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IMP Reference Guide  2.16.0
The Integrative Modeling Platform
argument_index.md
1 Argument Index {#argument_index}
2 ==============
3 
4 # Overview #
5 [TOC]
6 Functions that take objects of a given type as arguments:
7 
8 See also [Factory Index](@ref factory_index), [Argument Index](@ref argument_index), [Class Examples](@ref class_example_index), [Function Examples](@ref function_example_index)
9 # IMP (kernel) # {#argument_index_kernel}
10 <table><tr>
11 <th>Class</th><th>Users</th></tr>
12 <tr><td>@ref IMP::Array</td><td><a href="classIMP_1_1Array.html#a9549d191f4772f07777f5992a6f5ae4d">IMP::Array::compare()</a>, <a href="classIMP_1_1PairModifier.html#a1203f866809502706d3ddd3d5e1d930e">IMP::PairModifier::apply_index()</a>, <a href="classIMP_1_1PairPredicate.html#a812ced5db0cb09c670fedb3a900e0fcf">IMP::PairPredicate::get_value_index()</a>, <a href="classIMP_1_1PairPredicate.html#ab5f444057ff7abd671ffee74da71610f">IMP::PairPredicate::get_value_index_in_batch()</a>, <a href="classIMP_1_1PairPredicate.html#af1a76c20d0da0cb8091f70010abab1b3">IMP::PairPredicate::operator()()</a>, <a href="classIMP_1_1PairScore.html#ac3f53ee0daf867730b666ccfbfcbfa25">IMP::PairScore::create_current_decomposition()</a>, <a href="classIMP_1_1PairScore.html#a9353c185485691a3f4cc49fa2e85db84">IMP::PairScore::evaluate_if_good_index()</a>, <a href="classIMP_1_1PairScore.html#addfa4378ed7ec501350f1f70d96446de">IMP::PairScore::evaluate_index()</a>, <a href="classIMP_1_1PairScore.html#a39261041d14094111cb11a8d98f74241">IMP::PairScore::do_create_current_decomposition()</a>, <a href="classIMP_1_1QuadModifier.html#ab694ee2dc014bd33fbd125ebd2411b1a">IMP::QuadModifier::apply_index()</a>, <a href="classIMP_1_1QuadPredicate.html#a44d432e3d1746aea93562aa4778adb85">IMP::QuadPredicate::get_value_index()</a>, <a href="classIMP_1_1QuadPredicate.html#a10a8b17f369245507bfe891fd94dd507">IMP::QuadPredicate::get_value_index_in_batch()</a>, <a href="classIMP_1_1QuadPredicate.html#a2ab73aa13a7fc2ca8a37ee9b27633f6c">IMP::QuadPredicate::operator()()</a>, <a href="classIMP_1_1QuadScore.html#ae36391e637be084a570bf20cb6315f8e">IMP::QuadScore::create_current_decomposition()</a>, <a href="classIMP_1_1QuadScore.html#adfcf52bbb55dccf87eac762c158bcfc4">IMP::QuadScore::evaluate_if_good_index()</a>, <a href="classIMP_1_1QuadScore.html#a8811aa00b39851809b84403156adde47">IMP::QuadScore::evaluate_index()</a>, <a href="classIMP_1_1QuadScore.html#af8518e746dc7d2ccabaec558c16f0b6c">IMP::QuadScore::do_create_current_decomposition()</a>, <a href="classIMP_1_1TripletModifier.html#a56b9bd816c98bd67afe47b471ecfb21b">IMP::TripletModifier::apply_index()</a>, <a href="classIMP_1_1TripletPredicate.html#ab2cb55c8ca95d1d875d65fae9977ea88">IMP::TripletPredicate::get_value_index()</a>, <a href="classIMP_1_1TripletPredicate.html#a897085c21313ebf0669fea6be4d73db2">IMP::TripletPredicate::get_value_index_in_batch()</a>, <a href="classIMP_1_1TripletPredicate.html#aed542435fb88ad7c1703296651f4ef2e">IMP::TripletPredicate::operator()()</a>, <a href="classIMP_1_1TripletScore.html#a5f3906cbe68e8b3fd5b4fad2177dd700">IMP::TripletScore::create_current_decomposition()</a>, <a href="classIMP_1_1TripletScore.html#a3d24b25ec1320d6659c7475c07e63d5c">IMP::TripletScore::evaluate_if_good_index()</a>, <a href="classIMP_1_1TripletScore.html#a0d484717b416e3caeecae8064b4a547b">IMP::TripletScore::evaluate_index()</a>, <a href="classIMP_1_1TripletScore.html#ae356b8328fb4fb1f8e09ea9916ac3af0">IMP::TripletScore::do_create_current_decomposition()</a>, <a href="classIMP_1_1atom_1_1BondedPairFilter.html#ad23211bcfa456842db4455dc5127da12">IMP::atom::BondedPairFilter::get_value_index()</a>, <a href="classIMP_1_1atom_1_1CoulombPairScore.html#af11822aca9ef78f66806ff78a36ebf57">IMP::atom::CoulombPairScore::evaluate_index()</a>, <a href="classIMP_1_1atom_1_1LennardJonesPairScore.html#ad53cf37bfda254e9c32f7c3768864e14">IMP::atom::LennardJonesPairScore::evaluate_index()</a>, <a href="classIMP_1_1atom_1_1SameResiduePairFilter.html#a43beabad53a3baf1621b2fc9c66453d3">IMP::atom::SameResiduePairFilter::get_value_index()</a>, <a href="classIMP_1_1atom_1_1SoapPairFilter.html#a59bd711ee1e6399f0bba5626aeb5d844">IMP::atom::SoapPairFilter::get_value_index()</a>, <a href="classIMP_1_1atom_1_1StereochemistryPairFilter.html#ab97ead4da7fca308abe70743420d3195">IMP::atom::StereochemistryPairFilter::get_value_index()</a>, <a href="classIMP_1_1container_1_1ConsecutivePairContainer.html#a916805417bd4e38b437bd0714ad4ba35">IMP::container::ConsecutivePairContainer::get_contains()</a>, <a href="classIMP_1_1container_1_1ConsecutivePairFilter.html#a7066080e3e6b1259c22e041bf94b7bd4">IMP::container::ConsecutivePairFilter::get_value_index()</a>, <a href="classIMP_1_1container_1_1DynamicListPairContainer.html#a7340d80d5c31317ce9788b8b33067f37">IMP::container::DynamicListPairContainer::add()</a>, <a href="classIMP_1_1container_1_1DynamicListQuadContainer.html#a727e34ebe18cc054d5d22dd51617c083">IMP::container::DynamicListQuadContainer::add()</a>, <a href="classIMP_1_1container_1_1DynamicListTripletContainer.html#a22378aab7c4944448d6e92f4d0b06381">IMP::container::DynamicListTripletContainer::add()</a>, <a href="classIMP_1_1container_1_1ExclusiveConsecutivePairContainer.html#aa3491109e4451ea28b9983a0c300e694">IMP::container::ExclusiveConsecutivePairContainer::get_contains()</a>, <a href="classIMP_1_1container_1_1ExclusiveConsecutivePairFilter.html#a8666ee7c17737207b374642b34d2c462">IMP::container::ExclusiveConsecutivePairFilter::get_value_index()</a>, <a href="classIMP_1_1container_1_1InContainerPairFilter.html#ab377a426fde6f03e6aadc7dd71f47a02">IMP::container::InContainerPairFilter::get_value_index()</a>, <a href="classIMP_1_1container_1_1InContainerQuadFilter.html#a5efa677765e41243fe912815f08514c5">IMP::container::InContainerQuadFilter::get_value_index()</a>, <a href="classIMP_1_1container_1_1InContainerTripletFilter.html#a31fd10f59e06a0686bd5007ea2ace809">IMP::container::InContainerTripletFilter::get_value_index()</a>, <a href="classIMP_1_1container_1_1ListPairContainer.html#a9df2b8c7c684ebbba9bea04035562aea">IMP::container::ListPairContainer::add()</a>, <a href="classIMP_1_1container_1_1ListQuadContainer.html#a12e7f280f7e14ed4bc246fe526057c54">IMP::container::ListQuadContainer::add()</a>, <a href="classIMP_1_1container_1_1ListTripletContainer.html#ad8f21b6fdd92e7a487f5346b99b6d32d">IMP::container::ListTripletContainer::add()</a>, <a href="classIMP_1_1container_1_1MinimumPairScore.html#af0a6cfa5e602c8479d9cfd7b3632bffc">IMP::container::MinimumPairScore::do_create_current_decomposition()</a>, <a href="classIMP_1_1container_1_1MinimumPairScore.html#aadf933116206b7529022070fe28784e0">IMP::container::MinimumPairScore::evaluate_index()</a>, <a href="classIMP_1_1container_1_1MinimumQuadScore.html#a403b6f7b2c713a260b9a251922af5b54">IMP::container::MinimumQuadScore::do_create_current_decomposition()</a>, <a href="classIMP_1_1container_1_1MinimumQuadScore.html#aea9a974238cabbb952d8654c147190f7">IMP::container::MinimumQuadScore::evaluate_index()</a>, <a href="classIMP_1_1container_1_1MinimumTripletScore.html#ae34870dbf26f0f89612ad827a0644b19">IMP::container::MinimumTripletScore::do_create_current_decomposition()</a>, <a href="classIMP_1_1container_1_1MinimumTripletScore.html#ab27c7faa98447eeb691bdf5e7ae99b6b">IMP::container::MinimumTripletScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1AllSamePairPredicate.html#a2d25b9280bc314126e81ed8d1aba6f7c">IMP::core::AllSamePairPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1AllSameQuadPredicate.html#a8624ba1c088acc272aebd17cd2b17d82">IMP::core::AllSameQuadPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1AllSameTripletPredicate.html#a8338ade0c96e882f4b107e4609e30913">IMP::core::AllSameTripletPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1AngleTripletScore.html#a16b511c7018f830ad10a16c820440c98">IMP::core::AngleTripletScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1ClosePairsPairScore.html#a420c3c6bc7c982a4bde01d15249b1b5a">IMP::core::ClosePairsPairScore::get_close_pairs()</a>, <a href="classIMP_1_1core_1_1ClosePairsPairScore.html#aa989a2bd84f7f122736565abaef097b4">IMP::core::ClosePairsPairScore::create_current_decomposition()</a>, <a href="classIMP_1_1core_1_1ClosePairsPairScore.html#a4bbdf31e1ae0749a0345aa4b084eaa7b">IMP::core::ClosePairsPairScore::evaluate_if_good_index()</a>, <a href="classIMP_1_1core_1_1ClosePairsPairScore.html#a18eea2087eeccc46150a7c078e5db25e">IMP::core::ClosePairsPairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1CoinFlipPairPredicate.html#ab70e9932c662352f787132210607848e">IMP::core::CoinFlipPairPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1CoinFlipQuadPredicate.html#a0583e3296ba8350a16242897ae1fc398">IMP::core::CoinFlipQuadPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1CoinFlipTripletPredicate.html#ad98e5051634306c8af44c11f50ff882f">IMP::core::CoinFlipTripletPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1ConstantPairPredicate.html#a13760fc627b7f8d2c5cd65ad38eda041">IMP::core::ConstantPairPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1ConstantQuadPredicate.html#a15f6010220ab250a478b1c9520c0a3e0">IMP::core::ConstantQuadPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1ConstantTripletPredicate.html#a5451b6f49e9051683c2993b38de45783">IMP::core::ConstantTripletPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1DirectionAngle.html#a020224967fe2851b1cfd5ee4b4a7191d">IMP::core::DirectionAngle::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1DirectionAngle.html#ab6690f325dd3fdd9bb126d8c6afd31af">IMP::core::DirectionAngle::setup_particle()</a>, <a href="classIMP_1_1core_1_1DirectionAngle.html#a2de410c46019dad78a94d34435efcac1">IMP::core::DirectionAngle::setup_particle()</a>, <a href="classIMP_1_1core_1_1DistancePairScore.html#a1f69d849e2cd4451c580669d57b08a23">IMP::core::DistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1HarmonicDistancePairScore.html#aed2d6296770d0a56bc4cb4dd538bb885">IMP::core::HarmonicDistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1HarmonicSphereDistancePairScore.html#ae9466826ffafba100c7270bdca3d8fe0">IMP::core::HarmonicSphereDistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1HarmonicSurfaceDepthPairScore.html#a5df05ea8490df6d61ca1d805a1468c2d">IMP::core::HarmonicSurfaceDepthPairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1HarmonicSurfaceDistancePairScore.html#ab76420cbb54f896753104866c355dc11">IMP::core::HarmonicSurfaceDistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1HarmonicSurfaceHeightPairScore.html#a556f8d81f4bb461b2f5a21752cca7e89">IMP::core::HarmonicSurfaceHeightPairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1HarmonicUpperBoundSphereDiameterPairScore.html#a94f3ed8283c89625522a6d27bfbdf698">IMP::core::HarmonicUpperBoundSphereDiameterPairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1HarmonicUpperBoundSphereDistancePairScore.html#a6a007323ee38e5736fdcbb5bbe8f0161">IMP::core::HarmonicUpperBoundSphereDistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1IsCollisionPairPredicate.html#aaa4708e6e7eb2a09c19929749bbca27e">IMP::core::IsCollisionPairPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1KClosePairsPairScore.html#a8fbacd0eacaa1eae89881617242a7b49">IMP::core::KClosePairsPairScore::get_close_pairs()</a>, <a href="classIMP_1_1core_1_1KClosePairsPairScore.html#a6a487adec052f12f4fef2ddbf5720ce5">IMP::core::KClosePairsPairScore::create_current_decomposition()</a>, <a href="classIMP_1_1core_1_1KClosePairsPairScore.html#a6593d9626054e87ea59adeb7c42be34e">IMP::core::KClosePairsPairScore::evaluate_if_good_index()</a>, <a href="classIMP_1_1core_1_1KClosePairsPairScore.html#a96dcf52e4babae72bd0a193160641c77">IMP::core::KClosePairsPairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1MultipleBinormalRestraint.html#a43897a672f1efc428b5b196f788c281d">IMP::core::MultipleBinormalRestraint::MultipleBinormalRestraint()</a>, <a href="classIMP_1_1core_1_1NormalizedSphereDistancePairScore.html#a94af6c3fcd755f545fbb7fe4cd3f8565">IMP::core::NormalizedSphereDistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1OrderedTypePairPredicate.html#adf1d4d6022b7138fb686a40c7a960f99">IMP::core::OrderedTypePairPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1OrderedTypePairPredicate.html#a34439a8b8501fe3737ac2d9dd2c9034d">IMP::core::OrderedTypePairPredicate::get_value_index_in_batch()</a>, <a href="classIMP_1_1core_1_1OrderedTypeQuadPredicate.html#a9057e1acc8c6f06cef5902d4f512ef63">IMP::core::OrderedTypeQuadPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1OrderedTypeQuadPredicate.html#ab8e26fe261fe141adb30c5b9d0348085">IMP::core::OrderedTypeQuadPredicate::get_value_index_in_batch()</a>, <a href="classIMP_1_1core_1_1OrderedTypeTripletPredicate.html#a0daae64c51f2c40dbe2447e1c3530bbf">IMP::core::OrderedTypeTripletPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1OrderedTypeTripletPredicate.html#ad77c3a742cc7718e1f8771b2d1dbf34e">IMP::core::OrderedTypeTripletPredicate::get_value_index_in_batch()</a>, <a href="classIMP_1_1core_1_1PairConstraint.html#a6a5aac7fefc5fa599881d63482b4f639">IMP::core::PairConstraint::PairConstraint()</a>, <a href="classIMP_1_1core_1_1PairRestraint.html#a4153733cf2c74d9c87a379a631ff194f">IMP::core::PairRestraint::PairRestraint()</a>, <a href="classIMP_1_1core_1_1QuadConstraint.html#a6b3d5edb3fa7cdfaa35d37af9d439d18">IMP::core::QuadConstraint::QuadConstraint()</a>, <a href="classIMP_1_1core_1_1QuadRestraint.html#a613d76a32ec344886a02b1039100b8bd">IMP::core::QuadRestraint::QuadRestraint()</a>, <a href="classIMP_1_1core_1_1RefinedPairsPairScore.html#a3e51f509481e35942000264b59ea287d">IMP::core::RefinedPairsPairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1RigidBodyAnglePairScore.html#ac255f86cb1205429a47532616a4b8444">IMP::core::RigidBodyAnglePairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1SoftSpherePairScore.html#a4072dd6c5bf8f0863c60a450bc9b943d">IMP::core::SoftSpherePairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1SoftSubSurfacePairScore.html#a38120e0273c77f9a47a77ddedd41fe64">IMP::core::SoftSubSurfacePairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1SoftSuperSurfacePairScore.html#af9bf50705ca303d95ae729e374b46699">IMP::core::SoftSuperSurfacePairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1SphereDistancePairScore.html#a3e39ff56be09a4dbe371e69a0442ce1b">IMP::core::SphereDistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1SurfaceDepthPairScore.html#a42d7a6cad5ff2b4b340dea84c0f9eb53">IMP::core::SurfaceDepthPairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1SurfaceDistancePairScore.html#a613fdbe4aca8f1e004982b3982fffb35">IMP::core::SurfaceDistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1SurfaceHeightPairScore.html#aa1bb4ff369d3080ebc3f47875ed9b163">IMP::core::SurfaceHeightPairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1SurfaceSymmetryConstraint.html#acbe9fa76e03fcefd9219014f79411c39">IMP::core::SurfaceSymmetryConstraint::SurfaceSymmetryConstraint()</a>, <a href="classIMP_1_1core_1_1TransformedDistancePairScore.html#afad8b302e2264283b840e700a506a64b">IMP::core::TransformedDistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1TripletConstraint.html#ad99ccd052b261716671611a2cff4af79">IMP::core::TripletConstraint::TripletConstraint()</a>, <a href="classIMP_1_1core_1_1TripletRestraint.html#aa12a3dcb20c18236896d7523a355dd32">IMP::core::TripletRestraint::TripletRestraint()</a>, <a href="classIMP_1_1core_1_1TypedPairScore.html#a1ed4bcaaa82f6a137b77d16336b8dee6">IMP::core::TypedPairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1UnorderedTypePairPredicate.html#a7f07e5817ecd4b9c8b0eaba11d0b9ad6">IMP::core::UnorderedTypePairPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1UnorderedTypeQuadPredicate.html#a8600d0d803a08d0ac7973d2eca5f4ad3">IMP::core::UnorderedTypeQuadPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1UnorderedTypeTripletPredicate.html#aca472d3bfd587ca89c44263eecf0f97e">IMP::core::UnorderedTypeTripletPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1WeightedSphereDistancePairScore.html#ab83a5eaaaae5256e9e46a8b8c1cdc657">IMP::core::WeightedSphereDistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1example_1_1ExamplePairScore.html#ac4a6da957157e308a3226b3d73f478ff">IMP::example::ExamplePairScore::evaluate_index()</a>, <a href="classIMP_1_1isd_1_1AtomicCrossLinkMSRestraint.html#a379f971174248a8e9c66c8402a44e27d">IMP::isd::AtomicCrossLinkMSRestraint::add_contribution()</a>, <a href="classIMP_1_1isd_1_1CrossLinkMSRestraint.html#affc6a6cdbed7091cbe64018a53fbb2fe">IMP::isd::CrossLinkMSRestraint::add_contribution()</a>, <a href="classIMP_1_1isd_1_1RepulsiveDistancePairScore.html#a67fd255da53a5e6a9b4ae32102ff07f4">IMP::isd::RepulsiveDistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1misc_1_1CommonEndpointPairFilter.html#a15889422553c45aefa35638f1cc30960">IMP::misc::CommonEndpointPairFilter::get_value_index()</a>, <a href="classIMP_1_1misc_1_1LogPairScore.html#af6827dfecb55be161b7c6ea9f18ae184">IMP::misc::LogPairScore::evaluate_index()</a>, <a href="classIMP_1_1misc_1_1LowestRefinedPairScore.html#aa8a680cbf62bf672e3612f6adb50211c">IMP::misc::LowestRefinedPairScore::evaluate_index()</a>, <a href="classIMP_1_1misc_1_1SoftCylinderPairScore.html#aa29d2902b769e0fc842595c55e3c683a">IMP::misc::SoftCylinderPairScore::evaluate_index()</a>, <a href="classIMP_1_1npc_1_1MinimumSphereDistancePairScore.html#ae4c0e755b4f0ff815c1d12f30188632d">IMP::npc::MinimumSphereDistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1npctransport_1_1AnchorToCylidnricalPorePairScore.html#a77ba0dec47b4a09eda97b71fbbb6ea4c">IMP::npctransport::AnchorToCylidnricalPorePairScore::evaluate_index()</a>, <a href="classIMP_1_1npctransport_1_1HarmonicWellPairScore.html#a6112c2f581b093a6f400f10097705ffb">IMP::npctransport::HarmonicWellPairScore::evaluate_index()</a>, <a href="classIMP_1_1npctransport_1_1LinearInteraction.html#aa83af20b242348cbf39d45bea3eef124">IMP::npctransport::LinearInteraction::get_is_trivially_zero()</a>, <a href="classIMP_1_1npctransport_1_1LinearInteraction.html#a197f0b2c0799fc1a966f37dbc7708c19">IMP::npctransport::LinearInteraction::get_maximum_range()</a>, <a href="classIMP_1_1npctransport_1_1LinearInteraction.html#a92ba26bdbe6f1a7b119a10ce70da6a1e">IMP::npctransport::LinearInteraction::get_score()</a>, <a href="classIMP_1_1npctransport_1_1LinearInteraction.html#a16fcc958aec41ef02a4a701a50fb11d5">IMP::npctransport::LinearInteraction::get_score_and_derivative()</a>, <a href="classIMP_1_1npctransport_1_1LinearSoftSpherePairScore.html#a00c112ed25af75755c247427d80f9bd7">IMP::npctransport::LinearSoftSpherePairScore::evaluate_index()</a>, <a href="classIMP_1_1npctransport_1_1LinearWellPairScore.html#afb4ee96f18d024f2879d7e8d3a727048">IMP::npctransport::LinearWellPairScore::evaluate_index()</a>, <a href="classIMP_1_1npctransport_1_1SitesPairScore.html#a84202fb01032444b964e16ddd0be44a0">IMP::npctransport::SitesPairScore::evaluate_index()</a>, <a href="classIMP_1_1npctransport_1_1SitesPairScore.html#a0652d42fb895d6381b71909cc75bd4dc">IMP::npctransport::SitesPairScore::evaluate_site_contributions()</a>, <a href="classIMP_1_1npctransport_1_1SitesPairScore.html#a4f458d7972f6fd4b0a01c7d83d8f2534">IMP::npctransport::SitesPairScore::evaluate_site_contributions_with_internal_tables()</a>, <a href="classIMP_1_1npctransport_1_1SitesPairScore.html#afc69f1324198285ad999d480d442fa0f">IMP::npctransport::SitesPairScore::evaluate_index_with_internal_tables()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithCylindricalPorePairScore.html#a237792d9bd5d0afcf684e2b24695a491">IMP::npctransport::SlabWithCylindricalPorePairScore::evaluate_index()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithToroidalPorePairScore.html#ac038a2aa03536cc6a0265c2b0e06d84f">IMP::npctransport::SlabWithToroidalPorePairScore::evaluate_index()</a>, <a href="classIMP_1_1score__functor_1_1AddScores.html#ab9f8ad0e321f134213a560aa3877544d">IMP::score_functor::AddScores::get_is_trivially_zero()</a>, <a href="classIMP_1_1score__functor_1_1AddScores.html#a2dc8010737faa261c7d8bdf93781db1f">IMP::score_functor::AddScores::get_maximum_range()</a>, <a href="classIMP_1_1score__functor_1_1AddScores.html#aac21bb6a522f69372ea63f02eb34b986">IMP::score_functor::AddScores::get_score()</a>, <a href="classIMP_1_1score__functor_1_1AddScores.html#acc89f7565397789166f12981cbe4527b">IMP::score_functor::AddScores::get_score_and_derivative()</a>, <a href="classIMP_1_1score__functor_1_1DistancePairScore.html#a35e48061a5968d15b44686032a075968">IMP::score_functor::DistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1score__functor_1_1DistancePairScoreWithCache.html#a92420a5cbd9d73affefd4b8e9ff4e254">IMP::score_functor::DistancePairScoreWithCache::evaluate_index_with_cache()</a>, <a href="classIMP_1_1score__functor_1_1DistancePairScoreWithCache.html#ad012a8af9b447bb76fa9a30fc7852de2">IMP::score_functor::DistancePairScoreWithCache::evaluate_index()</a>, <a href="classIMP_1_1score__functor_1_1Harmonic.html#a9f2a4c42ec7cc14b6266478c06f97bb6">IMP::score_functor::Harmonic::get_score()</a>, <a href="classIMP_1_1score__functor_1_1Harmonic.html#af2a158ccffcf00f6ed73bfb4c007bba3">IMP::score_functor::Harmonic::get_score_and_derivative()</a>, <a href="classIMP_1_1score__functor_1_1HarmonicLowerBound.html#a2caf34ef9b4be1d268096bbc05c06c21">IMP::score_functor::HarmonicLowerBound::get_is_trivially_zero()</a>, <a href="classIMP_1_1score__functor_1_1HarmonicLowerBound.html#a235a4181cbff2b97cb20135ee2450bc7">IMP::score_functor::HarmonicLowerBound::get_maximum_range()</a>, <a href="classIMP_1_1score__functor_1_1HarmonicLowerBound.html#ad40a14f3265a4d875d9b65468f7f51e3">IMP::score_functor::HarmonicLowerBound::get_score()</a>, <a href="classIMP_1_1score__functor_1_1HarmonicLowerBound.html#a02f736fb7ffa1fa5e5b813cc24bb20f6">IMP::score_functor::HarmonicLowerBound::get_score_and_derivative()</a>, <a href="classIMP_1_1score__functor_1_1HarmonicUpperBound.html#ac8841db6f0a0c986417ce240a0b8b2d6">IMP::score_functor::HarmonicUpperBound::get_score()</a>, <a href="classIMP_1_1score__functor_1_1HarmonicUpperBound.html#abe1446ba2657e68709e055bed538d68a">IMP::score_functor::HarmonicUpperBound::get_score_and_derivative()</a>, <a href="classIMP_1_1score__functor_1_1LinearLowerBound.html#afa566e77a38fca1af75c4a2d3b25affd">IMP::score_functor::LinearLowerBound::get_is_trivially_zero()</a>, <a href="classIMP_1_1score__functor_1_1LinearLowerBound.html#aa1f94f2f5fe068ff4d4b8c581a78958b">IMP::score_functor::LinearLowerBound::get_maximum_range()</a>, <a href="classIMP_1_1score__functor_1_1LinearLowerBound.html#aff6459ee2e0cee12915183c9d4ba1387">IMP::score_functor::LinearLowerBound::get_score()</a>, <a href="classIMP_1_1score__functor_1_1LinearLowerBound.html#abb50e6bea33653e6a4f9bab35d786b7b">IMP::score_functor::LinearLowerBound::get_score_and_derivative()</a>, <a href="classIMP_1_1score__functor_1_1OpenCubicSpline.html#a0c5127070326f789ae8854d4a75d5cf2">IMP::score_functor::OpenCubicSpline::get_is_trivially_zero()</a>, <a href="classIMP_1_1score__functor_1_1OpenCubicSpline.html#a7525ecc9b139c06c2e15bec31f7a6750">IMP::score_functor::OpenCubicSpline::get_maximum_range()</a>, <a href="classIMP_1_1score__functor_1_1OpenCubicSpline.html#ad3c7db8d9846e9d1ee298459d6eb2d0b">IMP::score_functor::OpenCubicSpline::get_score()</a>, <a href="classIMP_1_1score__functor_1_1OpenCubicSpline.html#aaa8dc2858fb438020b5dcb8d7c31ee98">IMP::score_functor::OpenCubicSpline::get_score_and_derivative()</a>, <a href="classIMP_1_1score__functor_1_1OrientedSoap.html#aaa5b7042ff5845c00bf8d87785452b47">IMP::score_functor::OrientedSoap::get_is_trivially_zero_with_cache()</a>, <a href="classIMP_1_1score__functor_1_1OrientedSoap.html#a275f93bdfd934bbfa6bd7d26d4448ee0">IMP::score_functor::OrientedSoap::get_maximum_range()</a>, <a href="classIMP_1_1score__functor_1_1OrientedSoap.html#a0e7665fae253c917e440f4c64e97ef5d">IMP::score_functor::OrientedSoap::get_score_and_derivative_with_cache()</a>, <a href="classIMP_1_1score__functor_1_1OrientedSoap.html#a89c799a62cfa8faea3a6f10e6d71df15">IMP::score_functor::OrientedSoap::get_score_with_cache()</a>, <a href="classIMP_1_1score__functor_1_1PointToSphereDistance.html#ac48dfe14b8e4ef0e8ce90051481f1fab">IMP::score_functor::PointToSphereDistance::get_is_trivially_zero()</a>, <a href="classIMP_1_1score__functor_1_1PointToSphereDistance.html#a0c371b05f0433136ec27b667dc4f1fed">IMP::score_functor::PointToSphereDistance::get_maximum_range()</a>, <a href="classIMP_1_1score__functor_1_1PointToSphereDistance.html#a460d98bba47c59c22d1b621e70caaa3d">IMP::score_functor::PointToSphereDistance::get_score()</a>, <a href="classIMP_1_1score__functor_1_1PointToSphereDistance.html#a4d8180978b20a384aa4a6ad0ba53cc6a">IMP::score_functor::PointToSphereDistance::get_score_and_derivative()</a>, <a href="classIMP_1_1score__functor_1_1Shift.html#aef30bea2d7d5f8a2db5c5a8a6f73e5dd">IMP::score_functor::Shift::get_is_trivially_zero()</a>, <a href="classIMP_1_1score__functor_1_1Shift.html#a6578990b3ac6d1ad99f9d84568437891">IMP::score_functor::Shift::get_maximum_range()</a>, <a href="classIMP_1_1score__functor_1_1Shift.html#a308bb7a3cf51c89b9c698a486d12c7ff">IMP::score_functor::Shift::get_score()</a>, <a href="classIMP_1_1score__functor_1_1Shift.html#ac2e6cec31e35f5f3d256631ca521c301">IMP::score_functor::Shift::get_score_and_derivative()</a>, <a href="classIMP_1_1score__functor_1_1SphereDistance.html#a508d4c8920267bcaaf939199cf13a407">IMP::score_functor::SphereDistance::get_rsum()</a>, <a href="classIMP_1_1score__functor_1_1SphereDistance.html#aca12d8037ac827d0b09bf56a89295a10">IMP::score_functor::SphereDistance::get_is_trivially_zero()</a>, <a href="classIMP_1_1score__functor_1_1SphereDistance.html#a6a24c66fb3dbba22c2e6f4d586252266">IMP::score_functor::SphereDistance::get_maximum_range()</a>, <a href="classIMP_1_1score__functor_1_1SphereDistance.html#a17792ed42a40aaed674d50cfdd08199e">IMP::score_functor::SphereDistance::get_score()</a>, <a href="classIMP_1_1score__functor_1_1SphereDistance.html#a62de123203b4b80c46c47c40c4e94bc9">IMP::score_functor::SphereDistance::get_score_and_derivative()</a>, <a href="classIMP_1_1score__functor_1_1Statistical.html#a9a0b06f000f10df52abc02c60e7fba45">IMP::score_functor::Statistical::get_is_trivially_zero()</a>, <a href="classIMP_1_1score__functor_1_1Statistical.html#adac345083177391e03cdba6de9df8526">IMP::score_functor::Statistical::get_maximum_range()</a>, <a href="classIMP_1_1score__functor_1_1Statistical.html#ae09e75036b9fa07ea23a1b089a3d8134">IMP::score_functor::Statistical::get_score()</a>, <a href="classIMP_1_1score__functor_1_1Statistical.html#a431d126f973f232bb0017bdf42b8a229">IMP::score_functor::Statistical::get_score_and_derivative()</a>, <a href="classIMP_1_1score__functor_1_1SurfaceDistancePairScore.html#a3ec7c9c3010ecdb03fe565c7922d4a78">IMP::score_functor::SurfaceDistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1score__functor_1_1UnaryFunctionEvaluate.html#aaf42d5a71a06160c7c28c5eb08681fff">IMP::score_functor::UnaryFunctionEvaluate::get_score()</a>, <a href="classIMP_1_1score__functor_1_1UnaryFunctionEvaluate.html#abaaf3f9ba7f2f1b1c0bae2390dff7647">IMP::score_functor::UnaryFunctionEvaluate::get_score_and_derivative()</a>, <a href="classIMP_1_1score__functor_1_1WeightScore.html#aee210bba1d0a7582bda149ec90f62b71">IMP::score_functor::WeightScore::get_score()</a>, <a href="classIMP_1_1score__functor_1_1WeightScore.html#afaf226b6a937780c6fe3d1ff0c8ba8de">IMP::score_functor::WeightScore::get_score_and_derivative()</a>, <a href="classIMP_1_1spb_1_1AttributeDistancePairScore.html#ad703da3ed2ece907485501f6d5e3191b">IMP::spb::AttributeDistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1spb_1_1KinkPairScore.html#a054a2a261818a7b22fb893c5583a7b8c">IMP::spb::KinkPairScore::evaluate_index()</a>, <a href="classIMP_1_1spb_1_1RigidBodyPackingScore.html#a973b57cfcbe92c31b22370697b64ccb6">IMP::spb::RigidBodyPackingScore::evaluate_index()</a>, <a href="classIMP_1_1spb_1_1SameParticlePairFilter.html#a272699e9295a11087bf4a4c2fe805b73">IMP::spb::SameParticlePairFilter::get_value_index()</a>, <a href="classIMP_1_1spb_1_1SameRigidBodyPairFilter.html#a5d4a013ab99d797a37003931f9c566d8">IMP::spb::SameRigidBodyPairFilter::get_value_index()</a>, <a href="namespaceIMP_1_1npctransport.html#a656ab4ca89e8d22e30f474a6a15fe34d">IMP::npctransport::do_evaluate_index_harmonic()</a>, <a href="namespaceIMP_1_1npctransport.html#a795fe17c17d57c27a5b28f7a9d6d02a3">IMP::npctransport::make_unordered_particle_index_pair()</a></td></tr>
13 <tr><td>@ref IMP::Configuration</td><td><a href="classIMP_1_1Configuration.html#ac6ea0e2d7495231d46df0dfceeca9890">IMP::Configuration::Configuration()</a></td></tr>
14 <tr><td>@ref IMP::ConfigurationSet</td><td><a href="classIMP_1_1SaveToConfigurationSetOptimizerState.html#ac2f6d4c3a33e404de6a922af6fb5dd46">IMP::SaveToConfigurationSetOptimizerState::SaveToConfigurationSetOptimizerState()</a>, <a href="classIMP_1_1statistics_1_1ConfigurationSetRMSDMetric.html#a4a6365b3e39347130d20397aef8a8bad">IMP::statistics::ConfigurationSetRMSDMetric::ConfigurationSetRMSDMetric()</a>, <a href="classIMP_1_1statistics_1_1ConfigurationSetXYZEmbedding.html#a59f36e0f094ff45193a47939d8d93cd1">IMP::statistics::ConfigurationSetXYZEmbedding::ConfigurationSetXYZEmbedding()</a></td></tr>
15 <tr><td>@ref IMP::ConstVector</td><td><a href="classIMP_1_1ConstVector.html#a9f77fc91cb00ddf2b8d60577d877844d">IMP::ConstVector::compare()</a>, <a href="namespaceIMP.html#a4b749b9251eef8e7daa8ded9a61abe4e">IMP::swap()</a></td></tr>
16 <tr><td>@ref IMP::Container</td><td><a href="classIMP_1_1container_1_1DynamicListPairContainer.html#a6e9761b23a0132a9af1980e5e3749db9">IMP::container::DynamicListPairContainer::DynamicListPairContainer()</a>, <a href="classIMP_1_1container_1_1DynamicListQuadContainer.html#af4b3b9738040d6e073879056c7553be5">IMP::container::DynamicListQuadContainer::DynamicListQuadContainer()</a>, <a href="classIMP_1_1container_1_1DynamicListSingletonContainer.html#a3492d7b9a5f380642700c2f05146efc7">IMP::container::DynamicListSingletonContainer::DynamicListSingletonContainer()</a>, <a href="classIMP_1_1container_1_1DynamicListTripletContainer.html#a8024d47a46737c285cf41fe8e2de5248">IMP::container::DynamicListTripletContainer::DynamicListTripletContainer()</a>, <a href="namespaceIMP.html#a0fc9f9396c8c4473d9c298d531f77264">IMP::create_restraint()</a>, <a href="namespaceIMP.html#ae6ee6bad5ddcc6be1c4034f6daa51328">IMP::resize_to_fit()</a>, <a href="namespaceIMP_1_1container.html#a0e72bed2aebfee3bc2cf60a2a23cfa45">IMP::container::create_constraint()</a>, <a href="namespaceIMP_1_1container.html#a38623c7bf5f1b07e8f093aedce4f44ef">IMP::container::create_in_container_filter()</a>, <a href="namespaceIMP_1_1container.html#ad05b9be19e11c1364862cf8e032768e9">IMP::container::create_restraint()</a></td></tr>
17 <tr><td>@ref IMP::Decorator</td><td><a href="classIMP_1_1ParticleAdaptor.html#aa1ccdc4c6d666ff5fec1e97acf23cc19">IMP::ParticleAdaptor::ParticleAdaptor()</a>, <a href="classIMP_1_1ParticleIndexAdaptor.html#a1689883c40f7302fd86833b7c0d668db">IMP::ParticleIndexAdaptor::ParticleIndexAdaptor()</a>, <a href="classIMP_1_1atom_1_1AngularVelocity.html#a0c0a1b0bb984aa424ee4a4d35f3b01ef">IMP::atom::AngularVelocity::IMP_DECORATOR_METHODS()</a>, <a href="classIMP_1_1atom_1_1LinearVelocity.html#ac885de7b2294784c501d5a2f0c2c664a">IMP::atom::LinearVelocity::IMP_DECORATOR_METHODS()</a>, <a href="namespaceIMP.html#a1097ce195f15c7b70f67606a3138a9df">IMP::get_vector_geometry()</a>, <a href="namespaceIMP.html#a89524841bb4f39bcbac5ef704f2b9b84">IMP::set_vector_geometry()</a></td></tr>
18 <tr><td>@ref IMP::DerivativeAccumulator</td><td><a href="classIMP_1_1Constraint.html#a45a75409c59e5707dfd6d9ed617d400f">IMP::Constraint::do_after_evaluate()</a>, <a href="classIMP_1_1Constraint.html#a8eaa2c7f7ed8e50029705ab02b02ace0">IMP::Constraint::do_update_derivatives()</a>, <a href="classIMP_1_1DerivativeAccumulator.html#aa348f8327dfe74a5948c75f83b1beb3c">IMP::DerivativeAccumulator::DerivativeAccumulator()</a>, <a href="classIMP_1_1PairScore.html#a9353c185485691a3f4cc49fa2e85db84">IMP::PairScore::evaluate_if_good_index()</a>, <a href="classIMP_1_1PairScore.html#aaaebeddee8c8b2719360af5e5ee60467">IMP::PairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1PairScore.html#addfa4378ed7ec501350f1f70d96446de">IMP::PairScore::evaluate_index()</a>, <a href="classIMP_1_1PairScore.html#a2dca93e58717faf070de26c0095b5948">IMP::PairScore::evaluate_indexes()</a>, <a href="classIMP_1_1PairScore.html#a1e2eda017291b400ccaa6f5d4d4a1b53">IMP::PairScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1PairScore.html#a645eae1da1512fbd98ddca38f5a4cb7c">IMP::PairScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1QuadScore.html#adfcf52bbb55dccf87eac762c158bcfc4">IMP::QuadScore::evaluate_if_good_index()</a>, <a href="classIMP_1_1QuadScore.html#a23fe083ebd9ab41fae847c739c565e56">IMP::QuadScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1QuadScore.html#a8811aa00b39851809b84403156adde47">IMP::QuadScore::evaluate_index()</a>, <a href="classIMP_1_1QuadScore.html#a5998238ace6d73cdb32b11941a640fe0">IMP::QuadScore::evaluate_indexes()</a>, <a href="classIMP_1_1QuadScore.html#a58869d3e961b4fca71e86fa1a79540fc">IMP::QuadScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1QuadScore.html#ac239db0a3df1c7ab445b3f3aa0faf193">IMP::QuadScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1RestraintSet.html#aada3f8d09aeb05be5e51a9489eaed497">IMP::RestraintSet::unprotected_evaluate()</a>, <a href="classIMP_1_1ScoreState.html#a23aacfd7132adf7e82d4f99719297369">IMP::ScoreState::do_after_evaluate()</a>, <a href="classIMP_1_1ScoreState.html#a5a289a65663e993ebfc7ba335a24c87f">IMP::ScoreState::after_evaluate()</a>, <a href="classIMP_1_1SingletonScore.html#aceff09a984620d3e0fd287e5e1692304">IMP::SingletonScore::evaluate_if_good_index()</a>, <a href="classIMP_1_1SingletonScore.html#a72fedd1e026640d8dff579c8138cb543">IMP::SingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1SingletonScore.html#a65c2554625de92d0c0cfbabe108491c2">IMP::SingletonScore::evaluate_index()</a>, <a href="classIMP_1_1SingletonScore.html#a6b4756b83a12ad91eb5f6d5f943cde39">IMP::SingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1SingletonScore.html#a4212150dc45c60f04b7422491d0f919f">IMP::SingletonScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1SingletonScore.html#a2ddfa8309b6f3589864c028066777e59">IMP::SingletonScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1TripletScore.html#a3d24b25ec1320d6659c7475c07e63d5c">IMP::TripletScore::evaluate_if_good_index()</a>, <a href="classIMP_1_1TripletScore.html#aba77cc17c5736a22c4ba8678b97ca3d2">IMP::TripletScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1TripletScore.html#a0d484717b416e3caeecae8064b4a547b">IMP::TripletScore::evaluate_index()</a>, <a href="classIMP_1_1TripletScore.html#acac89a806de002ddd26368e3f73a79aa">IMP::TripletScore::evaluate_indexes()</a>, <a href="classIMP_1_1TripletScore.html#a094e729370c397cad9bd4190be908a2a">IMP::TripletScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1TripletScore.html#aa0afab007addd7a4852c7519ccf34307">IMP::TripletScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1atom_1_1AngleSingletonScore.html#a9d94065013e52688cec46fb3628b687e">IMP::atom::AngleSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1atom_1_1AngleSingletonScore.html#a854e1c08f59d9dd19b21511b18607be5">IMP::atom::AngleSingletonScore::evaluate_index()</a>, <a href="classIMP_1_1atom_1_1AngleSingletonScore.html#aaf636347f30a3bdb57c1efe85169b3ee">IMP::atom::AngleSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1atom_1_1AngleSingletonScore.html#ac98a1656980e03142588407436356652">IMP::atom::AngleSingletonScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1atom_1_1AngleSingletonScore.html#a9318fd68f16bbab979e4de1e1a586a65">IMP::atom::AngleSingletonScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1atom_1_1BondSingletonScore.html#aea653b8e4729b29f3b8ae867b185828d">IMP::atom::BondSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1atom_1_1BondSingletonScore.html#a6969ecb5ea9eb8fdaf6ed3624ef6c4ea">IMP::atom::BondSingletonScore::evaluate_index()</a>, <a href="classIMP_1_1atom_1_1BondSingletonScore.html#ac1f36ade2f5513cffc07e4dc5d1a9ca8">IMP::atom::BondSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1atom_1_1BondSingletonScore.html#af4566ccae002e42f23090fbe8460c9e1">IMP::atom::BondSingletonScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1atom_1_1BondSingletonScore.html#a817fcac36508aa396cbd9faa3b965801">IMP::atom::BondSingletonScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1atom_1_1CAAngleRestraint.html#a02ecd257fa25340ee57c1269ea83d9d1">IMP::atom::CAAngleRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1atom_1_1CADihedralRestraint.html#a0dba2a4c45f7aefbd18d47541e8874cc">IMP::atom::CADihedralRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1atom_1_1CHARMMStereochemistryRestraint.html#acedb1fe36d38668d3a73f433efbc60d7">IMP::atom::CHARMMStereochemistryRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1atom_1_1CoulombPairScore.html#aa6e2174d307e48930361e0dae3cccfb3">IMP::atom::CoulombPairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1atom_1_1CoulombPairScore.html#af11822aca9ef78f66806ff78a36ebf57">IMP::atom::CoulombPairScore::evaluate_index()</a>, <a href="classIMP_1_1atom_1_1CoulombPairScore.html#ad42ba80e1e05388e0f90c97618dd6239">IMP::atom::CoulombPairScore::evaluate_indexes()</a>, <a href="classIMP_1_1atom_1_1CoulombPairScore.html#aabb773a4552e28b1546a21e038cfa563">IMP::atom::CoulombPairScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1atom_1_1CoulombPairScore.html#a7c837e0d66a6cb38b01f204ee33bc321">IMP::atom::CoulombPairScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1atom_1_1DihedralSingletonScore.html#a7d32fc980bc2fbccfcd240859da6359d">IMP::atom::DihedralSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1atom_1_1DihedralSingletonScore.html#aee28679f7b4317c375a11c855e9fc3a6">IMP::atom::DihedralSingletonScore::evaluate_index()</a>, <a href="classIMP_1_1atom_1_1DihedralSingletonScore.html#a7c1c629afb4c9df8f171c1ede35f191f">IMP::atom::DihedralSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1atom_1_1DihedralSingletonScore.html#a39c7b481300fd153289bafaccd0adf94">IMP::atom::DihedralSingletonScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1atom_1_1DihedralSingletonScore.html#a84378fd00630c2db7101b39be013b0b8">IMP::atom::DihedralSingletonScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1atom_1_1EzRestraint.html#a9d986354f990c70aa42bc589914b7dcc">IMP::atom::EzRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1atom_1_1HelixRestraint.html#a60db5cc11ff5cf603c701da77123aed7">IMP::atom::HelixRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1atom_1_1ImproperSingletonScore.html#a9e4b75ae43efed67f5c0d429a740c94a">IMP::atom::ImproperSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1atom_1_1ImproperSingletonScore.html#a815b70b0e4f55d99633cbb3b3e8f8e0a">IMP::atom::ImproperSingletonScore::evaluate_index()</a>, <a href="classIMP_1_1atom_1_1ImproperSingletonScore.html#a74979e31e169663871126971dbb22ca6">IMP::atom::ImproperSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1atom_1_1ImproperSingletonScore.html#ac6c9b73eaf52d6178cd49389a07ad40a">IMP::atom::ImproperSingletonScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1atom_1_1ImproperSingletonScore.html#a6cc8536e3b4408cc29153e3bf0de4cd1">IMP::atom::ImproperSingletonScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1atom_1_1LennardJonesPairScore.html#a0559e17977150ff579dd16a67bcdedf0">IMP::atom::LennardJonesPairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1atom_1_1LennardJonesPairScore.html#ad53cf37bfda254e9c32f7c3768864e14">IMP::atom::LennardJonesPairScore::evaluate_index()</a>, <a href="classIMP_1_1atom_1_1LennardJonesPairScore.html#ae6f5a564ae21dedc18964bc7b20d0dcb">IMP::atom::LennardJonesPairScore::evaluate_indexes()</a>, <a href="classIMP_1_1atom_1_1LennardJonesPairScore.html#a61febfb6e0f4bae2efc5e651cfabd004">IMP::atom::LennardJonesPairScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1atom_1_1LennardJonesPairScore.html#a855fd8676d9c382c7835ec4807fc0072">IMP::atom::LennardJonesPairScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1bayesianem_1_1GaussianEMRestraint.html#abc2e64a980df57a59cd333768783ea55">IMP::bayesianem::GaussianEMRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1container_1_1DistributePairsScoreState.html#afac588a484ef18a2648d16d37948a276">IMP::container::DistributePairsScoreState::do_after_evaluate()</a>, <a href="classIMP_1_1container_1_1DistributeQuadsScoreState.html#a9dbf58c05b3531fa97156b06b415761b">IMP::container::DistributeQuadsScoreState::do_after_evaluate()</a>, <a href="classIMP_1_1container_1_1DistributeSingletonsScoreState.html#a7c41bfe41546385bc1677f5b9814a148">IMP::container::DistributeSingletonsScoreState::do_after_evaluate()</a>, <a href="classIMP_1_1container_1_1DistributeTripletsScoreState.html#a451f4cfc5fd99b0b3ca458865315e399">IMP::container::DistributeTripletsScoreState::do_after_evaluate()</a>, <a href="classIMP_1_1container_1_1MinimumPairRestraint.html#aa8f092ce69207d297d7f9d7e265d41b0">IMP::container::MinimumPairRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1container_1_1MinimumPairScore.html#a093437078a4c6cfd96e6564f76ecc5a8">IMP::container::MinimumPairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1container_1_1MinimumPairScore.html#aadf933116206b7529022070fe28784e0">IMP::container::MinimumPairScore::evaluate_index()</a>, <a href="classIMP_1_1container_1_1MinimumPairScore.html#a293ad87fce895b420bb8bb28ff19d0ad">IMP::container::MinimumPairScore::evaluate_indexes()</a>, <a href="classIMP_1_1container_1_1MinimumPairScore.html#af6c86e5fe57860987c4cfbf32308ad31">IMP::container::MinimumPairScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1container_1_1MinimumPairScore.html#ad5ea70d3c2f3410b0be186f85a831d24">IMP::container::MinimumPairScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1container_1_1MinimumQuadRestraint.html#a8b2274d953f908d4a7379f37bcb3af4b">IMP::container::MinimumQuadRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1container_1_1MinimumQuadScore.html#a86419c33fda9949ce91094f881674bf9">IMP::container::MinimumQuadScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1container_1_1MinimumQuadScore.html#aea9a974238cabbb952d8654c147190f7">IMP::container::MinimumQuadScore::evaluate_index()</a>, <a href="classIMP_1_1container_1_1MinimumQuadScore.html#a8053b92488d053ca3abb16403f800948">IMP::container::MinimumQuadScore::evaluate_indexes()</a>, <a href="classIMP_1_1container_1_1MinimumQuadScore.html#a21f967a4065e3be25c5baab88ada533c">IMP::container::MinimumQuadScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1container_1_1MinimumQuadScore.html#aee38323343aa1e116884e710403a0a17">IMP::container::MinimumQuadScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1container_1_1MinimumSingletonRestraint.html#a7ae2ef49b43adf416ea8f39052d5c303">IMP::container::MinimumSingletonRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1container_1_1MinimumSingletonScore.html#a5dcbfcdc0bee19b0c9c85211a482376e">IMP::container::MinimumSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1container_1_1MinimumSingletonScore.html#af4da1b4298727bc4c3e8c437550612a4">IMP::container::MinimumSingletonScore::evaluate_index()</a>, <a href="classIMP_1_1container_1_1MinimumSingletonScore.html#aba3c37a22496d69bdc8694ed3e64f85c">IMP::container::MinimumSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1container_1_1MinimumSingletonScore.html#ab592ddf3161a42aa7adbfb946f1e58ad">IMP::container::MinimumSingletonScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1container_1_1MinimumSingletonScore.html#aaaf11fddf57436514eba2b8260ac237b">IMP::container::MinimumSingletonScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1container_1_1MinimumTripletRestraint.html#aeb502a0766bb46e7cee24217aaf2960a">IMP::container::MinimumTripletRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1container_1_1MinimumTripletScore.html#ac26525589070e653665e332b37f512bb">IMP::container::MinimumTripletScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1container_1_1MinimumTripletScore.html#ab27c7faa98447eeb691bdf5e7ae99b6b">IMP::container::MinimumTripletScore::evaluate_index()</a>, <a href="classIMP_1_1container_1_1MinimumTripletScore.html#aa7cec24d49a9de3493c488164b0c79a6">IMP::container::MinimumTripletScore::evaluate_indexes()</a>, <a href="classIMP_1_1container_1_1MinimumTripletScore.html#a86425eb8757e8c18849b397cd2e71663">IMP::container::MinimumTripletScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1container_1_1MinimumTripletScore.html#ae7a6be3a483414c9e211603f36fd1173">IMP::container::MinimumTripletScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1container_1_1PairContainerStatistics.html#a925b3bba141ee6816450216f6d1ffc37">IMP::container::PairContainerStatistics::do_after_evaluate()</a>, <a href="classIMP_1_1container_1_1PairsConstraint.html#ae3eb0ba076119a1920cdc9894812086e">IMP::container::PairsConstraint::do_update_derivatives()</a>, <a href="classIMP_1_1container_1_1PairsRestraint.html#ab1d8f6f04efea2b56c6ed160e791102b">IMP::container::PairsRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1container_1_1QuadContainerStatistics.html#ad7512cf9b852c85532f901a37e7fede3">IMP::container::QuadContainerStatistics::do_after_evaluate()</a>, <a href="classIMP_1_1container_1_1QuadsConstraint.html#a20864d6bc38c8ae7978e370eb1048d9e">IMP::container::QuadsConstraint::do_update_derivatives()</a>, <a href="classIMP_1_1container_1_1QuadsRestraint.html#a65e9e9c6055568e4c95e494f5672c552">IMP::container::QuadsRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1container_1_1SingletonContainerStatistics.html#a05ede8bfea18c073ce24d653c10894d6">IMP::container::SingletonContainerStatistics::do_after_evaluate()</a>, <a href="classIMP_1_1container_1_1SingletonsConstraint.html#ad9beb4e1e754200f3dad439c4b4d8401">IMP::container::SingletonsConstraint::do_update_derivatives()</a>, <a href="classIMP_1_1container_1_1SingletonsRestraint.html#a3b2a3bff298c6b911b5de2a8a9b61944">IMP::container::SingletonsRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1container_1_1TripletContainerStatistics.html#a453236ace527c6eb6104b84a735662dc">IMP::container::TripletContainerStatistics::do_after_evaluate()</a>, <a href="classIMP_1_1container_1_1TripletsConstraint.html#acffc5e03f70999cc19bdc9d9a6f231d0">IMP::container::TripletsConstraint::do_update_derivatives()</a>, <a href="classIMP_1_1container_1_1TripletsRestraint.html#ad0165626b45526205c58ce4315fc4411">IMP::container::TripletsRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1core_1_1AngleTripletScore.html#aa3ad54b2c68335f37dee2ef9a9115002">IMP::core::AngleTripletScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1core_1_1AngleTripletScore.html#a16b511c7018f830ad10a16c820440c98">IMP::core::AngleTripletScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1AngleTripletScore.html#a593e8ebdd6dfa3e9c1f61b6526e14696">IMP::core::AngleTripletScore::evaluate_indexes()</a>, <a href="classIMP_1_1core_1_1AngleTripletScore.html#a9926c9ec4bed73b3bea3123ce75309eb">IMP::core::AngleTripletScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1core_1_1AngleTripletScore.html#a3d93c526c58b5aa48323e7efbe82f49e">IMP::core::AngleTripletScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1core_1_1ChecksScoreState.html#a393abb9375f2c23b64885ca611630b0a">IMP::core::ChecksScoreState::do_after_evaluate()</a>, <a href="classIMP_1_1core_1_1ClosePairsPairScore.html#a4bbdf31e1ae0749a0345aa4b084eaa7b">IMP::core::ClosePairsPairScore::evaluate_if_good_index()</a>, <a href="classIMP_1_1core_1_1ClosePairsPairScore.html#a96c436e7440e3ca896275efb75bfcbc0">IMP::core::ClosePairsPairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1core_1_1ClosePairsPairScore.html#a18eea2087eeccc46150a7c078e5db25e">IMP::core::ClosePairsPairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1ClosePairsPairScore.html#a47f3ad4d6a507f7c4971f2dd21b76c0d">IMP::core::ClosePairsPairScore::evaluate_indexes()</a>, <a href="classIMP_1_1core_1_1ClosePairsPairScore.html#a403711d274a28b57b8e889825eb9e0f9">IMP::core::ClosePairsPairScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1core_1_1ClosePairsPairScore.html#a51ef62441996b80bc54a2906ab0ed7c0">IMP::core::ClosePairsPairScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1core_1_1ConnectivityRestraint.html#a3d4b5e6a6a49881fedcde125d8f16571">IMP::core::ConnectivityRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1core_1_1ConstantRestraint.html#a5d97c3b5b65be1d3eeb876d5ed7e2943">IMP::core::ConstantRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1core_1_1DiameterRestraint.html#aea50108b757e44b7b896fff3b504e335">IMP::core::DiameterRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1core_1_1DihedralRestraint.html#af4c966e476a0b3b6b6db334786dc50e8">IMP::core::DihedralRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1core_1_1Direction.html#ab7b6e17001f735bb4d272842eab34edf">IMP::core::Direction::add_to_direction_derivative()</a>, <a href="classIMP_1_1core_1_1Direction.html#a36d0385a6ecb80ad27503530d60ca8b6">IMP::core::Direction::add_to_direction_derivatives()</a>, <a href="classIMP_1_1core_1_1DirectionAngle.html#ac3624eaedc2cfc66aac72c7cfe5fae24">IMP::core::DirectionAngle::add_to_angle_derivative()</a>, <a href="classIMP_1_1core_1_1DistancePairScore.html#a1f69d849e2cd4451c580669d57b08a23">IMP::core::DistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1ExcludedVolumeRestraint.html#a0fcc559c7dd9326814d4cf43b683bdf8">IMP::core::ExcludedVolumeRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1core_1_1GenericAttributeSingletonScore.html#ac08553a44f5431458ef1726cbf5fa412">IMP::core::GenericAttributeSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1core_1_1GenericAttributeSingletonScore.html#a6097af61a61ec8a1314efcacffd7c8d6">IMP::core::GenericAttributeSingletonScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1GenericAttributeSingletonScore.html#a1110467dc8c2d176d244a4fe7740afe5">IMP::core::GenericAttributeSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1core_1_1GenericAttributeSingletonScore.html#a7b88a951501e6ac69f59247148fc6721">IMP::core::GenericAttributeSingletonScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1core_1_1GenericAttributeSingletonScore.html#a33c00df5d2c0813886a637d5de0ed529">IMP::core::GenericAttributeSingletonScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1core_1_1GenericBoundingBox3DSingletonScore.html#a04625a228cade49bf22f3bb30475f4b8">IMP::core::GenericBoundingBox3DSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1core_1_1GenericBoundingBox3DSingletonScore.html#afcb4a6e63082a4ddd192791ad21fe79a">IMP::core::GenericBoundingBox3DSingletonScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1GenericBoundingBox3DSingletonScore.html#a0393df9fd8e034fcfe47e3e7bb7ec113">IMP::core::GenericBoundingBox3DSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1core_1_1GenericBoundingBox3DSingletonScore.html#a690cd1988db7fbf97811be8722822054">IMP::core::GenericBoundingBox3DSingletonScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1core_1_1GenericBoundingBox3DSingletonScore.html#a08383123609392bff2dd3cc6869631d4">IMP::core::GenericBoundingBox3DSingletonScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1core_1_1GenericBoundingSphere3DSingletonScore.html#ab712e8cbd70c00f776eacf8ef02fc37e">IMP::core::GenericBoundingSphere3DSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1core_1_1GenericBoundingSphere3DSingletonScore.html#a64244487203b279812fcf0420d1109f4">IMP::core::GenericBoundingSphere3DSingletonScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1GenericBoundingSphere3DSingletonScore.html#a49ec02d56efc9f7e949680934aadf0a5">IMP::core::GenericBoundingSphere3DSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1core_1_1GenericBoundingSphere3DSingletonScore.html#a1754cfe7b3d7f3ce30ea5c9c7cbeaaa7">IMP::core::GenericBoundingSphere3DSingletonScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1core_1_1GenericBoundingSphere3DSingletonScore.html#af209e14f62168fe09fef7e3e4ec2ff5a">IMP::core::GenericBoundingSphere3DSingletonScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1core_1_1GenericDistanceToSingletonScore.html#a1f787d0844c9a36fae2da0215afab271">IMP::core::GenericDistanceToSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1core_1_1GenericDistanceToSingletonScore.html#a65bbc6e5e434068c01d8333c8228c4d4">IMP::core::GenericDistanceToSingletonScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1GenericDistanceToSingletonScore.html#a1db4302e9f5afde1e643da0b6863fac7">IMP::core::GenericDistanceToSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1core_1_1GenericDistanceToSingletonScore.html#ac812e2e81f059642613603217b99d42a">IMP::core::GenericDistanceToSingletonScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1core_1_1GenericDistanceToSingletonScore.html#a0063febf20d887a0f353146daed7e14a">IMP::core::GenericDistanceToSingletonScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1core_1_1HarmonicDistancePairScore.html#aed2d6296770d0a56bc4cb4dd538bb885">IMP::core::HarmonicDistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1HarmonicSphereDistancePairScore.html#ae9466826ffafba100c7270bdca3d8fe0">IMP::core::HarmonicSphereDistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1HarmonicSurfaceDepthPairScore.html#a5df05ea8490df6d61ca1d805a1468c2d">IMP::core::HarmonicSurfaceDepthPairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1HarmonicSurfaceDistancePairScore.html#ab76420cbb54f896753104866c355dc11">IMP::core::HarmonicSurfaceDistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1HarmonicSurfaceHeightPairScore.html#a556f8d81f4bb461b2f5a21752cca7e89">IMP::core::HarmonicSurfaceHeightPairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1HarmonicUpperBoundSphereDiameterPairScore.html#af7c6caa5ab280c43dec5f27dea27e6c4">IMP::core::HarmonicUpperBoundSphereDiameterPairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1core_1_1HarmonicUpperBoundSphereDiameterPairScore.html#a94f3ed8283c89625522a6d27bfbdf698">IMP::core::HarmonicUpperBoundSphereDiameterPairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1HarmonicUpperBoundSphereDiameterPairScore.html#a0d94bea22e912440193e3cd0f2c76f0c">IMP::core::HarmonicUpperBoundSphereDiameterPairScore::evaluate_indexes()</a>, <a href="classIMP_1_1core_1_1HarmonicUpperBoundSphereDiameterPairScore.html#a09cb6cfc1e98676d8c9187c17cc98a62">IMP::core::HarmonicUpperBoundSphereDiameterPairScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1core_1_1HarmonicUpperBoundSphereDiameterPairScore.html#a9e79e760cc4e1f08e25bb1a7d0c7b7a2">IMP::core::HarmonicUpperBoundSphereDiameterPairScore::evaluate_indexes_scores()</a>, <a 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href="classIMP_1_1core_1_1KClosePairsPairScore.html#a87ebcdd22517a7e6890e02be1821eafe">IMP::core::KClosePairsPairScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1core_1_1LateralSurfaceConstraint.html#a9a5c79ab074fbcaa1c4eb09e38245505">IMP::core::LateralSurfaceConstraint::do_after_evaluate()</a>, <a href="classIMP_1_1core_1_1LateralSurfaceConstraint.html#a13b49b596d641a4bde8d19a946acfd39">IMP::core::LateralSurfaceConstraint::do_update_derivatives()</a>, <a href="classIMP_1_1core_1_1MSConnectivityRestraint.html#acb1a80f4698d6c883fbd63946ea0e809">IMP::core::MSConnectivityRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1core_1_1MinimumRestraint.html#abf85fa1e2a73fba4cbc31960b8a2f298">IMP::core::MinimumRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1core_1_1MoveStatisticsScoreState.html#a8bb48ae2ca9db887598eb97926745aac">IMP::core::MoveStatisticsScoreState::do_after_evaluate()</a>, <a 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href="classIMP_1_1core_1_1NormalizedSphereDistancePairScore.html#a94af6c3fcd755f545fbb7fe4cd3f8565">IMP::core::NormalizedSphereDistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1NormalizedSphereDistancePairScore.html#a8269a546af5f6e6be743c29f5c9009ba">IMP::core::NormalizedSphereDistancePairScore::evaluate_indexes()</a>, <a href="classIMP_1_1core_1_1NormalizedSphereDistancePairScore.html#af7956dd19c6e54530ec94c767feff3a9">IMP::core::NormalizedSphereDistancePairScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1core_1_1NormalizedSphereDistancePairScore.html#aa1646fe8eb02964f44c5f1f01f3d1c61">IMP::core::NormalizedSphereDistancePairScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1core_1_1PairConstraint.html#ae7f1e8aeebe4e84aec1897dcfc093767">IMP::core::PairConstraint::do_update_derivatives()</a>, <a href="classIMP_1_1core_1_1PairRestraint.html#a7a8085fa3a66010e2c4159f9c5caa707">IMP::core::PairRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1core_1_1PredicateSingletonScore.html#aa6f250ec1b7e2b3a6c316b4d8cc0bb37">IMP::core::PredicateSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1core_1_1PredicateSingletonScore.html#a807727fc8832d340dec557f9e9b8141b">IMP::core::PredicateSingletonScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1PredicateSingletonScore.html#af45e73299e2573c9e5db84608665278e">IMP::core::PredicateSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1core_1_1PredicateSingletonScore.html#ae2e30a890eb062400e507101eee59d54">IMP::core::PredicateSingletonScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1core_1_1PredicateSingletonScore.html#a8a23573ff201053c2cf7285d93dc38c4">IMP::core::PredicateSingletonScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1core_1_1QuadConstraint.html#a4b11f32c0d5d356f4813626cf9eaa982">IMP::core::QuadConstraint::do_update_derivatives()</a>, <a href="classIMP_1_1core_1_1QuadRestraint.html#af1dd15f17f01c856bad994391e8e5db3">IMP::core::QuadRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1core_1_1RefinedPairsPairScore.html#ad27ebd3c6882f169b9b3482d452b9cab">IMP::core::RefinedPairsPairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1core_1_1RefinedPairsPairScore.html#a3e51f509481e35942000264b59ea287d">IMP::core::RefinedPairsPairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1RefinedPairsPairScore.html#a9bd8677611fa1dc1af648b6f62d340ec">IMP::core::RefinedPairsPairScore::evaluate_indexes()</a>, <a href="classIMP_1_1core_1_1RefinedPairsPairScore.html#a7f56f3741d648c6847bf4ea702e2446e">IMP::core::RefinedPairsPairScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1core_1_1RefinedPairsPairScore.html#a1466a6f9490060a2a925db42b11a1567">IMP::core::RefinedPairsPairScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#aabf0d8453abcc3f28d4bf79c4d4992bd">IMP::core::RigidBody::add_to_derivatives()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#a91be8fde5bc2268a05b278e4b09ffd14">IMP::core::RigidBody::add_to_derivatives()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#adb1dbd74e7b5480c0827d699aac15be2">IMP::core::RigidBody::add_to_rotational_derivatives()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#a3f7f96649672956c8a6a310a73d27246">IMP::core::RigidBody::add_to_rotational_derivatives()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#aaa97333f82d88a313b50f49c8dc27282">IMP::core::RigidBody::add_to_torque()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#acd363de11c4b00cffe8168e4a24e98ab">IMP::core::RigidBody::pull_back_body_member_adjoints()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#aed2dde23e30fbcf168f174798fa911d1">IMP::core::RigidBody::pull_back_body_member_adjoints()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#a60c0f68f45958e090c6144b9b59e434c">IMP::core::RigidBody::pull_back_member_adjoints()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#a76e5fbad51df6a7b03992147afa7951d">IMP::core::RigidBody::pull_back_member_adjoints()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#a9dcdf464d9fda38db8d3acb760e4f814">IMP::core::RigidBody::pull_back_members_adjoints()</a>, <a href="classIMP_1_1core_1_1RigidBodyAnglePairScore.html#a77ee6203343417ea9350e258664728d6">IMP::core::RigidBodyAnglePairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1core_1_1RigidBodyAnglePairScore.html#ac255f86cb1205429a47532616a4b8444">IMP::core::RigidBodyAnglePairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1RigidBodyAnglePairScore.html#ab49116ba13ddbee3850a67671c5faac9">IMP::core::RigidBodyAnglePairScore::evaluate_indexes()</a>, <a href="classIMP_1_1core_1_1RigidBodyAnglePairScore.html#acb53dca0e3f1edc7063e4090d5313c25">IMP::core::RigidBodyAnglePairScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1core_1_1RigidBodyAnglePairScore.html#aec17357e0a3e5be57647b63e1d64d26d">IMP::core::RigidBodyAnglePairScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1core_1_1RigidBodyUmbrella.html#a09efb02eaef0b34bcab14f9c927a737a">IMP::core::RigidBodyUmbrella::unprotected_evaluate()</a>, <a href="classIMP_1_1core_1_1SingletonConstraint.html#a083237238d8d9ed0519af42076bab71c">IMP::core::SingletonConstraint::do_update_derivatives()</a>, <a href="classIMP_1_1core_1_1SingletonRestraint.html#a5d682d72bca5443f4d4499a880def61d">IMP::core::SingletonRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1core_1_1SoftSpherePairScore.html#a4072dd6c5bf8f0863c60a450bc9b943d">IMP::core::SoftSpherePairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1SoftSubSurfacePairScore.html#a38120e0273c77f9a47a77ddedd41fe64">IMP::core::SoftSubSurfacePairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1SoftSuperSurfacePairScore.html#af9bf50705ca303d95ae729e374b46699">IMP::core::SoftSuperSurfacePairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1SphereDistancePairScore.html#a3e39ff56be09a4dbe371e69a0442ce1b">IMP::core::SphereDistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1SphereDistanceToSingletonScore.html#ae1606d9a5c95f1a9c83ffecaff835c51">IMP::core::SphereDistanceToSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1core_1_1SphereDistanceToSingletonScore.html#af02cf511d3f40bf8c6ec9aab886897ea">IMP::core::SphereDistanceToSingletonScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1SphereDistanceToSingletonScore.html#ae84c1887eaff11bf6f332d67a8523e45">IMP::core::SphereDistanceToSingletonScore::evaluate_indexes()</a>, <a 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href="classIMP_1_1core_1_1SurfaceGeometryConstraint.html#a114be28ef9dfa5c5bddf851e8ad2ce3c">IMP::core::SurfaceGeometryConstraint::do_after_evaluate()</a>, <a href="classIMP_1_1core_1_1SurfaceGeometryConstraint.html#ab3f7902b79fb6bd3a1223f5864f18d22">IMP::core::SurfaceGeometryConstraint::do_update_derivatives()</a>, <a href="classIMP_1_1core_1_1SurfaceHeightPairScore.html#aa1bb4ff369d3080ebc3f47875ed9b163">IMP::core::SurfaceHeightPairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1SurfaceSymmetryConstraint.html#af99ada61d4825e6c12c8cc2bfb97eedd">IMP::core::SurfaceSymmetryConstraint::do_update_derivatives()</a>, <a href="classIMP_1_1core_1_1TransformedDistancePairScore.html#ada1c9d595076e186ff53f31420558395">IMP::core::TransformedDistancePairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1core_1_1TransformedDistancePairScore.html#afad8b302e2264283b840e700a506a64b">IMP::core::TransformedDistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1TransformedDistancePairScore.html#a9430b597c9aa935a28f054e0dd2b3fb3">IMP::core::TransformedDistancePairScore::evaluate_indexes()</a>, <a href="classIMP_1_1core_1_1TransformedDistancePairScore.html#a4b4b418ca257904da9327bb9ff4d41b3">IMP::core::TransformedDistancePairScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1core_1_1TransformedDistancePairScore.html#ac4daa6bb1547632e5b13f475435037a2">IMP::core::TransformedDistancePairScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1core_1_1TripletConstraint.html#a3acebcde3078b56e87f452664ac5b770">IMP::core::TripletConstraint::do_update_derivatives()</a>, <a href="classIMP_1_1core_1_1TripletRestraint.html#ab072fa0749adfe27a4e7bc671d744135">IMP::core::TripletRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1core_1_1TypedPairScore.html#aa404fc6299e5dbb3f70fc46920b1bd3f">IMP::core::TypedPairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1core_1_1TypedPairScore.html#a1ed4bcaaa82f6a137b77d16336b8dee6">IMP::core::TypedPairScore::evaluate_index()</a>, <a href="classIMP_1_1core_1_1TypedPairScore.html#a4157c25d4684efa01f5a02b890b64995">IMP::core::TypedPairScore::evaluate_indexes()</a>, <a href="classIMP_1_1core_1_1TypedPairScore.html#a0bfa089127a6920bf332e8ccd732b831">IMP::core::TypedPairScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1core_1_1TypedPairScore.html#a9a024fa1870c48ef42b3169bbe4de76d">IMP::core::TypedPairScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1core_1_1VolumeRestraint.html#a0d6011c108d3de21eae1c9a682eba476">IMP::core::VolumeRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1core_1_1WeightedSphereDistancePairScore.html#acf64e46c1a96f283936628d3c575e499">IMP::core::WeightedSphereDistancePairScore::evaluate_if_good_indexes()</a>, <a 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href="classIMP_1_1core_1_1XYZR.html#a553d9c8fb026a64e0ebe314db0729dd3">IMP::core::XYZR::add_to_radius_derivative()</a>, <a href="classIMP_1_1domino_1_1DependencyScoreState.html#abf2c152c7b1942f1f986734bcb18f3b6">IMP::domino::DependencyScoreState::do_after_evaluate()</a>, <a href="classIMP_1_1em2d_1_1DummyRestraint.html#a9f0202201cabc19da9841d7047ce57c0">IMP::em2d::DummyRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1em2d_1_1Em2DRestraint.html#ae5f820abb7785b95b5576cb5fcacf797">IMP::em2d::Em2DRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1em2d_1_1Fine2DRegistrationRestraint.html#a2e1d3015f782313eaa4bbc7033705453">IMP::em2d::Fine2DRegistrationRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1em2d_1_1PCAFitRestraint.html#a9cfd0a5eb4306b94189b17c52fbf10a0">IMP::em2d::PCAFitRestraint::unprotected_evaluate()</a>, <a 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href="classIMP_1_1em_1_1FitRestraint.html#a2d94c31c2db338417c5f141da5a940a5">IMP::em::FitRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1em_1_1FitRestraintBayesEM3D.html#a7a02af4d4addfdcbf4974c19ee9504a0">IMP::em::FitRestraintBayesEM3D::unprotected_evaluate()</a>, <a href="classIMP_1_1em_1_1PCAFitRestraint.html#a4235db8b0fa86db888579a55dad3af3e">IMP::em::PCAFitRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1example_1_1ExampleComplexRestraint.html#a6b7f3fbabb34b99f753ebb6b258c5627">IMP::example::ExampleComplexRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1example_1_1ExampleConstraint.html#ae3f5eea14b73d7ef538f715a8d30e151">IMP::example::ExampleConstraint::do_update_derivatives()</a>, <a href="classIMP_1_1example_1_1ExamplePairScore.html#a9f265046c5c001ced314701a19d8f420">IMP::example::ExamplePairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1example_1_1ExamplePairScore.html#ac4a6da957157e308a3226b3d73f478ff">IMP::example::ExamplePairScore::evaluate_index()</a>, <a href="classIMP_1_1example_1_1ExamplePairScore.html#a177f9b5efa1a234f21564f0d452f4e9c">IMP::example::ExamplePairScore::evaluate_indexes()</a>, <a href="classIMP_1_1example_1_1ExamplePairScore.html#a145439064a238d7606e00e46fddeb6d7">IMP::example::ExamplePairScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1example_1_1ExamplePairScore.html#abda5235092e6bfc7a19268e33b954719">IMP::example::ExamplePairScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1isd_1_1AmbiguousNOERestraint.html#a74e86d0521ea1a849be2373a3324f726">IMP::isd::AmbiguousNOERestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1AmbiguousRestraint.html#a09a5c2f7a30e5c3eb24dde72a589c5d5">IMP::isd::AmbiguousRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1AtomicCrossLinkMSRestraint.html#a665598a272032c7c355c0891c166b35c">IMP::isd::AtomicCrossLinkMSRestraint::evaluate_for_contributions()</a>, <a href="classIMP_1_1isd_1_1AtomicCrossLinkMSRestraint.html#ac87450e1986bdb7c4b03b847a4566436">IMP::isd::AtomicCrossLinkMSRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1BivariateFunction.html#a7c37b4ca75b7495b64e75d79b602651c">IMP::isd::BivariateFunction::add_to_derivatives()</a>, <a href="classIMP_1_1isd_1_1BivariateFunction.html#a820515ded9a817d40ca3ed1c6d4cc5c9">IMP::isd::BivariateFunction::add_to_particle_derivative()</a>, <a href="classIMP_1_1isd_1_1Covariance1DFunction.html#a702c5e7cb944f9e1b12e2c238754c75f">IMP::isd::Covariance1DFunction::add_to_derivatives()</a>, <a href="classIMP_1_1isd_1_1Covariance1DFunction.html#a97c4435da9ac10e5d34e396afdebf7d1">IMP::isd::Covariance1DFunction::add_to_particle_derivative()</a>, <a href="classIMP_1_1isd_1_1CrossLinkMSRestraint.html#a464dd562cfa6f8e729c4486b8511e980">IMP::isd::CrossLinkMSRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1CysteineCrossLinkRestraint.html#ad2c87e284393d2b7d857594013daed5c">IMP::isd::CysteineCrossLinkRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1FretRestraint.html#add1c6f000354065bd29a668c7b307e4a">IMP::isd::FretRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1GammaPrior.html#a91f8b220e4631c2a486a685398c755ea">IMP::isd::GammaPrior::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1GaussianAnchorEMRestraint.html#a9438918f67fb92c89bea1ad67c995f23">IMP::isd::GaussianAnchorEMRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1GaussianEMRestraint.html#a6554a36678c640d3169c3eed1ca5b351">IMP::isd::GaussianEMRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1GaussianProcessInterpolation.html#ab355cd74ffbc6ec3d225451028415c1b">IMP::isd::GaussianProcessInterpolation::add_to_m_particle_derivative()</a>, <a href="classIMP_1_1isd_1_1GaussianProcessInterpolation.html#a55d17b93b6e6e66d9d16c793f0dc4c95">IMP::isd::GaussianProcessInterpolation::add_to_Omega_particle_derivative()</a>, <a href="classIMP_1_1isd_1_1GaussianProcessInterpolationRestraint.html#ab44daa2028ad089af4137fc3003fc5b3">IMP::isd::GaussianProcessInterpolationRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1GaussianRestraint.html#a8ba282a40da68082969170a3e94c5340">IMP::isd::GaussianRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1GeneralizedGuinierPorodFunction.html#a2376feb4346659b99929bbca48a6295d">IMP::isd::GeneralizedGuinierPorodFunction::add_to_derivatives()</a>, <a href="classIMP_1_1isd_1_1GeneralizedGuinierPorodFunction.html#ac92728776ff35979e310525e600fa471">IMP::isd::GeneralizedGuinierPorodFunction::add_to_particle_derivative()</a>, <a href="classIMP_1_1isd_1_1ISDRestraint.html#a85f80cb8a1c163b53c68bdad45a21e3b">IMP::isd::ISDRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1JeffreysRestraint.html#ad9284de3e435443d6c6453bd9daa0f5a">IMP::isd::JeffreysRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1Linear1DFunction.html#a1cce9f29722819905f0cec887f9b5f49">IMP::isd::Linear1DFunction::add_to_derivatives()</a>, <a href="classIMP_1_1isd_1_1Linear1DFunction.html#aeedfae66d663e515dfc2c4ff1a40993e">IMP::isd::Linear1DFunction::add_to_particle_derivative()</a>, <a href="classIMP_1_1isd_1_1LogWrapper.html#ab176d5909f19dcb90d42241f5349f99d">IMP::isd::LogWrapper::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1LogWrapper.html#a5142469b8e566bb953dfc9584a486dd8">IMP::isd::LogWrapper::unprotected_evaluate_moved()</a>, <a href="classIMP_1_1isd_1_1LognormalAmbiguousRestraint.html#a871bf4ecfb2f704b3ae417b55c89eff9">IMP::isd::LognormalAmbiguousRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1LognormalRestraint.html#afe206145a41dc7b2d44d5bb2b0d75be6">IMP::isd::LognormalRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1MarginalHBondRestraint.html#a6b43ececaa09880c2111d9fdab69abeb">IMP::isd::MarginalHBondRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1MarginalNOERestraint.html#a5737599ba3f5f4d1c830d54ecf2a57a1">IMP::isd::MarginalNOERestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1NOERestraint.html#a6ca68d4359f2acdae6e6f880475314bf">IMP::isd::NOERestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1NormalSigmaPCRestraint.html#a6ab7c604f3447c4a52284a97b7fb2b26">IMP::isd::NormalSigmaPCRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1Nuisance.html#a46afd4c51e289fa1ba38d6221b7379c7">IMP::isd::Nuisance::add_to_nuisance_derivative()</a>, <a href="classIMP_1_1isd_1_1RepulsiveDistancePairScore.html#a9557ccab40bc8051fd5911ca9a12f68a">IMP::isd::RepulsiveDistancePairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1isd_1_1RepulsiveDistancePairScore.html#a67fd255da53a5e6a9b4ae32102ff07f4">IMP::isd::RepulsiveDistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1isd_1_1RepulsiveDistancePairScore.html#afb354bf17e26b6643e212e7abadb4056">IMP::isd::RepulsiveDistancePairScore::evaluate_indexes()</a>, <a href="classIMP_1_1isd_1_1RepulsiveDistancePairScore.html#a9c149f53b6fba2c0097d2a618c5c90b5">IMP::isd::RepulsiveDistancePairScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1isd_1_1RepulsiveDistancePairScore.html#a8edfec5a43654bc34384200017df9fb2">IMP::isd::RepulsiveDistancePairScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1isd_1_1Scale.html#af55aa24c314c30f4953b8fbf2ab85821">IMP::isd::Scale::add_to_scale_derivative()</a>, <a href="classIMP_1_1isd_1_1StudentTRestraint.html#a350349f8f2d6caa43154c634b46abe6a">IMP::isd::StudentTRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1Switching.html#af0055c458c9b69ebdac628ff9bfcf556">IMP::isd::Switching::add_to_switching_derivative()</a>, <a href="classIMP_1_1isd_1_1TALOSRestraint.html#a155b3c588ec41f4eb83fad4f2401fea8">IMP::isd::TALOSRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1UniformPrior.html#affde93fda96ec1582be514dc7e597360">IMP::isd::UniformPrior::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1UnivariateFunction.html#afe6f16c49b043203baa74ea289b1dbbb">IMP::isd::UnivariateFunction::add_to_derivatives()</a>, <a href="classIMP_1_1isd_1_1UnivariateFunction.html#a79ae543aef5c6911c2ef4c99b1d27ffd">IMP::isd::UnivariateFunction::add_to_particle_derivative()</a>, <a href="classIMP_1_1isd_1_1Weight.html#a5011bbab25979e157b8facacf7b13295">IMP::isd::Weight::add_to_weight_derivative()</a>, <a href="classIMP_1_1isd_1_1Weight.html#adf3c062686fa4344880e07cadca76a60">IMP::isd::Weight::add_to_weights_derivatives()</a>, <a href="classIMP_1_1isd_1_1WeightRestraint.html#a77920bbb351bc19dbced87ade5a8d17b">IMP::isd::WeightRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1vonMisesKappaConjugateRestraint.html#a1369d919ed1faa96111c457e44b5762f">IMP::isd::vonMisesKappaConjugateRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1isd_1_1vonMisesKappaJeffreysRestraint.html#ae16fe28f3c0edb644e2cb99939634d1a">IMP::isd::vonMisesKappaJeffreysRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1kinematics_1_1KinematicForestScoreState.html#a591d7293a283c1a265d58469d78382a3">IMP::kinematics::KinematicForestScoreState::do_after_evaluate()</a>, <a href="classIMP_1_1misc_1_1CustomXYZR.html#abbeaea01860116473babd3cffb8ac942">IMP::misc::CustomXYZR::add_to_radius_derivative()</a>, <a href="classIMP_1_1misc_1_1LogPairScore.html#af6827dfecb55be161b7c6ea9f18ae184">IMP::misc::LogPairScore::evaluate_index()</a>, <a href="classIMP_1_1misc_1_1LowestRefinedPairScore.html#a746384a8c50e6cd1559923d00d147858">IMP::misc::LowestRefinedPairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1misc_1_1LowestRefinedPairScore.html#aa8a680cbf62bf672e3612f6adb50211c">IMP::misc::LowestRefinedPairScore::evaluate_index()</a>, <a href="classIMP_1_1misc_1_1LowestRefinedPairScore.html#a1cdb5f4d8cad0071891420908ec153cb">IMP::misc::LowestRefinedPairScore::evaluate_indexes()</a>, <a href="classIMP_1_1misc_1_1LowestRefinedPairScore.html#a55b1572a8d1040bdbad7b3841832a9bc">IMP::misc::LowestRefinedPairScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1misc_1_1LowestRefinedPairScore.html#ace151f4f97e0d5f5e6a230b81bfc4c21">IMP::misc::LowestRefinedPairScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1misc_1_1SoftCylinderPairScore.html#a3c3720248e16cb26a2825086b8a59c9c">IMP::misc::SoftCylinderPairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1misc_1_1SoftCylinderPairScore.html#aa29d2902b769e0fc842595c55e3c683a">IMP::misc::SoftCylinderPairScore::evaluate_index()</a>, <a href="classIMP_1_1misc_1_1SoftCylinderPairScore.html#a0181fb4dc8f01ba9d44d133c510b779b">IMP::misc::SoftCylinderPairScore::evaluate_indexes()</a>, <a href="classIMP_1_1misc_1_1SoftCylinderPairScore.html#aa439ce0d33a443422d3f037e4cdb6724">IMP::misc::SoftCylinderPairScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1misc_1_1SoftCylinderPairScore.html#a14fac6c2a244f6b3725ea48bcb100bda">IMP::misc::SoftCylinderPairScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1misc_1_1StateAdaptor.html#aa1a407433d676e7fa6f861dc02775861">IMP::misc::StateAdaptor::do_after_evaluate()</a>, <a href="classIMP_1_1multifit_1_1ComplementarityRestraint.html#a910029be0b4dd96f0fe93e96f7364d97">IMP::multifit::ComplementarityRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1multifit_1_1DummyRestraint.html#a029c49322c58a7f9f14f8f6ec8a6276e">IMP::multifit::DummyRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1multifit_1_1RadiusOfGyrationRestraint.html#a6b82e09f1471edc10fce781b321b8c30">IMP::multifit::RadiusOfGyrationRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1multifit_1_1WeightedExcludedVolumeRestraint.html#a85ec29b54b556c8532a55bdaac67894c">IMP::multifit::WeightedExcludedVolumeRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1npc_1_1AssemblySymmetryByDihedralRestraint.html#ae5da68ff1959ef4ff642205fa98068e8">IMP::npc::AssemblySymmetryByDihedralRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1npc_1_1AssemblySymmetryByDistanceRestraint.html#aa69efb552dca3e9942b0f5db60344add">IMP::npc::AssemblySymmetryByDistanceRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1npc_1_1CompositeRestraint.html#a8623850dcf6ab4367212c513839757e0">IMP::npc::CompositeRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1npc_1_1MembraneExclusionRestraint.html#a3274ece4c8b344010fe414097b0fec9d">IMP::npc::MembraneExclusionRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1npc_1_1MembraneSurfaceLocationConditionalRestraint.html#a9b0ac09ce8a62c5524d8d90908e31e4e">IMP::npc::MembraneSurfaceLocationConditionalRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1npc_1_1MembraneSurfaceLocationRestraint.html#a56a0189abdb2fa6703b49a0a399e8a4e">IMP::npc::MembraneSurfaceLocationRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1npc_1_1MinimumSphereDistancePairScore.html#aa8a17940758efc05d6de148feaa2409e">IMP::npc::MinimumSphereDistancePairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1npc_1_1MinimumSphereDistancePairScore.html#ae4c0e755b4f0ff815c1d12f30188632d">IMP::npc::MinimumSphereDistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1npc_1_1MinimumSphereDistancePairScore.html#abd81da44c15d26d9de41a8cc47bbf387">IMP::npc::MinimumSphereDistancePairScore::evaluate_indexes()</a>, <a href="classIMP_1_1npc_1_1MinimumSphereDistancePairScore.html#a11f6b2ba6b2a1f22e730538e89e0e338">IMP::npc::MinimumSphereDistancePairScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1npc_1_1MinimumSphereDistancePairScore.html#a7663f7a2deba8cba94761e562de3682b">IMP::npc::MinimumSphereDistancePairScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1npc_1_1PerinuclearVolumeLocationRestraint.html#a7762b9127b98d10065ad5909a94df18f">IMP::npc::PerinuclearVolumeLocationRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1npc_1_1PoreSideVolumeLocationRestraint.html#abba63c738c969159d94ccfe8f2a78c30">IMP::npc::PoreSideVolumeLocationRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1npc_1_1ProteinChainRestraint.html#aff6c8d8019b036f05e3aae357be75fab">IMP::npc::ProteinChainRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1npc_1_1ProteinContactRestraint.html#a9c8dfe09ab4b2f33f598d2b4584e3ef3">IMP::npc::ProteinContactRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1npc_1_1ProteinProximityRestraint.html#a249b9b9db45c30223dbb63050c0738d3">IMP::npc::ProteinProximityRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1npc_1_1XYRadialPositionLowerRestraint.html#a85fc2c0b0b511e65f9854dc2c8db7126">IMP::npc::XYRadialPositionLowerRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1npc_1_1XYRadialPositionRestraint.html#a5501fb3213bf560fb3e573096d18fe72">IMP::npc::XYRadialPositionRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1npc_1_1XYRadialPositionUpperRestraint.html#ab9a1ec49a4292374e3a13024d3ad38d6">IMP::npc::XYRadialPositionUpperRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1npc_1_1YAxialPositionLowerRestraint.html#aec405205cd4deeea4e3b89b120a4a7ed">IMP::npc::YAxialPositionLowerRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1npc_1_1YAxialPositionRestraint.html#af83234d789e3fcd05535e1b0d40d575b">IMP::npc::YAxialPositionRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1npc_1_1YAxialPositionUpperRestraint.html#a827ca7d932df85dd265c12b202f78209">IMP::npc::YAxialPositionUpperRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1npc_1_1ZAxialPositionLowerRestraint.html#a03b47fa55a2fbfb01b09966241e712e7">IMP::npc::ZAxialPositionLowerRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1npc_1_1ZAxialPositionRestraint.html#a7d74ace78cb28d18132922bc41598f03">IMP::npc::ZAxialPositionRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1npc_1_1ZAxialPositionUpperRestraint.html#a36267729ed4c27ee71ebd8eb34a99735">IMP::npc::ZAxialPositionUpperRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1npctransport_1_1AnchorToCylidnricalPorePairScore.html#ad88a285076129f7c75c47cc8723c70d1">IMP::npctransport::AnchorToCylidnricalPorePairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1npctransport_1_1AnchorToCylidnricalPorePairScore.html#a77ba0dec47b4a09eda97b71fbbb6ea4c">IMP::npctransport::AnchorToCylidnricalPorePairScore::evaluate_index()</a>, <a href="classIMP_1_1npctransport_1_1AnchorToCylidnricalPorePairScore.html#a1ab10319e14e6b3b818060c31a4ccdb6">IMP::npctransport::AnchorToCylidnricalPorePairScore::evaluate_indexes()</a>, <a href="classIMP_1_1npctransport_1_1AnchorToCylidnricalPorePairScore.html#a0e35e4651f87b997fac79d5f685aaf7a">IMP::npctransport::AnchorToCylidnricalPorePairScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1npctransport_1_1AnchorToCylidnricalPorePairScore.html#a3dd98abd190c8fda3b53a957603906dc">IMP::npctransport::AnchorToCylidnricalPorePairScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1npctransport_1_1ExcludeZRangeSingletonScore.html#a99575f81936d3bc57d00497ca101b4db">IMP::npctransport::ExcludeZRangeSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1npctransport_1_1ExcludeZRangeSingletonScore.html#a3964d7a479b58b473c1790db0955b956">IMP::npctransport::ExcludeZRangeSingletonScore::evaluate_index()</a>, <a href="classIMP_1_1npctransport_1_1ExcludeZRangeSingletonScore.html#abf31640a5fa6dda862b734a6c952617c">IMP::npctransport::ExcludeZRangeSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1npctransport_1_1ExcludeZRangeSingletonScore.html#a3a26a8f2a61b1535654c80bcdae9ee6c">IMP::npctransport::ExcludeZRangeSingletonScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1npctransport_1_1ExcludeZRangeSingletonScore.html#a4b34774352dcfcadbc1f625915ee0df3">IMP::npctransport::ExcludeZRangeSingletonScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1npctransport_1_1HarmonicSpringSingletonScore.html#ac6a7456dc5976e823587ba97d5cc966c">IMP::npctransport::HarmonicSpringSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1npctransport_1_1HarmonicSpringSingletonScore.html#a25f453cf760ce1b694c7f3089925299b">IMP::npctransport::HarmonicSpringSingletonScore::evaluate_index()</a>, <a href="classIMP_1_1npctransport_1_1HarmonicSpringSingletonScore.html#a360dd53f41fbf8705b0b909da10e0b19">IMP::npctransport::HarmonicSpringSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1npctransport_1_1HarmonicSpringSingletonScore.html#a488ff9a3dc0f8e3ff5475d76a4a1edb1">IMP::npctransport::HarmonicSpringSingletonScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1npctransport_1_1HarmonicSpringSingletonScore.html#a7bdd92c3af3650aeeaa38978b41b0a94">IMP::npctransport::HarmonicSpringSingletonScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1npctransport_1_1HarmonicWellPairScore.html#a09e884d92d155e0029443e2f2b571224">IMP::npctransport::HarmonicWellPairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1npctransport_1_1HarmonicWellPairScore.html#a6112c2f581b093a6f400f10097705ffb">IMP::npctransport::HarmonicWellPairScore::evaluate_index()</a>, <a href="classIMP_1_1npctransport_1_1HarmonicWellPairScore.html#afb65f1c65f7a1ac94098292df89be652">IMP::npctransport::HarmonicWellPairScore::evaluate_indexes()</a>, <a href="classIMP_1_1npctransport_1_1HarmonicWellPairScore.html#aa64b6368f782e95e246a048c7edb7d2e">IMP::npctransport::HarmonicWellPairScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1npctransport_1_1HarmonicWellPairScore.html#a0c009ed367b0b3ca54b3a656fd57d77e">IMP::npctransport::HarmonicWellPairScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1npctransport_1_1LinearInteractionPairScore.html#aca9ea98ff4513f4de765d18d3828a9c7">IMP::npctransport::LinearInteractionPairScore::evaluate_index()</a>, <a href="classIMP_1_1npctransport_1_1LinearInteractionPairScore.html#a06c7acf9cf91b0b70f5d7360e1290f27">IMP::npctransport::LinearInteractionPairScore::evaluate_if_good_index()</a>, <a href="classIMP_1_1npctransport_1_1LinearInteractionPairScore.html#aad31e4c06f68e70640f91104e17bcf46">IMP::npctransport::LinearInteractionPairScore::evaluate_indexes()</a>, <a href="classIMP_1_1npctransport_1_1LinearSoftSpherePairScore.html#aae44155552c1719e618a66a0fe5054bb">IMP::npctransport::LinearSoftSpherePairScore::evaluate_index()</a>, <a href="classIMP_1_1npctransport_1_1LinearSoftSpherePairScore.html#a2e3b41ce74e861659cb7fa7960880d1b">IMP::npctransport::LinearSoftSpherePairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1npctransport_1_1LinearSoftSpherePairScore.html#a00c112ed25af75755c247427d80f9bd7">IMP::npctransport::LinearSoftSpherePairScore::evaluate_index()</a>, <a href="classIMP_1_1npctransport_1_1LinearSoftSpherePairScore.html#a510e15e619d75da578728a39679faddc">IMP::npctransport::LinearSoftSpherePairScore::evaluate_indexes()</a>, <a href="classIMP_1_1npctransport_1_1LinearWellPairScore.html#ae6de67c774716a45e191b06ceddad9e7">IMP::npctransport::LinearWellPairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1npctransport_1_1LinearWellPairScore.html#afb4ee96f18d024f2879d7e8d3a727048">IMP::npctransport::LinearWellPairScore::evaluate_index()</a>, <a href="classIMP_1_1npctransport_1_1LinearWellPairScore.html#a78c641c231c72d0b1ff056689cca2bac">IMP::npctransport::LinearWellPairScore::evaluate_indexes()</a>, <a href="classIMP_1_1npctransport_1_1LinearWellPairScore.html#ad4f201e9ac653983a204eaaf2503fd9f">IMP::npctransport::LinearWellPairScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1npctransport_1_1LinearWellPairScore.html#a1979ea44779ce084a4700e8a7bf17b42">IMP::npctransport::LinearWellPairScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1npctransport_1_1RelaxingSpring.html#a00c37e225cce336b3ba7ab7999db21f1">IMP::npctransport::RelaxingSpring::add_to_rest_length_derivative()</a>, <a href="classIMP_1_1npctransport_1_1SitesPairScore.html#adca8192f602abf374e5dcad3e7c2db4a">IMP::npctransport::SitesPairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1npctransport_1_1SitesPairScore.html#a84202fb01032444b964e16ddd0be44a0">IMP::npctransport::SitesPairScore::evaluate_index()</a>, <a href="classIMP_1_1npctransport_1_1SitesPairScore.html#aefe53963a5d17cd3dba6a8124b1e7e31">IMP::npctransport::SitesPairScore::evaluate_indexes()</a>, <a href="classIMP_1_1npctransport_1_1SitesPairScore.html#a0652d42fb895d6381b71909cc75bd4dc">IMP::npctransport::SitesPairScore::evaluate_site_contributions()</a>, <a href="classIMP_1_1npctransport_1_1SitesPairScore.html#a4f458d7972f6fd4b0a01c7d83d8f2534">IMP::npctransport::SitesPairScore::evaluate_site_contributions_with_internal_tables()</a>, <a href="classIMP_1_1npctransport_1_1SitesPairScore.html#afc69f1324198285ad999d480d442fa0f">IMP::npctransport::SitesPairScore::evaluate_index_with_internal_tables()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithCylindricalPorePairScore.html#aacc13979a2eb16762901fe95b12f5dfa">IMP::npctransport::SlabWithCylindricalPorePairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithCylindricalPorePairScore.html#a237792d9bd5d0afcf684e2b24695a491">IMP::npctransport::SlabWithCylindricalPorePairScore::evaluate_index()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithCylindricalPorePairScore.html#a2ad579397e11683b9c88cdb51848f5f5">IMP::npctransport::SlabWithCylindricalPorePairScore::evaluate_indexes()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithPore.html#a8b3be5efd113369fd41b7f1902d987fd">IMP::npctransport::SlabWithPore::add_to_pore_radius_derivative()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithToroidalPorePairScore.html#a6ab34004310542d304a5659de61b1223">IMP::npctransport::SlabWithToroidalPorePairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithToroidalPorePairScore.html#ac038a2aa03536cc6a0265c2b0e06d84f">IMP::npctransport::SlabWithToroidalPorePairScore::evaluate_index()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithToroidalPorePairScore.html#a63cad160e76611b2e8eec2158842483b">IMP::npctransport::SlabWithToroidalPorePairScore::evaluate_indexes()</a>, <a href="classIMP_1_1npctransport_1_1ZBiasSingletonScore.html#afc2372d9d5912790c9bd711ae247371f">IMP::npctransport::ZBiasSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1npctransport_1_1ZBiasSingletonScore.html#a64fe0edf6b1014ea87219cecbc7ad83a">IMP::npctransport::ZBiasSingletonScore::evaluate_index()</a>, <a href="classIMP_1_1npctransport_1_1ZBiasSingletonScore.html#a5fcbc10bd5dac71d600a68cf9583c235">IMP::npctransport::ZBiasSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1npctransport_1_1ZBiasSingletonScore.html#a629f3b7227f818ea15b2201af1aec8ad">IMP::npctransport::ZBiasSingletonScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1npctransport_1_1ZBiasSingletonScore.html#ac4310eb3df7994295143de787dd44b90">IMP::npctransport::ZBiasSingletonScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1pmi1_1_1CompositeRestraint.html#a01436a16b88f77ea1b6f795fe55ef07c">IMP::pmi1::CompositeRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1pmi1_1_1MembraneRestraint.html#a54396d1b8fee9b0c62ece1d47e24c60c">IMP::pmi1::MembraneRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1pmi1_1_1SigmoidRestraintSphere.html#ac5ae7c504a0f46387b6537b121d0a8f1">IMP::pmi1::SigmoidRestraintSphere::unprotected_evaluate()</a>, <a href="classIMP_1_1pmi_1_1CompositeRestraint.html#ad26874383f6a1045fc97a14f47971b57">IMP::pmi::CompositeRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1pmi_1_1MembraneRestraint.html#a343c2c4114a7ce0158cc83c112d89b9c">IMP::pmi::MembraneRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1saxs_1_1RadiusOfGyrationRestraint.html#afa6789a8b317951a22c7ca0acfda8e69">IMP::saxs::RadiusOfGyrationRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1saxs_1_1Restraint.html#abd2aa7d1418b69dfcabd0c3bf98000ab">IMP::saxs::Restraint::unprotected_evaluate()</a>, <a href="classIMP_1_1saxs_1_1RigidBodiesProfileHandler.html#a67d3fe4fac308624da7c39df74702ba5">IMP::saxs::RigidBodiesProfileHandler::compute_derivatives()</a>, <a href="classIMP_1_1score__functor_1_1DistancePairScore.html#a2f30c0deeb1f287308cc9e527de068e7">IMP::score_functor::DistancePairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1score__functor_1_1DistancePairScore.html#a35e48061a5968d15b44686032a075968">IMP::score_functor::DistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1score__functor_1_1DistancePairScore.html#ab2fda99dbd160cc3ebbaa7e14981efc2">IMP::score_functor::DistancePairScore::evaluate_indexes()</a>, <a href="classIMP_1_1score__functor_1_1DistancePairScore.html#a367db1fd00238dbf5a6f5f54a9a65692">IMP::score_functor::DistancePairScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1score__functor_1_1DistancePairScore.html#a412d8dc4c549f4609fde767d196b126a">IMP::score_functor::DistancePairScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1score__functor_1_1DistancePairScoreWithCache.html#a92420a5cbd9d73affefd4b8e9ff4e254">IMP::score_functor::DistancePairScoreWithCache::evaluate_index_with_cache()</a>, <a href="classIMP_1_1score__functor_1_1DistancePairScoreWithCache.html#ad012a8af9b447bb76fa9a30fc7852de2">IMP::score_functor::DistancePairScoreWithCache::evaluate_index()</a>, <a href="classIMP_1_1score__functor_1_1DistancePairScoreWithCache.html#ac6cc237bacf8f596ab48eb6089fbd792">IMP::score_functor::DistancePairScoreWithCache::evaluate_indexes()</a>, <a href="classIMP_1_1score__functor_1_1DistancePairScoreWithCache.html#a94058904a9b0c2eb60044e2eb52bb7b4">IMP::score_functor::DistancePairScoreWithCache::evaluate_indexes_delta()</a>, <a href="classIMP_1_1score__functor_1_1DistancePairScoreWithCache.html#af4c6260d1ff99271cda7df1910723cba">IMP::score_functor::DistancePairScoreWithCache::evaluate_indexes_scores()</a>, <a href="classIMP_1_1score__functor_1_1SurfaceDistancePairScore.html#ac5dab9a200f01e781cb1550fe5150a53">IMP::score_functor::SurfaceDistancePairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1score__functor_1_1SurfaceDistancePairScore.html#a3ec7c9c3010ecdb03fe565c7922d4a78">IMP::score_functor::SurfaceDistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1score__functor_1_1SurfaceDistancePairScore.html#a8ef796b187bf269f865d3fe14c95f151">IMP::score_functor::SurfaceDistancePairScore::evaluate_indexes()</a>, <a href="classIMP_1_1score__functor_1_1SurfaceDistancePairScore.html#aab119bd0d9622b04191df4c7a961dc06">IMP::score_functor::SurfaceDistancePairScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1score__functor_1_1SurfaceDistancePairScore.html#ad0050f08806e87aeec8d55b800dc22f8">IMP::score_functor::SurfaceDistancePairScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1spb_1_1AttributeDistancePairScore.html#acc356c75b27a919e7a3085876b9f40d5">IMP::spb::AttributeDistancePairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1spb_1_1AttributeDistancePairScore.html#ad703da3ed2ece907485501f6d5e3191b">IMP::spb::AttributeDistancePairScore::evaluate_index()</a>, <a href="classIMP_1_1spb_1_1AttributeDistancePairScore.html#a5aaf275ad63cd6e50667365f15be51fc">IMP::spb::AttributeDistancePairScore::evaluate_indexes()</a>, <a href="classIMP_1_1spb_1_1AttributeDistancePairScore.html#a155276a378e85ccf3e77955c18b0bd7b">IMP::spb::AttributeDistancePairScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1spb_1_1AttributeDistancePairScore.html#a97b29bf5b65fad892e4db0b80ca857f4">IMP::spb::AttributeDistancePairScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1spb_1_1DiameterRgyrRestraint.html#a6941a1b4177ec42dade6cab6ad52916e">IMP::spb::DiameterRgyrRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1spb_1_1DistanceTerminiRestraint.html#a3cd3af49180a059e7570666f3eda293c">IMP::spb::DistanceTerminiRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1spb_1_1EM2DRestraint.html#ac05a6732d4c4131993afac2a59931640">IMP::spb::EM2DRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1spb_1_1KinkPairScore.html#ababcac4e6a17b39a34338f4014d189bf">IMP::spb::KinkPairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1spb_1_1KinkPairScore.html#a054a2a261818a7b22fb893c5583a7b8c">IMP::spb::KinkPairScore::evaluate_index()</a>, <a href="classIMP_1_1spb_1_1KinkPairScore.html#aa543f7b5e0a77ec8196bb70636eb8b18">IMP::spb::KinkPairScore::evaluate_indexes()</a>, <a href="classIMP_1_1spb_1_1KinkPairScore.html#a5947ca466c128b47588d8741c6a3aaff">IMP::spb::KinkPairScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1spb_1_1KinkPairScore.html#ae9671e913583a4c296f5bf052acb753c">IMP::spb::KinkPairScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1spb_1_1RigidBodyPackingScore.html#a84a2a27af1a86a46f36171ad87f72119">IMP::spb::RigidBodyPackingScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1spb_1_1RigidBodyPackingScore.html#a973b57cfcbe92c31b22370697b64ccb6">IMP::spb::RigidBodyPackingScore::evaluate_index()</a>, <a href="classIMP_1_1spb_1_1RigidBodyPackingScore.html#a28db3fabb8e63080b54045b421ea324b">IMP::spb::RigidBodyPackingScore::evaluate_indexes()</a>, <a href="classIMP_1_1spb_1_1RigidBodyPackingScore.html#ab6aa49962ea53a1b4abfa75be3d7fab5">IMP::spb::RigidBodyPackingScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1spb_1_1RigidBodyPackingScore.html#a206bdf9a88a3253f46e39fe6b7fae74b">IMP::spb::RigidBodyPackingScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1spb_1_1TiltSingletonScore.html#a21e290585cc6cb0b5cbda2575c644ab2">IMP::spb::TiltSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1spb_1_1TiltSingletonScore.html#adb5eca3a3fbe47d39ab45b573c9cd7ed">IMP::spb::TiltSingletonScore::evaluate_index()</a>, <a href="classIMP_1_1spb_1_1TiltSingletonScore.html#a05ccd61cda83d04de1944c3b735b703c">IMP::spb::TiltSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1spb_1_1TiltSingletonScore.html#ab3925a2ae9226bcfef7853c674e36e9c">IMP::spb::TiltSingletonScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1spb_1_1TiltSingletonScore.html#aca29e2823e17d7d94ce6d240bd0c1a72">IMP::spb::TiltSingletonScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1spb_1_1TwoStateGoModelRestraint.html#a4b6e1067ce6470bf012336a6d54e747b">IMP::spb::TwoStateGoModelRestraint::unprotected_evaluate()</a>, <a href="classIMP_1_1spb_1_1UniformBoundedRestraint.html#ac270867980d13911526cbdcf6667b7af">IMP::spb::UniformBoundedRestraint::unprotected_evaluate()</a>, <a href="namespaceIMP_1_1npctransport.html#aeeafcd1dbc23081c85d3b450cf9d3474">IMP::npctransport::do_evaluate_index()</a>, <a href="namespaceIMP_1_1npctransport.html#a656ab4ca89e8d22e30f474a6a15fe34d">IMP::npctransport::do_evaluate_index_harmonic()</a></td></tr>
19 <tr><td>@ref IMP::Index</td><td><a href="classIMP_1_1Index.html#ac6c2cc368c5239ac08e19537b1a82095">IMP::Index::IMP_COMPARISONS_1()</a>, <a href="classIMP_1_1Index.html#aa75dff1705ffc85ebcc32e630379e470">IMP::Index::IMP_HASHABLE_INLINE()</a>, <a href="classIMP_1_1IndexVector.html#a199d90a9ea4faa0ee617eb5355dfb184">IMP::IndexVector::at()</a>, <a href="classIMP_1_1IndexVector.html#a83934608ec5e9cdf69f21f5c38cff5af">IMP::IndexVector::at()</a>, <a href="classIMP_1_1IndexVector.html#ab5927b935406c01c180274f2ce0d751e">IMP::IndexVector::operator[]()</a>, <a href="classIMP_1_1IndexVector.html#a5e3d8c81e61d1daa711605d761540903">IMP::IndexVector::operator[]()</a>, <a href="namespaceIMP.html#af313d47627f11fef05efac53312f7e7a">IMP::get_as_unsigned_int()</a>, <a href="namespaceIMP.html#ae6ee6bad5ddcc6be1c4034f6daa51328">IMP::resize_to_fit()</a></td></tr>
20 <tr><td>@ref IMP::Key</td><td><a href="classIMP_1_1Key.html#af693f942a3d828618581b1d99eed633b">IMP::Key::add_alias()</a>, <a href="classIMP_1_1ScopedAddCacheAttribute.html#a8af77bca25f204c29b0b5787e2b8788d">IMP::ScopedAddCacheAttribute::ScopedAddCacheAttribute()</a>, <a href="classIMP_1_1ScopedAddCacheAttribute.html#a950aa06fe61aafec097d962eb556714a">IMP::ScopedAddCacheAttribute::set()</a>, <a href="classIMP_1_1ScopedSetAttribute.html#a99b2803e357b09f6de49e93ce6cfefbd">IMP::ScopedSetAttribute::ScopedSetAttribute()</a>, <a href="classIMP_1_1ScopedSetAttribute.html#a7adf89db75ee85754c433440f37eb3ad">IMP::ScopedSetAttribute::set()</a>, <a href="classIMP_1_1misc_1_1CustomXYZR.html#aced3d45ac55147fc868b5d48b1252cce">IMP::misc::CustomXYZR::setup_particle()</a>, <a href="classIMP_1_1misc_1_1CustomXYZR.html#abf188a677aa7ebfee43ca5a544bfdfd2">IMP::misc::CustomXYZR::setup_particle()</a>, <a href="classIMP_1_1misc_1_1CustomXYZR.html#a02af81dba92ccd8b980d954907ee105b">IMP::misc::CustomXYZR::setup_particle()</a>, <a href="classIMP_1_1misc_1_1CustomXYZR.html#ad73b6ff63c8a45379366ab9634163f8c">IMP::misc::CustomXYZR::setup_particle()</a>, <a href="classIMP_1_1misc_1_1CustomXYZR.html#a4dc8e38f4ea04f1815e9d45c43ecb6d6">IMP::misc::CustomXYZR::setup_particle()</a>, <a href="classIMP_1_1misc_1_1CustomXYZR.html#a658ca7eefa1b70fbc5372d54293d02e1">IMP::misc::CustomXYZR::setup_particle()</a></td></tr>
21 <tr><td>@ref IMP::Model</td><td><a href="classIMP_1_1AttributeOptimizer.html#aa45005a0e8501328862fce1809386dba">IMP::AttributeOptimizer::AttributeOptimizer()</a>, <a href="classIMP_1_1Configuration.html#a9aedb6724d083eadc2fb3c470ea9d181">IMP::Configuration::Configuration()</a>, <a href="classIMP_1_1Configuration.html#ac6ea0e2d7495231d46df0dfceeca9890">IMP::Configuration::Configuration()</a>, <a href="classIMP_1_1ConfigurationSet.html#a07bc7f0bfa7d0deb9358bd86560bf51b">IMP::ConfigurationSet::ConfigurationSet()</a>, <a href="classIMP_1_1Constraint.html#a2ad695ef750ed6d0a5cb72a92a91d4c5">IMP::Constraint::Constraint()</a>, <a href="classIMP_1_1Container.html#a36fe59f2bf9d8dc4133e29a88f6a9553">IMP::Container::Container()</a>, <a href="classIMP_1_1Decorator.html#a55afb5d7cb57325d03bf53134faf9792">IMP::Decorator::Decorator()</a>, <a href="classIMP_1_1ModelObject.html#a89c6a16b5cd05661fee64f1dba02c503">IMP::ModelObject::set_model()</a>, <a href="classIMP_1_1ModelObject.html#a8e48b3af28cee5894c894eeffcb9513f">IMP::ModelObject::ModelObject()</a>, <a href="classIMP_1_1Optimizer.html#a9ee454dc936ef3f2e555ce720ed4cff7">IMP::Optimizer::Optimizer()</a>, <a href="classIMP_1_1OptimizerState.html#ad6c2225465a62144555ff0a350e2c1e7">IMP::OptimizerState::OptimizerState()</a>, <a href="classIMP_1_1PairContainer.html#af9f066b76e9b027aec3844ecc018a887">IMP::PairContainer::PairContainer()</a>, <a href="classIMP_1_1PairModifier.html#a1203f866809502706d3ddd3d5e1d930e">IMP::PairModifier::apply_index()</a>, <a href="classIMP_1_1PairModifier.html#ae71e356ac6257d8c65b3b2415b768e85">IMP::PairModifier::apply_indexes()</a>, <a href="classIMP_1_1PairModifier.html#aa5d8ffc0c3a1e03d5d1c23cd5b35602c">IMP::PairModifier::apply_indexes_moved()</a>, <a href="classIMP_1_1PairPredicate.html#a812ced5db0cb09c670fedb3a900e0fcf">IMP::PairPredicate::get_value_index()</a>, <a href="classIMP_1_1PairPredicate.html#ad13ff551feda00ee3affd9d694425dfa">IMP::PairPredicate::get_value_index()</a>, <a href="classIMP_1_1PairPredicate.html#ab5f444057ff7abd671ffee74da71610f">IMP::PairPredicate::get_value_index_in_batch()</a>, <a href="classIMP_1_1PairPredicate.html#af1a76c20d0da0cb8091f70010abab1b3">IMP::PairPredicate::operator()()</a>, <a href="classIMP_1_1PairPredicate.html#af48cdb44570360fcae3b3e3596954ff4">IMP::PairPredicate::setup_for_get_value_index_in_batch()</a>, <a href="classIMP_1_1PairScore.html#ac3f53ee0daf867730b666ccfbfcbfa25">IMP::PairScore::create_current_decomposition()</a>, <a href="classIMP_1_1PairScore.html#a9353c185485691a3f4cc49fa2e85db84">IMP::PairScore::evaluate_if_good_index()</a>, <a href="classIMP_1_1PairScore.html#aaaebeddee8c8b2719360af5e5ee60467">IMP::PairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1PairScore.html#addfa4378ed7ec501350f1f70d96446de">IMP::PairScore::evaluate_index()</a>, <a href="classIMP_1_1PairScore.html#a2dca93e58717faf070de26c0095b5948">IMP::PairScore::evaluate_indexes()</a>, <a href="classIMP_1_1PairScore.html#a1e2eda017291b400ccaa6f5d4d4a1b53">IMP::PairScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1PairScore.html#a645eae1da1512fbd98ddca38f5a4cb7c">IMP::PairScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1PairScore.html#a39261041d14094111cb11a8d98f74241">IMP::PairScore::do_create_current_decomposition()</a>, <a href="classIMP_1_1Particle.html#a6caf01fd20050cd3a9db409ef073fc3b">IMP::Particle::Particle()</a>, <a href="classIMP_1_1Particle.html#ac64c5db6063037526f0c0065b5e2fa5e">IMP::Particle::Particle()</a>, <a href="classIMP_1_1ParticleInputs.html#a117b8901ab831bde1b2badb3599447c9">IMP::ParticleInputs::get_inputs()</a>, <a href="classIMP_1_1ParticleInputs.html#a98f8a3455c3d69f08eebdb2b659c3317">IMP::ParticleInputs::do_get_inputs()</a>, <a href="classIMP_1_1ParticleOutputs.html#a319cf644ab7d3d1b4041c3bc21318009">IMP::ParticleOutputs::get_outputs()</a>, <a href="classIMP_1_1ParticleOutputs.html#ac90bae015c3ee606281cead2719631ff">IMP::ParticleOutputs::do_get_outputs()</a>, <a href="classIMP_1_1QuadContainer.html#afb126a3d0366dad4f2d8fa00a566b9b6">IMP::QuadContainer::QuadContainer()</a>, <a href="classIMP_1_1QuadModifier.html#ab694ee2dc014bd33fbd125ebd2411b1a">IMP::QuadModifier::apply_index()</a>, <a href="classIMP_1_1QuadModifier.html#acbc547917363142e0ccd74fbfe0f31ab">IMP::QuadModifier::apply_indexes()</a>, <a href="classIMP_1_1QuadModifier.html#ace28229b91ce1475a4de2dea5fa235b9">IMP::QuadModifier::apply_indexes_moved()</a>, <a href="classIMP_1_1QuadPredicate.html#a44d432e3d1746aea93562aa4778adb85">IMP::QuadPredicate::get_value_index()</a>, <a href="classIMP_1_1QuadPredicate.html#a27ce599f0259c55e23ba165045849765">IMP::QuadPredicate::get_value_index()</a>, <a href="classIMP_1_1QuadPredicate.html#a10a8b17f369245507bfe891fd94dd507">IMP::QuadPredicate::get_value_index_in_batch()</a>, <a href="classIMP_1_1QuadPredicate.html#a2ab73aa13a7fc2ca8a37ee9b27633f6c">IMP::QuadPredicate::operator()()</a>, <a href="classIMP_1_1QuadPredicate.html#a1cfb9e54d01416f23d1a67674860d02c">IMP::QuadPredicate::setup_for_get_value_index_in_batch()</a>, <a href="classIMP_1_1QuadScore.html#ae36391e637be084a570bf20cb6315f8e">IMP::QuadScore::create_current_decomposition()</a>, <a href="classIMP_1_1QuadScore.html#adfcf52bbb55dccf87eac762c158bcfc4">IMP::QuadScore::evaluate_if_good_index()</a>, <a href="classIMP_1_1QuadScore.html#a23fe083ebd9ab41fae847c739c565e56">IMP::QuadScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1QuadScore.html#a8811aa00b39851809b84403156adde47">IMP::QuadScore::evaluate_index()</a>, <a href="classIMP_1_1QuadScore.html#a5998238ace6d73cdb32b11941a640fe0">IMP::QuadScore::evaluate_indexes()</a>, <a href="classIMP_1_1QuadScore.html#a58869d3e961b4fca71e86fa1a79540fc">IMP::QuadScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1QuadScore.html#ac239db0a3df1c7ab445b3f3aa0faf193">IMP::QuadScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1QuadScore.html#af8518e746dc7d2ccabaec558c16f0b6c">IMP::QuadScore::do_create_current_decomposition()</a>, <a href="classIMP_1_1Refiner.html#a93aea26b1bfc67c1b704fd25df6ba3da">IMP::Refiner::get_refined_indexes()</a>, <a href="classIMP_1_1Refiner.html#aa56cac7a4534bc17640ca939e4e8fcee">IMP::Refiner::get_refined_indexes_by_ref()</a>, <a href="classIMP_1_1Restraint.html#a65f5bfc07a342897b316c4cd0bc6f06c">IMP::Restraint::Restraint()</a>, <a href="classIMP_1_1RestraintSet.html#a8879e7a6fc3143465b5aa5e5e49f5ea1">IMP::RestraintSet::RestraintSet()</a>, <a href="classIMP_1_1RestraintSet.html#a815c2a582544773485481f97c3c2d96e">IMP::RestraintSet::RestraintSet()</a>, <a href="classIMP_1_1Sampler.html#a4e4587f5feb2ea71987687601dc7d056">IMP::Sampler::Sampler()</a>, <a href="classIMP_1_1ScoreState.html#ab08d40336a1e88402979963a33bf692d">IMP::ScoreState::ScoreState()</a>, <a href="classIMP_1_1ScoringFunction.html#ae6d2e6cc6e717a44ae7ead5d7ec0e607">IMP::ScoringFunction::ScoringFunction()</a>, <a href="classIMP_1_1SingletonContainer.html#aef8c8a572f4cacbfe09d4cf4234c5d3a">IMP::SingletonContainer::SingletonContainer()</a>, <a href="classIMP_1_1SingletonModifier.html#a20017115e6adc4aef22a45918beb77f9">IMP::SingletonModifier::apply_index()</a>, <a href="classIMP_1_1SingletonModifier.html#a80231ec89eb82fa05d6b525fa6ed849f">IMP::SingletonModifier::apply_indexes()</a>, <a href="classIMP_1_1SingletonModifier.html#a5a299e609e143eb15b9453681a85f8dc">IMP::SingletonModifier::apply_indexes_moved()</a>, <a href="classIMP_1_1SingletonPredicate.html#a64a04d72baf5b56f35cf28cf758e1746">IMP::SingletonPredicate::get_value_index()</a>, <a href="classIMP_1_1SingletonPredicate.html#a875dca49aaa39bffb277075e186e57ff">IMP::SingletonPredicate::get_value_index()</a>, <a href="classIMP_1_1SingletonPredicate.html#a7b51f2837f9b2b429d2245eb8c80beac">IMP::SingletonPredicate::get_value_index_in_batch()</a>, <a href="classIMP_1_1SingletonPredicate.html#a3fe80fa98a4011cee2ffec3a391c513b">IMP::SingletonPredicate::operator()()</a>, <a href="classIMP_1_1SingletonPredicate.html#a2c20739d37be0db235f6b5aeb6567cc2">IMP::SingletonPredicate::setup_for_get_value_index_in_batch()</a>, <a href="classIMP_1_1SingletonScore.html#ada1d3df437cff3117db1aaa65870a9f7">IMP::SingletonScore::create_current_decomposition()</a>, <a href="classIMP_1_1SingletonScore.html#aceff09a984620d3e0fd287e5e1692304">IMP::SingletonScore::evaluate_if_good_index()</a>, <a href="classIMP_1_1SingletonScore.html#a72fedd1e026640d8dff579c8138cb543">IMP::SingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1SingletonScore.html#a65c2554625de92d0c0cfbabe108491c2">IMP::SingletonScore::evaluate_index()</a>, <a href="classIMP_1_1SingletonScore.html#a6b4756b83a12ad91eb5f6d5f943cde39">IMP::SingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1SingletonScore.html#a4212150dc45c60f04b7422491d0f919f">IMP::SingletonScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1SingletonScore.html#a2ddfa8309b6f3589864c028066777e59">IMP::SingletonScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1SingletonScore.html#ad96fd46369829929bb48e4da6b63494e">IMP::SingletonScore::do_create_current_decomposition()</a>, <a href="classIMP_1_1TripletContainer.html#ac0f5fc0c81a680cdd65504be26f3505b">IMP::TripletContainer::TripletContainer()</a>, <a href="classIMP_1_1TripletModifier.html#a56b9bd816c98bd67afe47b471ecfb21b">IMP::TripletModifier::apply_index()</a>, <a href="classIMP_1_1TripletModifier.html#a8b1cd25d9895fd9e7d1c689fdbd7c325">IMP::TripletModifier::apply_indexes()</a>, <a href="classIMP_1_1TripletModifier.html#aaa5dd7e8b3bcadc69f59f9eaf6540bd8">IMP::TripletModifier::apply_indexes_moved()</a>, <a href="classIMP_1_1TripletPredicate.html#ab2cb55c8ca95d1d875d65fae9977ea88">IMP::TripletPredicate::get_value_index()</a>, <a href="classIMP_1_1TripletPredicate.html#a56269f29dea452b725e0c9158b49957a">IMP::TripletPredicate::get_value_index()</a>, <a href="classIMP_1_1TripletPredicate.html#a897085c21313ebf0669fea6be4d73db2">IMP::TripletPredicate::get_value_index_in_batch()</a>, <a href="classIMP_1_1TripletPredicate.html#aed542435fb88ad7c1703296651f4ef2e">IMP::TripletPredicate::operator()()</a>, <a href="classIMP_1_1TripletPredicate.html#a30cc08c4b00790b2e47efd830ce96779">IMP::TripletPredicate::setup_for_get_value_index_in_batch()</a>, <a href="classIMP_1_1TripletScore.html#a5f3906cbe68e8b3fd5b4fad2177dd700">IMP::TripletScore::create_current_decomposition()</a>, <a href="classIMP_1_1TripletScore.html#a3d24b25ec1320d6659c7475c07e63d5c">IMP::TripletScore::evaluate_if_good_index()</a>, <a href="classIMP_1_1TripletScore.html#aba77cc17c5736a22c4ba8678b97ca3d2">IMP::TripletScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1TripletScore.html#a0d484717b416e3caeecae8064b4a547b">IMP::TripletScore::evaluate_index()</a>, <a href="classIMP_1_1TripletScore.html#acac89a806de002ddd26368e3f73a79aa">IMP::TripletScore::evaluate_indexes()</a>, <a href="classIMP_1_1TripletScore.html#a094e729370c397cad9bd4190be908a2a">IMP::TripletScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1TripletScore.html#aa0afab007addd7a4852c7519ccf34307">IMP::TripletScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1TripletScore.html#ae356b8328fb4fb1f8e09ea9916ac3af0">IMP::TripletScore::do_create_current_decomposition()</a>, <a href="classIMP_1_1Undecorator.html#a173f34fdd37b2de2e8641fecff4bd3ea">IMP::Undecorator::Undecorator()</a>, <a href="classIMP_1_1atom_1_1Angle.html#abf8e9da4ebd4f545e4bce03ac6f0dc50">IMP::atom::Angle::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Angle.html#a0e926023b01db3176075aa14558c5132">IMP::atom::Angle::Angle()</a>, <a href="classIMP_1_1atom_1_1Angle.html#ade4c44561dcf44eaadbef64701a51e05">IMP::atom::Angle::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Angle.html#ac05c3945ed23762560f6d065d2626981">IMP::atom::Angle::setup_particle()</a>, <a href="classIMP_1_1atom_1_1AngleSingletonScore.html#a50b498ed409a4299d4e7a42dbb6de0aa">IMP::atom::AngleSingletonScore::do_get_inputs()</a>, <a href="classIMP_1_1atom_1_1AngleSingletonScore.html#a9d94065013e52688cec46fb3628b687e">IMP::atom::AngleSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1atom_1_1AngleSingletonScore.html#a854e1c08f59d9dd19b21511b18607be5">IMP::atom::AngleSingletonScore::evaluate_index()</a>, <a href="classIMP_1_1atom_1_1AngleSingletonScore.html#aaf636347f30a3bdb57c1efe85169b3ee">IMP::atom::AngleSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1atom_1_1AngleSingletonScore.html#ac98a1656980e03142588407436356652">IMP::atom::AngleSingletonScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1atom_1_1AngleSingletonScore.html#a9318fd68f16bbab979e4de1e1a586a65">IMP::atom::AngleSingletonScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1atom_1_1AngularVelocity.html#a8464def8551231166a94469a13792030">IMP::atom::AngularVelocity::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1AngularVelocity.html#aa284222b4fe8bbd1883256209d667948">IMP::atom::AngularVelocity::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Atom.html#a129e3c38ccce94e7468e7cb504a040a3">IMP::atom::Atom::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Atom.html#a2b24077e12488f4f1370697fc0776755">IMP::atom::Atom::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Atom.html#ad6d5e72902aa1b05cc43847b2bf9632d">IMP::atom::Atom::Atom()</a>, <a href="classIMP_1_1atom_1_1Atom.html#a85674bedb99e0a3e6248b08329e17d0c">IMP::atom::Atom::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Atom.html#a8673b3453596560cdbe50d3dbf4815a0">IMP::atom::Atom::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Atom.html#ae77d0503f22ce6b6902900807ee92829">IMP::atom::Atom::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Bond.html#a134b4197f5256c49d4709ed054589194">IMP::atom::Bond::Bond()</a>, <a href="classIMP_1_1atom_1_1Bond.html#a983a19f216b2e4caa4e8f4e3d25f4bf9">IMP::atom::Bond::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1BondEndpointsRefiner.html#a8fd096183681aa3e0b8ccce1798ac419">IMP::atom::BondEndpointsRefiner::do_get_inputs()</a>, <a href="classIMP_1_1atom_1_1BondSingletonScore.html#ad927da7b5ce1613b32941e73ef877296">IMP::atom::BondSingletonScore::do_get_inputs()</a>, <a href="classIMP_1_1atom_1_1BondSingletonScore.html#aea653b8e4729b29f3b8ae867b185828d">IMP::atom::BondSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1atom_1_1BondSingletonScore.html#a6969ecb5ea9eb8fdaf6ed3624ef6c4ea">IMP::atom::BondSingletonScore::evaluate_index()</a>, <a href="classIMP_1_1atom_1_1BondSingletonScore.html#ac1f36ade2f5513cffc07e4dc5d1a9ca8">IMP::atom::BondSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1atom_1_1BondSingletonScore.html#af4566ccae002e42f23090fbe8460c9e1">IMP::atom::BondSingletonScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1atom_1_1BondSingletonScore.html#a817fcac36508aa396cbd9faa3b965801">IMP::atom::BondSingletonScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1atom_1_1Bonded.html#aaa219f1b5e76fd5bd1608249c5bda98a">IMP::atom::Bonded::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Bonded.html#a85e4732f8ee944e2d8b90f80509230df">IMP::atom::Bonded::Bonded()</a>, <a href="classIMP_1_1atom_1_1Bonded.html#ada5f04e195d7920821855ee175217a3f">IMP::atom::Bonded::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Bonded.html#a48b39e583b48f1dd403a80d6aac5e2f1">IMP::atom::Bonded::setup_particle()</a>, <a href="classIMP_1_1atom_1_1BondedPairFilter.html#ab4d33f448adb5b06ed1826aa3d62ef7d">IMP::atom::BondedPairFilter::do_get_inputs()</a>, <a href="classIMP_1_1atom_1_1BondedPairFilter.html#ad23211bcfa456842db4455dc5127da12">IMP::atom::BondedPairFilter::get_value_index()</a>, <a href="classIMP_1_1atom_1_1BondedPairFilter.html#a4edd408626923cc9a79a36711f0c0c40">IMP::atom::BondedPairFilter::get_value_index()</a>, <a href="classIMP_1_1atom_1_1BrownianDynamics.html#abebe1768377662ed6c45c79220aec587">IMP::atom::BrownianDynamics::BrownianDynamics()</a>, <a href="classIMP_1_1atom_1_1BrownianDynamicsTAMD.html#a132d62c6c7f2a19b8a34a28be6591f8f">IMP::atom::BrownianDynamicsTAMD::BrownianDynamicsTAMD()</a>, <a href="classIMP_1_1atom_1_1CAAngleRestraint.html#af83e92f9462a7527e13ffa74f7a03211">IMP::atom::CAAngleRestraint::CAAngleRestraint()</a>, <a href="classIMP_1_1atom_1_1CADihedralRestraint.html#a54eb14f1925d6914c24a212dfbad0364">IMP::atom::CADihedralRestraint::CADihedralRestraint()</a>, <a href="classIMP_1_1atom_1_1CHARMMAtom.html#a4651094c5840cc5258bba4d031ad1aa3">IMP::atom::CHARMMAtom::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1CHARMMAtom.html#ac4d4d135e0b8ca0efd9e43a919475921">IMP::atom::CHARMMAtom::CHARMMAtom()</a>, <a href="classIMP_1_1atom_1_1CHARMMAtom.html#a829c0cb6c1884d248760a85166da49b3">IMP::atom::CHARMMAtom::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1CHARMMAtom.html#abe9de32622eb206706e744ad97412084">IMP::atom::CHARMMAtom::setup_particle()</a>, <a href="classIMP_1_1atom_1_1CHARMMTopology.html#a3d3e69d8d1d90294c5cedd6c0f33ca2c">IMP::atom::CHARMMTopology::create_hierarchy()</a>, <a href="classIMP_1_1atom_1_1CenterOfMass.html#a0195cdb1ec740e305a5be28f9668c427">IMP::atom::CenterOfMass::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1CenterOfMass.html#a67206a3eda48a7d490c2701ad56ca7a2">IMP::atom::CenterOfMass::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1CenterOfMass.html#a5a9d6ca22223df96ebd669df4acd20f6">IMP::atom::CenterOfMass::set_constraint()</a>, <a href="classIMP_1_1atom_1_1CenterOfMass.html#a6ffe59c882facc432e75d8a18d6bae7b">IMP::atom::CenterOfMass::CenterOfMass()</a>, <a href="classIMP_1_1atom_1_1CenterOfMass.html#a3a9f580bb7f1d94b8f04ea527ffe0ec3">IMP::atom::CenterOfMass::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1CenterOfMass.html#af645b19c442b1e76ad1c4aacda45e81d">IMP::atom::CenterOfMass::setup_particle()</a>, <a href="classIMP_1_1atom_1_1CenterOfMass.html#a05b61bbc3ccc220788567089208071bf">IMP::atom::CenterOfMass::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Chain.html#a1eed24ab7bc6ec0d7431f9e2a06be513">IMP::atom::Chain::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Chain.html#ac2a0a74b412ccaf946a5c03af63ce5d1">IMP::atom::Chain::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Chain.html#a177a82bf81cb3793fc3d07e1a670e841">IMP::atom::Chain::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Chain.html#ac332c1020834251ea61b73b8405b803c">IMP::atom::Chain::Chain()</a>, <a href="classIMP_1_1atom_1_1Chain.html#a759f769249133f6647ad24544ffcd235">IMP::atom::Chain::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Chain.html#a07e5b5a1bfa7e0c8ac52799bec365e30">IMP::atom::Chain::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Chain.html#a6336a07dd312f7c56db369121e73ae81">IMP::atom::Chain::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Chain.html#a1a39ce6772b2575cbe7cf3478c504f1e">IMP::atom::Chain::setup_particle()</a>, <a 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href="classIMP_1_1core_1_1ConstantQuadPredicate.html#af4ab630bd0863a7eef60d5e9834cdcb6">IMP::core::ConstantQuadPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1ConstantRestraint.html#aa2aa7b206e738f3c03ff754f0303c8d9">IMP::core::ConstantRestraint::ConstantRestraint()</a>, <a href="classIMP_1_1core_1_1ConstantSingletonPredicate.html#acca07750d9840f52e22b49547f6d4418">IMP::core::ConstantSingletonPredicate::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1ConstantSingletonPredicate.html#a77de0a827189c446d3f5d9026cb01353">IMP::core::ConstantSingletonPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1ConstantSingletonPredicate.html#a06f8c07a0ff02a80e264c44f9143c264">IMP::core::ConstantSingletonPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1ConstantTripletPredicate.html#a39b8e9fd479ae7f80935f7ab8f7e14ca">IMP::core::ConstantTripletPredicate::do_get_inputs()</a>, <a 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href="classIMP_1_1core_1_1Cover.html#a18b4345f9d9ea754ab7d5dd909e1d85a">IMP::core::Cover::setup_particle()</a>, <a href="classIMP_1_1core_1_1CoverRefined.html#a7fb58728802c4bf0b5242ce09b3fbc87">IMP::core::CoverRefined::apply_index()</a>, <a href="classIMP_1_1core_1_1CoverRefined.html#afe0c430053195537421b9f5f3be433db">IMP::core::CoverRefined::apply_indexes()</a>, <a href="classIMP_1_1core_1_1CoverRefined.html#ac8093b20bf4415549a275b15b0504ef0">IMP::core::CoverRefined::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1CoverRefined.html#ae2ceba8c4a8d4f342c55bf4e63ff1f2d">IMP::core::CoverRefined::do_get_outputs()</a>, <a href="classIMP_1_1core_1_1DerivativesFromRefined.html#a3c0ba82b6c858e09b436e49ab194e4aa">IMP::core::DerivativesFromRefined::apply_index()</a>, <a href="classIMP_1_1core_1_1DerivativesFromRefined.html#ae0507498d1d954720230b21103987cb0">IMP::core::DerivativesFromRefined::apply_indexes()</a>, <a href="classIMP_1_1core_1_1DerivativesFromRefined.html#a10636b33468e5c72e21ce7567781e288">IMP::core::DerivativesFromRefined::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1DerivativesFromRefined.html#a824136ecb4b046ac246ce79149e72bd2">IMP::core::DerivativesFromRefined::do_get_outputs()</a>, <a href="classIMP_1_1core_1_1DerivativesToRefined.html#a8a55111883dca1044bfece5446a40551">IMP::core::DerivativesToRefined::apply_index()</a>, <a href="classIMP_1_1core_1_1DerivativesToRefined.html#ac913d70f2591ee438ac8e4926d4db32c">IMP::core::DerivativesToRefined::apply_indexes()</a>, <a href="classIMP_1_1core_1_1DerivativesToRefined.html#a9dbf014826795d90d055982bf1e07c51">IMP::core::DerivativesToRefined::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1DerivativesToRefined.html#ae56c30905324ad0e97b9770b03704448">IMP::core::DerivativesToRefined::do_get_outputs()</a>, <a 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href="classIMP_1_1core_1_1DirectionAngle.html#afe832f2f6a553bbf86894fdeb7eec42d">IMP::core::DirectionAngle::DirectionAngle()</a>, <a href="classIMP_1_1core_1_1DirectionAngle.html#a4fea00872ac8e064f1d2c68578759575">IMP::core::DirectionAngle::get_is_setup()</a>, <a href="classIMP_1_1core_1_1DirectionAngle.html#ab6690f325dd3fdd9bb126d8c6afd31af">IMP::core::DirectionAngle::setup_particle()</a>, <a href="classIMP_1_1core_1_1DirectionAngle.html#a237b38371936220cd3c3ca1785cc091f">IMP::core::DirectionAngle::setup_particle()</a>, <a href="classIMP_1_1core_1_1DirectionMover.html#a226b498a820763d43c7f507f89059e36">IMP::core::DirectionMover::DirectionMover()</a>, <a href="classIMP_1_1core_1_1DistancePairScore.html#a71740d22e71f6d713b37c5690f83b9a6">IMP::core::DistancePairScore::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1DistancePairScore.html#a1f69d849e2cd4451c580669d57b08a23">IMP::core::DistancePairScore::evaluate_index()</a>, <a 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href="classIMP_1_1core_1_1FixedRefiner.html#a71409c5169fd02437048f3a65057b912">IMP::core::FixedRefiner::FixedRefiner()</a>, <a href="classIMP_1_1core_1_1FixedRefiner.html#a05bf207d25fd1e0646bf7bd9f608180f">IMP::core::FixedRefiner::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1FixedRefiner.html#aff0ca83fbd69bede60b4c58b9ada9b1f">IMP::core::FixedRefiner::get_refined_indexes()</a>, <a href="classIMP_1_1core_1_1FixedRefiner.html#a1955d711ba5cb632dcc9e8036c6d6be9">IMP::core::FixedRefiner::get_refined_indexes_by_ref()</a>, <a href="classIMP_1_1core_1_1Gaussian.html#af603d7210e63fdbc74733250d9726f01">IMP::core::Gaussian::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1Gaussian.html#a2485c4d8d99ba29b1a408e698f0db2ac">IMP::core::Gaussian::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1Gaussian.html#ac3c88808a7f0a477e629760c3a1edbeb">IMP::core::Gaussian::Gaussian()</a>, <a 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href="classIMP_1_1core_1_1GenericAttributeSingletonScore.html#a1110467dc8c2d176d244a4fe7740afe5">IMP::core::GenericAttributeSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1core_1_1GenericAttributeSingletonScore.html#a7b88a951501e6ac69f59247148fc6721">IMP::core::GenericAttributeSingletonScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1core_1_1GenericAttributeSingletonScore.html#a33c00df5d2c0813886a637d5de0ed529">IMP::core::GenericAttributeSingletonScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1core_1_1GenericBoundingBox3DSingletonScore.html#ad29972b4e5dca87ab4ab0718baaf8a62">IMP::core::GenericBoundingBox3DSingletonScore::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1GenericBoundingBox3DSingletonScore.html#a04625a228cade49bf22f3bb30475f4b8">IMP::core::GenericBoundingBox3DSingletonScore::evaluate_if_good_indexes()</a>, <a 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href="classIMP_1_1core_1_1GenericDistanceToSingletonScore.html#a0063febf20d887a0f353146daed7e14a">IMP::core::GenericDistanceToSingletonScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1core_1_1GridClosePairsFinder.html#a225d46ec6e2d652085bf7482534e876a">IMP::core::GridClosePairsFinder::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1GridClosePairsFinder.html#adb27193de7ef63f08562aca372fe9ebf">IMP::core::GridClosePairsFinder::get_close_pairs()</a>, <a href="classIMP_1_1core_1_1GridClosePairsFinder.html#a562c0d5780f2d63841aab1d8bd3044f6">IMP::core::GridClosePairsFinder::get_close_pairs()</a>, <a href="classIMP_1_1core_1_1HarmonicDistancePairScore.html#a3d33f3730fc301345d93c0fedd0b00f1">IMP::core::HarmonicDistancePairScore::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1HarmonicDistancePairScore.html#aed2d6296770d0a56bc4cb4dd538bb885">IMP::core::HarmonicDistancePairScore::evaluate_index()</a>, <a 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href="classIMP_1_1core_1_1XYZR.html#ad07b9838ed1c4ad55ae8d46535ec0f56">IMP::core::XYZR::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1XYZR.html#a25702be3a57bd5546719624e9644c633">IMP::core::XYZR::XYZR()</a>, <a href="classIMP_1_1core_1_1XYZR.html#ad57d9400bc1e93292e927dfc208f62fb">IMP::core::XYZR::get_is_setup()</a>, <a href="classIMP_1_1core_1_1XYZR.html#a2972fe8c69de14cce2a4261f52c635a1">IMP::core::XYZR::setup_particle()</a>, <a href="classIMP_1_1core_1_1XYZR.html#a4c60eba2dc7581429ebb119a0b918131">IMP::core::XYZR::setup_particle()</a>, <a href="classIMP_1_1core_1_1XYZR.html#a918f7247568b4dd55613fb66c25d2bee">IMP::core::XYZR::setup_particle()</a>, <a href="classIMP_1_1display_1_1Colored.html#a37d69f63a128fa2fbf0413f41b97bb05">IMP::display::Colored::do_setup_particle()</a>, <a href="classIMP_1_1display_1_1Colored.html#afb3020bcc3e737c8832052bdbb513a14">IMP::display::Colored::Colored()</a>, <a href="classIMP_1_1display_1_1Colored.html#a6c6b8f4f59e8d32e2b5872181fc15f04">IMP::display::Colored::get_is_setup()</a>, <a href="classIMP_1_1display_1_1Colored.html#a1f682cba5427be0068b38d6c126da974">IMP::display::Colored::setup_particle()</a>, <a href="classIMP_1_1display_1_1RestraintGeometry.html#a305119c98092eaa981746cc8c035fc1a">IMP::display::RestraintGeometry::RestraintGeometry()</a>, <a href="classIMP_1_1display_1_1WriteOptimizerState.html#a51ae42814a3cf03a8d4003bc94508de7">IMP::display::WriteOptimizerState::WriteOptimizerState()</a>, <a href="classIMP_1_1domino_1_1BranchAndBoundSampler.html#a6731519ba2c15c8de889184c7d8d1285">IMP::domino::BranchAndBoundSampler::BranchAndBoundSampler()</a>, <a href="classIMP_1_1domino_1_1BranchAndBoundSampler.html#a8246e854a8ba9054935a9c75cb9c3a5b">IMP::domino::BranchAndBoundSampler::BranchAndBoundSampler()</a>, <a 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href="classIMP_1_1example_1_1ExampleDecorator.html#aea68bd2cc5dc18edc92d804e486e43b6">IMP::example::ExampleDecorator::ExampleDecorator()</a>, <a href="classIMP_1_1example_1_1ExamplePairScore.html#a8a028bafe90b65cc304667b7a32d60eb">IMP::example::ExamplePairScore::do_get_inputs()</a>, <a href="classIMP_1_1example_1_1ExamplePairScore.html#a9f265046c5c001ced314701a19d8f420">IMP::example::ExamplePairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1example_1_1ExamplePairScore.html#ac4a6da957157e308a3226b3d73f478ff">IMP::example::ExamplePairScore::evaluate_index()</a>, <a href="classIMP_1_1example_1_1ExamplePairScore.html#a177f9b5efa1a234f21564f0d452f4e9c">IMP::example::ExamplePairScore::evaluate_indexes()</a>, <a href="classIMP_1_1example_1_1ExamplePairScore.html#a145439064a238d7606e00e46fddeb6d7">IMP::example::ExamplePairScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1example_1_1ExamplePairScore.html#abda5235092e6bfc7a19268e33b954719">IMP::example::ExamplePairScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1example_1_1ExampleRestraint.html#a63477f355b12a71baeac254e88b2face">IMP::example::ExampleRestraint::ExampleRestraint()</a>, <a href="classIMP_1_1example_1_1ExampleSingletonModifier.html#aca4703e6377d8d0e327bd547bb1f5fb4">IMP::example::ExampleSingletonModifier::apply_index()</a>, <a href="classIMP_1_1example_1_1ExampleSingletonModifier.html#acd99bc31a1ab70b64cb68d45d191f79d">IMP::example::ExampleSingletonModifier::apply_indexes()</a>, <a href="classIMP_1_1example_1_1ExampleSingletonModifier.html#a8484194417f33950297c36b1e5d73f94">IMP::example::ExampleSingletonModifier::do_get_inputs()</a>, <a href="classIMP_1_1example_1_1ExampleSingletonModifier.html#a183ee092d168ed48d889d5061a9d83ea">IMP::example::ExampleSingletonModifier::do_get_outputs()</a>, <a 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href="classIMP_1_1npctransport_1_1SlabWithToroidalPore.html#aa583897ead8362d4c84b92c78aa54a18">IMP::npctransport::SlabWithToroidalPore::do_setup_particle()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithToroidalPore.html#a9f9b17a2c451419f329c6c058318dfba">IMP::npctransport::SlabWithToroidalPore::SlabWithToroidalPore()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithToroidalPore.html#acfa3d5d3fcf813c02f3cc30c13ac4876">IMP::npctransport::SlabWithToroidalPore::get_is_setup()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithToroidalPore.html#aaf307e24380fdacb3c205d5073d0144a">IMP::npctransport::SlabWithToroidalPore::setup_particle()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithToroidalPore.html#a07871738b01b66c32412e600bbcebf83">IMP::npctransport::SlabWithToroidalPore::setup_particle()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithToroidalPorePairScore.html#afbaed12df9e9bd455f2e5f07bb6cb66b">IMP::npctransport::SlabWithToroidalPorePairScore::do_get_inputs()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithToroidalPorePairScore.html#a6ab34004310542d304a5659de61b1223">IMP::npctransport::SlabWithToroidalPorePairScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithToroidalPorePairScore.html#ac038a2aa03536cc6a0265c2b0e06d84f">IMP::npctransport::SlabWithToroidalPorePairScore::evaluate_index()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithToroidalPorePairScore.html#a63cad160e76611b2e8eec2158842483b">IMP::npctransport::SlabWithToroidalPorePairScore::evaluate_indexes()</a>, <a href="classIMP_1_1npctransport_1_1Transporting.html#a8b0046417777bf557d86cb525ec691ec">IMP::npctransport::Transporting::do_setup_particle()</a>, <a href="classIMP_1_1npctransport_1_1Transporting.html#acd8d5842a2af1aed596023a8163bfbf6">IMP::npctransport::Transporting::Transporting()</a>, <a href="classIMP_1_1npctransport_1_1Transporting.html#a5e1e6ea2eeb8996e721e3e2542317ed8">IMP::npctransport::Transporting::get_is_setup()</a>, <a href="classIMP_1_1npctransport_1_1Transporting.html#a4040a253b333196bd955a5945a079283">IMP::npctransport::Transporting::setup_particle()</a>, <a href="classIMP_1_1npctransport_1_1ZBiasSingletonScore.html#a967c3986bb37a1a16b761f8d9e4c8f21">IMP::npctransport::ZBiasSingletonScore::do_get_inputs()</a>, <a href="classIMP_1_1npctransport_1_1ZBiasSingletonScore.html#afc2372d9d5912790c9bd711ae247371f">IMP::npctransport::ZBiasSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1npctransport_1_1ZBiasSingletonScore.html#a64fe0edf6b1014ea87219cecbc7ad83a">IMP::npctransport::ZBiasSingletonScore::evaluate_index()</a>, <a href="classIMP_1_1npctransport_1_1ZBiasSingletonScore.html#a5fcbc10bd5dac71d600a68cf9583c235">IMP::npctransport::ZBiasSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1npctransport_1_1ZBiasSingletonScore.html#a629f3b7227f818ea15b2201af1aec8ad">IMP::npctransport::ZBiasSingletonScore::evaluate_indexes_delta()</a>, <a 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href="classIMP_1_1pmi1_1_1Symmetric.html#ab44fdcb72562d56b8b10f6b081cb4598">IMP::pmi1::Symmetric::get_is_setup()</a>, <a href="classIMP_1_1pmi1_1_1Symmetric.html#a14e50dfbe30e8c3b38a9bba3b723bc9c">IMP::pmi1::Symmetric::setup_particle()</a>, <a href="classIMP_1_1pmi1_1_1Symmetric.html#a86fec61bb6ee044d0fd13987753cf687">IMP::pmi1::Symmetric::Symmetric()</a>, <a href="classIMP_1_1pmi1_1_1TransformMover.html#ae41d15d8ba410ce9d770530de450a2af">IMP::pmi1::TransformMover::TransformMover()</a>, <a href="classIMP_1_1pmi1_1_1TransformMover.html#af5dad5161b60a8a51c26e961c22b2796">IMP::pmi1::TransformMover::TransformMover()</a>, <a href="classIMP_1_1pmi1_1_1TransformMover.html#ac6d359cb8cfb6ad468c5f276aa6f3554">IMP::pmi1::TransformMover::TransformMover()</a>, <a href="classIMP_1_1pmi1_1_1Uncertainty.html#aa62db02fa4b5dfb30f510670a40e90a7">IMP::pmi1::Uncertainty::do_setup_particle()</a>, <a 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href="classIMP_1_1pmi_1_1Resolution.html#afe33425fc9b6e30f6fef08e644ae23d6">IMP::pmi::Resolution::setup_particle()</a>, <a href="classIMP_1_1pmi_1_1Resolution.html#abcb78bb60d33258844aa77855f82206c">IMP::pmi::Resolution::Resolution()</a>, <a href="classIMP_1_1pmi_1_1Symmetric.html#a4450c1e56dcf5284b0b53872f92560e0">IMP::pmi::Symmetric::do_setup_particle()</a>, <a href="classIMP_1_1pmi_1_1Symmetric.html#a69e607c3919cd684b5cd35f6b633a362">IMP::pmi::Symmetric::get_is_setup()</a>, <a href="classIMP_1_1pmi_1_1Symmetric.html#ae95167db885a60e540bcf7b66abbdaac">IMP::pmi::Symmetric::setup_particle()</a>, <a href="classIMP_1_1pmi_1_1Symmetric.html#adfe6846fca255d7d275cfc373544e595">IMP::pmi::Symmetric::Symmetric()</a>, <a href="classIMP_1_1pmi_1_1TransformMover.html#a28dcded10bac77035ef8430ce0d28bd3">IMP::pmi::TransformMover::TransformMover()</a>, <a href="classIMP_1_1pmi_1_1TransformMover.html#a46d160c066d8fd9b9d40f087ac2a59d1">IMP::pmi::TransformMover::TransformMover()</a>, <a href="classIMP_1_1pmi_1_1TransformMover.html#ac85464e8d64888b3e83ef9bcfa951718">IMP::pmi::TransformMover::TransformMover()</a>, <a href="classIMP_1_1pmi_1_1Uncertainty.html#aa36498a2d12dcc936e1db0c88848537e">IMP::pmi::Uncertainty::do_setup_particle()</a>, <a href="classIMP_1_1pmi_1_1Uncertainty.html#a1e6736bc8ecbb44e72152ea1017b4b79">IMP::pmi::Uncertainty::get_is_setup()</a>, <a href="classIMP_1_1pmi_1_1Uncertainty.html#ab5afc06397b7e14477e106a2475d3706">IMP::pmi::Uncertainty::setup_particle()</a>, <a href="classIMP_1_1pmi_1_1Uncertainty.html#ad78ad0b3a55a6d4c635ba82528b74ab2">IMP::pmi::Uncertainty::Uncertainty()</a>, <a href="classIMP_1_1rmf_1_1HierarchyLoadLink.html#a457f6759860d684136f977bda083e6c6">IMP::rmf::HierarchyLoadLink::add_link_recursive()</a>, <a href="classIMP_1_1rmf_1_1HierarchyLoadLink.html#adb414343f11c2bf660fc4c2eb15cc85c">IMP::rmf::HierarchyLoadLink::create_one_provenance()</a>, <a 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href="classIMP_1_1rmf_1_1HierarchySaveLink.html#a9a269c9979c9d3e889d093e286aaf46d">IMP::rmf::HierarchySaveLink::add_recursive()</a>, <a href="classIMP_1_1rmf_1_1HierarchySaveLink.html#acad2966f5813309997bdb1b89a4106f4">IMP::rmf::HierarchySaveLink::do_save_hierarchy()</a>, <a href="classIMP_1_1rmf_1_1HierarchySaveLink.html#acb5c102fbadac34930f053c2ed03bd42">IMP::rmf::HierarchySaveLink::do_setup_node()</a>, <a href="classIMP_1_1rmf_1_1SaveOptimizerState.html#aba24e4f4ffe8503079a40eb80852c6da">IMP::rmf::SaveOptimizerState::SaveOptimizerState()</a>, <a href="classIMP_1_1rmf_1_1SimpleLoadLink.html#aae0cb5f069acf827712f0543f62be5cc">IMP::rmf::SimpleLoadLink::do_create()</a>, <a href="classIMP_1_1rmf_1_1SimpleLoadLink.html#acb250839c30652b3b67bb63c8beb3429">IMP::rmf::SimpleLoadLink::create()</a>, <a href="classIMP_1_1score__functor_1_1AddScores.html#a99a269b65f1a4d78a3f0b1d64d5798b7">IMP::score_functor::AddScores::get_inputs()</a>, <a 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href="namespaceIMP_1_1example.html#ae4f0f8060682cb190fcc18eb72322b62">IMP::example::optimize_balls()</a>, <a href="namespaceIMP_1_1multifit.html#a3ae2f2b63f2b07f548e4fd095871d9b8">IMP::multifit::create_coarse_molecule_from_density()</a>, <a href="namespaceIMP_1_1multifit.html#a990fc248adf46233d96011ab77130eec">IMP::multifit::load_ensemble()</a>, <a href="namespaceIMP_1_1npctransport.html#af4eac42b841cb74c967c2f4284ddb1d0">IMP::npctransport::create_hierarchies_with_sites()</a>, <a href="namespaceIMP_1_1npctransport.html#a656ab4ca89e8d22e30f474a6a15fe34d">IMP::npctransport::do_evaluate_index_harmonic()</a>, <a href="namespaceIMP_1_1rmf.html#a34bff2a310116bc205e199ae6442be5d">IMP::rmf::create_hierarchies()</a>, <a href="namespaceIMP_1_1rmf.html#af3c5165b1f2cb083d98c36bd202ef275">IMP::rmf::create_particles()</a>, <a href="namespaceIMP_1_1rmf.html#ae393fe01981d8d3b03b431d3d4b26722">IMP::rmf::create_restraints()</a>, <a href="namespaceIMP_1_1saxs.html#a48a6e99f77380532e66b861ecd6ff64c">IMP::saxs::read_files()</a>, <a href="namespaceIMP_1_1saxs.html#abd840b58460b2d3c4874fe738272f80b">IMP::saxs::read_pdb()</a>, <a href="namespaceIMP_1_1spb.html#a6a49d172ebb893d6a3b0de6234cb318e">IMP::spb::add_GFP_restraint()</a>, <a href="namespaceIMP_1_1spb.html#a23e14d249f701c421fd66833c044539a">IMP::spb::add_internal_restraint()</a>, <a href="namespaceIMP_1_1spb.html#ae1bbb466a333fd88c5c6307d628165b9">IMP::spb::add_ISD_particles()</a>, <a href="namespaceIMP_1_1spb.html#ac82266395d7d5fcf26defd3c2f2f9f06">IMP::spb::add_link()</a>, <a href="namespaceIMP_1_1spb.html#a2e319d74f871dffac11765e34a748794">IMP::spb::add_link()</a>, <a href="namespaceIMP_1_1spb.html#ac5d9e593d188cd0afbeb276881d82996">IMP::spb::add_my_connectivity()</a>, <a href="namespaceIMP_1_1spb.html#a1d50546bf0502a542c492062c8f0f42b">IMP::spb::add_restrain_coiledcoil_to_cterm()</a>, <a href="namespaceIMP_1_1spb.html#a238100618f48d22ed7acd619702caea9">IMP::spb::add_SPBexcluded_volume()</a>, <a href="namespaceIMP_1_1spb.html#ac09f34c6ac78e8632549a693c32154e7">IMP::spb::add_stay_close_restraint()</a>, <a href="namespaceIMP_1_1spb.html#a575f993823c11b8c6d9b11c1fcd089f0">IMP::spb::add_stay_close_restraint()</a>, <a href="namespaceIMP_1_1spb.html#aaf1e29ff21dfe105c06b225967d4849e">IMP::spb::add_stay_on_plane_restraint()</a>, <a href="namespaceIMP_1_1spb.html#a06b534d7a1f9697f71f4a75366ba0a93">IMP::spb::add_symmetry_restraint()</a>, <a href="namespaceIMP_1_1spb.html#a69efcfb24ba7b76acf747b54f9c8ce75">IMP::spb::add_tilt()</a>, <a href="namespaceIMP_1_1spb.html#acf08490a12bf75b525b03a2b88f55ada">IMP::spb::add_tilt_restraint()</a>, <a href="namespaceIMP_1_1spb.html#af9854762e7ddee17e6b588f2a8502c20">IMP::spb::create_coiled_coil()</a>, <a href="namespaceIMP_1_1spb.html#ae8957e05a946a61598e363e00de9763c">IMP::spb::create_GFP()</a>, <a href="namespaceIMP_1_1spb.html#abeff346a43c51e4d81a56567357880a1">IMP::spb::create_merged_protein()</a>, <a href="namespaceIMP_1_1spb.html#a78b1fb512e1db9c6362bb36df94293be">IMP::spb::create_protein()</a>, <a href="namespaceIMP_1_1spb.html#a994bd0fe39346bf4f08cbc6693a230f3">IMP::spb::create_protein()</a>, <a href="namespaceIMP_1_1spb.html#ae9d935784a933409cd306c7c046cfff6">IMP::spb::create_representation()</a>, <a href="namespaceIMP_1_1spb.html#a76fc05e5b9a81702e8c5a6d560695b08">IMP::spb::do_bipartite_mindist()</a>, <a href="namespaceIMP_1_1spb.html#a034798d478f68b2f5cab9cb68ac983d4">IMP::spb::do_bipartite_mindist()</a>, <a href="namespaceIMP_1_1spb.html#ab58214204b446b5e3784249004b1ed9d">IMP::spb::setup_SPBMonteCarlo()</a>, <a href="namespaceIMP_1_1spb.html#a7c113921b584fd1fce234cdb478f354b">IMP::spb::spb_assemble_restraints()</a>, <a href="namespaceIMP_1_1spb.html#adc86ba90554da52601fc2e10c42cf016">IMP::spb::y2h_restraint()</a>, <a href="namespaceIMP_1_1spb.html#ab5e2abcde6e2dd7c9578b1f952808e38">IMP::spb::y2h_restraint()</a>, <a href="namespaceIMP_1_1spb.html#ac4ef731aae34f16b158cc7ab451ccd38">IMP::spb::y2h_restraint()</a>, <a href="namespaceIMP_1_1spb.html#ab16e77716acf17384a5092aa7ae86294">IMP::spb::y2h_restraint()</a></td></tr>
22 <tr><td>@ref IMP::ModelObject</td><td><a href="classIMP_1_1Model.html#ad465454c3c7e87a2d91e962f18976973">IMP::Model::check_dependency_invariants()</a>, <a href="classIMP_1_1Model.html#a3896c96f9714e42c432c4a16330a1dda">IMP::Model::do_add_dependencies()</a>, <a href="classIMP_1_1Model.html#a2670fa43a049966d0cbef9029c642783">IMP::Model::do_add_model_object()</a>, <a href="classIMP_1_1Model.html#aafaf6973a7a2d50e3a665a6f6f49d7f8">IMP::Model::do_check_inputs_and_outputs()</a>, <a href="classIMP_1_1Model.html#aa5c4acab97a8fbdf57716d0348b45ff9">IMP::Model::do_check_not_in_readers_and_writers()</a>, <a href="classIMP_1_1Model.html#a599ca74aa41fc54ad303d67199bc3c41">IMP::Model::do_check_readers_and_writers()</a>, <a href="classIMP_1_1Model.html#ab9be3faa5fdeac3b557ee462947ff50c">IMP::Model::do_check_required_score_states()</a>, <a href="classIMP_1_1Model.html#a6e8061a710fa61d89a7c2369ae15f496">IMP::Model::do_clear_dependencies()</a>, <a href="classIMP_1_1Model.html#ab0d7ad034ee31e452c89c621220ce6c3">IMP::Model::do_clear_required_score_states()</a>, <a href="classIMP_1_1Model.html#a1a6df87f12ee72179bca3a7dccc24763">IMP::Model::do_get_has_dependencies()</a>, <a href="classIMP_1_1Model.html#a8595ab61604a7251b5295069e09c6a25">IMP::Model::do_get_has_required_score_states()</a>, <a href="classIMP_1_1Model.html#a53a623d9a1d08e8f1ed4f357fb35b49d">IMP::Model::do_get_required_score_states()</a>, <a href="classIMP_1_1Model.html#a67d50c7852ecf5009f751fdbeb19d705">IMP::Model::do_remove_model_object()</a>, <a href="classIMP_1_1Model.html#a321c18bab7495b752d62f07523aa6c99">IMP::Model::do_set_has_dependencies()</a>, <a href="classIMP_1_1Model.html#ac0451c02b223c536d7a501445a7277e5">IMP::Model::do_set_has_required_score_states()</a>, <a href="classIMP_1_1Model.html#a0c1d7d62603b2d7710fb742ec4b658aa">IMP::Model::get_ancestor_score_states()</a>, <a href="classIMP_1_1Model.html#aafc1673e0a163d3bd1d3dc92ee884a57">IMP::Model::get_dependency_graph_inputs()</a>, <a href="classIMP_1_1Model.html#a816914bece10937fa02eb124f4ce6ae2">IMP::Model::get_dependency_graph_outputs()</a>, <a href="classIMP_1_1Model.html#a9e4c4578f3ad6e6e56890670b1083dee">IMP::Model::get_descendent_score_states()</a>, <a href="namespaceIMP.html#ae762869ee2f6a3888dcd62a1f4213566">IMP::get_dependent_particles()</a>, <a href="namespaceIMP.html#a02c846056b00408e6c39242c0aa0af1f">IMP::get_required_score_states()</a></td></tr>
23 <tr><td>@ref IMP::Object</td><td><a href="classIMP_1_1CreateLogContext.html#aac0978da0bf0dd317f4c46e33472cfce">IMP::CreateLogContext::CreateLogContext()</a>, <a href="classIMP_1_1CreateLogContext.html#a6599201fcefd6bd0fdad2d33c36518db">IMP::CreateLogContext::CreateLogContext()</a>, <a href="classIMP_1_1CreateLogContext.html#a75c6da5833b963ecf839b02f660791e1">IMP::CreateLogContext::set()</a>, <a href="classIMP_1_1Decorator.html#acd28629125399c8073f04f4cb15b6ccd">IMP::Decorator::compare()</a>, <a href="classIMP_1_1Model.html#ab6f2323f70ce6ae41b012712c2320347">IMP::Model::add_data()</a>, <a href="classIMP_1_1Object.html#a82f7afeeeedf5437068009c31ed0b862">IMP::Object::add_live_object()</a>, <a href="classIMP_1_1Object.html#a8a314aeb1194db2f37865791f7ed83d5">IMP::Object::remove_live_object()</a>, <a href="classIMP_1_1Object.html#a1d12f52d4b5235d723433dcaa42016e5">IMP::Object::compare()</a>, <a href="classIMP_1_1SetCheckState.html#aee6f6ca36023959691ab29db58b457aa">IMP::SetCheckState::do_set()</a>, <a href="classIMP_1_1SetCheckState.html#af3c629aea0fc699de8ebfccda3c5e9dd">IMP::SetCheckState::SetCheckState()</a>, <a href="classIMP_1_1SetCheckState.html#aefc4eaea42c097c397f18cfe172de163">IMP::SetCheckState::set()</a>, <a href="classIMP_1_1SetLogState.html#a428c85ba5ee2de2f7a0c0229d268aa6f">IMP::SetLogState::do_set()</a>, <a href="classIMP_1_1SetLogState.html#a50645d667e2e83b9068525e32369e35b">IMP::SetLogState::SetLogState()</a>, <a href="classIMP_1_1SetLogState.html#ab9da0857b9c5cd09e20e096eac7f3e5f">IMP::SetLogState::set()</a>, <a href="namespaceIMP.html#a7e5cb87b915025d9948ecc762db49136">IMP::object_cast()</a>, <a href="namespaceIMP_1_1rmf.html#ae9ce729d949656bb507f384f5220d05a">IMP::rmf::get_node_from_association()</a>, <a href="namespaceIMP_1_1rmf.html#a91e1e8ae4ea55d0e06fa26d626970d92">IMP::rmf::get_node_from_association()</a>, <a href="namespaceIMP_1_1rmf.html#a74acc7e3e31eab6ceaad0fe0131f0cfe">IMP::rmf::get_has_associated_node()</a>, <a href="namespaceIMP_1_1rmf.html#a6be38fec78e589e2c5368b4c34522edd">IMP::rmf::set_association()</a></td></tr>
24 <tr><td>@ref IMP::Optimizer</td><td><a href="classIMP_1_1Optimizer.html#a9b34441cf099f14439410719053f147e">IMP::Optimizer::set_optimizer_state_optimizer()</a>, <a href="classIMP_1_1OptimizerState.html#a384158c2ee465855137bc03ce7d5a090">IMP::OptimizerState::set_optimizer()</a>, <a href="classIMP_1_1core_1_1MCCGSampler.html#aa307180bc674357cb82b6ecdd2904889">IMP::core::MCCGSampler::set_local_optimizer()</a>, <a href="classIMP_1_1core_1_1MonteCarloWithBasinHopping.html#a6356051316cf0e8dc0fe5468225a5a10">IMP::core::MonteCarloWithBasinHopping::MonteCarloWithBasinHopping()</a>, <a href="classIMP_1_1core_1_1MonteCarloWithLocalOptimization.html#a67c5c29ced1b207546e6832689bc5859">IMP::core::MonteCarloWithLocalOptimization::MonteCarloWithLocalOptimization()</a>, <a href="classIMP_1_1npctransport_1_1Statistics.html#a551002c191a92fe34f8743c110549028">IMP::npctransport::Statistics::add_optimizer_states()</a>, <a href="namespaceIMP_1_1container.html#ac8965a95934fc142a9797c44fdc03d88">IMP::container::get_slack_estimate()</a>, <a href="namespaceIMP_1_1container.html#a10c42d60066d5eeb4b9cd5fa4a6d72d9">IMP::container::get_slack_estimate()</a></td></tr>
25 <tr><td>@ref IMP::OptimizerState</td><td><a href="classIMP_1_1Optimizer.html#a7f67c83ebe09b47f6aaf4bc0c250b3d9">IMP::Optimizer::remove_optimizer_state()</a>, <a href="classIMP_1_1Optimizer.html#a8c9bf2d71403d3b8f7c178e4e5dfc047">IMP::Optimizer::add_optimizer_state()</a>, <a href="classIMP_1_1Optimizer.html#a9b34441cf099f14439410719053f147e">IMP::Optimizer::set_optimizer_state_optimizer()</a>, <a href="classIMP_1_1core_1_1MCCGSampler.html#ac1f397db11f8df64c72a6361b0e7d772">IMP::core::MCCGSampler::remove_optimizer_state()</a>, <a href="classIMP_1_1core_1_1MCCGSampler.html#ae6cfef11cada50f400e6da98269dd207">IMP::core::MCCGSampler::add_optimizer_state()</a>, <a href="classIMP_1_1misc_1_1StateAdaptor.html#a20254b90bcaebe823d0613bdf8dcde80">IMP::misc::StateAdaptor::StateAdaptor()</a></td></tr>
26 <tr><td>@ref IMP::PairContainer</td><td><a href="classIMP_1_1PairContainerAdaptor.html#ad6224f22244c6a5bd3df68d444268644">IMP::PairContainerAdaptor::PairContainerAdaptor()</a>, <a href="classIMP_1_1container_1_1InContainerPairFilter.html#a258e31fbf56d9f7f5ed0dd0fc79f0ac2">IMP::container::InContainerPairFilter::InContainerPairFilter()</a>, <a href="classIMP_1_1container_1_1InContainerPairFilter.html#a27947488ae62dc8691b21561417a50ac">IMP::container::InContainerPairFilter::InContainerPairFilter()</a>, <a href="classIMP_1_1container_1_1PairContainerSet.html#a565965267d826a85995db52e08a615eb">IMP::container::PairContainerSet::remove_pair_container()</a>, <a href="classIMP_1_1container_1_1PairContainerSet.html#a2a33cfa37f8b6f22d9bb82739145eb29">IMP::container::PairContainerSet::add_pair_container()</a>, <a href="classIMP_1_1container_1_1PairContainerSet.html#ad73b337edcd61026138832c505587c47">IMP::container::PairContainerSet::get_set()</a>, <a href="classIMP_1_1core_1_1EdgePairsGeometry.html#ab49030c10717d6f2966f7b5867650ce2">IMP::core::EdgePairsGeometry::EdgePairsGeometry()</a>, <a href="classIMP_1_1core_1_1NeighborsTable.html#ab43ed9debb21ab81155181faabd7b262">IMP::core::NeighborsTable::NeighborsTable()</a>, <a href="classIMP_1_1display_1_1PairsGeometry.html#a1a82af0664dd2d3206b5e4f4aeb0ca5d">IMP::display::PairsGeometry::PairsGeometry()</a>, <a href="classIMP_1_1display_1_1PairsGeometry.html#ac2fcc0543e40dafd7129d0fe1317334b">IMP::display::PairsGeometry::PairsGeometry()</a>, <a href="classIMP_1_1isd_1_1AmbiguousNOERestraint.html#ae3ab78cb324e0b0d604bea494c6b4e7a">IMP::isd::AmbiguousNOERestraint::AmbiguousNOERestraint()</a>, <a href="classIMP_1_1isd_1_1MarginalHBondRestraint.html#a3e7e45bd707ac8ffaa52f80692015fe1">IMP::isd::MarginalHBondRestraint::add_contribution()</a>, <a href="classIMP_1_1isd_1_1MarginalNOERestraint.html#a3e2610a86de5cc54d941d83118032d58">IMP::isd::MarginalNOERestraint::add_contribution()</a>, <a href="classIMP_1_1npctransport_1_1Scoring.html#a4652f839b606cd0de7efbe2220510a22">IMP::npctransport::Scoring::create_predicates_pair_restraint()</a></td></tr>
27 <tr><td>@ref IMP::PairContainerAdaptor</td><td><a href="classIMP_1_1container_1_1DistributePairsScoreState.html#a7ac43f8453d5a0f453c007a24652a38f">IMP::container::DistributePairsScoreState::DistributePairsScoreState()</a>, <a href="classIMP_1_1container_1_1EventPairsOptimizerState.html#afdb7ee1a3d227a9c08c73d26065469d9">IMP::container::EventPairsOptimizerState::EventPairsOptimizerState()</a>, <a href="classIMP_1_1container_1_1MinimumPairRestraint.html#a9eb8eb9fdfcfe383257055de264ae393">IMP::container::MinimumPairRestraint::MinimumPairRestraint()</a>, <a href="classIMP_1_1container_1_1PairContainerStatistics.html#a1b0661cecd4ff309fb9847ab6a4d1ae5">IMP::container::PairContainerStatistics::PairContainerStatistics()</a>, <a href="classIMP_1_1container_1_1PairsConstraint.html#a26a23d76b5e516905ca31cb7ae426e6a">IMP::container::PairsConstraint::PairsConstraint()</a>, <a href="classIMP_1_1container_1_1PairsOptimizerState.html#ac34edec94ea948a2010887bac5862e01">IMP::container::PairsOptimizerState::PairsOptimizerState()</a>, <a href="classIMP_1_1container_1_1PairsRestraint.html#a537b01ba86efb40dd99bb270cf197054">IMP::container::PairsRestraint::PairsRestraint()</a>, <a href="classIMP_1_1container_1_1PredicatePairsRestraint.html#a71d534ebe79712a2697c44d45f103190">IMP::container::PredicatePairsRestraint::PredicatePairsRestraint()</a></td></tr>
28 <tr><td>@ref IMP::PairModifier</td><td><a href="classIMP_1_1PairContainer.html#ae4d131f42b91dfea7785493ea3092ce7">IMP::PairContainer::apply()</a>, <a href="classIMP_1_1PairContainer.html#a22536a01bbe9a437b59fa3d39fb4b453">IMP::PairContainer::apply_generic()</a>, <a href="classIMP_1_1PairContainer.html#a7bbb919465a48da1f8875030af040737">IMP::PairContainer::apply_generic_moved()</a>, <a href="classIMP_1_1PairContainer.html#a4056f063501464a662a6d34a665b1ea8">IMP::PairContainer::apply_moved()</a>, <a href="classIMP_1_1PairContainer.html#ab88751a332573bb3149469272f8dd727">IMP::PairContainer::do_apply()</a>, <a href="classIMP_1_1PairContainer.html#a7043f56aa5f4d0cac63fd6574bbb8fc0">IMP::PairContainer::do_apply_moved()</a>, <a href="classIMP_1_1atom_1_1BondPairContainer.html#a825b0459698d7501bb5134b708580460">IMP::atom::BondPairContainer::do_apply()</a>, <a href="classIMP_1_1atom_1_1BondPairContainer.html#acbd0f3193d77767c73c1f36095822f95">IMP::atom::BondPairContainer::do_apply_moved()</a>, <a href="classIMP_1_1container_1_1AllBipartitePairContainer.html#a3c22bc0a3888bb4db26056868f981d35">IMP::container::AllBipartitePairContainer::do_apply()</a>, <a href="classIMP_1_1container_1_1AllBipartitePairContainer.html#a30dfb397ab67c6bcba25584b12bd06d2">IMP::container::AllBipartitePairContainer::do_apply_moved()</a>, <a href="classIMP_1_1container_1_1AllPairContainer.html#ad1136fc157f7d8712ce12f15ac01ac38">IMP::container::AllPairContainer::do_apply()</a>, <a href="classIMP_1_1container_1_1AllPairContainer.html#a00a9690723d71692283269cf8120dec9">IMP::container::AllPairContainer::do_apply_moved()</a>, <a href="classIMP_1_1container_1_1CloseBipartitePairContainer.html#ae8b9e9ca10f09789fafd590f1a5e70d6">IMP::container::CloseBipartitePairContainer::do_apply()</a>, <a href="classIMP_1_1container_1_1ClosePairContainer.html#a107d3802b7665878b31d54da2877eacd">IMP::container::ClosePairContainer::do_apply()</a>, <a href="classIMP_1_1container_1_1ConnectingPairContainer.html#a379aa9875e9eed78a6b598b882923ef5">IMP::container::ConnectingPairContainer::do_apply()</a>, <a href="classIMP_1_1container_1_1ConsecutivePairContainer.html#a8cf3b244c8f3e8ef1c7f41cc4a3504f8">IMP::container::ConsecutivePairContainer::do_apply()</a>, <a href="classIMP_1_1container_1_1ConsecutivePairContainer.html#a66ac10b97eb22da7cb99c35e0548d939">IMP::container::ConsecutivePairContainer::do_apply_moved()</a>, <a href="classIMP_1_1container_1_1ExclusiveConsecutivePairContainer.html#a7168018a82e58d6b08ae007e4b6ae999">IMP::container::ExclusiveConsecutivePairContainer::do_apply()</a>, <a href="classIMP_1_1container_1_1ExclusiveConsecutivePairContainer.html#a8712a0ebaffb01da001c0b5ddcb3ff3c">IMP::container::ExclusiveConsecutivePairContainer::do_apply_moved()</a>, <a href="classIMP_1_1container_1_1PairsConstraint.html#a26a23d76b5e516905ca31cb7ae426e6a">IMP::container::PairsConstraint::PairsConstraint()</a>, <a href="classIMP_1_1container_1_1PairsOptimizerState.html#ac34edec94ea948a2010887bac5862e01">IMP::container::PairsOptimizerState::PairsOptimizerState()</a>, <a href="classIMP_1_1core_1_1PairConstraint.html#a6e7ff0a21fc61701d4382687ed3a68b7">IMP::core::PairConstraint::PairConstraint()</a>, <a href="classIMP_1_1core_1_1PairConstraint.html#a6a5aac7fefc5fa599881d63482b4f639">IMP::core::PairConstraint::PairConstraint()</a></td></tr>
29 <tr><td>@ref IMP::PairPredicate</td><td><a href="classIMP_1_1container_1_1CloseBipartitePairContainer.html#ab2e5ddbe66a7c653ddc5bdc61087074e">IMP::container::CloseBipartitePairContainer::remove_pair_filter()</a>, <a href="classIMP_1_1container_1_1CloseBipartitePairContainer.html#a8399cf4bcbe2f4a46843590efc2bb3b3">IMP::container::CloseBipartitePairContainer::add_pair_filter()</a>, <a href="classIMP_1_1container_1_1ClosePairContainer.html#adb8d32e342474ab606f657a83151f770">IMP::container::ClosePairContainer::remove_pair_filter()</a>, <a href="classIMP_1_1container_1_1ClosePairContainer.html#a45cfe9be7d6167cf1372dd3ba41ded93">IMP::container::ClosePairContainer::add_pair_filter()</a>, <a href="classIMP_1_1container_1_1DistributePairsScoreState.html#a905137252f92c0e5df1ce56f59dcc8ef">IMP::container::DistributePairsScoreState::add_predicate()</a>, <a href="classIMP_1_1container_1_1EventPairsOptimizerState.html#afdb7ee1a3d227a9c08c73d26065469d9">IMP::container::EventPairsOptimizerState::EventPairsOptimizerState()</a>, <a href="classIMP_1_1container_1_1PredicatePairsRestraint.html#a71d534ebe79712a2697c44d45f103190">IMP::container::PredicatePairsRestraint::PredicatePairsRestraint()</a>, <a href="classIMP_1_1core_1_1ClosePairsFinder.html#a8df0a924b119f07a1abc653d45fe4a9e">IMP::core::ClosePairsFinder::remove_pair_filter()</a>, <a href="classIMP_1_1core_1_1ClosePairsFinder.html#ad062dd05e45e4edd2691aa3c8db1f1cb">IMP::core::ClosePairsFinder::add_pair_filter()</a>, <a href="classIMP_1_1core_1_1ExcludedVolumeRestraint.html#aa8abf15d5bd6a0e953494d440c9d5cc3">IMP::core::ExcludedVolumeRestraint::add_pair_filter()</a>, <a href="classIMP_1_1core_1_1ExcludedVolumeRestraint.html#a1bb358d5544925bf3d7c7888b08ae0c7">IMP::core::ExcludedVolumeRestraint::remove_pair_filter()</a>, <a href="classIMP_1_1misc_1_1DecayPairContainerOptimizerState.html#a5429de10f2384359ecc4f41676eefef6">IMP::misc::DecayPairContainerOptimizerState::DecayPairContainerOptimizerState()</a></td></tr>
30 <tr><td>@ref IMP::PairScore</td><td><a href="classIMP_1_1container_1_1MinimumPairRestraint.html#a9eb8eb9fdfcfe383257055de264ae393">IMP::container::MinimumPairRestraint::MinimumPairRestraint()</a>, <a href="classIMP_1_1container_1_1PairsRestraint.html#a537b01ba86efb40dd99bb270cf197054">IMP::container::PairsRestraint::PairsRestraint()</a>, <a href="classIMP_1_1container_1_1PredicatePairsRestraint.html#a6ba78aca8bc79b159a22b8f178911ff7">IMP::container::PredicatePairsRestraint::set_score()</a>, <a href="classIMP_1_1container_1_1PredicatePairsRestraint.html#aca389681d4a5bafd230f16cc9443bfa1">IMP::container::PredicatePairsRestraint::set_unknown_score()</a>, <a href="classIMP_1_1core_1_1ClosePairsPairScore.html#aa14e8e87a96d8e1bb5388301e89c8553">IMP::core::ClosePairsPairScore::ClosePairsPairScore()</a>, <a href="classIMP_1_1core_1_1ConnectivityRestraint.html#ab3f9acf18ba9cb254034c8f9ae1ddd1f">IMP::core::ConnectivityRestraint::ConnectivityRestraint()</a>, <a href="classIMP_1_1core_1_1IncrementalScoringFunction.html#acca3149b72ff1f2229bbb901de87c6eb">IMP::core::IncrementalScoringFunction::add_close_pair_score()</a>, <a href="classIMP_1_1core_1_1IncrementalScoringFunction.html#a59a77878cc2ce50f5d81c336435eaf07">IMP::core::IncrementalScoringFunction::add_close_pair_score()</a>, <a href="classIMP_1_1core_1_1KClosePairsPairScore.html#a2a23964f1fa3d3f05bd6d9504d071880">IMP::core::KClosePairsPairScore::KClosePairsPairScore()</a>, <a href="classIMP_1_1core_1_1MSConnectivityRestraint.html#a5615f33fd0a9e8554834467ee315bc76">IMP::core::MSConnectivityRestraint::MSConnectivityRestraint()</a>, <a href="classIMP_1_1core_1_1PairRestraint.html#a4153733cf2c74d9c87a379a631ff194f">IMP::core::PairRestraint::PairRestraint()</a>, <a href="classIMP_1_1core_1_1RefinedPairsPairScore.html#adb30d6b0d713e0b78829e7da0685335d">IMP::core::RefinedPairsPairScore::RefinedPairsPairScore()</a>, <a href="classIMP_1_1core_1_1RigidBodyDistancePairScore.html#a4975b55d39c224707d50b2a3e187b30f">IMP::core::RigidBodyDistancePairScore::RigidBodyDistancePairScore()</a>, <a href="classIMP_1_1core_1_1TypedPairScore.html#aa22066494d15fcbe1255a04634f09d50">IMP::core::TypedPairScore::set_pair_score()</a>, <a href="classIMP_1_1misc_1_1LowestRefinedPairScore.html#ae522bb65cfacf6dfcb2eed7adc4094e4">IMP::misc::LowestRefinedPairScore::LowestRefinedPairScore()</a>, <a href="classIMP_1_1npc_1_1CompositeRestraint.html#a645448ed2623fd3793167938f50f7038">IMP::npc::CompositeRestraint::CompositeRestraint()</a>, <a href="classIMP_1_1rotamer_1_1RotamerCalculator.html#a7b2c4dcc21cd3cf6cee2430993a1e756">IMP::rotamer::RotamerCalculator::transform()</a>, <a href="namespaceIMP_1_1example.html#aa485f4a9129b84b2b1296b4e150edb51">IMP::example::optimize_assembly()</a></td></tr>
31 <tr><td>@ref IMP::Particle</td><td><a href="classIMP_1_1Model.html#abb61bcf757787fdf43eeb6b71f603113">IMP::Model::add_particle_internal()</a>, <a href="classIMP_1_1ParticleAdaptor.html#a37b3a8366e47946b8312d7a5fd7e5279">IMP::ParticleAdaptor::ParticleAdaptor()</a>, <a href="classIMP_1_1ParticleAdaptor.html#a594eac780f0f2f616ddf7cddaf806ac8">IMP::ParticleAdaptor::ParticleAdaptor()</a>, <a href="classIMP_1_1ParticleAdaptor.html#a1401c5a1ef221ce471b4b601ad6eaa68">IMP::ParticleAdaptor::ParticleAdaptor()</a>, <a href="classIMP_1_1ParticleAdaptor.html#a860e974a3c2b9c0333cc8a095802283d">IMP::ParticleAdaptor::ParticleAdaptor()</a>, <a href="classIMP_1_1ParticleIndexAdaptor.html#a3c7e0d061a26af456ca08b2c55ac4c0c">IMP::ParticleIndexAdaptor::ParticleIndexAdaptor()</a>, <a href="classIMP_1_1Refiner.html#aa48af13c4fcdeb23171a3b3d7fdf8f83">IMP::Refiner::refined_begin()</a>, <a href="classIMP_1_1Refiner.html#a001cb3c2275e480aaf56b93deb4e4098">IMP::Refiner::refined_end()</a>, <a href="classIMP_1_1Refiner.html#a88fd0c21d615aca9bc30f651a2d4df24">IMP::Refiner::get_can_refine()</a>, <a href="classIMP_1_1Refiner.html#a86526ae1b5275cf0d1c42c3201f2e366">IMP::Refiner::get_number_of_refined()</a>, <a href="classIMP_1_1Refiner.html#a5472c3ed2b59a73d39ca58fba0aad9d9">IMP::Refiner::get_refined()</a>, <a href="classIMP_1_1Refiner.html#aee8d61be106d561f9be0e7ace3bbef34">IMP::Refiner::get_refined()</a>, <a href="classIMP_1_1ScopedAddCacheAttribute.html#a8af77bca25f204c29b0b5787e2b8788d">IMP::ScopedAddCacheAttribute::ScopedAddCacheAttribute()</a>, <a href="classIMP_1_1ScopedAddCacheAttribute.html#a950aa06fe61aafec097d962eb556714a">IMP::ScopedAddCacheAttribute::set()</a>, <a href="classIMP_1_1ScopedSetAttribute.html#a99b2803e357b09f6de49e93ce6cfefbd">IMP::ScopedSetAttribute::ScopedSetAttribute()</a>, <a href="classIMP_1_1ScopedSetAttribute.html#a7adf89db75ee85754c433440f37eb3ad">IMP::ScopedSetAttribute::set()</a>, <a href="classIMP_1_1atom_1_1BondEndpointsRefiner.html#a2d780adb4f74e5a3670cedb6e8626bf3">IMP::atom::BondEndpointsRefiner::get_can_refine()</a>, <a href="classIMP_1_1atom_1_1BondEndpointsRefiner.html#abb282e495e86d776e420b43fbbd3990f">IMP::atom::BondEndpointsRefiner::get_refined()</a>, <a href="classIMP_1_1atom_1_1BondGeometry.html#a82f2458d6fd04ef2720cd81eddd01b91">IMP::atom::BondGeometry::BondGeometry()</a>, <a href="classIMP_1_1atom_1_1CHARMMParameters.html#a2b698cd7b5a6946cc7949cc0a832b166">IMP::atom::CHARMMParameters::add_angle()</a>, <a href="classIMP_1_1atom_1_1CHARMMParameters.html#adabf60c9c911d1b15505a18de1a5223f">IMP::atom::CHARMMParameters::add_dihedral()</a>, <a href="classIMP_1_1atom_1_1SecondaryStructureResidue.html#aea26f9048af0cd495d711e7a5c842673">IMP::atom::SecondaryStructureResidue::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Selection.html#af55e3cfb3c4fa8ebd94c1b1f12f1fdb0">IMP::atom::Selection::Selection()</a>, <a href="classIMP_1_1atom_1_1Simulator.html#acb81041648a4b4890c4025b6839c3e14">IMP::atom::Simulator::remove_particle()</a>, <a href="classIMP_1_1atom_1_1Simulator.html#ae42a436cc82b22dd5d1fe81e305f480e">IMP::atom::Simulator::add_particle()</a>, <a href="classIMP_1_1atom_1_1TAMDParticle.html#a4983decc8a054f5b2e572b19f0939781">IMP::atom::TAMDParticle::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1TAMDParticle.html#acd4a1f68a13134872c27ab0ae85b9267">IMP::atom::TAMDParticle::setup_particle()</a>, <a href="classIMP_1_1atom_1_1TAMDParticle.html#abe2e84b9f10bc225c845fa6ca457bd2f">IMP::atom::TAMDParticle::setup_particle()</a>, <a href="classIMP_1_1container_1_1InContainerSingletonFilter.html#ae18787a0258620fde9386c9131b7b96f">IMP::container::InContainerSingletonFilter::get_value()</a>, <a href="classIMP_1_1core_1_1AllSameSingletonPredicate.html#aef27264063ebf318402c97f3f8334d13">IMP::core::AllSameSingletonPredicate::get_value()</a>, <a href="classIMP_1_1core_1_1AttributeSingletonPredicate.html#ab4225888eb9e6d0dfc402a227545aec9">IMP::core::AttributeSingletonPredicate::get_value()</a>, <a href="classIMP_1_1core_1_1ChildrenRefiner.html#a49d4b353ef4921e0b05171857a77086c">IMP::core::ChildrenRefiner::get_can_refine()</a>, <a href="classIMP_1_1core_1_1ChildrenRefiner.html#afeda09ff69e4e16706f8d3f7a71cfa0a">IMP::core::ChildrenRefiner::get_refined()</a>, <a href="classIMP_1_1core_1_1CoinFlipSingletonPredicate.html#adcbe9b617c93536d52760905bebc0b0e">IMP::core::CoinFlipSingletonPredicate::get_value()</a>, <a href="classIMP_1_1core_1_1ConstantSingletonPredicate.html#a3af63316bfcd9a884e052522f206c0f3">IMP::core::ConstantSingletonPredicate::get_value()</a>, <a href="classIMP_1_1core_1_1FixedRefiner.html#a9a577b7f3250a7cd05b9a2a4d41c284e">IMP::core::FixedRefiner::get_can_refine()</a>, <a href="classIMP_1_1core_1_1FixedRefiner.html#aa5dd9970b9e75b2b90d98b2303147995">IMP::core::FixedRefiner::get_refined()</a>, <a href="classIMP_1_1core_1_1InBoundingBox3DSingletonPredicate.html#aa47c7745726beca0872390a6729dd660">IMP::core::InBoundingBox3DSingletonPredicate::get_value()</a>, <a href="classIMP_1_1core_1_1LeavesRefiner.html#a55ab69c2607bdf68aa998edfeaf2555b">IMP::core::LeavesRefiner::get_can_refine()</a>, <a href="classIMP_1_1core_1_1LeavesRefiner.html#ad1f7d37021aa45239a572034bb340b0e">IMP::core::LeavesRefiner::get_refined()</a>, <a href="classIMP_1_1core_1_1OrderedTypeSingletonPredicate.html#a4d7e5bc03e26e71c52e893392a7eadc2">IMP::core::OrderedTypeSingletonPredicate::get_value()</a>, <a href="classIMP_1_1core_1_1QuadraticClosePairsFinder.html#aceb8fc137d4a06bcc35d11d0a0da0342">IMP::core::QuadraticClosePairsFinder::get_are_close_and_filtered()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#a6cb67f5f077f0ee3a9197641ee0ac74a">IMP::core::RigidBody::add_member_internal()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#ad9ca7d53e048d063ad3dcb9376ef8c88">IMP::core::RigidBody::teardown_constraints()</a>, <a href="classIMP_1_1core_1_1RigidBodyDerivativeGeometry.html#a380c2f5221b286669e50d1a3c1adc235">IMP::core::RigidBodyDerivativeGeometry::RigidBodyDerivativeGeometry()</a>, <a href="classIMP_1_1core_1_1RigidBodyFrameGeometry.html#af04c9e63e1b0e4082cf324606d845e5a">IMP::core::RigidBodyFrameGeometry::RigidBodyFrameGeometry()</a>, <a href="classIMP_1_1core_1_1RigidBodyTorque.html#a799b8bbd20a5f67426fc210e634d1e2d">IMP::core::RigidBodyTorque::extract_geometry()</a>, <a href="classIMP_1_1core_1_1RigidBodyTorque.html#afc9919799ce7dbd3d142b9ac490031d2">IMP::core::RigidBodyTorque::RigidBodyTorque()</a>, <a href="classIMP_1_1core_1_1SingletonConstraint.html#a313647b6559bce11d4088c029332bcb2">IMP::core::SingletonConstraint::SingletonConstraint()</a>, <a href="classIMP_1_1core_1_1TableRefiner.html#afcfaf9a69ca5747a1a0d887bdcec9ebf">IMP::core::TableRefiner::add_particle()</a>, <a href="classIMP_1_1core_1_1TableRefiner.html#a8a81de41ad29718c5df5afd0ec8d33ff">IMP::core::TableRefiner::get_can_refine()</a>, <a href="classIMP_1_1core_1_1TableRefiner.html#a466ed7d73f725c9ad9d0ea82f51a64d9">IMP::core::TableRefiner::get_refined()</a>, <a href="classIMP_1_1core_1_1TableRefiner.html#a7bedc730004885f8147f9b239994b313">IMP::core::TableRefiner::remove_particle()</a>, <a href="classIMP_1_1core_1_1TableRefiner.html#a1b5c10798a6f72040ebf6b9e70b0bfd7">IMP::core::TableRefiner::set_particle()</a>, <a href="classIMP_1_1core_1_1TypedPairScore.html#aae80b4cb6e0a0d6f240d60e2c5da48b8">IMP::core::TypedPairScore::set_particle_type()</a>, <a href="classIMP_1_1core_1_1UnorderedTypeSingletonPredicate.html#aae3fe46edcacc97f756a200ed2da442e">IMP::core::UnorderedTypeSingletonPredicate::get_value()</a>, <a href="classIMP_1_1core_1_1XYZDerivativeGeometry.html#a92d2d30e539aa11edd19c8edb4815ca0">IMP::core::XYZDerivativeGeometry::XYZDerivativeGeometry()</a>, <a href="classIMP_1_1core_1_1XYZRGeometry.html#ab980cd97a4ff3c40d99ba63a20192a07">IMP::core::XYZRGeometry::XYZRGeometry()</a>, <a href="classIMP_1_1display_1_1SingletonGeometry.html#ab0c4559eca9051a847fa7431041d103c">IMP::display::SingletonGeometry::SingletonGeometry()</a>, <a href="classIMP_1_1domino_1_1CompoundStates.html#ad197cfe069ced7d7372ec59852607730">IMP::domino::CompoundStates::load_particle_state()</a>, <a href="classIMP_1_1domino_1_1DiscreteSampler.html#af01fe0f3283adc61bdb94b716afca5cd">IMP::domino::DiscreteSampler::set_particle_states()</a>, <a href="classIMP_1_1domino_1_1DisjointSetsSubsetFilterTable.html#a3805c30908b11f8e72daddb3fbc3c7a7">IMP::domino::DisjointSetsSubsetFilterTable::get_index()</a>, <a href="classIMP_1_1domino_1_1IndexStates.html#a1e6f99d5a2e5def2d0d4af73ca370ba5">IMP::domino::IndexStates::load_particle_state()</a>, <a href="classIMP_1_1domino_1_1ListSubsetFilterTable.html#a969b5d728ed81870e36a51fac6887b8e">IMP::domino::ListSubsetFilterTable::get_number_of_particle_states()</a>, <a href="classIMP_1_1domino_1_1ListSubsetFilterTable.html#abcb5b2e0ec46754f150167b60c8b85b6">IMP::domino::ListSubsetFilterTable::set_allowed_states()</a>, <a href="classIMP_1_1domino_1_1NestedRigidBodyStates.html#a5c17442c1bdd70f33d433185894e183c">IMP::domino::NestedRigidBodyStates::load_particle_state()</a>, <a href="classIMP_1_1domino_1_1ParticleStates.html#ac11a066be2c5812768068f4126e94f53">IMP::domino::ParticleStates::load_particle_state()</a>, <a href="classIMP_1_1domino_1_1ParticleStatesTable.html#aec6d179af9b27c2de8eddfe424192d6c">IMP::domino::ParticleStatesTable::get_has_particle()</a>, <a href="classIMP_1_1domino_1_1ParticleStatesTable.html#aeeaf96e9b2425dae382e391e2a0dfa01">IMP::domino::ParticleStatesTable::get_particle_states()</a>, <a href="classIMP_1_1domino_1_1ParticleStatesTable.html#a9ad869bd5d88c52e03c4395d8ab36e9e">IMP::domino::ParticleStatesTable::set_particle_states()</a>, <a href="classIMP_1_1domino_1_1PermutationStates.html#a2ca26d2df0035aaf25ff038a503c88e4">IMP::domino::PermutationStates::load_particle_state()</a>, <a href="classIMP_1_1domino_1_1RecursiveStates.html#a64d119281ac852e97227186e68b69c0c">IMP::domino::RecursiveStates::RecursiveStates()</a>, <a href="classIMP_1_1domino_1_1RecursiveStates.html#a3b3f761f6b969769a4faadb29d20bf2c">IMP::domino::RecursiveStates::load_particle_state()</a>, <a href="classIMP_1_1domino_1_1RigidBodyStates.html#a5c049aedcde939064feeaaabea3465f2">IMP::domino::RigidBodyStates::load_particle_state()</a>, <a 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href="classIMP_1_1spb_1_1PbcBoxedRigidBodyMover.html#a71a75e5182b952b8fb0b4a4e5ca49eeb">IMP::spb::PbcBoxedRigidBodyMover::PbcBoxedRigidBodyMover()</a>, <a href="classIMP_1_1spb_1_1TransformationSymmetry.html#abbd918cd369d5b315141934b20ac0868">IMP::spb::TransformationSymmetry::TransformationSymmetry()</a>, <a href="classIMP_1_1spb_1_1UniformBoundedRestraint.html#ad778f9dd80c267b5860c40d80a7d6da9">IMP::spb::UniformBoundedRestraint::UniformBoundedRestraint()</a>, <a href="classIMP_1_1symmetry_1_1BallMover.html#aa31ed479ef4b404d06981ac681f99667">IMP::symmetry::BallMover::BallMover()</a>, <a href="namespaceIMP.html#a4b39d171e19de7d77b18712a1d53371b">IMP::get_vector_geometry()</a>, <a href="namespaceIMP.html#a46baf60a90040d52b44c798099aa6304">IMP::get_vector_geometry()</a>, <a href="namespaceIMP.html#a924bebd6d5a6197265f68b798de457ff">IMP::get_vector_geometry()</a>, <a href="namespaceIMP.html#af7eb121360be9b6e4c0468e6677bb8d0">IMP::set_vector_geometry()</a>, <a href="namespaceIMP.html#a61ee62a2ede595280473bffc1f1ee19d">IMP::set_vector_geometry()</a>, <a href="namespaceIMP.html#a35e75da7a2e6761f503887aa48a25211">IMP::set_vector_geometry()</a>, <a href="namespaceIMP_1_1atom.html#a6eb0ed1c738a5d6b223b3628b09533f6">IMP::atom::setup_as_approximation()</a>, <a href="namespaceIMP_1_1em.html#acf93458d53bb786095f8fcfc32782929">IMP::em::bayesem3d_get_value()</a>, <a href="namespaceIMP_1_1em.html#a7cc0ae516db501ad39635d0066092094">IMP::em::bayesem3d_get_value_no_deriv()</a>, <a href="namespaceIMP_1_1em.html#a300a1ede18ac26749a961beca4c971e3">IMP::em::local_rigid_fitting()</a>, <a href="namespaceIMP_1_1em.html#a46543f4001a8c31276003433db00f776">IMP::em::local_rigid_fitting_around_point()</a>, <a href="namespaceIMP_1_1em.html#a729f3b19106724e0dbc8c7e98336ff64">IMP::em::local_rigid_fitting_around_points()</a>, <a href="namespaceIMP_1_1multifit.html#a72317593e3aff9f9e43e2e4f92481f47">IMP::multifit::get_close_to_point()</a>, <a href="namespaceIMP_1_1npctransport.html#a1b69574be5151ac787bd44f6f33d8383">IMP::npctransport::copy_hierarchy_reference_frame_recursive()</a>, <a href="namespaceIMP_1_1npctransport.html#a7def529ac221a63d72836659cfa0f3cf">IMP::npctransport::copy_particle_reference_frame_if_applicable()</a>, <a href="namespaceIMP_1_1npctransport.html#ae7a91516eb510beba957bd253626e22b">IMP::npctransport::get_fg_chain()</a>, <a href="namespaceIMP_1_1npctransport.html#a0affdade87f4dedc26d84d57faf2009e">IMP::npctransport::get_global_from_local_v3()</a>, <a href="namespaceIMP_1_1rmf.html#abf6e3fa733ef668bb985ed3e52f88187">IMP::rmf::add_particle()</a>, <a href="namespaceIMP_1_1spb.html#a4f4e29033718c00197737912b750ef5b">IMP::spb::add_bayesian_layer_restraint()</a>, <a href="namespaceIMP_1_1spb.html#a647eefa83fcb00316337141fc940792b">IMP::spb::add_NuisanceMover()</a>, <a href="namespaceIMP_1_1spb.html#ac8ec6f7f84c9684326f06ce1e0f9e74e">IMP::spb::add_PbcBoxedMover()</a>, <a href="namespaceIMP_1_1spb.html#aec465b74f8f98da4682c157f396f8a7f">IMP::spb::add_PbcBoxedRigidBodyMover()</a>, <a href="namespaceIMP_1_1spb.html#a1d50546bf0502a542c492062c8f0f42b">IMP::spb::add_restrain_coiledcoil_to_cterm()</a>, <a href="namespaceIMP_1_1spb.html#ada54561155757e22856d4066515ecca0">IMP::spb::add_restrain_protein_length()</a>, <a href="namespaceIMP_1_1spb.html#a06b534d7a1f9697f71f4a75366ba0a93">IMP::spb::add_symmetry_restraint()</a>, <a href="namespaceIMP_1_1spb.html#acf08490a12bf75b525b03a2b88f55ada">IMP::spb::add_tilt_restraint()</a>, <a href="namespaceIMP_1_1spb.html#ae8957e05a946a61598e363e00de9763c">IMP::spb::create_GFP()</a>, <a href="namespaceIMP_1_1spb.html#ae9d935784a933409cd306c7c046cfff6">IMP::spb::create_representation()</a>, <a href="namespaceIMP_1_1spb.html#ae9d0b23db782452a116f737439adcd0f">IMP::spb::em2d_restraint()</a>, <a href="namespaceIMP_1_1spb.html#a8a576f8cb8828bb3f7bf1853ed9e9f21">IMP::spb::fret_restraint()</a>, <a href="namespaceIMP_1_1spb.html#acfc148835c56484d4e992d107aa55bee">IMP::spb::fret_restraint()</a>, <a href="namespaceIMP_1_1spb.html#abdbc7bac876d7baf8c690b92ed9d5208">IMP::spb::fret_restraint()</a>, <a href="namespaceIMP_1_1spb.html#a7c113921b584fd1fce234cdb478f354b">IMP::spb::spb_assemble_restraints()</a></td></tr>
32 <tr><td>@ref IMP::ParticleAdaptor</td><td><a href="classIMP_1_1Decorator.html#a5471c1fb7bbca6af40422b8e4b154e06">IMP::Decorator::Decorator()</a>, <a href="classIMP_1_1atom_1_1Angle.html#abfb2f957caf4180db5815cdffeaa7cc2">IMP::atom::Angle::Angle()</a>, <a href="classIMP_1_1atom_1_1Angle.html#a6adf83fc3dd6fdd4385b6b014b0ab3ca">IMP::atom::Angle::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Angle.html#a85dc3dea18311ca858192b5a8e1087d7">IMP::atom::Angle::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Atom.html#a47d9d544104e223d1d704b5a1249507f">IMP::atom::Atom::Atom()</a>, <a href="classIMP_1_1atom_1_1Atom.html#ae168af7bc14e10acd7fe45890389ede8">IMP::atom::Atom::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Atom.html#aa05431b15bea7b5c936623226d4501c1">IMP::atom::Atom::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Atom.html#a0001e1b21f8f133618a3dd12482eb910">IMP::atom::Atom::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Bond.html#a8a0e803730058b888a1e16f15a779c76">IMP::atom::Bond::Bond()</a>, <a href="classIMP_1_1atom_1_1Bond.html#a7d8d1265ecb539678095f287bb7604f3">IMP::atom::Bond::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Bonded.html#aea2e0541b4a421c0c6ae9440cdbcfb4b">IMP::atom::Bonded::Bonded()</a>, <a href="classIMP_1_1atom_1_1Bonded.html#aebb3d09e50f1e3ff25ccab5e1b157bdd">IMP::atom::Bonded::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Bonded.html#ad09f82f4e129050b69dd718b0c0965f4">IMP::atom::Bonded::setup_particle()</a>, <a href="classIMP_1_1atom_1_1CHARMMAtom.html#ac9edcbee5a60df79d5c457f497402bd1">IMP::atom::CHARMMAtom::CHARMMAtom()</a>, <a href="classIMP_1_1atom_1_1CHARMMAtom.html#a6818c14c1d7ed4b595830d2d93157bca">IMP::atom::CHARMMAtom::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1CHARMMAtom.html#a0a9a48d48a627533669e338c1b0c1a91">IMP::atom::CHARMMAtom::setup_particle()</a>, <a href="classIMP_1_1atom_1_1CenterOfMass.html#af0f08c47a335320e0d4978ce8badc74b">IMP::atom::CenterOfMass::CenterOfMass()</a>, <a href="classIMP_1_1atom_1_1CenterOfMass.html#a77134887ce0479384a13aadc51c0e307">IMP::atom::CenterOfMass::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1CenterOfMass.html#a8b410c8db67479ac85541ea142e7d21e">IMP::atom::CenterOfMass::setup_particle()</a>, <a href="classIMP_1_1atom_1_1CenterOfMass.html#af441d973d432424c6e565f85197ee48e">IMP::atom::CenterOfMass::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Chain.html#adf1a15a60efe5aa69326847d0ea56a0d">IMP::atom::Chain::Chain()</a>, <a href="classIMP_1_1atom_1_1Chain.html#a0a7ba2828e24db3bb5ff98096818c51d">IMP::atom::Chain::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Chain.html#a5d18c9c7513ba44d34dfce18be257e61">IMP::atom::Chain::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Chain.html#a0130cdf0e73e878257209d02081dbcbb">IMP::atom::Chain::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Chain.html#ab65be1b3500bbf38bc1223075d66db16">IMP::atom::Chain::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Charged.html#a1381e5d8c92bd73a5cfb144499f9dd79">IMP::atom::Charged::Charged()</a>, <a href="classIMP_1_1atom_1_1Charged.html#a70b6adcc600820dc02736f07cd543ef2">IMP::atom::Charged::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Charged.html#a777a4ffb00b4bdd99234dc37e9d9ac23">IMP::atom::Charged::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Charged.html#a0c1728090ac4b7987dea00841554a5ac">IMP::atom::Charged::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Copy.html#ac38918184cfaeec184327f378b6bde20">IMP::atom::Copy::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Copy.html#a7d07850e2a347b041b1bf669e27ba1d7">IMP::atom::Copy::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Copy.html#aaac41c0a8e20cd477136ef8e98450994">IMP::atom::Copy::Copy()</a>, <a href="classIMP_1_1atom_1_1Diffusion.html#ac62c3712ca6f12f35d8f83de947a84e3">IMP::atom::Diffusion::Diffusion()</a>, <a href="classIMP_1_1atom_1_1Diffusion.html#aaf791f9133914f65722ff5273bbea89b">IMP::atom::Diffusion::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Diffusion.html#a00f1cff665ce88629f5fac43a603d0af">IMP::atom::Diffusion::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Diffusion.html#aa18f2a8df7e350e75e92084032c2c54d">IMP::atom::Diffusion::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Diffusion.html#a44caa4dffad3e5e1b823c7e3aae3a2a3">IMP::atom::Diffusion::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Dihedral.html#a2d73668e3436286d73890e29157fd5cf">IMP::atom::Dihedral::Dihedral()</a>, <a href="classIMP_1_1atom_1_1Dihedral.html#ad11169b8244abc37e6e13ab2dc463705">IMP::atom::Dihedral::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Dihedral.html#a7fd379c8d46a632cbe59b22f2a9043e5">IMP::atom::Dihedral::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Domain.html#a1995f6d0412bb0085d0cbbea0a75ec89">IMP::atom::Domain::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Domain.html#a5584f87cb8159c5de3b8c59e40d73a5e">IMP::atom::Domain::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Domain.html#ad0fb27e9620f14f9dc6a4fec0aadfde0">IMP::atom::Domain::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Domain.html#a0ae88409c0cfb1d20a160ec3518931f1">IMP::atom::Domain::Domain()</a>, <a href="classIMP_1_1atom_1_1Fragment.html#ac0871a2e7093a46d8830f6ae6b2c2cd6">IMP::atom::Fragment::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Fragment.html#ae352ab0184f9e44f77e821f49c1ba1af">IMP::atom::Fragment::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Fragment.html#a666570dc72f118be1ddf31cfcd960661">IMP::atom::Fragment::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Fragment.html#a3b814fa79bf1f037f7ff55694524436b">IMP::atom::Fragment::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Fragment.html#ab162e2c1337380b2fe6daff09ad276ad">IMP::atom::Fragment::Fragment()</a>, <a href="classIMP_1_1atom_1_1Hierarchy.html#ac247ff98ffe02eae0a3c48c4cf767f63">IMP::atom::Hierarchy::Hierarchy()</a>, <a href="classIMP_1_1atom_1_1LennardJones.html#a64bda90615e1736f7b64b89c11479ede">IMP::atom::LennardJones::LennardJones()</a>, <a href="classIMP_1_1atom_1_1LennardJones.html#a481142b1cea07071a6e7493de0cd5676">IMP::atom::LennardJones::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1LennardJones.html#afe637e075f1359c8c72f60ac8cad7f1e">IMP::atom::LennardJones::setup_particle()</a>, <a href="classIMP_1_1atom_1_1LennardJones.html#a1df5d20c20e6a6c8e8e3a3e56baad6cc">IMP::atom::LennardJones::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Mass.html#a833bedc38bf16e621d5131872f5694ec">IMP::atom::Mass::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Mass.html#a5df5aaecd758b65ca95b9813dbfd5df9">IMP::atom::Mass::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Mass.html#aed7e8decd2da73941a27bb4d8fa22fcb">IMP::atom::Mass::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Mass.html#a007b2d47bf0f859b84cd277ea564ec48">IMP::atom::Mass::Mass()</a>, <a href="classIMP_1_1atom_1_1Molecule.html#aaa15a951b7ac9adad5185ebbd5bd0a9f">IMP::atom::Molecule::Molecule()</a>, <a href="classIMP_1_1atom_1_1Molecule.html#a27e346fb2a090de06fc2ead1d30bf7ba">IMP::atom::Molecule::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Molecule.html#a4d02b52443d77f6cc5ef339d526ebd01">IMP::atom::Molecule::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Molecule.html#ac719cd07adab9dac805eebb8d2fe51c9">IMP::atom::Molecule::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Representation.html#a20ad6d4662339efa8cbc33afb2e4597e">IMP::atom::Representation::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Representation.html#ae89627390c9dae590f241107c5ca1273">IMP::atom::Representation::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Representation.html#afc4aa97989f756ff65f32e0dc4efd659">IMP::atom::Representation::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Representation.html#af24e26b69812ec688ef7265f8f5c0bc1">IMP::atom::Representation::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Representation.html#aa9c7c0ae153bdf5dab8fca0a2f4a0738">IMP::atom::Representation::Representation()</a>, <a href="classIMP_1_1atom_1_1Residue.html#afaa9067f7012baeadadd0a82e5f161e7">IMP::atom::Residue::Residue()</a>, <a href="classIMP_1_1atom_1_1Residue.html#ad7ce8a8e860e4f470001b28ee185888f">IMP::atom::Residue::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1Residue.html#ad00f788c4a62ba2039b3d0e19696c627">IMP::atom::Residue::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Residue.html#a432006d0924f45aeaf4d0a313948865a">IMP::atom::Residue::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Residue.html#a649753abdd11818384bfb4322b273205">IMP::atom::Residue::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Residue.html#a8f192aba52a14ffc0c9e0ee30b948e0b">IMP::atom::Residue::setup_particle()</a>, <a href="classIMP_1_1atom_1_1RigidBodyDiffusion.html#ad1e5c29410b18183c1801b11c845b6a5">IMP::atom::RigidBodyDiffusion::RigidBodyDiffusion()</a>, <a href="classIMP_1_1atom_1_1RigidBodyDiffusion.html#a80984e336630dda7ab19f4240931d4c5">IMP::atom::RigidBodyDiffusion::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1RigidBodyDiffusion.html#a371ba52920f1dceb79de0307716d3a8e">IMP::atom::RigidBodyDiffusion::setup_particle()</a>, <a href="classIMP_1_1atom_1_1SecondaryStructureResidue.html#ada63e7096f60d6a3ef38dc01480d4675">IMP::atom::SecondaryStructureResidue::SecondaryStructureResidue()</a>, <a href="classIMP_1_1atom_1_1SecondaryStructureResidue.html#a8e1836fe3fff314ca7712b14c5193090">IMP::atom::SecondaryStructureResidue::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1SecondaryStructureResidue.html#a83c7a31db0047e87f410d11551c9686c">IMP::atom::SecondaryStructureResidue::setup_particle()</a>, <a href="classIMP_1_1atom_1_1State.html#ae008980d9dc649956831fd1f6913d925">IMP::atom::State::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1State.html#a4773b1168da0d566d9a0bbb99489f8aa">IMP::atom::State::setup_particle()</a>, <a href="classIMP_1_1atom_1_1State.html#a81848e10ddf84cdf61ab74770229ab65">IMP::atom::State::setup_particle()</a>, <a href="classIMP_1_1atom_1_1State.html#ae144fe6b70d29b15ce1c2c09dda0cb04">IMP::atom::State::State()</a>, <a href="classIMP_1_1atom_1_1StructureSource.html#abdac9b235adf6c3f65ba6f7600c31cba">IMP::atom::StructureSource::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1StructureSource.html#ac05f522e56e1aa8288463605ab2de755">IMP::atom::StructureSource::setup_particle()</a>, <a href="classIMP_1_1atom_1_1StructureSource.html#a661072573a972cc40d8506108b6d6171">IMP::atom::StructureSource::StructureSource()</a>, <a href="classIMP_1_1atom_1_1TAMDCentroid.html#a9e6dbc026e582b0ed1c3081acefdb1ee">IMP::atom::TAMDCentroid::TAMDCentroid()</a>, <a href="classIMP_1_1atom_1_1TAMDCentroid.html#a521d35d4c278819cf31b37ea63a9ea7b">IMP::atom::TAMDCentroid::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1TAMDCentroid.html#a11ddc2c0d0a85fd50ec344cd4476479b">IMP::atom::TAMDCentroid::setup_particle()</a>, <a href="classIMP_1_1atom_1_1TAMDCentroid.html#ac39e34eb4cc3b69fa3e02149d7dad644">IMP::atom::TAMDCentroid::setup_particle()</a>, <a href="classIMP_1_1atom_1_1TAMDParticle.html#a5b5ee826761713ba371afb54deecf3e9">IMP::atom::TAMDParticle::TAMDParticle()</a>, <a href="classIMP_1_1atom_1_1TAMDParticle.html#a0f0b89bbd44116157705e9f433b87006">IMP::atom::TAMDParticle::get_is_setup()</a>, <a href="classIMP_1_1atom_1_1TAMDParticle.html#a6e1d23f313828675b431f3e9a3427e97">IMP::atom::TAMDParticle::setup_particle()</a>, <a href="classIMP_1_1atom_1_1TAMDParticle.html#abe2e84b9f10bc225c845fa6ca457bd2f">IMP::atom::TAMDParticle::setup_particle()</a>, <a href="classIMP_1_1core_1_1Centroid.html#a36bb5e04f43ef7ef532eedd3a6398204">IMP::core::Centroid::Centroid()</a>, <a href="classIMP_1_1core_1_1Centroid.html#a163c087bd6e60efa7646118a3953917c">IMP::core::Centroid::get_is_setup()</a>, <a href="classIMP_1_1core_1_1Centroid.html#a336d27cf05f8679da8ab1067f6e32f98">IMP::core::Centroid::setup_particle()</a>, <a href="classIMP_1_1core_1_1Centroid.html#ab17c86f104301a4f7d074ad1a56ed4b3">IMP::core::Centroid::setup_particle()</a>, <a href="classIMP_1_1core_1_1ClusterProvenance.html#a253704f3edac78be10d02046412d035c">IMP::core::ClusterProvenance::get_is_setup()</a>, <a href="classIMP_1_1core_1_1ClusterProvenance.html#af1c8b779a902f913c004538b631bc59e">IMP::core::ClusterProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1ClusterProvenance.html#a2c04488f3e8f10f2506bd5d5a9576f62">IMP::core::ClusterProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1ClusterProvenance.html#aab2e679a2e036e459948fac47d144b41">IMP::core::ClusterProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1ClusterProvenance.html#a5b750ffcdf47f2a97db99091a3aca15c">IMP::core::ClusterProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1ClusterProvenance.html#a188a4c45160345efca5079fe1ac3f250">IMP::core::ClusterProvenance::ClusterProvenance()</a>, <a href="classIMP_1_1core_1_1CombineProvenance.html#a4c5bfa141d16c0a427c6a12b3ff9a0d4">IMP::core::CombineProvenance::get_is_setup()</a>, <a href="classIMP_1_1core_1_1CombineProvenance.html#a75e9eb9b35f6bf3d23001a4b14bd160c">IMP::core::CombineProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1CombineProvenance.html#a108e878f8abbef6d9ef5013d5df15c97">IMP::core::CombineProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1CombineProvenance.html#a45bdc5a42e57d54da54b9abd7d9409fe">IMP::core::CombineProvenance::CombineProvenance()</a>, <a href="classIMP_1_1core_1_1Cover.html#a754f3d2966c7022ef2925c2255215ef0">IMP::core::Cover::Cover()</a>, <a href="classIMP_1_1core_1_1Cover.html#a1311a2d6cdd00e454283a2e5269755bb">IMP::core::Cover::get_is_setup()</a>, <a href="classIMP_1_1core_1_1Cover.html#a1cd025934cb393d6547e202edcab792f">IMP::core::Cover::setup_particle()</a>, <a href="classIMP_1_1core_1_1Cover.html#a6bab5f7ffe16f1dce0f351bb221974f4">IMP::core::Cover::setup_particle()</a>, <a href="classIMP_1_1core_1_1Direction.html#ad9ac92a5adc8f6062ffdab2e1ec1b6df">IMP::core::Direction::get_is_setup()</a>, <a href="classIMP_1_1core_1_1Direction.html#a357e04db48501894e3e10af25bd9b3be">IMP::core::Direction::setup_particle()</a>, <a href="classIMP_1_1core_1_1Direction.html#a8b80b7ac791d777126850a0954469f95">IMP::core::Direction::Direction()</a>, <a href="classIMP_1_1core_1_1DirectionAngle.html#a5122e2ba42519ed19f1dc9deeaceb3f6">IMP::core::DirectionAngle::DirectionAngle()</a>, <a href="classIMP_1_1core_1_1DirectionAngle.html#a5c1c2edaa1578c94b4b0f2358e73e07c">IMP::core::DirectionAngle::get_is_setup()</a>, <a href="classIMP_1_1core_1_1DirectionAngle.html#a2de410c46019dad78a94d34435efcac1">IMP::core::DirectionAngle::setup_particle()</a>, <a href="classIMP_1_1core_1_1DirectionAngle.html#abd8f87cbb5c0d3780666263b0ea14793">IMP::core::DirectionAngle::setup_particle()</a>, <a href="classIMP_1_1core_1_1FilterProvenance.html#a2c467c88565c67eb80c59057918a873d">IMP::core::FilterProvenance::get_is_setup()</a>, <a href="classIMP_1_1core_1_1FilterProvenance.html#ab4c7a7d1e88c993881bc7edf33b32655">IMP::core::FilterProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1FilterProvenance.html#af157b1d08abda33e13e8b9833e2776b9">IMP::core::FilterProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1FilterProvenance.html#ad348038defa8f5924fb243ed543dab50">IMP::core::FilterProvenance::FilterProvenance()</a>, <a href="classIMP_1_1core_1_1Gaussian.html#a4ceb930c942f43bf96b9cfe461f08bb0">IMP::core::Gaussian::Gaussian()</a>, <a href="classIMP_1_1core_1_1Gaussian.html#a27f66b0db63750a196835c0573c7e13b">IMP::core::Gaussian::get_is_setup()</a>, <a href="classIMP_1_1core_1_1Gaussian.html#a7384461f177072170c3d82d2b3c4c888">IMP::core::Gaussian::setup_particle()</a>, <a href="classIMP_1_1core_1_1Gaussian.html#a03345ca51aeba0893a3280bbb2435ee6">IMP::core::Gaussian::setup_particle()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#a5ad401d6e66517fdbe9813c5abf93421">IMP::core::Hierarchy::Hierarchy()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#aa257f3f243db94bb9f9c6c42ad7e8680">IMP::core::Hierarchy::get_is_setup()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#aa66644bbb2c9feefcc49e439d5623f78">IMP::core::Hierarchy::setup_particle()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#ad3309b0bfcb19888094814f4d3310a63">IMP::core::Hierarchy::setup_particle()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#a34cd5c036aac3d8cd71c18dae9e6595c">IMP::core::Hierarchy::setup_particle()</a>, <a href="classIMP_1_1core_1_1NonRigidMember.html#a29762bcedae6d9438f1ebd3c82a8e66b">IMP::core::NonRigidMember::NonRigidMember()</a>, <a href="classIMP_1_1core_1_1NonRigidMember.html#ad2f9f54dba0e3d3ef4928ed1909d0906">IMP::core::NonRigidMember::get_is_setup()</a>, <a href="classIMP_1_1core_1_1Provenance.html#a9d385cf5e7c62d2f5530bb1cace2f8f8">IMP::core::Provenance::get_is_setup()</a>, <a href="classIMP_1_1core_1_1Provenance.html#a09e5fa6b786c7fd7bc77d22a5b306d52">IMP::core::Provenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1Provenance.html#a8614cad5d6c4fb3830127c94e8284d87">IMP::core::Provenance::Provenance()</a>, <a href="classIMP_1_1core_1_1Provenanced.html#a108bb86a11f3d096b8fde6b43f42d855">IMP::core::Provenanced::get_is_setup()</a>, <a href="classIMP_1_1core_1_1Provenanced.html#a3aea98306c09aee470fc1f540f5ea7e0">IMP::core::Provenanced::setup_particle()</a>, <a href="classIMP_1_1core_1_1Provenanced.html#a2d668ace9374bc74037c27c267666aa7">IMP::core::Provenanced::Provenanced()</a>, <a href="classIMP_1_1core_1_1Reference.html#a00483eac8663b31ed3b1a3330877dc4c">IMP::core::Reference::Reference()</a>, <a href="classIMP_1_1core_1_1Reference.html#a203510d0f9babdcc08e26fa74676f1da">IMP::core::Reference::get_is_setup()</a>, <a href="classIMP_1_1core_1_1Reference.html#a34a714765f6e9fa4536b33560828d357">IMP::core::Reference::setup_particle()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#afbe1be7314537c5128fe5d931cae1d44">IMP::core::RigidBody::RigidBody()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#abbb143123495ac7de28e84289a78f6cd">IMP::core::RigidBody::get_is_setup()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#aca1a74bd404b30b7c3ebf0f072ec7cdc">IMP::core::RigidBody::setup_particle()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#a568f76829966c6cdc02e10b93a30251b">IMP::core::RigidBody::setup_particle()</a>, <a href="classIMP_1_1core_1_1RigidBodyMember.html#aeaf2f61111bc3802103848672f6b4233">IMP::core::RigidBodyMember::RigidBodyMember()</a>, <a href="classIMP_1_1core_1_1RigidBodyMember.html#a6f83adf1e5dd3c640380c40af9b7f9f2">IMP::core::RigidBodyMember::get_is_setup()</a>, <a href="classIMP_1_1core_1_1RigidMember.html#ad224b1dcfa5943f6a85b88db22fcc372">IMP::core::RigidMember::RigidMember()</a>, <a href="classIMP_1_1core_1_1RigidMember.html#aace62ae322ca8cd166167ff70ce32316">IMP::core::RigidMember::get_is_setup()</a>, <a href="classIMP_1_1core_1_1SampleProvenance.html#a878339d564ba495a370cd7d5470b8762">IMP::core::SampleProvenance::get_is_setup()</a>, <a href="classIMP_1_1core_1_1SampleProvenance.html#a27e6c32e3963b1777889fe12c9928da6">IMP::core::SampleProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1SampleProvenance.html#a0429a1bd87cbe895a618ce878b27498e">IMP::core::SampleProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1SampleProvenance.html#a2162a2c167f1a332b3c6c71d2da8ebc2">IMP::core::SampleProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1SampleProvenance.html#a70a8e67420865491129ae3e50aa91e78">IMP::core::SampleProvenance::SampleProvenance()</a>, <a href="classIMP_1_1core_1_1ScriptProvenance.html#ae100800ebc552f87d624357b16d8ca89">IMP::core::ScriptProvenance::get_is_setup()</a>, <a href="classIMP_1_1core_1_1ScriptProvenance.html#a35612ef5d269d51a7b59e0fda21167f2">IMP::core::ScriptProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1ScriptProvenance.html#a50f3d03183437ba64252c917645b79ae">IMP::core::ScriptProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1ScriptProvenance.html#aca0a1facbfe06082a9d5b3a6b7688024">IMP::core::ScriptProvenance::ScriptProvenance()</a>, <a href="classIMP_1_1core_1_1SoftwareProvenance.html#ae782fc2dc1361a5c17fa182d57343d21">IMP::core::SoftwareProvenance::get_is_setup()</a>, <a href="classIMP_1_1core_1_1SoftwareProvenance.html#a5b30be2e2200d6919be03e752070a37b">IMP::core::SoftwareProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1SoftwareProvenance.html#a0fdc3df205b116a9ec891ba68fdf9a48">IMP::core::SoftwareProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1SoftwareProvenance.html#aff2ae6940ac1bf19a864b5bbe4caf445">IMP::core::SoftwareProvenance::SoftwareProvenance()</a>, <a href="classIMP_1_1core_1_1StructureProvenance.html#a472f98d2b24f0daf5d3e563b8f6ca9e4">IMP::core::StructureProvenance::get_is_setup()</a>, <a href="classIMP_1_1core_1_1StructureProvenance.html#aa3f21fa92ed0f24c12e3ef1a13578c84">IMP::core::StructureProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1StructureProvenance.html#a12f171e01c89e043ba8db13dca9ede31">IMP::core::StructureProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1StructureProvenance.html#a5905f04f65df6b6ecb322e533bf0ecd0">IMP::core::StructureProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1StructureProvenance.html#ada0211021130821b82429f1917b7ffea">IMP::core::StructureProvenance::StructureProvenance()</a>, <a href="classIMP_1_1core_1_1Surface.html#a59dcbd26257615edf4541aae65a728b2">IMP::core::Surface::get_is_setup()</a>, <a href="classIMP_1_1core_1_1Surface.html#a6ddc2907dcd9dbdce2117fed65d895ac">IMP::core::Surface::setup_particle()</a>, <a href="classIMP_1_1core_1_1Surface.html#afbd39b286d5a68edf1248a602af7f18c">IMP::core::Surface::setup_particle()</a>, <a href="classIMP_1_1core_1_1Surface.html#afc989143678b92ebf5602ab187b704a1">IMP::core::Surface::setup_particle()</a>, <a href="classIMP_1_1core_1_1Surface.html#aa9cea052e8fc3933182c873ad3fe3d80">IMP::core::Surface::setup_particle()</a>, <a href="classIMP_1_1core_1_1Surface.html#a6c749db5ba439877932e9e92edc72d43">IMP::core::Surface::Surface()</a>, <a href="classIMP_1_1core_1_1Typed.html#a242400e29a223312b8d888ce3fb73be4">IMP::core::Typed::get_is_setup()</a>, <a href="classIMP_1_1core_1_1Typed.html#a3d6ef0964495dafd482ab201a451c5c4">IMP::core::Typed::setup_particle()</a>, <a href="classIMP_1_1core_1_1Typed.html#a6eb704084f010d1e342298cdfbb2fe33">IMP::core::Typed::Typed()</a>, <a href="classIMP_1_1core_1_1XYZ.html#a523017e686601b23a2687a86e3c4f43f">IMP::core::XYZ::get_is_setup()</a>, <a href="classIMP_1_1core_1_1XYZ.html#ae0cb94d288a442d2aec90a0f8853c597">IMP::core::XYZ::setup_particle()</a>, <a href="classIMP_1_1core_1_1XYZ.html#a50d393f50f368b469b25f256fe6fc0de">IMP::core::XYZ::setup_particle()</a>, <a href="classIMP_1_1core_1_1XYZ.html#aadb6c09df5fb7c9665b54b2f58a4d0a3">IMP::core::XYZ::XYZ()</a>, <a href="classIMP_1_1core_1_1XYZR.html#aa0e2b81d6d67c37569662f42e0b50239">IMP::core::XYZR::XYZR()</a>, <a href="classIMP_1_1core_1_1XYZR.html#aec41c392a03fa60f552f6d7336baf2c0">IMP::core::XYZR::get_is_setup()</a>, <a href="classIMP_1_1core_1_1XYZR.html#a034b3d51dbe1733bc733fa8b71630857">IMP::core::XYZR::setup_particle()</a>, <a href="classIMP_1_1core_1_1XYZR.html#ac83e5d10a8c3aea86721d2d4c83f9838">IMP::core::XYZR::setup_particle()</a>, <a href="classIMP_1_1core_1_1XYZR.html#a73236be015dcb13fee6cd488e13f8e85">IMP::core::XYZR::setup_particle()</a>, <a href="classIMP_1_1display_1_1Colored.html#a3f913276366f6f32b83ed73926a0f25b">IMP::display::Colored::Colored()</a>, <a href="classIMP_1_1display_1_1Colored.html#a1b03ebe43f5628f5686ad6f2dd21c664">IMP::display::Colored::get_is_setup()</a>, <a href="classIMP_1_1display_1_1Colored.html#ac7a6985811693a52c964d64d650a881c">IMP::display::Colored::setup_particle()</a>, <a href="classIMP_1_1em2d_1_1ProjectionParameters.html#a316b8807a2c7b62bfcb9e2821a8813d4">IMP::em2d::ProjectionParameters::ProjectionParameters()</a>, <a href="classIMP_1_1em2d_1_1ProjectionParameters.html#a3e4bd76b0639de68020f0f1e44620d1d">IMP::em2d::ProjectionParameters::get_is_setup()</a>, <a href="classIMP_1_1em2d_1_1ProjectionParameters.html#a65f19d3d9f9b0796997ba4ee41c88fc7">IMP::em2d::ProjectionParameters::setup_particle()</a>, <a href="classIMP_1_1em_1_1Voxel.html#a0256f8ac30df4b0af51f869974441e70">IMP::em::Voxel::get_is_setup()</a>, <a href="classIMP_1_1em_1_1Voxel.html#aedeb9d266c2539700d65875090a62e45">IMP::em::Voxel::setup_particle()</a>, <a href="classIMP_1_1em_1_1Voxel.html#acf4c0b7a005e63c740103347f30614a0">IMP::em::Voxel::Voxel()</a>, <a href="classIMP_1_1example_1_1ExampleDecorator.html#a372c4193645cf40d6598ed9d214d498e">IMP::example::ExampleDecorator::get_is_setup()</a>, <a href="classIMP_1_1example_1_1ExampleDecorator.html#a3d3a231b75bea58f400c94f2ebd6976a">IMP::example::ExampleDecorator::setup_particle()</a>, <a href="classIMP_1_1example_1_1ExampleDecorator.html#a37e75134ddde85054ad7bc4bf7b8bb5b">IMP::example::ExampleDecorator::ExampleDecorator()</a>, <a href="classIMP_1_1isd_1_1Nuisance.html#a6b92ea3ab13db1997d46d71ef2599c38">IMP::isd::Nuisance::Nuisance()</a>, <a href="classIMP_1_1isd_1_1Nuisance.html#a6b42ae60c81c045b26a8b58d1069a80d">IMP::isd::Nuisance::get_is_setup()</a>, <a href="classIMP_1_1isd_1_1Nuisance.html#aab055ae58fe5bdf2b31dd2d423c7f6ae">IMP::isd::Nuisance::setup_particle()</a>, <a href="classIMP_1_1isd_1_1Nuisance.html#ac09f4230ac7bf3af3a20f757d0882753">IMP::isd::Nuisance::setup_particle()</a>, <a href="classIMP_1_1isd_1_1Scale.html#a4133d088c179f880fdec6bec10cd38f2">IMP::isd::Scale::Scale()</a>, <a href="classIMP_1_1isd_1_1Scale.html#a9001e72ca9ef7f3644076bdec39027e0">IMP::isd::Scale::get_is_setup()</a>, <a href="classIMP_1_1isd_1_1Scale.html#af388b87ed923bc92235e76fffb1991af">IMP::isd::Scale::setup_particle()</a>, <a href="classIMP_1_1isd_1_1Scale.html#ad33c9eccdf56d12f18c40cb6f98394e6">IMP::isd::Scale::setup_particle()</a>, <a href="classIMP_1_1isd_1_1Switching.html#accc26142617bf0ff37599b013a52376b">IMP::isd::Switching::Switching()</a>, <a href="classIMP_1_1isd_1_1Switching.html#a5a6e211b88f95162a4c9c7b0a612e237">IMP::isd::Switching::get_is_setup()</a>, <a href="classIMP_1_1isd_1_1Switching.html#ada60e22d851fd0e2f7aab3d5f76994c0">IMP::isd::Switching::setup_particle()</a>, <a href="classIMP_1_1isd_1_1Switching.html#a7c7f23c19c47a019a668c1d47853c7cc">IMP::isd::Switching::setup_particle()</a>, <a href="classIMP_1_1isd_1_1Weight.html#a34de5fe907b9023a630214c4b0a10c86">IMP::isd::Weight::Weight()</a>, <a href="classIMP_1_1isd_1_1Weight.html#a934ebec711cb2ba3355dfe25c353ba4b">IMP::isd::Weight::get_is_setup()</a>, <a href="classIMP_1_1isd_1_1Weight.html#aad7d240451cff13a6a94424f85328d37">IMP::isd::Weight::setup_particle()</a>, <a href="classIMP_1_1isd_1_1Weight.html#aba2e9713cd0ba5bf94aad4ae83126ab4">IMP::isd::Weight::setup_particle()</a>, <a href="classIMP_1_1isd_1_1Weight.html#a8b40d3acd2f4563b2c2252bef6c4ac33">IMP::isd::Weight::setup_particle()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#af99f66580d68e500ae0e537fa570a489">IMP::kinematics::KinematicNode::KinematicNode()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#a98341d20611a9b7b20dad5ac5071f3ac">IMP::kinematics::KinematicNode::get_is_setup()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#abc4cd7cbbcd2fc955adf9b53e6f0026c">IMP::kinematics::KinematicNode::setup_particle()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#ab124f751588f8c4f28f24efe321bddea">IMP::kinematics::KinematicNode::setup_particle()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#a42c150181046d83c51d8799f14326c96">IMP::kinematics::KinematicNode::setup_particle()</a>, <a href="classIMP_1_1misc_1_1CustomXYZR.html#ab6e661b06ed9442c181e93447cbbf717">IMP::misc::CustomXYZR::CustomXYZR()</a>, <a href="classIMP_1_1misc_1_1CustomXYZR.html#a9b7625533ff1f910ac1857a3e3d213b5">IMP::misc::CustomXYZR::get_is_setup()</a>, <a href="classIMP_1_1misc_1_1CustomXYZR.html#aced3d45ac55147fc868b5d48b1252cce">IMP::misc::CustomXYZR::setup_particle()</a>, <a href="classIMP_1_1misc_1_1CustomXYZR.html#ad73b6ff63c8a45379366ab9634163f8c">IMP::misc::CustomXYZR::setup_particle()</a>, <a href="classIMP_1_1misc_1_1CustomXYZR.html#a4dc8e38f4ea04f1815e9d45c43ecb6d6">IMP::misc::CustomXYZR::setup_particle()</a>, <a href="classIMP_1_1npctransport_1_1RelaxingSpring.html#aa2583c6aa190625cdfbf1f3a764c3449">IMP::npctransport::RelaxingSpring::RelaxingSpring()</a>, <a href="classIMP_1_1npctransport_1_1RelaxingSpring.html#a6c1c7fe80c3456d8f9729241d6e6ef21">IMP::npctransport::RelaxingSpring::get_is_setup()</a>, <a href="classIMP_1_1npctransport_1_1RelaxingSpring.html#aa0a2da6f9b633d32409d8bf0d77b044c">IMP::npctransport::RelaxingSpring::setup_particle()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithCylindricalPore.html#a354a90993ffaecc522980ed1142106c6">IMP::npctransport::SlabWithCylindricalPore::SlabWithCylindricalPore()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithCylindricalPore.html#af7134101b328ded18bff09597121896b">IMP::npctransport::SlabWithCylindricalPore::get_is_setup()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithCylindricalPore.html#acb36b8642b771ed9f4d127a80fe93618">IMP::npctransport::SlabWithCylindricalPore::setup_particle()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithPore.html#a9b092e54834fda1cbda9ade13d5f1440">IMP::npctransport::SlabWithPore::SlabWithPore()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithPore.html#a30adc73f268e10b5b2760fcaa7ce95ac">IMP::npctransport::SlabWithPore::get_is_setup()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithPore.html#af2b72108b548978af51c7ad84f0bb2d4">IMP::npctransport::SlabWithPore::setup_particle()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithToroidalPore.html#a1d09afe6de1b0c54676f4b5d0ab5f2fa">IMP::npctransport::SlabWithToroidalPore::SlabWithToroidalPore()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithToroidalPore.html#ac573a2469522fc27470798aa89d36cd6">IMP::npctransport::SlabWithToroidalPore::get_is_setup()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithToroidalPore.html#afa0cd47834b4bd164ad8a1fa99502a4f">IMP::npctransport::SlabWithToroidalPore::setup_particle()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithToroidalPore.html#ae4083742cdce5310ea4c2010283d50ea">IMP::npctransport::SlabWithToroidalPore::setup_particle()</a>, <a href="classIMP_1_1npctransport_1_1Transporting.html#a9ebc9766921d97d7c45ed8ca584ca2af">IMP::npctransport::Transporting::Transporting()</a>, <a href="classIMP_1_1npctransport_1_1Transporting.html#a9629539c6c8a90e6b453adbb8bc326b6">IMP::npctransport::Transporting::get_is_setup()</a>, <a href="classIMP_1_1npctransport_1_1Transporting.html#a5df7e2a693c50fb43c24ee4c051385a6">IMP::npctransport::Transporting::setup_particle()</a>, <a href="classIMP_1_1pmi1_1_1Resolution.html#a1bce8bf867ac542d552a02d5373aa3af">IMP::pmi1::Resolution::get_is_setup()</a>, <a href="classIMP_1_1pmi1_1_1Resolution.html#a4fd1805426bb0020017bcba3ce03bf9d">IMP::pmi1::Resolution::setup_particle()</a>, <a href="classIMP_1_1pmi1_1_1Resolution.html#aff49323d47c34fa00335187f5a880115">IMP::pmi1::Resolution::Resolution()</a>, <a href="classIMP_1_1pmi1_1_1Symmetric.html#a782ce5d17229e120737ec25135683f8c">IMP::pmi1::Symmetric::get_is_setup()</a>, <a href="classIMP_1_1pmi1_1_1Symmetric.html#a4a9f87bb73a52b176124d541e0340eb2">IMP::pmi1::Symmetric::setup_particle()</a>, <a href="classIMP_1_1pmi1_1_1Symmetric.html#accdeb0b96e7ae60fe842157b78745488">IMP::pmi1::Symmetric::Symmetric()</a>, <a href="classIMP_1_1pmi1_1_1Uncertainty.html#a4ab2275d957d90c2c5c3d8f7b935499c">IMP::pmi1::Uncertainty::get_is_setup()</a>, <a href="classIMP_1_1pmi1_1_1Uncertainty.html#ac7c77714aa6f645224a0d7aadb9f0c06">IMP::pmi1::Uncertainty::setup_particle()</a>, <a href="classIMP_1_1pmi1_1_1Uncertainty.html#ab9ed4bfcf2bb55d9d4a74efca7780ac1">IMP::pmi1::Uncertainty::Uncertainty()</a>, <a href="classIMP_1_1pmi_1_1Resolution.html#afe643637e60191d3af84c0096af008d6">IMP::pmi::Resolution::get_is_setup()</a>, <a href="classIMP_1_1pmi_1_1Resolution.html#a8481894a76a7e06fcc0cf85664c6d10d">IMP::pmi::Resolution::setup_particle()</a>, <a href="classIMP_1_1pmi_1_1Resolution.html#ab44f0f0c80191310dd655cf874de7fac">IMP::pmi::Resolution::Resolution()</a>, <a href="classIMP_1_1pmi_1_1Symmetric.html#a82e75a6c22ce186cd00baeecc458fc47">IMP::pmi::Symmetric::get_is_setup()</a>, <a href="classIMP_1_1pmi_1_1Symmetric.html#a743fff47616d0b1caa92bba3dda73fdb">IMP::pmi::Symmetric::setup_particle()</a>, <a href="classIMP_1_1pmi_1_1Symmetric.html#aeeee2ce35d32277699005460a1ffb868">IMP::pmi::Symmetric::Symmetric()</a>, <a href="classIMP_1_1pmi_1_1Uncertainty.html#ae28ad955b57814fc72ce7050f3a90a0a">IMP::pmi::Uncertainty::get_is_setup()</a>, <a href="classIMP_1_1pmi_1_1Uncertainty.html#a7e09f1108753b299b7f824237468ab60">IMP::pmi::Uncertainty::setup_particle()</a>, <a href="classIMP_1_1pmi_1_1Uncertainty.html#ad3a1d062501b22fc4d0a0b4767529681">IMP::pmi::Uncertainty::Uncertainty()</a>, <a href="classIMP_1_1spb_1_1HelixDecorator.html#a2a2866201561eb03be940d7dd558786e">IMP::spb::HelixDecorator::HelixDecorator()</a>, <a href="classIMP_1_1spb_1_1HelixDecorator.html#ade35a69f558117d6ddc786e28f9330c4">IMP::spb::HelixDecorator::get_is_setup()</a></td></tr>
33 <tr><td>@ref IMP::ParticleIndexAdaptor</td><td><a href="classIMP_1_1atom_1_1CAAngleRestraint.html#af83e92f9462a7527e13ffa74f7a03211">IMP::atom::CAAngleRestraint::CAAngleRestraint()</a>, <a href="classIMP_1_1atom_1_1CADihedralRestraint.html#a54eb14f1925d6914c24a212dfbad0364">IMP::atom::CADihedralRestraint::CADihedralRestraint()</a>, <a href="classIMP_1_1atom_1_1Representation.html#a497d5d3f19d928884b03edd16fbab99e">IMP::atom::Representation::add_representation()</a>, <a href="classIMP_1_1atom_1_1Representation.html#a34c82c9da8203b70518b44260d5bef6d">IMP::atom::Representation::remove_representation()</a>, <a href="classIMP_1_1core_1_1AngleRestraint.html#a8d804a5e089cdfaf9d92bca151824a75">IMP::core::AngleRestraint::AngleRestraint()</a>, <a href="classIMP_1_1core_1_1DihedralRestraint.html#a44a074b10c84117cf6f05bbec9348026">IMP::core::DihedralRestraint::DihedralRestraint()</a>, <a href="classIMP_1_1core_1_1DirectionAngle.html#abe2b5b0af2a8372aa8ff349346758568">IMP::core::DirectionAngle::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1DirectionAngle.html#a237b38371936220cd3c3ca1785cc091f">IMP::core::DirectionAngle::setup_particle()</a>, <a href="classIMP_1_1core_1_1DirectionAngle.html#abd8f87cbb5c0d3780666263b0ea14793">IMP::core::DirectionAngle::setup_particle()</a>, <a href="classIMP_1_1core_1_1DistanceRestraint.html#ad9a7eb6292db99b8df339ea289202632">IMP::core::DistanceRestraint::DistanceRestraint()</a>, <a href="classIMP_1_1core_1_1Reference.html#a34a714765f6e9fa4536b33560828d357">IMP::core::Reference::setup_particle()</a>, <a href="classIMP_1_1core_1_1Reference.html#a71b485271947fe268a60fe762642fb87">IMP::core::Reference::setup_particle()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#ab1f022c6ae1db3d76af81fdc1b15f18b">IMP::core::RigidBody::add_member()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#ad6afb8be1ab840d31c0e7a6b5fcda4a4">IMP::core::RigidBody::add_non_rigid_member()</a>, <a href="classIMP_1_1core_1_1RigidBodyMember.html#ad07bb2a3ac4655c35961f69e80ce450a">IMP::core::RigidBodyMember::get_is_setup()</a>, <a href="classIMP_1_1core_1_1RigidMember.html#a2db92354804a38e5ea63fdbe7f9c5f85">IMP::core::RigidMember::get_is_setup()</a>, <a href="classIMP_1_1isd_1_1AmbiguousNOERestraint.html#ae3ab78cb324e0b0d604bea494c6b4e7a">IMP::isd::AmbiguousNOERestraint::AmbiguousNOERestraint()</a>, <a href="classIMP_1_1isd_1_1CrossLinkMSRestraint.html#a729662a17459751472e61537fd9b15c9">IMP::isd::CrossLinkMSRestraint::CrossLinkMSRestraint()</a>, <a href="classIMP_1_1isd_1_1CysteineCrossLinkRestraint.html#add9b9dde6bf243b14dc3abac501e4d24">IMP::isd::CysteineCrossLinkRestraint::CysteineCrossLinkRestraint()</a>, <a href="classIMP_1_1isd_1_1CysteineCrossLinkRestraint.html#a5a9d77f313f04238dffb52b016ddac66">IMP::isd::CysteineCrossLinkRestraint::CysteineCrossLinkRestraint()</a>, <a href="classIMP_1_1isd_1_1CysteineCrossLinkRestraint.html#a4f4dd26f6be312e9ad7e4701bb90ddcf">IMP::isd::CysteineCrossLinkRestraint::add_contribution()</a>, <a href="classIMP_1_1isd_1_1StudentTRestraint.html#a0dec14ace731838982054e9f3949773e">IMP::isd::StudentTRestraint::StudentTRestraint()</a>, <a href="classIMP_1_1isd_1_1StudentTRestraint.html#a0cf3e2d47f558f4feca099dd0290b02a">IMP::isd::StudentTRestraint::StudentTRestraint()</a>, <a href="classIMP_1_1isd_1_1StudentTRestraint.html#ae46a18c6ab26358369811a2f461a38d9">IMP::isd::StudentTRestraint::StudentTRestraint()</a>, <a href="classIMP_1_1isd_1_1StudentTRestraint.html#af9f3128720b032cf40f31ed7b1036e28">IMP::isd::StudentTRestraint::StudentTRestraint()</a>, <a href="classIMP_1_1isd_1_1StudentTRestraint.html#af9947545697b58403588ba9b9a4a5cf7">IMP::isd::StudentTRestraint::StudentTRestraint()</a>, <a href="classIMP_1_1isd_1_1StudentTRestraint.html#ad56764c43daea454a47eb62c28b3e874">IMP::isd::StudentTRestraint::StudentTRestraint()</a>, <a href="classIMP_1_1isd_1_1StudentTRestraint.html#a238f1987465bb9d74f45bab9ca18b8ca">IMP::isd::StudentTRestraint::StudentTRestraint()</a>, <a href="classIMP_1_1isd_1_1StudentTRestraint.html#aead0de81025afa2307b69991a03b36ff">IMP::isd::StudentTRestraint::StudentTRestraint()</a>, <a href="classIMP_1_1isd_1_1StudentTRestraint.html#acd4afa1ce8154882be89e726d701b2c0">IMP::isd::StudentTRestraint::StudentTRestraint()</a>, <a href="classIMP_1_1isd_1_1StudentTRestraint.html#abd14eb8a4c1e22d7e4530c48ff01a882">IMP::isd::StudentTRestraint::StudentTRestraint()</a>, <a href="classIMP_1_1isd_1_1StudentTRestraint.html#a57b98f6cf740c724e047ea87cdef76e8">IMP::isd::StudentTRestraint::StudentTRestraint()</a>, <a href="classIMP_1_1isd_1_1StudentTRestraint.html#ac881378098f4e3e3e695fca7a79f0424">IMP::isd::StudentTRestraint::StudentTRestraint()</a>, <a href="classIMP_1_1isd_1_1StudentTRestraint.html#abfc3362498f8fa88e90b69c521e68741">IMP::isd::StudentTRestraint::StudentTRestraint()</a>, <a href="classIMP_1_1isd_1_1StudentTRestraint.html#ae57fa3adb311704327cd20381e26fc07">IMP::isd::StudentTRestraint::StudentTRestraint()</a>, <a href="classIMP_1_1isd_1_1StudentTRestraint.html#a85067252262443088a1d641759bf533f">IMP::isd::StudentTRestraint::StudentTRestraint()</a>, <a href="classIMP_1_1pmi1_1_1SigmoidRestraintSphere.html#a6c6d08563da661764df750fe520139ce">IMP::pmi1::SigmoidRestraintSphere::SigmoidRestraintSphere()</a>, <a href="classIMP_1_1pmi1_1_1TransformMover.html#ac6d359cb8cfb6ad468c5f276aa6f3554">IMP::pmi1::TransformMover::TransformMover()</a>, <a href="classIMP_1_1pmi1_1_1TransformMover.html#a3d3c4f6597fbc894dd808d7694fcb1f4">IMP::pmi1::TransformMover::add_rigid_body_particle()</a>, <a href="classIMP_1_1pmi1_1_1TransformMover.html#ac163544d3410221d5c22650a05cf192c">IMP::pmi1::TransformMover::add_xyz_particle()</a>, <a href="classIMP_1_1pmi_1_1TransformMover.html#ac85464e8d64888b3e83ef9bcfa951718">IMP::pmi::TransformMover::TransformMover()</a>, <a href="classIMP_1_1pmi_1_1TransformMover.html#a8f1e32dd9f95085b2c612cb6dd8c01f7">IMP::pmi::TransformMover::add_rigid_body_particle()</a>, <a href="classIMP_1_1pmi_1_1TransformMover.html#ab6a7f30a95cb6d9ba9b285803833470d">IMP::pmi::TransformMover::add_xyz_particle()</a></td></tr>
34 <tr><td>@ref IMP::ParticleIndexesAdaptor</td><td><a href="classIMP_1_1atom_1_1CenterOfMass.html#af645b19c442b1e76ad1c4aacda45e81d">IMP::atom::CenterOfMass::setup_particle()</a>, <a href="classIMP_1_1atom_1_1CenterOfMass.html#a8b410c8db67479ac85541ea142e7d21e">IMP::atom::CenterOfMass::setup_particle()</a>, <a href="classIMP_1_1atom_1_1EzRestraint.html#ab0622696250e6e9c465b633869ba59cc">IMP::atom::EzRestraint::EzRestraint()</a>, <a href="classIMP_1_1atom_1_1Hierarchy.html#a56ea228dde7abf072de82f4d9c82b629">IMP::atom::Hierarchy::setup_particle()</a>, <a href="classIMP_1_1atom_1_1LangevinThermostatOptimizerState.html#ab4d3951090ea83b5875eda37543e58e3">IMP::atom::LangevinThermostatOptimizerState::LangevinThermostatOptimizerState()</a>, <a href="classIMP_1_1atom_1_1RemoveRigidMotionOptimizerState.html#a74b14ca50923bcc14a227757242b8440">IMP::atom::RemoveRigidMotionOptimizerState::RemoveRigidMotionOptimizerState()</a>, <a href="classIMP_1_1atom_1_1RemoveTranslationOptimizerState.html#a82f19dc724f92784fd15cc9d61371b6a">IMP::atom::RemoveTranslationOptimizerState::RemoveTranslationOptimizerState()</a>, <a href="classIMP_1_1atom_1_1TAMDCentroid.html#a0798b30e5e80229807b08bbdcd8502a6">IMP::atom::TAMDCentroid::setup_particle()</a>, <a href="classIMP_1_1atom_1_1TAMDCentroid.html#a11ddc2c0d0a85fd50ec344cd4476479b">IMP::atom::TAMDCentroid::setup_particle()</a>, <a href="classIMP_1_1atom_1_1VelocityScalingOptimizerState.html#aec6d4c8c4840146f61e2ba17bd78f8f8">IMP::atom::VelocityScalingOptimizerState::VelocityScalingOptimizerState()</a>, <a href="classIMP_1_1atom_1_1WritePDBOptimizerState.html#a1addc65cdfb5d782bdfa42547b5a4e9f">IMP::atom::WritePDBOptimizerState::WritePDBOptimizerState()</a>, <a href="classIMP_1_1core_1_1Centroid.html#ab17c86f104301a4f7d074ad1a56ed4b3">IMP::core::Centroid::setup_particle()</a>, <a href="classIMP_1_1core_1_1Centroid.html#a25fd05c17e081907c3059e5522c4db0e">IMP::core::Centroid::setup_particle()</a>, <a href="classIMP_1_1core_1_1Cover.html#a6bab5f7ffe16f1dce0f351bb221974f4">IMP::core::Cover::setup_particle()</a>, <a href="classIMP_1_1core_1_1Cover.html#a18b4345f9d9ea754ab7d5dd909e1d85a">IMP::core::Cover::setup_particle()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#a4a86a52c9581c9056021a7e1b4266280">IMP::core::RigidBody::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#aca1a74bd404b30b7c3ebf0f072ec7cdc">IMP::core::RigidBody::setup_particle()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#ade7dc68a77c0397fd7bc1711e8d85c7c">IMP::core::RigidBody::setup_particle()</a>, <a href="classIMP_1_1pmi1_1_1CompositeRestraint.html#ab47ac587dcc28a81ae538afc3fc079f8">IMP::pmi1::CompositeRestraint::CompositeRestraint()</a>, <a href="classIMP_1_1pmi1_1_1CompositeRestraint.html#a61ee84cd4df627da38e733a2f147c5be">IMP::pmi1::CompositeRestraint::add_composite_particle()</a>, <a href="classIMP_1_1pmi_1_1CompositeRestraint.html#ae074c9b992d2959c99ac2a24d0f23060">IMP::pmi::CompositeRestraint::CompositeRestraint()</a>, <a href="classIMP_1_1pmi_1_1CompositeRestraint.html#a4d3e54795c8ec7eb4acfc88f8aaff128">IMP::pmi::CompositeRestraint::add_composite_particle()</a></td></tr>
35 <tr><td>@ref IMP::QuadContainer</td><td><a href="classIMP_1_1QuadContainerAdaptor.html#ac170cad8e100bbed73e7292a6f686620">IMP::QuadContainerAdaptor::QuadContainerAdaptor()</a>, <a href="classIMP_1_1container_1_1InContainerQuadFilter.html#ab6cceebb5b5072652264816d67027724">IMP::container::InContainerQuadFilter::InContainerQuadFilter()</a>, <a href="classIMP_1_1container_1_1InContainerQuadFilter.html#a82b102c116493b92f1c91abf8de24695">IMP::container::InContainerQuadFilter::InContainerQuadFilter()</a>, <a href="classIMP_1_1container_1_1QuadContainerSet.html#a85bf432d0c59fae7a17503fc64ac85da">IMP::container::QuadContainerSet::remove_quad_container()</a>, <a href="classIMP_1_1container_1_1QuadContainerSet.html#a0c9c7d48780ad3782febebeb2db8c30a">IMP::container::QuadContainerSet::add_quad_container()</a>, <a href="classIMP_1_1container_1_1QuadContainerSet.html#ac2a1a54aa5fed2f2d5394c0a4734229c">IMP::container::QuadContainerSet::get_set()</a></td></tr>
36 <tr><td>@ref IMP::QuadContainerAdaptor</td><td><a href="classIMP_1_1container_1_1DistributeQuadsScoreState.html#a2bce106792c76d2ca4209c1f92ef28e4">IMP::container::DistributeQuadsScoreState::DistributeQuadsScoreState()</a>, <a href="classIMP_1_1container_1_1EventQuadsOptimizerState.html#a0882313e029cfa10e33a5eef530d671b">IMP::container::EventQuadsOptimizerState::EventQuadsOptimizerState()</a>, <a href="classIMP_1_1container_1_1MinimumQuadRestraint.html#a5e4ef73d56f6be06820b101556f9a2d4">IMP::container::MinimumQuadRestraint::MinimumQuadRestraint()</a>, <a href="classIMP_1_1container_1_1PredicateQuadsRestraint.html#a3dada94ed0273c9b063546c9dac025d8">IMP::container::PredicateQuadsRestraint::PredicateQuadsRestraint()</a>, <a href="classIMP_1_1container_1_1QuadContainerStatistics.html#abb8e28a564c402cbfbc0487e854ee79c">IMP::container::QuadContainerStatistics::QuadContainerStatistics()</a>, <a href="classIMP_1_1container_1_1QuadsConstraint.html#a93c4a08113b8ab7fa391cda89f9d672f">IMP::container::QuadsConstraint::QuadsConstraint()</a>, <a href="classIMP_1_1container_1_1QuadsOptimizerState.html#a657cdc918c306205a3f7274ed8efd4ac">IMP::container::QuadsOptimizerState::QuadsOptimizerState()</a>, <a href="classIMP_1_1container_1_1QuadsRestraint.html#a1fa60ee163ed082964365e60ab6fe483">IMP::container::QuadsRestraint::QuadsRestraint()</a></td></tr>
37 <tr><td>@ref IMP::QuadModifier</td><td><a href="classIMP_1_1QuadContainer.html#a7b1ba7958e70ba7c3411e2d949839ac2">IMP::QuadContainer::apply()</a>, <a href="classIMP_1_1QuadContainer.html#a7a5945aff269bdc6f7e8e27d327e1974">IMP::QuadContainer::apply_generic()</a>, <a href="classIMP_1_1QuadContainer.html#af2e0fe21fe427f811178c0a1704f1ba7">IMP::QuadContainer::apply_generic_moved()</a>, <a href="classIMP_1_1QuadContainer.html#a69b4c8cb88a2162dc18b7f07a6f7e60c">IMP::QuadContainer::apply_moved()</a>, <a href="classIMP_1_1QuadContainer.html#a13d56c22f9b8fa5fad24c4143e6d9df1">IMP::QuadContainer::do_apply()</a>, <a href="classIMP_1_1QuadContainer.html#a58852e2742e9b0c2a5f7582e00f28eb1">IMP::QuadContainer::do_apply_moved()</a>, <a href="classIMP_1_1container_1_1QuadsConstraint.html#a93c4a08113b8ab7fa391cda89f9d672f">IMP::container::QuadsConstraint::QuadsConstraint()</a>, <a href="classIMP_1_1container_1_1QuadsOptimizerState.html#a657cdc918c306205a3f7274ed8efd4ac">IMP::container::QuadsOptimizerState::QuadsOptimizerState()</a>, <a href="classIMP_1_1core_1_1QuadConstraint.html#a1e80827a35fdf4bb2a66f0800dd03e75">IMP::core::QuadConstraint::QuadConstraint()</a>, <a href="classIMP_1_1core_1_1QuadConstraint.html#a6b3d5edb3fa7cdfaa35d37af9d439d18">IMP::core::QuadConstraint::QuadConstraint()</a></td></tr>
38 <tr><td>@ref IMP::QuadPredicate</td><td><a href="classIMP_1_1container_1_1DistributeQuadsScoreState.html#a5fd9074e32c95ec367b06b5a40fd72ab">IMP::container::DistributeQuadsScoreState::add_predicate()</a>, <a href="classIMP_1_1container_1_1EventQuadsOptimizerState.html#a0882313e029cfa10e33a5eef530d671b">IMP::container::EventQuadsOptimizerState::EventQuadsOptimizerState()</a>, <a href="classIMP_1_1container_1_1PredicateQuadsRestraint.html#a3dada94ed0273c9b063546c9dac025d8">IMP::container::PredicateQuadsRestraint::PredicateQuadsRestraint()</a></td></tr>
39 <tr><td>@ref IMP::QuadScore</td><td><a href="classIMP_1_1container_1_1MinimumQuadRestraint.html#a5e4ef73d56f6be06820b101556f9a2d4">IMP::container::MinimumQuadRestraint::MinimumQuadRestraint()</a>, <a href="classIMP_1_1container_1_1PredicateQuadsRestraint.html#ac3e2a5033fdd0a6d83c6b096c38e1710">IMP::container::PredicateQuadsRestraint::set_score()</a>, <a href="classIMP_1_1container_1_1PredicateQuadsRestraint.html#a96b12e640900a821b0cb10f2613430b7">IMP::container::PredicateQuadsRestraint::set_unknown_score()</a>, <a href="classIMP_1_1container_1_1QuadsRestraint.html#a1fa60ee163ed082964365e60ab6fe483">IMP::container::QuadsRestraint::QuadsRestraint()</a>, <a href="classIMP_1_1core_1_1QuadRestraint.html#a613d76a32ec344886a02b1039100b8bd">IMP::core::QuadRestraint::QuadRestraint()</a></td></tr>
40 <tr><td>@ref IMP::Refiner</td><td><a href="classIMP_1_1atom_1_1CenterOfMass.html#a67206a3eda48a7d490c2701ad56ca7a2">IMP::atom::CenterOfMass::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1CenterOfMass.html#a05b61bbc3ccc220788567089208071bf">IMP::atom::CenterOfMass::setup_particle()</a>, <a href="classIMP_1_1atom_1_1CenterOfMass.html#af441d973d432424c6e565f85197ee48e">IMP::atom::CenterOfMass::setup_particle()</a>, <a href="classIMP_1_1atom_1_1TAMDCentroid.html#a42e93336dc50cdf13b8237da98ab5fb7">IMP::atom::TAMDCentroid::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1TAMDCentroid.html#afb8fd3568091ed55121b653a390a3c45">IMP::atom::TAMDCentroid::setup_particle()</a>, <a href="classIMP_1_1atom_1_1TAMDCentroid.html#ac39e34eb4cc3b69fa3e02149d7dad644">IMP::atom::TAMDCentroid::setup_particle()</a>, <a href="classIMP_1_1core_1_1Centroid.html#a40180c819422a60f1be5715534de2fc5">IMP::core::Centroid::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1Centroid.html#a336d27cf05f8679da8ab1067f6e32f98">IMP::core::Centroid::setup_particle()</a>, <a href="classIMP_1_1core_1_1Centroid.html#a533b86af3d87e81c676e50f5651f52b1">IMP::core::Centroid::setup_particle()</a>, <a href="classIMP_1_1core_1_1CentroidOfRefined.html#a68dc0bfe69a80b4f64c8dc16071f0ce4">IMP::core::CentroidOfRefined::CentroidOfRefined()</a>, <a href="classIMP_1_1core_1_1ClosePairsPairScore.html#aa14e8e87a96d8e1bb5388301e89c8553">IMP::core::ClosePairsPairScore::ClosePairsPairScore()</a>, <a href="classIMP_1_1core_1_1Cover.html#ab5213b236dae346ff153bac0db23adbd">IMP::core::Cover::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1Cover.html#a1cd025934cb393d6547e202edcab792f">IMP::core::Cover::setup_particle()</a>, <a href="classIMP_1_1core_1_1Cover.html#a673af3098e2e4c0f054a2a750d50f977">IMP::core::Cover::setup_particle()</a>, <a href="classIMP_1_1core_1_1CoverRefined.html#a45b7edfe7946a02e25dffc8c14b5663a">IMP::core::CoverRefined::CoverRefined()</a>, <a href="classIMP_1_1core_1_1DerivativesFromRefined.html#a8000da2c305d871cdab633cbd148dd9f">IMP::core::DerivativesFromRefined::DerivativesFromRefined()</a>, <a href="classIMP_1_1core_1_1DerivativesToRefined.html#a9924217fcda26cf50f5f7562671fa725">IMP::core::DerivativesToRefined::DerivativesToRefined()</a>, <a href="classIMP_1_1core_1_1KClosePairsPairScore.html#a2a23964f1fa3d3f05bd6d9504d071880">IMP::core::KClosePairsPairScore::KClosePairsPairScore()</a>, <a href="classIMP_1_1core_1_1RefinedPairsPairScore.html#adb30d6b0d713e0b78829e7da0685335d">IMP::core::RefinedPairsPairScore::RefinedPairsPairScore()</a>, <a href="classIMP_1_1core_1_1RigidBodyDistancePairScore.html#a4975b55d39c224707d50b2a3e187b30f">IMP::core::RigidBodyDistancePairScore::RigidBodyDistancePairScore()</a>, <a href="classIMP_1_1core_1_1WeightedDerivativesToRefined.html#ae94d358573870e97b5527e9454ccdcea">IMP::core::WeightedDerivativesToRefined::WeightedDerivativesToRefined()</a>, <a href="classIMP_1_1misc_1_1LowestRefinedPairScore.html#ae522bb65cfacf6dfcb2eed7adc4094e4">IMP::misc::LowestRefinedPairScore::LowestRefinedPairScore()</a>, <a href="classIMP_1_1multifit_1_1WeightedExcludedVolumeRestraint.html#a1b6c81a897d408afc71a09df136738c3">IMP::multifit::WeightedExcludedVolumeRestraint::WeightedExcludedVolumeRestraint()</a>, <a href="namespaceIMP_1_1em.html#ab8beedad8915dcd1aa22b5ba75a61439">IMP::em::compute_fitting_scores()</a>, <a href="namespaceIMP_1_1em.html#a300a1ede18ac26749a961beca4c971e3">IMP::em::local_rigid_fitting()</a>, <a href="namespaceIMP_1_1em.html#a46543f4001a8c31276003433db00f776">IMP::em::local_rigid_fitting_around_point()</a>, <a href="namespaceIMP_1_1em.html#a729f3b19106724e0dbc8c7e98336ff64">IMP::em::local_rigid_fitting_around_points()</a>, <a href="namespaceIMP_1_1multifit.html#a3359231b0601df5803958afcd8d93184">IMP::multifit::create_hit_map()</a>, <a href="namespaceIMP_1_1multifit.html#a45c8385d6183240ec7216ae97374c7a9">IMP::multifit::pca_based_rigid_fitting()</a></td></tr>
41 <tr><td>@ref IMP::Restraint</td><td><a href="classIMP_1_1RestraintSet.html#a2b6227d446afc88b0adce7884c57bd1b">IMP::RestraintSet::remove_restraint()</a>, <a href="classIMP_1_1RestraintSet.html#a96f88196ad13df7a9e69f62b3022e1ad">IMP::RestraintSet::add_restraint()</a>, <a href="classIMP_1_1RestraintSet.html#afc7732ec283f1b5595700898d44191dd">IMP::RestraintSet::on_add()</a>, <a href="classIMP_1_1RestraintSet.html#a3c0ed84d7535ddb3330a249c804f6783">IMP::RestraintSet::on_remove()</a>, <a href="classIMP_1_1RestraintsAdaptor.html#a4480138e5bbff398b8f3bc2aeb516b22">IMP::RestraintsAdaptor::get()</a>, <a href="classIMP_1_1RestraintsAdaptor.html#a44c377153bfec221ec4592b550d702e8">IMP::RestraintsAdaptor::RestraintsAdaptor()</a>, <a href="classIMP_1_1ScoreAccumulator.html#a02c104d9f192ea011f0a7f8b69612bfa">IMP::ScoreAccumulator::ScoreAccumulator()</a>, <a href="classIMP_1_1ScoringFunctionAdaptor.html#a8703032ecda559760ce1c4a8c2a8c1e3">IMP::ScoringFunctionAdaptor::get()</a>, <a href="classIMP_1_1ScoringFunctionAdaptor.html#ab6cb78fd9052b8ffec3e0989c255da78">IMP::ScoringFunctionAdaptor::ScoringFunctionAdaptor()</a>, <a href="classIMP_1_1core_1_1IncrementalScoringFunction.html#adaec7d61ac31420872ba793183198498">IMP::core::IncrementalScoringFunction::create_data()</a>, <a href="classIMP_1_1core_1_1MinimumRestraint.html#a5529776c7009eabe6eeb2267e43834e4">IMP::core::MinimumRestraint::add_restraint()</a>, <a href="classIMP_1_1core_1_1MinimumRestraint.html#ab39a892c852feab0a8962cd0a6567457">IMP::core::MinimumRestraint::remove_restraint()</a>, <a href="classIMP_1_1display_1_1RestraintGeometry.html#a305119c98092eaa981746cc8c035fc1a">IMP::display::RestraintGeometry::RestraintGeometry()</a>, <a href="classIMP_1_1display_1_1RestraintGeometry.html#afedc559ed5cb937a04986d87d9f0c005">IMP::display::RestraintGeometry::RestraintGeometry()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#ab63563966e52189ed4944e938c148660">IMP::domino::RestraintCache::add_restraint_internal()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#afec39699a2c73dfbe5176b6564c02124">IMP::domino::RestraintCache::add_restraint_set_child_internal()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#abfeee91ee10e51b2dcf53e0daaf3fd37">IMP::domino::RestraintCache::get_subset()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#a900c1be619f7302ade5f53c08b86f8b8">IMP::domino::RestraintCache::get_score()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#a277af62358d51335e22c3c5419ced30a">IMP::domino::RestraintCache::get_score()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#a15f1f5513308176b4eaccc9e411277f2">IMP::domino::RestraintCache::get_slice()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#a7cb8d67a4032980ccdbbb2393c4a8aad">IMP::domino::RestraintCache::load_last_score()</a>, <a href="classIMP_1_1isd_1_1AmbiguousRestraint.html#a7455431ce0eb1ccd1cc68d37f8e773e1">IMP::isd::AmbiguousRestraint::AmbiguousRestraint()</a>, <a href="classIMP_1_1npctransport_1_1Scoring.html#a313bae5df7a2e611258f439e29492eff">IMP::npctransport::Scoring::add_custom_restraint()</a>, <a href="namespaceIMP_1_1rmf.html#a2308cb4a180c1c885f7dda0c13592b8f">IMP::rmf::add_restraint()</a></td></tr>
42 <tr><td>@ref IMP::RestraintSet</td><td><a href="classIMP_1_1RestraintSet.html#a3c0ed84d7535ddb3330a249c804f6783">IMP::RestraintSet::on_remove()</a>, <a href="classIMP_1_1display_1_1RestraintSetGeometry.html#a7828db7c00604e67e3b38057638fef9e">IMP::display::RestraintSetGeometry::RestraintSetGeometry()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#ab63563966e52189ed4944e938c148660">IMP::domino::RestraintCache::add_restraint_internal()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#afec39699a2c73dfbe5176b6564c02124">IMP::domino::RestraintCache::add_restraint_set_child_internal()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#ae7e20f6f1ca49677a51ed9bd7b1884e0">IMP::domino::RestraintCache::add_restraint_set_internal()</a>, <a href="classIMP_1_1spb_1_1MonteCarloWithWte.html#afac90eb879ea01493498a4a753bee8aa">IMP::spb::MonteCarloWithWte::MonteCarloWithWte()</a>, <a href="namespaceIMP_1_1domino.html#ab0efd3e3db335ea082bf9b7567011958">IMP::domino::get_restraints()</a>, <a href="namespaceIMP_1_1spb.html#a4f4e29033718c00197737912b750ef5b">IMP::spb::add_bayesian_layer_restraint()</a>, <a href="namespaceIMP_1_1spb.html#a5cf4889f38b10df0422f43533e1efa71">IMP::spb::add_diameter_rgyr_restraint()</a>, <a href="namespaceIMP_1_1spb.html#a6a49d172ebb893d6a3b0de6234cb318e">IMP::spb::add_GFP_restraint()</a>, <a href="namespaceIMP_1_1spb.html#a23e14d249f701c421fd66833c044539a">IMP::spb::add_internal_restraint()</a>, <a href="namespaceIMP_1_1spb.html#ae1bbb466a333fd88c5c6307d628165b9">IMP::spb::add_ISD_particles()</a>, <a href="namespaceIMP_1_1spb.html#a89c91f69eb459a1a6ef9a2da1c9d885a">IMP::spb::add_layer_restraint()</a>, <a href="namespaceIMP_1_1spb.html#ac82266395d7d5fcf26defd3c2f2f9f06">IMP::spb::add_link()</a>, <a href="namespaceIMP_1_1spb.html#a2e319d74f871dffac11765e34a748794">IMP::spb::add_link()</a>, <a href="namespaceIMP_1_1spb.html#ac5d9e593d188cd0afbeb276881d82996">IMP::spb::add_my_connectivity()</a>, <a href="namespaceIMP_1_1spb.html#a1d50546bf0502a542c492062c8f0f42b">IMP::spb::add_restrain_coiledcoil_to_cterm()</a>, <a href="namespaceIMP_1_1spb.html#ada54561155757e22856d4066515ecca0">IMP::spb::add_restrain_protein_length()</a>, <a href="namespaceIMP_1_1spb.html#a238100618f48d22ed7acd619702caea9">IMP::spb::add_SPBexcluded_volume()</a>, <a href="namespaceIMP_1_1spb.html#ac09f34c6ac78e8632549a693c32154e7">IMP::spb::add_stay_close_restraint()</a>, <a href="namespaceIMP_1_1spb.html#a575f993823c11b8c6d9b11c1fcd089f0">IMP::spb::add_stay_close_restraint()</a>, <a href="namespaceIMP_1_1spb.html#aaf1e29ff21dfe105c06b225967d4849e">IMP::spb::add_stay_on_plane_restraint()</a>, <a href="namespaceIMP_1_1spb.html#a69efcfb24ba7b76acf747b54f9c8ce75">IMP::spb::add_tilt()</a>, <a href="namespaceIMP_1_1spb.html#acf08490a12bf75b525b03a2b88f55ada">IMP::spb::add_tilt_restraint()</a>, <a href="namespaceIMP_1_1spb.html#abeff346a43c51e4d81a56567357880a1">IMP::spb::create_merged_protein()</a>, <a href="namespaceIMP_1_1spb.html#a78b1fb512e1db9c6362bb36df94293be">IMP::spb::create_protein()</a>, <a href="namespaceIMP_1_1spb.html#ae9d935784a933409cd306c7c046cfff6">IMP::spb::create_representation()</a>, <a href="namespaceIMP_1_1spb.html#a7c113921b584fd1fce234cdb478f354b">IMP::spb::spb_assemble_restraints()</a></td></tr>
43 <tr><td>@ref IMP::RestraintsAdaptor</td><td><a href="classIMP_1_1core_1_1RestraintsScoringFunction.html#ac1d88a47376f4b06be4c1c1c36f78f5f">IMP::core::RestraintsScoringFunction::RestraintsScoringFunction()</a>, <a href="classIMP_1_1core_1_1RestraintsScoringFunction.html#aa6523603cfdce508edce495b91cf43dd">IMP::core::RestraintsScoringFunction::RestraintsScoringFunction()</a>, <a href="classIMP_1_1domino_1_1DiscreteSampler.html#aa88d60254ee2cf156c3405437af23ee1">IMP::domino::DiscreteSampler::set_restraints()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#a7f717d32d3a03455618395539b261846">IMP::domino::RestraintCache::add_restraints()</a>, <a href="classIMP_1_1domino_1_1RestraintScoreSubsetFilterTable.html#a27a72d5b2d3000fa72df9c45755db866">IMP::domino::RestraintScoreSubsetFilterTable::RestraintScoreSubsetFilterTable()</a></td></tr>
44 <tr><td>@ref IMP::Sampler</td><td><a href="classIMP_1_1core_1_1MCCGSampler.html#a459aa19964e0315139fdbfb378bcaa7f">IMP::core::MCCGSampler::MCCGSampler()</a></td></tr>
45 <tr><td>@ref IMP::ScoreAccumulator</td><td><a href="classIMP_1_1Restraint.html#a580b9df5d4094f07703cce8093f59bac">IMP::Restraint::add_score_and_derivatives()</a>, <a href="classIMP_1_1Restraint.html#a844a93798189fbad836f6b16baecbbe6">IMP::Restraint::add_score_and_derivatives_moved()</a>, <a href="classIMP_1_1Restraint.html#a537cbd8ac265fa5cd0690c11d3fd16d1">IMP::Restraint::do_add_score_and_derivatives()</a>, <a href="classIMP_1_1Restraint.html#acc57c8055191bb2a77c78a594ecb4257">IMP::Restraint::do_add_score_and_derivatives_moved()</a>, <a href="classIMP_1_1ScoreAccumulator.html#a02c104d9f192ea011f0a7f8b69612bfa">IMP::ScoreAccumulator::ScoreAccumulator()</a>, <a href="classIMP_1_1ScoreAccumulator.html#ac46b358820c2a6e1faa379873b786390">IMP::ScoreAccumulator::ScoreAccumulator()</a>, <a href="classIMP_1_1ScoringFunction.html#a1dbb15f117f7ae2e6398ddc1acfe5316">IMP::ScoringFunction::do_add_score_and_derivatives()</a>, <a href="classIMP_1_1ScoringFunction.html#a0a3b283bf930c2dfabf13192ef617fa6">IMP::ScoringFunction::do_add_score_and_derivatives_moved()</a>, <a href="classIMP_1_1container_1_1PredicatePairsRestraint.html#a1b4220f06cf860b3345a4aeb69f08f8a">IMP::container::PredicatePairsRestraint::do_add_score_and_derivatives()</a>, <a href="classIMP_1_1container_1_1PredicateQuadsRestraint.html#ad99dbedd16f83586eec81446a58fe853">IMP::container::PredicateQuadsRestraint::do_add_score_and_derivatives()</a>, <a href="classIMP_1_1container_1_1PredicateSingletonsRestraint.html#a9488c2fbe9f45c079c5142bd5c2a34d9">IMP::container::PredicateSingletonsRestraint::do_add_score_and_derivatives()</a>, <a href="classIMP_1_1container_1_1PredicateTripletsRestraint.html#a563b82cd5f0647d0bf6e7742e2f48b37">IMP::container::PredicateTripletsRestraint::do_add_score_and_derivatives()</a>, <a href="classIMP_1_1core_1_1IncrementalScoringFunction.html#af6628421a520ff52efc7732643a48b1d">IMP::core::IncrementalScoringFunction::do_add_score_and_derivatives()</a>, <a href="classIMP_1_1example_1_1ExampleRestraint.html#ac8c02104f995e7a43a91d24d94cecf01">IMP::example::ExampleRestraint::do_add_score_and_derivatives()</a>, <a href="classIMP_1_1isd_1_1LogWrapper.html#a76560e61dba0633ced0f498d4e7ae64a">IMP::isd::LogWrapper::do_add_score_and_derivatives()</a>, <a href="classIMP_1_1isd_1_1LogWrapper.html#aff10b0471ed44a25b1e4d3b0ce70b0fd">IMP::isd::LogWrapper::do_add_score_and_derivatives_moved()</a></td></tr>
46 <tr><td>@ref IMP::ScoreState</td><td><a href="classIMP_1_1Model.html#a494d49b1b9b42964f24c0e8fc29368c9">IMP::Model::remove_score_state()</a>, <a href="classIMP_1_1Model.html#a80d90d7b926b5e2f3b4896f2f5d5dbb4">IMP::Model::add_score_state()</a>, <a href="classIMP_1_1Model.html#a8aca3d3b9f325fb7919c4d951bfa5410">IMP::Model::do_add_score_state()</a>, <a href="classIMP_1_1Model.html#aa9e5cbf0e859559156083bad92858bb0">IMP::Model::do_check_update_order()</a>, <a href="classIMP_1_1Model.html#af1148b36863dddee994121fe0c08cc1f">IMP::Model::do_remove_score_state()</a></td></tr>
47 <tr><td>@ref IMP::ScoringFunction</td><td><a href="classIMP_1_1ScoringFunctionAdaptor.html#aad09f1973c5383ea3d1d0430910beeb6">IMP::ScoringFunctionAdaptor::get()</a>, <a href="classIMP_1_1ScoringFunctionAdaptor.html#a53ffc834fe3c4731d1c2f0b232e7d4f1">IMP::ScoringFunctionAdaptor::ScoringFunctionAdaptor()</a>, <a href="classIMP_1_1kinematics_1_1LocalPlanner.html#ae1a5e3af8bdac8533a6cf66ff496456e">IMP::kinematics::LocalPlanner::is_valid()</a>, <a href="classIMP_1_1kinematics_1_1LocalPlanner.html#aa3e2c3f33045da082ccbc0c57cf98fae">IMP::kinematics::LocalPlanner::plan()</a>, <a href="classIMP_1_1kinematics_1_1PathLocalPlanner.html#a67f80137a9768983eb7c54911f00e158">IMP::kinematics::PathLocalPlanner::plan()</a>, <a href="classIMP_1_1kinematics_1_1RRT.html#abe1880ea81bd556626392e5da325a29f">IMP::kinematics::RRT::check_initial_configuration()</a>, <a href="namespaceIMP.html#ab557e028ce1a3dfda4936f2f86a89b36">IMP::create_decomposition()</a></td></tr>
48 <tr><td>@ref IMP::ScoringFunctionAdaptor</td><td><a href="classIMP_1_1Optimizer.html#a0f6b4b9b00d0e5d766cbd1f498a5e575">IMP::Optimizer::set_scoring_function()</a>, <a href="classIMP_1_1Sampler.html#a252d7090be151052cd7e244651150eb1">IMP::Sampler::set_scoring_function()</a>, <a href="namespaceIMP.html#a0fcf04bcd228de32bba2cde04f75b66e">IMP::show_restraint_hierarchy()</a>, <a href="namespaceIMP_1_1domino.html#a7745ea629841a6a4475211ba0a134b44">IMP::domino::get_interaction_graph()</a>, <a href="namespaceIMP_1_1domino.html#a32c0b82e732879cbf0d77bbea28541bb">IMP::domino::get_interaction_graph()</a>, <a href="namespaceIMP_1_1domino.html#a52b8de54766ce0eeaece21adff2c9bd1">IMP::domino::get_merge_tree()</a>, <a href="namespaceIMP_1_1domino.html#ab0eb2c05d5eb0c9e64fba8c85011ad01">IMP::domino::get_restraint_graph()</a></td></tr>
49 <tr><td>@ref IMP::SingletonContainer</td><td><a href="classIMP_1_1SingletonContainerAdaptor.html#a87a965e7f45d6062b4bd9b2de90e07d6">IMP::SingletonContainerAdaptor::SingletonContainerAdaptor()</a>, <a href="classIMP_1_1atom_1_1BondPairContainer.html#a29746aefa377d639d76290e766cde29a">IMP::atom::BondPairContainer::BondPairContainer()</a>, <a href="classIMP_1_1atom_1_1BondsGeometry.html#ab8515165c8c88285cd53a08c49c20027">IMP::atom::BondsGeometry::BondsGeometry()</a>, <a href="classIMP_1_1atom_1_1HierarchiesGeometry.html#a99fd0e79a857e374e71b0747535021a6">IMP::atom::HierarchiesGeometry::HierarchiesGeometry()</a>, <a href="classIMP_1_1container_1_1ConnectingPairContainer.html#a382caf3731ab7ff9342a3ddd5edbabd6">IMP::container::ConnectingPairContainer::initialize()</a>, <a href="classIMP_1_1container_1_1ConnectingPairContainer.html#a35da194925a5f1cbf02b5ae6c86a49a5">IMP::container::ConnectingPairContainer::ConnectingPairContainer()</a>, <a href="classIMP_1_1container_1_1InContainerSingletonFilter.html#a68fbe4b0e18b81e11a16e8aeb0901e50">IMP::container::InContainerSingletonFilter::InContainerSingletonFilter()</a>, <a href="classIMP_1_1container_1_1InContainerSingletonFilter.html#ac0ceafc7e624e431fd483096a1f3cea0">IMP::container::InContainerSingletonFilter::InContainerSingletonFilter()</a>, <a href="classIMP_1_1container_1_1SingletonContainerSet.html#a3f1d9a259ba319a2091f077cf59b42e4">IMP::container::SingletonContainerSet::remove_singleton_container()</a>, <a href="classIMP_1_1container_1_1SingletonContainerSet.html#a445f478c983c1304767c94cc47db65f4">IMP::container::SingletonContainerSet::add_singleton_container()</a>, <a href="classIMP_1_1container_1_1SingletonContainerSet.html#a3053d32ea57216bae48fa420198bcf95">IMP::container::SingletonContainerSet::get_set()</a>, <a href="classIMP_1_1core_1_1DiameterRestraint.html#a686dadc8304340cc099efc0e6d725841">IMP::core::DiameterRestraint::DiameterRestraint()</a>, <a href="classIMP_1_1core_1_1RigidBodyDerivativesGeometry.html#a0096a1f0c7b5b08b92f30ec46238f299">IMP::core::RigidBodyDerivativesGeometry::RigidBodyDerivativesGeometry()</a>, <a href="classIMP_1_1core_1_1RigidBodyFramesGeometry.html#a417f60df35bd50228cbbd78454167d7f">IMP::core::RigidBodyFramesGeometry::RigidBodyFramesGeometry()</a>, <a href="classIMP_1_1core_1_1VolumeRestraint.html#ae1b60894c5cda0839c7100261563e5a8">IMP::core::VolumeRestraint::VolumeRestraint()</a>, <a href="classIMP_1_1core_1_1XYZDerivativesGeometry.html#af6ebb040ac13ac913c8630dc8f660170">IMP::core::XYZDerivativesGeometry::XYZDerivativesGeometry()</a>, <a href="classIMP_1_1core_1_1XYZRsGeometry.html#aca80015235b9af92bfa758f798f0e187">IMP::core::XYZRsGeometry::XYZRsGeometry()</a>, <a href="classIMP_1_1em2d_1_1Em2DRestraint.html#a4fff039bf0e2bf49c06583f83d254afa">IMP::em2d::Em2DRestraint::set_particles()</a>, <a href="classIMP_1_1em2d_1_1ParticlesDummyRestraint.html#a6282d6bb36aaeb6f2af32b5c03c49dc4">IMP::em2d::ParticlesDummyRestraint::ParticlesDummyRestraint()</a>, <a href="classIMP_1_1example_1_1ExampleComplexRestraint.html#a2fdc2b737dd01072a9d87e90e3dee5b3">IMP::example::ExampleComplexRestraint::ExampleComplexRestraint()</a>, <a href="classIMP_1_1statistics_1_1ConfigurationSetRMSDMetric.html#a4a6365b3e39347130d20397aef8a8bad">IMP::statistics::ConfigurationSetRMSDMetric::ConfigurationSetRMSDMetric()</a></td></tr>
50 <tr><td>@ref IMP::SingletonContainerAdaptor</td><td><a href="classIMP_1_1container_1_1AllBipartitePairContainer.html#adcb03395abbfa62560b4067687d976c3">IMP::container::AllBipartitePairContainer::AllBipartitePairContainer()</a>, <a href="classIMP_1_1container_1_1AllPairContainer.html#af3b744e61af8d9d982321faa2f3f1d1b">IMP::container::AllPairContainer::AllPairContainer()</a>, <a href="classIMP_1_1container_1_1CloseBipartitePairContainer.html#afa0bdd7250c318333de927ea873b11c6">IMP::container::CloseBipartitePairContainer::CloseBipartitePairContainer()</a>, <a href="classIMP_1_1container_1_1ClosePairContainer.html#aa7b183795bd28ab268e5e84a5ad0cd99">IMP::container::ClosePairContainer::ClosePairContainer()</a>, <a href="classIMP_1_1container_1_1ClosePairContainer.html#a19f52fd2b6c1f34261b304f5870ac9ca">IMP::container::ClosePairContainer::ClosePairContainer()</a>, <a href="classIMP_1_1container_1_1DistributeSingletonsScoreState.html#abb7c58bb403b0f0927a94408dfd14556">IMP::container::DistributeSingletonsScoreState::DistributeSingletonsScoreState()</a>, <a href="classIMP_1_1container_1_1EventSingletonsOptimizerState.html#a98cfbd1e195b6fbfd606df3f9016ce55">IMP::container::EventSingletonsOptimizerState::EventSingletonsOptimizerState()</a>, <a href="classIMP_1_1container_1_1MinimumSingletonRestraint.html#afc6016d7b8306d113c7aac80f9fad916">IMP::container::MinimumSingletonRestraint::MinimumSingletonRestraint()</a>, <a href="classIMP_1_1container_1_1PredicateSingletonsRestraint.html#a84f8347debda23cf2d99b2e2b0695ddb">IMP::container::PredicateSingletonsRestraint::PredicateSingletonsRestraint()</a>, <a href="classIMP_1_1container_1_1SingletonContainerStatistics.html#a25aa3889891c205a80f490dc8f0d8c01">IMP::container::SingletonContainerStatistics::SingletonContainerStatistics()</a>, <a href="classIMP_1_1container_1_1SingletonsConstraint.html#a760702d2cb759a7966c3eb443234c5b6">IMP::container::SingletonsConstraint::SingletonsConstraint()</a>, <a href="classIMP_1_1container_1_1SingletonsOptimizerState.html#adcee3152351b3236bdad5d08366b71f9">IMP::container::SingletonsOptimizerState::SingletonsOptimizerState()</a>, <a href="classIMP_1_1container_1_1SingletonsRestraint.html#a999b26a2d8543e33cf373b469e7b84f9">IMP::container::SingletonsRestraint::SingletonsRestraint()</a>, <a href="classIMP_1_1core_1_1ConnectivityRestraint.html#ab3f9acf18ba9cb254034c8f9ae1ddd1f">IMP::core::ConnectivityRestraint::ConnectivityRestraint()</a>, <a href="classIMP_1_1core_1_1ExcludedVolumeRestraint.html#a3901b13b7a361386dfe813d43384b05e">IMP::core::ExcludedVolumeRestraint::ExcludedVolumeRestraint()</a>, <a href="classIMP_1_1core_1_1ExcludedVolumeRestraint.html#aafdb5271265f58bdc71b60dacc22387b">IMP::core::ExcludedVolumeRestraint::ExcludedVolumeRestraint()</a>, <a href="classIMP_1_1display_1_1SingletonsGeometry.html#a6bfeea07e40dfd0843f9174ed55189a4">IMP::display::SingletonsGeometry::SingletonsGeometry()</a>, <a href="classIMP_1_1display_1_1SingletonsGeometry.html#af290142275852a92acfa8470ca2d7ab4">IMP::display::SingletonsGeometry::SingletonsGeometry()</a>, <a href="classIMP_1_1npc_1_1AssemblySymmetryByDihedralRestraint.html#a4d4cb73e4b24ee491659349d823efc87">IMP::npc::AssemblySymmetryByDihedralRestraint::AssemblySymmetryByDihedralRestraint()</a>, <a href="classIMP_1_1npc_1_1AssemblySymmetryByDistanceRestraint.html#a10ece457dfaa48a3669b39559d855af5">IMP::npc::AssemblySymmetryByDistanceRestraint::AssemblySymmetryByDistanceRestraint()</a>, <a href="classIMP_1_1npc_1_1MembraneExclusionRestraint.html#aabe833698158da230b3c9b0876bcc4bb">IMP::npc::MembraneExclusionRestraint::MembraneExclusionRestraint()</a>, <a href="classIMP_1_1npc_1_1MembraneSurfaceLocationConditionalRestraint.html#a9d1e118957941e5bd79ef3ddcfeb5e79">IMP::npc::MembraneSurfaceLocationConditionalRestraint::MembraneSurfaceLocationConditionalRestraint()</a>, <a href="classIMP_1_1npc_1_1MembraneSurfaceLocationRestraint.html#a6d22056f1058bab236f21513254b67e3">IMP::npc::MembraneSurfaceLocationRestraint::MembraneSurfaceLocationRestraint()</a>, <a href="classIMP_1_1npc_1_1PerinuclearVolumeLocationRestraint.html#ad22a7acc34ee3856ffbb8a08a569fc24">IMP::npc::PerinuclearVolumeLocationRestraint::PerinuclearVolumeLocationRestraint()</a>, <a href="classIMP_1_1npc_1_1PoreSideVolumeLocationRestraint.html#aa170d32aef12da22f9d5f17dada3a534">IMP::npc::PoreSideVolumeLocationRestraint::PoreSideVolumeLocationRestraint()</a>, <a href="classIMP_1_1npc_1_1ProteinChainRestraint.html#af3f66d8f208f99fd51ba4338f1c2029f">IMP::npc::ProteinChainRestraint::ProteinChainRestraint()</a>, <a href="classIMP_1_1npc_1_1ProteinContactRestraint.html#a50ba64a0841d0e1db90f64fc35aefd83">IMP::npc::ProteinContactRestraint::ProteinContactRestraint()</a>, <a href="classIMP_1_1npc_1_1ProteinProximityRestraint.html#a7705475b8e7ce39cba357651c6103694">IMP::npc::ProteinProximityRestraint::ProteinProximityRestraint()</a>, <a href="classIMP_1_1npc_1_1XYRadialPositionLowerRestraint.html#a2ae61a4679697f0d670fde46d26033d9">IMP::npc::XYRadialPositionLowerRestraint::XYRadialPositionLowerRestraint()</a>, <a href="classIMP_1_1npc_1_1XYRadialPositionRestraint.html#ab0c60baefbd3e5cbd4a3c4b6b47bf52e">IMP::npc::XYRadialPositionRestraint::XYRadialPositionRestraint()</a>, <a href="classIMP_1_1npc_1_1XYRadialPositionUpperRestraint.html#a85c4871e05eab28e448b8dcac5e03460">IMP::npc::XYRadialPositionUpperRestraint::XYRadialPositionUpperRestraint()</a>, <a href="classIMP_1_1npc_1_1YAxialPositionLowerRestraint.html#a1fe76a94b18be8cbedaa7d926a75b1ab">IMP::npc::YAxialPositionLowerRestraint::YAxialPositionLowerRestraint()</a>, <a href="classIMP_1_1npc_1_1YAxialPositionRestraint.html#a2311027e2bd2388c3bce8f3e1530a084">IMP::npc::YAxialPositionRestraint::YAxialPositionRestraint()</a>, <a href="classIMP_1_1npc_1_1YAxialPositionUpperRestraint.html#ae0922ea2155fa175c2823b184b066645">IMP::npc::YAxialPositionUpperRestraint::YAxialPositionUpperRestraint()</a>, <a href="classIMP_1_1npc_1_1ZAxialPositionLowerRestraint.html#aea595905e32aeac385ef639555b841e4">IMP::npc::ZAxialPositionLowerRestraint::ZAxialPositionLowerRestraint()</a>, <a href="classIMP_1_1npc_1_1ZAxialPositionRestraint.html#a8606bf0dabe6e6e5427666325195adeb">IMP::npc::ZAxialPositionRestraint::ZAxialPositionRestraint()</a>, <a href="classIMP_1_1npc_1_1ZAxialPositionUpperRestraint.html#ab20dba21955290cc0a060366f3f4385e">IMP::npc::ZAxialPositionUpperRestraint::ZAxialPositionUpperRestraint()</a>, <a href="classIMP_1_1npctransport_1_1Scoring.html#a7c79f71a7354a360368115ba1ff7c38c">IMP::npctransport::Scoring::add_z_bias_restraint()</a>, <a href="classIMP_1_1npctransport_1_1Scoring.html#a5af15fec4f0f1153c0a5d8c9042a3536">IMP::npctransport::Scoring::create_bounding_volume_restraint()</a>, <a href="classIMP_1_1npctransport_1_1Scoring.html#a4e4f841b03e335318b0617e5cf5a1b5b">IMP::npctransport::Scoring::create_close_beads_container()</a>, <a href="classIMP_1_1npctransport_1_1Scoring.html#aedd0b42cf991b9980138d60ee29a7838">IMP::npctransport::Scoring::create_close_beads_container()</a>, <a href="classIMP_1_1npctransport_1_1Scoring.html#a9e946acc8b600f31d8c01edf59534dd7">IMP::npctransport::Scoring::create_slab_restraint()</a>, <a href="classIMP_1_1npctransport_1_1Scoring.html#a871ed833b15dcb500c7e8e733e709be5">IMP::npctransport::Scoring::create_z_bias_restraint()</a>, <a href="classIMP_1_1npctransport_1_1Scoring.html#a240419d2434543e30736dacdff5aa444">IMP::npctransport::Scoring::get_chain_restraints_on()</a>, <a href="classIMP_1_1npctransport_1_1Scoring.html#aae1d68d893a9cc874ae24552a5a24540">IMP::npctransport::Scoring::get_custom_scoring_function()</a>, <a href="classIMP_1_1npctransport_1_1Scoring.html#adb5e855a526b1a707bcb0ba40ffbd9bb">IMP::npctransport::Scoring::get_custom_scoring_function()</a>, <a href="classIMP_1_1npctransport_1_1TypedSitesGeometry.html#abaf08a2599e01c26498264a393c4ee5b">IMP::npctransport::TypedSitesGeometry::TypedSitesGeometry()</a>, <a href="classIMP_1_1statistics_1_1ConfigurationSetXYZEmbedding.html#a59f36e0f094ff45193a47939d8d93cd1">IMP::statistics::ConfigurationSetXYZEmbedding::ConfigurationSetXYZEmbedding()</a>, <a href="namespaceIMP_1_1npctransport.html#a5fc61bf3d6e02c39e648b153ae6f1dbb">IMP::npctransport::load_pb_conformation()</a>, <a href="namespaceIMP_1_1npctransport.html#a314fcf4d4eafa0e7c58ac7b2513f7673">IMP::npctransport::save_pb_conformation()</a></td></tr>
51 <tr><td>@ref IMP::SingletonModifier</td><td><a href="classIMP_1_1SingletonContainer.html#abc33d2f583c005dcddc80985e31be519">IMP::SingletonContainer::apply()</a>, <a href="classIMP_1_1SingletonContainer.html#a9379f8eba15a16219eccc38f9f7ca827">IMP::SingletonContainer::apply_generic()</a>, <a href="classIMP_1_1SingletonContainer.html#a881db3daef9944eb98dfa40eea54b028">IMP::SingletonContainer::apply_generic_moved()</a>, <a href="classIMP_1_1SingletonContainer.html#aaa76cfad0e04e47ac27c9ee508e3485a">IMP::SingletonContainer::apply_moved()</a>, <a href="classIMP_1_1SingletonContainer.html#a56a378db72a4d989308ef4cbc31444af">IMP::SingletonContainer::do_apply()</a>, <a href="classIMP_1_1SingletonContainer.html#a3835d8d6659e174cb57a24b8bec5709e">IMP::SingletonContainer::do_apply_moved()</a>, <a href="classIMP_1_1atom_1_1CenterOfMass.html#a5a9d6ca22223df96ebd669df4acd20f6">IMP::atom::CenterOfMass::set_constraint()</a>, <a href="classIMP_1_1container_1_1SingletonsConstraint.html#a760702d2cb759a7966c3eb443234c5b6">IMP::container::SingletonsConstraint::SingletonsConstraint()</a>, <a href="classIMP_1_1container_1_1SingletonsOptimizerState.html#adcee3152351b3236bdad5d08366b71f9">IMP::container::SingletonsOptimizerState::SingletonsOptimizerState()</a>, <a href="classIMP_1_1core_1_1Centroid.html#a507bf2af81049919f5aecb8a8bc1f519">IMP::core::Centroid::set_constraint()</a>, <a href="classIMP_1_1core_1_1Cover.html#a66cb1c335414df432226e0aa1c43e467">IMP::core::Cover::set_constraint()</a>, <a href="classIMP_1_1core_1_1ModifierVisitor.html#aec2680b943876bd3f0156bd4b539458a">IMP::core::ModifierVisitor::ModifierVisitor()</a>, <a href="classIMP_1_1core_1_1SingletonConstraint.html#a313647b6559bce11d4088c029332bcb2">IMP::core::SingletonConstraint::SingletonConstraint()</a>, <a href="classIMP_1_1core_1_1SingletonConstraint.html#a18a1741964162c7403596756aa9b392e">IMP::core::SingletonConstraint::SingletonConstraint()</a></td></tr>
52 <tr><td>@ref IMP::SingletonPredicate</td><td><a href="classIMP_1_1container_1_1DistributeSingletonsScoreState.html#aace32527df07ef4c4e84dfd4f96ac46c">IMP::container::DistributeSingletonsScoreState::add_predicate()</a>, <a href="classIMP_1_1container_1_1EventSingletonsOptimizerState.html#a98cfbd1e195b6fbfd606df3f9016ce55">IMP::container::EventSingletonsOptimizerState::EventSingletonsOptimizerState()</a>, <a href="classIMP_1_1container_1_1PredicateSingletonsRestraint.html#a84f8347debda23cf2d99b2e2b0695ddb">IMP::container::PredicateSingletonsRestraint::PredicateSingletonsRestraint()</a></td></tr>
53 <tr><td>@ref IMP::SingletonScore</td><td><a href="classIMP_1_1container_1_1MinimumSingletonRestraint.html#afc6016d7b8306d113c7aac80f9fad916">IMP::container::MinimumSingletonRestraint::MinimumSingletonRestraint()</a>, <a href="classIMP_1_1container_1_1PredicateSingletonsRestraint.html#a6cd441a03c4a29e87aa738f98fb3ce91">IMP::container::PredicateSingletonsRestraint::set_score()</a>, <a href="classIMP_1_1container_1_1PredicateSingletonsRestraint.html#aeb4a59190b8b6035ca4f61e007e4bad0">IMP::container::PredicateSingletonsRestraint::set_unknown_score()</a>, <a href="classIMP_1_1container_1_1SingletonsRestraint.html#a999b26a2d8543e33cf373b469e7b84f9">IMP::container::SingletonsRestraint::SingletonsRestraint()</a>, <a href="classIMP_1_1core_1_1SingletonRestraint.html#ae3d07f96fc76707658b5ddea1fd14088">IMP::core::SingletonRestraint::SingletonRestraint()</a></td></tr>
54 <tr><td>@ref IMP::TextInput</td><td><a href="classIMP_1_1atom_1_1CHARMMParameters.html#acbdb37f228ea45a7fadf426566353725">IMP::atom::CHARMMParameters::read_parameter_file()</a>, <a href="classIMP_1_1atom_1_1CHARMMParameters.html#acca5467e6636e6a15a12cbbb3d5e4117">IMP::atom::CHARMMParameters::read_topology_file()</a>, <a href="classIMP_1_1atom_1_1CHARMMParameters.html#ad3268fabf7026f20fdb6c99c0d6c8be8">IMP::atom::CHARMMParameters::CHARMMParameters()</a>, <a href="classIMP_1_1atom_1_1DopePairScore.html#a880e9729dbfb41c5352ac31a74ab7b26">IMP::atom::DopePairScore::DopePairScore()</a>, <a href="classIMP_1_1atom_1_1LoopStatisticalPairScore.html#a432f07cd2669ed0be7e40f08e13b1023">IMP::atom::LoopStatisticalPairScore::LoopStatisticalPairScore()</a>, <a href="classIMP_1_1atom_1_1ProteinLigandAtomPairScore.html#a0ffe52d45c1ae528cb5548602bc199df">IMP::atom::ProteinLigandAtomPairScore::ProteinLigandAtomPairScore()</a>, <a href="classIMP_1_1atom_1_1ProteinLigandRestraint.html#abc3c5536068dfa6656755334f3430c77">IMP::atom::ProteinLigandRestraint::ProteinLigandRestraint()</a>, <a href="classIMP_1_1core_1_1StatisticalPairScore.html#a44e0c53a5108a702a14749ba813303da">IMP::core::StatisticalPairScore::StatisticalPairScore()</a>, <a href="classIMP_1_1core_1_1StatisticalPairScore.html#aec58d0b096b9c8e80a6bde0dfeeb286e">IMP::core::StatisticalPairScore::StatisticalPairScore()</a>, <a href="classIMP_1_1score__functor_1_1Dope.html#a3dc442630ef41b0cbd97de37a3d38562">IMP::score_functor::Dope::Dope()</a>, <a href="classIMP_1_1score__functor_1_1LoopStatistical.html#a5077600016cceffd9e50a34b244695cb">IMP::score_functor::LoopStatistical::LoopStatistical()</a>, <a href="classIMP_1_1score__functor_1_1SingletonStatistical.html#a68d45e37f5968532b98762482e1fd4b9">IMP::score_functor::SingletonStatistical::SingletonStatistical()</a>, <a href="classIMP_1_1score__functor_1_1Soap.html#aa43b57f68bf7ae5b3961b2a77dfce147">IMP::score_functor::Soap::Soap()</a>, <a href="classIMP_1_1score__functor_1_1Statistical.html#ab0f8bda15288865292e58494fdd37200">IMP::score_functor::Statistical::Statistical()</a>, <a href="classIMP_1_1score__functor_1_1Statistical.html#acfa23222824ef5e35558596f3bcfb3b0">IMP::score_functor::Statistical::Statistical()</a>, <a href="namespaceIMP_1_1algebra.html#aacb10c1707e3fa5a66481d9332c5b162">IMP::algebra::read_pts()</a>, <a href="namespaceIMP_1_1algebra.html#a9bf0a264f35a8de115575dedbfd136f5">IMP::algebra::read_spheres()</a>, <a href="namespaceIMP_1_1atom.html#a63d0f55dbe0f5805915a028a15bf1b1f">IMP::atom::read_mol2()</a>, <a href="namespaceIMP_1_1atom.html#ae3392202746ce0960f27d6acb66c3523">IMP::atom::read_pdb()</a>, <a href="namespaceIMP_1_1atom.html#a0176b83aca48c8580d80b88f6d91ef6f">IMP::atom::read_pdb()</a>, <a href="namespaceIMP_1_1atom.html#a4383e2b7c2330222eaba39867aa4b12d">IMP::atom::read_multimodel_pdb()</a>, <a href="namespaceIMP_1_1atom.html#a293b1fa9409fb92e7830afe81571c03b">IMP::atom::read_psipred()</a>, <a href="namespaceIMP_1_1atom.html#a1b00eeb0093e23eb053c3686e71dbee3">IMP::atom::read_psipred()</a>, <a href="namespaceIMP_1_1atom.html#a2efb72426efcdea0d7566faa78d793ae">IMP::atom::read_mmcif()</a>, <a href="namespaceIMP_1_1atom.html#a8dd513ff4e39c4c40c56e11f2d23da94">IMP::atom::read_multimodel_mmcif()</a>, <a href="namespaceIMP_1_1atom.html#ae2befbe269f1b12d6ccfd31fff5d4673">IMP::atom::read_multimodel_pdb_or_mmcif()</a>, <a href="namespaceIMP_1_1atom.html#afa75d21223f20565d1cc585ec7ebc9af">IMP::atom::read_pdb_or_mmcif()</a>, <a href="namespaceIMP_1_1spb.html#a74a565a80cd426faecd53074703dfcf2">IMP::spb::get_SPBParameters()</a></td></tr>
55 <tr><td>@ref IMP::TextOutput</td><td><a href="classIMP_1_1SetLogTarget.html#affb259b20b780a7eeda3e1321ecbb449">IMP::SetLogTarget::SetLogTarget()</a>, <a href="classIMP_1_1SetLogTarget.html#a9d2e1fa326b32ea584eb948c212897d4">IMP::SetLogTarget::set()</a>, <a href="classIMP_1_1core_1_1WriteRestraintScoresOptimizerState.html#ae7c0af8098f8e5ea6ec7ac278eb2a90c">IMP::core::WriteRestraintScoresOptimizerState::WriteRestraintScoresOptimizerState()</a>, <a href="classIMP_1_1display_1_1PymolWriter.html#a9a6b475762a39dfe0c647a20956e5b4e">IMP::display::PymolWriter::PymolWriter()</a>, <a href="classIMP_1_1display_1_1TextWriter.html#ad5b09bf8ae667c97b3e89a41a18ecf3d">IMP::display::TextWriter::TextWriter()</a>, <a href="namespaceIMP.html#a53851bd4b9e93a219fc7a2b8da3811f7">IMP::set_log_target()</a>, <a href="namespaceIMP.html#ac2464e42d01d49f1e57e3d748887ad99">IMP::show_as_graphviz()</a>, <a href="namespaceIMP_1_1algebra.html#a9a6b26aefeb9ea250ade1e86dff7ea64">IMP::algebra::write_pts()</a>, <a href="namespaceIMP_1_1algebra.html#a6ea7d6d317811b817f9a13410783668a">IMP::algebra::write_spheres()</a>, <a href="namespaceIMP_1_1atom.html#abfcacb973482471e99c5fb1ca306f20b">IMP::atom::write_mol2()</a>, <a href="namespaceIMP_1_1atom.html#a73e18e3fed07044ae62a1fb2954b5784">IMP::atom::write_pdb()</a>, <a href="namespaceIMP_1_1atom.html#a6eee9382831652975bf689feeab8d508">IMP::atom::write_pdb_of_c_alphas()</a>, <a href="namespaceIMP_1_1atom.html#a27cddb5d82fc586eee446fa630c58fc2">IMP::atom::write_multimodel_pdb()</a>, <a href="namespaceIMP_1_1atom.html#a7fa09044850d52574ea2e5fe2f7ec4d9">IMP::atom::show_as_graphviz()</a>, <a href="namespaceIMP_1_1core.html#ad2e0faca3653d6acca9edc09af19ef99">IMP::core::show_rigid_body_hierarchy()</a>, <a href="namespaceIMP_1_1domino.html#a2d03716c9c16a8174cab8627835cf716">IMP::domino::show_as_graphviz()</a>, <a href="namespaceIMP_1_1multifit.html#ad3f92bb765e32aee3d6f1c0d15366d5a">IMP::multifit::write_connolly_surface()</a></td></tr>
56 <tr><td>@ref IMP::TripletContainer</td><td><a href="classIMP_1_1TripletContainerAdaptor.html#a27446f85c68928fe7a13642b342d2b13">IMP::TripletContainerAdaptor::TripletContainerAdaptor()</a>, <a href="classIMP_1_1container_1_1InContainerTripletFilter.html#a0628132a1b0e09cbb9ae74e91e4b7fb5">IMP::container::InContainerTripletFilter::InContainerTripletFilter()</a>, <a href="classIMP_1_1container_1_1InContainerTripletFilter.html#ab9d2b11a24ec46abd6e85038c7585613">IMP::container::InContainerTripletFilter::InContainerTripletFilter()</a>, <a href="classIMP_1_1container_1_1TripletContainerSet.html#a2a79bf7f98f3e405427718ac4fdad9ec">IMP::container::TripletContainerSet::remove_triplet_container()</a>, <a href="classIMP_1_1container_1_1TripletContainerSet.html#a62f2b724a721d1c726ad11a155596259">IMP::container::TripletContainerSet::add_triplet_container()</a>, <a href="classIMP_1_1container_1_1TripletContainerSet.html#a5650d9c2999046961450a95b98d1ff26">IMP::container::TripletContainerSet::get_set()</a></td></tr>
57 <tr><td>@ref IMP::TripletContainerAdaptor</td><td><a href="classIMP_1_1container_1_1DistributeTripletsScoreState.html#a1144f56a3369c719081db5934f0e4177">IMP::container::DistributeTripletsScoreState::DistributeTripletsScoreState()</a>, <a href="classIMP_1_1container_1_1EventTripletsOptimizerState.html#a5a3acac26466ec547977360373e67154">IMP::container::EventTripletsOptimizerState::EventTripletsOptimizerState()</a>, <a href="classIMP_1_1container_1_1MinimumTripletRestraint.html#ab3fe22bd709e5092001fb5475fb20162">IMP::container::MinimumTripletRestraint::MinimumTripletRestraint()</a>, <a href="classIMP_1_1container_1_1PredicateTripletsRestraint.html#a0cc4d122667f0c06bb990a3124d58b23">IMP::container::PredicateTripletsRestraint::PredicateTripletsRestraint()</a>, <a href="classIMP_1_1container_1_1TripletContainerStatistics.html#ac475db4e968f2a7c31842c433d06e0ac">IMP::container::TripletContainerStatistics::TripletContainerStatistics()</a>, <a href="classIMP_1_1container_1_1TripletsConstraint.html#a0a627cc40dcc275e1abe2b162834b877">IMP::container::TripletsConstraint::TripletsConstraint()</a>, <a href="classIMP_1_1container_1_1TripletsOptimizerState.html#af3ab8492a4f6033a1fdbadaa95981c8f">IMP::container::TripletsOptimizerState::TripletsOptimizerState()</a>, <a href="classIMP_1_1container_1_1TripletsRestraint.html#aef8856afade7ff7d64a9a54852b150a1">IMP::container::TripletsRestraint::TripletsRestraint()</a></td></tr>
58 <tr><td>@ref IMP::TripletModifier</td><td><a href="classIMP_1_1TripletContainer.html#a4a6b9e2955f3b48a34bafe045692cb7c">IMP::TripletContainer::apply()</a>, <a href="classIMP_1_1TripletContainer.html#a53b7f6552eb455c99db57feb1efff7e6">IMP::TripletContainer::apply_generic()</a>, <a href="classIMP_1_1TripletContainer.html#a3ee0a2b797304469888071bf682a1f7d">IMP::TripletContainer::apply_generic_moved()</a>, <a href="classIMP_1_1TripletContainer.html#a47b9edc68b3e7f1b1f10153845659090">IMP::TripletContainer::apply_moved()</a>, <a href="classIMP_1_1TripletContainer.html#af3ec425bcba40a5515c35fc2ae5a5922">IMP::TripletContainer::do_apply()</a>, <a href="classIMP_1_1TripletContainer.html#aff31674d754101e8934dc993861b1083">IMP::TripletContainer::do_apply_moved()</a>, <a href="classIMP_1_1container_1_1TripletsConstraint.html#a0a627cc40dcc275e1abe2b162834b877">IMP::container::TripletsConstraint::TripletsConstraint()</a>, <a href="classIMP_1_1container_1_1TripletsOptimizerState.html#af3ab8492a4f6033a1fdbadaa95981c8f">IMP::container::TripletsOptimizerState::TripletsOptimizerState()</a>, <a href="classIMP_1_1core_1_1TripletConstraint.html#aeed25782c5964acea034fa541f870269">IMP::core::TripletConstraint::TripletConstraint()</a>, <a href="classIMP_1_1core_1_1TripletConstraint.html#ad99ccd052b261716671611a2cff4af79">IMP::core::TripletConstraint::TripletConstraint()</a></td></tr>
59 <tr><td>@ref IMP::TripletPredicate</td><td><a href="classIMP_1_1container_1_1DistributeTripletsScoreState.html#a73b67981a22dc16bb6dc985ff85e26ae">IMP::container::DistributeTripletsScoreState::add_predicate()</a>, <a href="classIMP_1_1container_1_1EventTripletsOptimizerState.html#a5a3acac26466ec547977360373e67154">IMP::container::EventTripletsOptimizerState::EventTripletsOptimizerState()</a>, <a href="classIMP_1_1container_1_1PredicateTripletsRestraint.html#a0cc4d122667f0c06bb990a3124d58b23">IMP::container::PredicateTripletsRestraint::PredicateTripletsRestraint()</a></td></tr>
60 <tr><td>@ref IMP::TripletScore</td><td><a href="classIMP_1_1container_1_1MinimumTripletRestraint.html#ab3fe22bd709e5092001fb5475fb20162">IMP::container::MinimumTripletRestraint::MinimumTripletRestraint()</a>, <a href="classIMP_1_1container_1_1PredicateTripletsRestraint.html#a6fa8b5fc0f53c9c22b67085342ad8e72">IMP::container::PredicateTripletsRestraint::set_score()</a>, <a href="classIMP_1_1container_1_1PredicateTripletsRestraint.html#abb02987a9c403f856a81a45133168d39">IMP::container::PredicateTripletsRestraint::set_unknown_score()</a>, <a href="classIMP_1_1container_1_1TripletsRestraint.html#aef8856afade7ff7d64a9a54852b150a1">IMP::container::TripletsRestraint::TripletsRestraint()</a>, <a href="classIMP_1_1core_1_1TripletRestraint.html#aa12a3dcb20c18236896d7523a355dd32">IMP::core::TripletRestraint::TripletRestraint()</a></td></tr>
61 <tr><td>@ref IMP::UnaryFunction</td><td><a href="classIMP_1_1atom_1_1AngleSingletonScore.html#a025212d2429602e2f25e91de4806bf2c">IMP::atom::AngleSingletonScore::AngleSingletonScore()</a>, <a href="classIMP_1_1atom_1_1BondSingletonScore.html#abaa89a38a7990656cce91dde514fbdda">IMP::atom::BondSingletonScore::BondSingletonScore()</a>, <a href="classIMP_1_1atom_1_1ImproperSingletonScore.html#a0dd47b6f1b201fff0dc338e0f6fc18c5">IMP::atom::ImproperSingletonScore::ImproperSingletonScore()</a>, <a href="classIMP_1_1core_1_1AngleRestraint.html#a8d804a5e089cdfaf9d92bca151824a75">IMP::core::AngleRestraint::AngleRestraint()</a>, <a href="classIMP_1_1core_1_1AngleTripletScore.html#afdf1cc12de696eb65446e35b364cd3d1">IMP::core::AngleTripletScore::AngleTripletScore()</a>, <a href="classIMP_1_1core_1_1DiameterRestraint.html#a686dadc8304340cc099efc0e6d725841">IMP::core::DiameterRestraint::DiameterRestraint()</a>, <a href="classIMP_1_1core_1_1DihedralRestraint.html#a44a074b10c84117cf6f05bbec9348026">IMP::core::DihedralRestraint::DihedralRestraint()</a>, <a href="classIMP_1_1core_1_1DistancePairScore.html#a53e6966c14b4be2932d68d079ae191cc">IMP::core::DistancePairScore::DistancePairScore()</a>, <a href="classIMP_1_1core_1_1DistanceRestraint.html#ad9a7eb6292db99b8df339ea289202632">IMP::core::DistanceRestraint::DistanceRestraint()</a>, <a href="classIMP_1_1core_1_1NormalizedSphereDistancePairScore.html#a80720c55fbfe7ffbbab6c974e2c79aef">IMP::core::NormalizedSphereDistancePairScore::NormalizedSphereDistancePairScore()</a>, <a href="classIMP_1_1core_1_1RigidBodyAnglePairScore.html#a9762d9d1a687ec7016b06ae7f831a9be">IMP::core::RigidBodyAnglePairScore::RigidBodyAnglePairScore()</a>, <a href="classIMP_1_1core_1_1SphereDistancePairScore.html#a6e35c99828c2c596a5c3bf4eb3fef0dd">IMP::core::SphereDistancePairScore::SphereDistancePairScore()</a>, <a href="classIMP_1_1core_1_1SphereDistanceToSingletonScore.html#a552fa42fd52a039d38e2085bc78a27c3">IMP::core::SphereDistanceToSingletonScore::SphereDistanceToSingletonScore()</a>, <a href="classIMP_1_1core_1_1SurfaceDepthPairScore.html#a6528dea7f4283cd1f48ad8cd744dd666">IMP::core::SurfaceDepthPairScore::SurfaceDepthPairScore()</a>, <a href="classIMP_1_1core_1_1SurfaceDistancePairScore.html#a4e971d8bcecd53097ef78370fb0c8d3b">IMP::core::SurfaceDistancePairScore::SurfaceDistancePairScore()</a>, <a href="classIMP_1_1core_1_1SurfaceHeightPairScore.html#ac6822276921a98a82610d483883a8669">IMP::core::SurfaceHeightPairScore::SurfaceHeightPairScore()</a>, <a href="classIMP_1_1core_1_1TransformedDistancePairScore.html#a18d9ea122d7eb647fbd53c3a17cb110c">IMP::core::TransformedDistancePairScore::TransformedDistancePairScore()</a>, <a href="classIMP_1_1core_1_1VolumeRestraint.html#ae1b60894c5cda0839c7100261563e5a8">IMP::core::VolumeRestraint::VolumeRestraint()</a>, <a href="classIMP_1_1core_1_1WeightedSphereDistancePairScore.html#a00fd4a9c9030740bbcdc4c1a1bee7730">IMP::core::WeightedSphereDistancePairScore::WeightedSphereDistancePairScore()</a>, <a href="classIMP_1_1example_1_1ExampleComplexRestraint.html#a2fdc2b737dd01072a9d87e90e3dee5b3">IMP::example::ExampleComplexRestraint::ExampleComplexRestraint()</a>, <a href="classIMP_1_1npc_1_1MinimumSphereDistancePairScore.html#af4a2fe6a0d60822438d81bcbc247818d">IMP::npc::MinimumSphereDistancePairScore::MinimumSphereDistancePairScore()</a>, <a href="classIMP_1_1score__functor_1_1UnaryFunctionEvaluate.html#aed62f4dd0e91566bb17435c1f019047d">IMP::score_functor::UnaryFunctionEvaluate::UnaryFunctionEvaluate()</a>, <a href="classIMP_1_1spb_1_1AttributeDistancePairScore.html#abd9f3f36a0742a1dbf85cb6021e905da">IMP::spb::AttributeDistancePairScore::AttributeDistancePairScore()</a>, <a href="classIMP_1_1spb_1_1KinkPairScore.html#a429783aa9cdf3119f1d8b66d85289c43">IMP::spb::KinkPairScore::KinkPairScore()</a>, <a href="classIMP_1_1spb_1_1TiltSingletonScore.html#a342433901f7f30ddc1d221ea9a2ea5c7">IMP::spb::TiltSingletonScore::TiltSingletonScore()</a>, <a href="namespaceIMP_1_1core.html#a2d189bddcf9e654a50e9ce934a9a4ac6">IMP::core::create_bounding_box_3d_singleton_score()</a>, <a href="namespaceIMP_1_1core.html#a90cbfde8c69b48bb7751c5d34491537e">IMP::core::create_bounding_sphere_3d_singleton_score()</a>, <a href="namespaceIMP_1_1core.html#a03101e1d8dcabef1d4f117d96c3ce803">IMP::core::create_distance_to_singleton_score()</a></td></tr>
62 <tr><td>@ref IMP::Undecorator</td><td><a href="classIMP_1_1Model.html#a542551beb5170eedbd3488b636942351">IMP::Model::add_undecorator()</a></td></tr>
63 <tr><td>@ref IMP::Value</td><td><a href="classIMP_1_1ScopedAddCacheAttribute.html#a8af77bca25f204c29b0b5787e2b8788d">IMP::ScopedAddCacheAttribute::ScopedAddCacheAttribute()</a>, <a href="classIMP_1_1ScopedAddCacheAttribute.html#a950aa06fe61aafec097d962eb556714a">IMP::ScopedAddCacheAttribute::set()</a>, <a href="classIMP_1_1ScopedSetAttribute.html#a99b2803e357b09f6de49e93ce6cfefbd">IMP::ScopedSetAttribute::ScopedSetAttribute()</a>, <a href="classIMP_1_1ScopedSetAttribute.html#a7adf89db75ee85754c433440f37eb3ad">IMP::ScopedSetAttribute::set()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#a97ccb184c448edc82741a0b8126ec750">IMP::algebra::GridD::GridD()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#aa575da807c4f8427657289c1725587c2">IMP::algebra::GridD::GridD()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#ab96be5a02e7d8a1729e6b47e8f6b93da">IMP::algebra::GridD::GridD()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#adb32bd20c18445dd15609b6d71ab6eff">IMP::algebra::GridD::GridD()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#a1331afb93fdf474e352ce38076a1dd56">IMP::algebra::GridD::GridD()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#a24ba706b342d7dc7e3c5cb42ed64fccf">IMP::algebra::GridD::add_voxel()</a>, <a href="classIMP_1_1display_1_1IsosurfaceGeometry.html#aee4743136bd5d0a62b41fd956ab1d7da">IMP::display::IsosurfaceGeometry::IsosurfaceGeometry()</a>, <a href="namespaceIMP_1_1algebra.html#a9ed792e2cc65d410fdcce57c0850eb92">IMP::algebra::get_bounding_box()</a>, <a href="namespaceIMP_1_1algebra.html#adb4e0a724bc2f1f9c54e3ebc9437c260">IMP::algebra::get_linearly_interpolated()</a></td></tr>
64 <tr><td>@ref IMP::Vector</td><td><a href="classIMP_1_1ConstVector.html#aea5e00cd3a596d70b5e5691c23f1d487">IMP::ConstVector::ConstVector()</a>, <a href="classIMP_1_1PairContainer.html#a7bbb919465a48da1f8875030af040737">IMP::PairContainer::apply_generic_moved()</a>, <a href="classIMP_1_1PairContainer.html#a4056f063501464a662a6d34a665b1ea8">IMP::PairContainer::apply_moved()</a>, <a href="classIMP_1_1PairContainer.html#a7043f56aa5f4d0cac63fd6574bbb8fc0">IMP::PairContainer::do_apply_moved()</a>, <a href="classIMP_1_1PairModifier.html#aa5d8ffc0c3a1e03d5d1c23cd5b35602c">IMP::PairModifier::apply_indexes_moved()</a>, <a href="classIMP_1_1ParticleIndexesAdaptor.html#a4eb604539b50fde0988a21aad2dc243e">IMP::ParticleIndexesAdaptor::ParticleIndexesAdaptor()</a>, <a href="classIMP_1_1ParticleIndexesAdaptor.html#a1bb1ea98119c8ef61e3f1eda030100d8">IMP::ParticleIndexesAdaptor::ParticleIndexesAdaptor()</a>, <a href="classIMP_1_1ParticleIndexesAdaptor.html#a184e015c92f8c7ff1cd7446fbc313bc0">IMP::ParticleIndexesAdaptor::ParticleIndexesAdaptor()</a>, <a href="classIMP_1_1ParticleInputs.html#a117b8901ab831bde1b2badb3599447c9">IMP::ParticleInputs::get_inputs()</a>, <a href="classIMP_1_1ParticleInputs.html#a98f8a3455c3d69f08eebdb2b659c3317">IMP::ParticleInputs::do_get_inputs()</a>, <a href="classIMP_1_1ParticleOutputs.html#a319cf644ab7d3d1b4041c3bc21318009">IMP::ParticleOutputs::get_outputs()</a>, <a href="classIMP_1_1ParticleOutputs.html#ac90bae015c3ee606281cead2719631ff">IMP::ParticleOutputs::do_get_outputs()</a>, <a href="classIMP_1_1QuadContainer.html#af2e0fe21fe427f811178c0a1704f1ba7">IMP::QuadContainer::apply_generic_moved()</a>, <a href="classIMP_1_1QuadContainer.html#a69b4c8cb88a2162dc18b7f07a6f7e60c">IMP::QuadContainer::apply_moved()</a>, <a href="classIMP_1_1QuadContainer.html#a58852e2742e9b0c2a5f7582e00f28eb1">IMP::QuadContainer::do_apply_moved()</a>, <a href="classIMP_1_1QuadModifier.html#ace28229b91ce1475a4de2dea5fa235b9">IMP::QuadModifier::apply_indexes_moved()</a>, <a href="classIMP_1_1Restraint.html#a844a93798189fbad836f6b16baecbbe6">IMP::Restraint::add_score_and_derivatives_moved()</a>, <a href="classIMP_1_1Restraint.html#acc57c8055191bb2a77c78a594ecb4257">IMP::Restraint::do_add_score_and_derivatives_moved()</a>, <a href="classIMP_1_1RestraintInfo.html#a3c4509787a136fc0c28f92c2468764ed">IMP::RestraintInfo::add_particle_indexes()</a>, <a href="classIMP_1_1ScoringFunction.html#a6057913cc43610fd70d25d57bc2af293">IMP::ScoringFunction::get_moved_required_score_states()</a>, <a href="classIMP_1_1ScoringFunction.html#a0a3b283bf930c2dfabf13192ef617fa6">IMP::ScoringFunction::do_add_score_and_derivatives_moved()</a>, <a href="classIMP_1_1ScoringFunction.html#ab58935a06c3a9c2a4c956987ce30cada">IMP::ScoringFunction::evaluate_moved()</a>, <a href="classIMP_1_1ScoringFunction.html#a00c293b023caf9802c2c2ed29c202d04">IMP::ScoringFunction::evaluate_moved_if_below()</a>, <a href="classIMP_1_1ScoringFunction.html#acbc17a5c000c36602ff1e76963a17a54">IMP::ScoringFunction::evaluate_moved_if_good()</a>, <a href="classIMP_1_1SingletonContainer.html#a881db3daef9944eb98dfa40eea54b028">IMP::SingletonContainer::apply_generic_moved()</a>, <a href="classIMP_1_1SingletonContainer.html#aaa76cfad0e04e47ac27c9ee508e3485a">IMP::SingletonContainer::apply_moved()</a>, <a href="classIMP_1_1SingletonContainer.html#a3835d8d6659e174cb57a24b8bec5709e">IMP::SingletonContainer::do_apply_moved()</a>, <a href="classIMP_1_1SingletonContainerAdaptor.html#a0a71a74b5dfe5e02ccb1468471330920">IMP::SingletonContainerAdaptor::SingletonContainerAdaptor()</a>, <a href="classIMP_1_1SingletonModifier.html#a80231ec89eb82fa05d6b525fa6ed849f">IMP::SingletonModifier::apply_indexes()</a>, <a href="classIMP_1_1SingletonModifier.html#a5a299e609e143eb15b9453681a85f8dc">IMP::SingletonModifier::apply_indexes_moved()</a>, <a href="classIMP_1_1SingletonPredicate.html#a875dca49aaa39bffb277075e186e57ff">IMP::SingletonPredicate::get_value_index()</a>, <a href="classIMP_1_1SingletonScore.html#a72fedd1e026640d8dff579c8138cb543">IMP::SingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1SingletonScore.html#a6b4756b83a12ad91eb5f6d5f943cde39">IMP::SingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1SingletonScore.html#a4212150dc45c60f04b7422491d0f919f">IMP::SingletonScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1SingletonScore.html#a2ddfa8309b6f3589864c028066777e59">IMP::SingletonScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1SparseSymmetricPairMemoizer.html#a61bd8ee88638273069c46592973f1af6">IMP::SparseSymmetricPairMemoizer::SparseSymmetricPairMemoizer()</a>, <a href="classIMP_1_1TripletContainer.html#a3ee0a2b797304469888071bf682a1f7d">IMP::TripletContainer::apply_generic_moved()</a>, <a href="classIMP_1_1TripletContainer.html#a47b9edc68b3e7f1b1f10153845659090">IMP::TripletContainer::apply_moved()</a>, <a href="classIMP_1_1TripletContainer.html#aff31674d754101e8934dc993861b1083">IMP::TripletContainer::do_apply_moved()</a>, <a href="classIMP_1_1TripletModifier.html#aaa5dd7e8b3bcadc69f59f9eaf6540bd8">IMP::TripletModifier::apply_indexes_moved()</a>, <a href="classIMP_1_1algebra_1_1BoundingBoxD.html#a612cedf52eea6d53f4ce2d5e219541b7">IMP::algebra::BoundingBoxD::BoundingBoxD()</a>, <a href="classIMP_1_1algebra_1_1NearestNeighborD.html#aa7bdb458b64d199dc003b10a6a25d951">IMP::algebra::NearestNeighborD::NearestNeighborD()</a>, <a href="classIMP_1_1algebra_1_1PrincipalComponentAnalysisD.html#a446bf7701bd38a6e6aa307aa4031e419">IMP::algebra::PrincipalComponentAnalysisD::PrincipalComponentAnalysisD()</a>, <a href="classIMP_1_1atom_1_1AngleSingletonScore.html#a50b498ed409a4299d4e7a42dbb6de0aa">IMP::atom::AngleSingletonScore::do_get_inputs()</a>, <a href="classIMP_1_1atom_1_1AngleSingletonScore.html#a9d94065013e52688cec46fb3628b687e">IMP::atom::AngleSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1atom_1_1AngleSingletonScore.html#aaf636347f30a3bdb57c1efe85169b3ee">IMP::atom::AngleSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1atom_1_1AngleSingletonScore.html#ac98a1656980e03142588407436356652">IMP::atom::AngleSingletonScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1atom_1_1AngleSingletonScore.html#a9318fd68f16bbab979e4de1e1a586a65">IMP::atom::AngleSingletonScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1atom_1_1BerendsenThermostatOptimizerState.html#a362cca5a6a7d02e9ed49cc0d91797a3c">IMP::atom::BerendsenThermostatOptimizerState::BerendsenThermostatOptimizerState()</a>, <a href="classIMP_1_1atom_1_1BerendsenThermostatOptimizerState.html#a255b5e7e2f091cdcd819cf73039c0ec7">IMP::atom::BerendsenThermostatOptimizerState::set_particles()</a>, <a href="classIMP_1_1atom_1_1BondEndpointsRefiner.html#a8fd096183681aa3e0b8ccce1798ac419">IMP::atom::BondEndpointsRefiner::do_get_inputs()</a>, <a href="classIMP_1_1atom_1_1BondPairContainer.html#acbd0f3193d77767c73c1f36095822f95">IMP::atom::BondPairContainer::do_apply_moved()</a>, <a href="classIMP_1_1atom_1_1BondSingletonScore.html#ad927da7b5ce1613b32941e73ef877296">IMP::atom::BondSingletonScore::do_get_inputs()</a>, <a href="classIMP_1_1atom_1_1BondSingletonScore.html#aea653b8e4729b29f3b8ae867b185828d">IMP::atom::BondSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1atom_1_1BondSingletonScore.html#ac1f36ade2f5513cffc07e4dc5d1a9ca8">IMP::atom::BondSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1atom_1_1BondSingletonScore.html#af4566ccae002e42f23090fbe8460c9e1">IMP::atom::BondSingletonScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1atom_1_1BondSingletonScore.html#a817fcac36508aa396cbd9faa3b965801">IMP::atom::BondSingletonScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1atom_1_1BondedPairFilter.html#ab4d33f448adb5b06ed1826aa3d62ef7d">IMP::atom::BondedPairFilter::do_get_inputs()</a>, <a href="classIMP_1_1atom_1_1BrownianDynamics.html#a48bb410933daba74bc10c097320ea7cb">IMP::atom::BrownianDynamics::do_advance_chunk()</a>, <a href="classIMP_1_1atom_1_1BrownianDynamics.html#af396db4decb30333a95da5d8e714ba36">IMP::atom::BrownianDynamics::do_step()</a>, <a href="classIMP_1_1atom_1_1BrownianDynamics.html#acf6fecd07636ebba7cb79284cdfdeced">IMP::atom::BrownianDynamics::setup()</a>, <a href="classIMP_1_1atom_1_1BrownianDynamicsTAMD.html#a034166252b16862634e364d2c82d3d2f">IMP::atom::BrownianDynamicsTAMD::do_advance_chunk()</a>, <a href="classIMP_1_1atom_1_1CHARMMConnection.html#a9625d8ee87f5a2d67148cf1c47a12e95">IMP::atom::CHARMMConnection::CHARMMConnection()</a>, <a href="classIMP_1_1atom_1_1CHARMMInternalCoordinate.html#a6dea63854f3357e4abf39965864726c8">IMP::atom::CHARMMInternalCoordinate::CHARMMInternalCoordinate()</a>, <a href="classIMP_1_1atom_1_1CHARMMParameters.html#a2b698cd7b5a6946cc7949cc0a832b166">IMP::atom::CHARMMParameters::add_angle()</a>, <a href="classIMP_1_1atom_1_1CHARMMParameters.html#adabf60c9c911d1b15505a18de1a5223f">IMP::atom::CHARMMParameters::add_dihedral()</a>, <a href="classIMP_1_1atom_1_1CHARMMParameters.html#a629d4fad7858d635635acc80d38c1474">IMP::atom::CHARMMParameters::parse_dihedrals_parameters_line()</a>, <a href="classIMP_1_1atom_1_1CHARMMParameters.html#a0605f8d59691de7afd2436348dfdc991">IMP::atom::CHARMMParameters::create_angles()</a>, <a href="classIMP_1_1atom_1_1CHARMMParameters.html#a7aafc32e901ac77cb2b68a944945f8cd">IMP::atom::CHARMMParameters::create_dihedrals()</a>, <a href="classIMP_1_1atom_1_1CHARMMStereochemistryRestraint.html#ae55a4983c41e935a811d933ba32a60c8">IMP::atom::CHARMMStereochemistryRestraint::CHARMMStereochemistryRestraint()</a>, <a href="classIMP_1_1atom_1_1CenterOfMass.html#a0195cdb1ec740e305a5be28f9668c427">IMP::atom::CenterOfMass::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1CoulombPairScore.html#ad6b7e53fafe298179fec9ff942bd8d08">IMP::atom::CoulombPairScore::do_get_inputs()</a>, <a href="classIMP_1_1atom_1_1CoverBond.html#abb800e91ae09f4486d7f0896487c7181">IMP::atom::CoverBond::apply_indexes()</a>, <a href="classIMP_1_1atom_1_1CoverBond.html#aaf5f81c253baab818a55460c3fb98d92">IMP::atom::CoverBond::do_get_inputs()</a>, <a href="classIMP_1_1atom_1_1CoverBond.html#a0c4a7d315e0d0df61d01a7b2a85fe6bf">IMP::atom::CoverBond::do_get_outputs()</a>, <a href="classIMP_1_1atom_1_1DihedralSingletonScore.html#adea15478f4c6db4876b24b6e9a27e701">IMP::atom::DihedralSingletonScore::do_get_inputs()</a>, <a href="classIMP_1_1atom_1_1DihedralSingletonScore.html#a7d32fc980bc2fbccfcd240859da6359d">IMP::atom::DihedralSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1atom_1_1DihedralSingletonScore.html#a7c1c629afb4c9df8f171c1ede35f191f">IMP::atom::DihedralSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1atom_1_1DihedralSingletonScore.html#a39c7b481300fd153289bafaccd0adf94">IMP::atom::DihedralSingletonScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1atom_1_1DihedralSingletonScore.html#a84378fd00630c2db7101b39be013b0b8">IMP::atom::DihedralSingletonScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1atom_1_1HelixRestraint.html#a17fb141c2258da3cfe1df1fcea58b58f">IMP::atom::HelixRestraint::HelixRestraint()</a>, <a href="classIMP_1_1atom_1_1Hierarchy.html#aea222a9dc8798d5ac1bcc492b73e72dd">IMP::atom::Hierarchy::create_fragment()</a>, <a href="classIMP_1_1atom_1_1Hierarchy.html#aa8687c81bbcdd0a54c247d9b6b4a2821">IMP::atom::Hierarchy::get_leaves()</a>, <a href="classIMP_1_1atom_1_1ImproperSingletonScore.html#adad1f87ff456b104e745109ebb35e2e6">IMP::atom::ImproperSingletonScore::do_get_inputs()</a>, <a href="classIMP_1_1atom_1_1ImproperSingletonScore.html#a9e4b75ae43efed67f5c0d429a740c94a">IMP::atom::ImproperSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1atom_1_1ImproperSingletonScore.html#a74979e31e169663871126971dbb22ca6">IMP::atom::ImproperSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1atom_1_1ImproperSingletonScore.html#ac6c9b73eaf52d6178cd49389a07ad40a">IMP::atom::ImproperSingletonScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1atom_1_1ImproperSingletonScore.html#a6cc8536e3b4408cc29153e3bf0de4cd1">IMP::atom::ImproperSingletonScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1atom_1_1LangevinThermostatOptimizerState.html#a9fe023e16134a6aac7f62de3210ba139">IMP::atom::LangevinThermostatOptimizerState::set_particles()</a>, <a href="classIMP_1_1atom_1_1LennardJonesPairScore.html#aa7104149d7f0349051b87171e17f675a">IMP::atom::LennardJonesPairScore::do_get_inputs()</a>, <a href="classIMP_1_1atom_1_1MolecularDynamics.html#a90e2329bfd4420247712ee83d0b4aa36">IMP::atom::MolecularDynamics::do_step()</a>, <a href="classIMP_1_1atom_1_1MolecularDynamics.html#a98ef7000ad208974eed21ad0dd671306">IMP::atom::MolecularDynamics::setup()</a>, <a href="classIMP_1_1atom_1_1MolecularDynamics.html#ab8ecae703fc70f75db37f1428e928f73">IMP::atom::MolecularDynamics::propagate_coordinates()</a>, <a href="classIMP_1_1atom_1_1MolecularDynamics.html#a754fe04e1c1dad0b675cf811f0ebdcbb">IMP::atom::MolecularDynamics::propagate_velocities()</a>, <a href="classIMP_1_1atom_1_1MolecularDynamics.html#aa11e2c9c8663da38dec9a91a8e673ac0">IMP::atom::MolecularDynamics::setup_degrees_of_freedom()</a>, <a href="classIMP_1_1atom_1_1RemoveRigidMotionOptimizerState.html#ab8a93cc8210611c95b2378ef9ff35e6f">IMP::atom::RemoveRigidMotionOptimizerState::set_particles()</a>, <a href="classIMP_1_1atom_1_1RemoveTranslationOptimizerState.html#adc7fc75835bdc0cd9bf1013a9f940280">IMP::atom::RemoveTranslationOptimizerState::set_particles()</a>, <a href="classIMP_1_1atom_1_1SameResiduePairFilter.html#af0f16d162e0c00c2a2681b17eb724ebe">IMP::atom::SameResiduePairFilter::do_get_inputs()</a>, <a href="classIMP_1_1atom_1_1Selection.html#af604ff145912972c35d5c5b1fbaf13a8">IMP::atom::Selection::set_hierarchies()</a>, <a href="classIMP_1_1atom_1_1Selection.html#a1aa9fab76bf21cfdab1e7b25751a094a">IMP::atom::Selection::Selection()</a>, <a href="classIMP_1_1atom_1_1Selection.html#a295b2ca7b091238de1de1351724c7a93">IMP::atom::Selection::Selection()</a>, <a href="classIMP_1_1atom_1_1Selection.html#aa382f78f97cb063e198413d0bc25bce9">IMP::atom::Selection::Selection()</a>, <a href="classIMP_1_1atom_1_1Selection.html#a7a8d2e710da2b8b3f23cd8ab6563d7c2">IMP::atom::Selection::Selection()</a>, <a href="classIMP_1_1atom_1_1Simulator.html#aedf7514f6090e50b0c2ef091fc991738">IMP::atom::Simulator::remove_particles()</a>, <a href="classIMP_1_1atom_1_1Simulator.html#a47972c0f296eb9a03ff98a61f1af7584">IMP::atom::Simulator::set_particles()</a>, <a href="classIMP_1_1atom_1_1Simulator.html#a120db92c9aec57b210c21e83e5e21771">IMP::atom::Simulator::set_particles_order()</a>, <a href="classIMP_1_1atom_1_1Simulator.html#afab6f05fc52a5219217ef8644eafa9b4">IMP::atom::Simulator::add_particles()</a>, <a href="classIMP_1_1atom_1_1Simulator.html#abcaab2f1616305dc3654245bcf67472a">IMP::atom::Simulator::do_step()</a>, <a href="classIMP_1_1atom_1_1Simulator.html#a2b6f2117677bbbe1bf114a8e50fe6f1b">IMP::atom::Simulator::setup()</a>, <a href="classIMP_1_1atom_1_1SoapPairFilter.html#ae757d610f7161567ef40e7d7ff92a8a7">IMP::atom::SoapPairFilter::do_get_inputs()</a>, <a href="classIMP_1_1atom_1_1StereochemistryPairFilter.html#aca06160174516c892c200e1c55725e84">IMP::atom::StereochemistryPairFilter::do_get_inputs()</a>, <a href="classIMP_1_1atom_1_1StereochemistryPairFilter.html#a005a8a55cd3870c714fd9ba05633cda0">IMP::atom::StereochemistryPairFilter::set_angles()</a>, <a href="classIMP_1_1atom_1_1StereochemistryPairFilter.html#a257236e289c76bd9efc7e12ad41a8850">IMP::atom::StereochemistryPairFilter::set_bonds()</a>, <a href="classIMP_1_1atom_1_1StereochemistryPairFilter.html#a9a21e9e76ffb6c18a1211f0e67e15ff0">IMP::atom::StereochemistryPairFilter::set_dihedrals()</a>, <a href="classIMP_1_1atom_1_1TAMDCentroid.html#ad3823563f3a3aa417f6e1a074a0d364e">IMP::atom::TAMDCentroid::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1VelocityScalingOptimizerState.html#a042d1b4e6716cd86bd519e06253d3857">IMP::atom::VelocityScalingOptimizerState::set_particles()</a>, <a href="classIMP_1_1atom_1_1WritePDBOptimizerState.html#af7ba603a6120146394b50f1077b50445">IMP::atom::WritePDBOptimizerState::WritePDBOptimizerState()</a>, <a href="classIMP_1_1bayesianem_1_1GaussianEMRestraint.html#a7fdad0e2f2f2e3d08cc98f0157f296dc">IMP::bayesianem::GaussianEMRestraint::GaussianEMRestraint()</a>, <a href="classIMP_1_1cnmultifit_1_1AlignSymmetric.html#af93bae09db2484418fa09368248b1a4a">IMP::cnmultifit::AlignSymmetric::get_symm_axis_alignments_from_model_to_density()</a>, <a href="classIMP_1_1cnmultifit_1_1AlignSymmetric.html#ab72d66d8b1e06812715b6949a5abcb1f">IMP::cnmultifit::AlignSymmetric::score_alignment()</a>, <a href="classIMP_1_1cnmultifit_1_1CnSymmAxisDetector.html#aee82a5869b8d5ee3201710eb9f92b632">IMP::cnmultifit::CnSymmAxisDetector::CnSymmAxisDetector()</a>, <a href="classIMP_1_1cnmultifit_1_1MolCnSymmAxisDetector.html#ad7ed1782f8ebbf7c4d3d15afd0fa4f24">IMP::cnmultifit::MolCnSymmAxisDetector::MolCnSymmAxisDetector()</a>, <a href="classIMP_1_1container_1_1AllBipartitePairContainer.html#a30dfb397ab67c6bcba25584b12bd06d2">IMP::container::AllBipartitePairContainer::do_apply_moved()</a>, <a href="classIMP_1_1container_1_1AllPairContainer.html#a00a9690723d71692283269cf8120dec9">IMP::container::AllPairContainer::do_apply_moved()</a>, <a href="classIMP_1_1container_1_1ConsecutivePairContainer.html#ad5ffcfc76685db8857c7a7031c904456">IMP::container::ConsecutivePairContainer::ConsecutivePairContainer()</a>, <a href="classIMP_1_1container_1_1ConsecutivePairContainer.html#a66ac10b97eb22da7cb99c35e0548d939">IMP::container::ConsecutivePairContainer::do_apply_moved()</a>, <a href="classIMP_1_1container_1_1ConsecutivePairFilter.html#a9bbb0f5ce0d54232d5ca5df48243532a">IMP::container::ConsecutivePairFilter::do_get_inputs()</a>, <a href="classIMP_1_1container_1_1DynamicListSingletonContainer.html#ac8845bc5f91c593e0bd9e489b1d5f22b">IMP::container::DynamicListSingletonContainer::add()</a>, <a href="classIMP_1_1container_1_1DynamicListSingletonContainer.html#aabbbd02197c4883608a9337caa5d45b9">IMP::container::DynamicListSingletonContainer::set()</a>, <a href="classIMP_1_1container_1_1ExclusiveConsecutivePairContainer.html#a0652689701ff99821061df450725ca21">IMP::container::ExclusiveConsecutivePairContainer::ExclusiveConsecutivePairContainer()</a>, <a href="classIMP_1_1container_1_1ExclusiveConsecutivePairContainer.html#a8712a0ebaffb01da001c0b5ddcb3ff3c">IMP::container::ExclusiveConsecutivePairContainer::do_apply_moved()</a>, <a href="classIMP_1_1container_1_1ExclusiveConsecutivePairFilter.html#acd39349b2221e9a20a6fef5bf8e58a08">IMP::container::ExclusiveConsecutivePairFilter::do_get_inputs()</a>, <a href="classIMP_1_1container_1_1InContainerPairFilter.html#ad3f78ba827d74f22367e6400cbbbdabd">IMP::container::InContainerPairFilter::do_get_inputs()</a>, <a href="classIMP_1_1container_1_1InContainerQuadFilter.html#a40819caf661628d891a72cf392d0f60f">IMP::container::InContainerQuadFilter::do_get_inputs()</a>, <a href="classIMP_1_1container_1_1InContainerSingletonFilter.html#a3eb9247a86ff0699b9b7fa2b39ff2bbb">IMP::container::InContainerSingletonFilter::do_get_inputs()</a>, <a href="classIMP_1_1container_1_1InContainerSingletonFilter.html#ac37386123fcd1c39ea258f660f63be2d">IMP::container::InContainerSingletonFilter::get_value()</a>, <a href="classIMP_1_1container_1_1InContainerSingletonFilter.html#ae34050c2277ef4456abaaa29844299b4">IMP::container::InContainerSingletonFilter::get_value_index()</a>, <a href="classIMP_1_1container_1_1InContainerTripletFilter.html#a0ccb161d156da4ad8ba32d70083fef54">IMP::container::InContainerTripletFilter::do_get_inputs()</a>, <a href="classIMP_1_1container_1_1ListSingletonContainer.html#a64d6eb9cde6ab16b39dd3049753f9442">IMP::container::ListSingletonContainer::ListSingletonContainer()</a>, <a href="classIMP_1_1container_1_1ListSingletonContainer.html#a62e07f863f02e2719084e724ee41e501">IMP::container::ListSingletonContainer::add()</a>, <a href="classIMP_1_1container_1_1ListSingletonContainer.html#a0d1c58a0cf8fcedab37c9b7796c5a338">IMP::container::ListSingletonContainer::set()</a>, <a href="classIMP_1_1container_1_1MinimumPairScore.html#a46d8cc09b2266267a7d030428a5324ad">IMP::container::MinimumPairScore::do_get_inputs()</a>, <a href="classIMP_1_1container_1_1MinimumQuadScore.html#a5c6633130fdaa79bd516446add760391">IMP::container::MinimumQuadScore::do_get_inputs()</a>, <a href="classIMP_1_1container_1_1MinimumSingletonScore.html#ac0c837d7136029968896483c77e3b5b7">IMP::container::MinimumSingletonScore::do_get_inputs()</a>, <a href="classIMP_1_1container_1_1MinimumSingletonScore.html#a5dcbfcdc0bee19b0c9c85211a482376e">IMP::container::MinimumSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1container_1_1MinimumSingletonScore.html#aba3c37a22496d69bdc8694ed3e64f85c">IMP::container::MinimumSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1container_1_1MinimumSingletonScore.html#ab592ddf3161a42aa7adbfb946f1e58ad">IMP::container::MinimumSingletonScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1container_1_1MinimumSingletonScore.html#aaaf11fddf57436514eba2b8260ac237b">IMP::container::MinimumSingletonScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1container_1_1MinimumTripletScore.html#a33208999f177468e3be4094a7995f70e">IMP::container::MinimumTripletScore::do_get_inputs()</a>, <a href="classIMP_1_1container_1_1PairContainerSet.html#a5be8075a45665d990ecf9c4011156733">IMP::container::PairContainerSet::apply_generic_moved()</a>, <a href="classIMP_1_1container_1_1QuadContainerSet.html#a747d755bc45fc2c71bf881bced8f22c9">IMP::container::QuadContainerSet::apply_generic_moved()</a>, <a href="classIMP_1_1container_1_1SingletonContainerSet.html#a1a63f20f9db5eb002854935729abe2ec">IMP::container::SingletonContainerSet::apply_generic_moved()</a>, <a href="classIMP_1_1container_1_1SingletonContainerSet.html#a32e37b38a68cf34eb32f810219e0f1cb">IMP::container::SingletonContainerSet::get_indexes_in_place()</a>, <a href="classIMP_1_1container_1_1TripletContainerSet.html#af311a7e776f3e50679768408d20616f2">IMP::container::TripletContainerSet::apply_generic_moved()</a>, <a href="classIMP_1_1core_1_1AllSamePairPredicate.html#ac27b36dd0d19876ea239aefd4ec9d211">IMP::core::AllSamePairPredicate::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1AllSameQuadPredicate.html#a0aeaeb39a45847019158b9d7e3360e1c">IMP::core::AllSameQuadPredicate::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1AllSameSingletonPredicate.html#acf4a334a140de46ba03cdc5802580875">IMP::core::AllSameSingletonPredicate::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1AllSameSingletonPredicate.html#a74804e4fce336a0819b39f7d0eb13147">IMP::core::AllSameSingletonPredicate::get_value()</a>, <a href="classIMP_1_1core_1_1AllSameSingletonPredicate.html#a43bf518b51791164d2645931b239f49e">IMP::core::AllSameSingletonPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1AllSameTripletPredicate.html#afc3ec596e94eea2c0e3abb7207414b88">IMP::core::AllSameTripletPredicate::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1AngleTripletScore.html#a2fb9d5e4b89124538c9f25f53573fec0">IMP::core::AngleTripletScore::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1AttributeSingletonPredicate.html#a4ea0aadb8324369572773f971d7f4863">IMP::core::AttributeSingletonPredicate::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1AttributeSingletonPredicate.html#a6e20b5dfb6c281aaffaa1f10030c92c4">IMP::core::AttributeSingletonPredicate::get_value()</a>, <a href="classIMP_1_1core_1_1AttributeSingletonPredicate.html#a11613a23b19cf401d03b442e37e62d79">IMP::core::AttributeSingletonPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1BallMover.html#a866136a164fb590516235d7c6001422f">IMP::core::BallMover::initialize()</a>, <a href="classIMP_1_1core_1_1BallMover.html#a5fe39f69bfb134ac69897ce58d82d9e1">IMP::core::BallMover::BallMover()</a>, <a href="classIMP_1_1core_1_1BallMover.html#a69d2b6affbca13893654613949fa91a1">IMP::core::BallMover::BallMover()</a>, <a href="classIMP_1_1core_1_1BoxSweepClosePairsFinder.html#aefcca8f30501a0a9227fa10a9647fb41">IMP::core::BoxSweepClosePairsFinder::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1BoxSweepClosePairsFinder.html#a6f8e9ba6c3c195db0afc3082b4f6ab34">IMP::core::BoxSweepClosePairsFinder::get_close_pairs()</a>, <a href="classIMP_1_1core_1_1BoxSweepClosePairsFinder.html#ab282be2e2dc0e89db5a09c319621f0e7">IMP::core::BoxSweepClosePairsFinder::get_close_pairs()</a>, <a href="classIMP_1_1core_1_1Centroid.html#a831ca6ca18d28ec5cfb0a2c73b46cdfe">IMP::core::Centroid::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1CentroidOfRefined.html#a81f9b2be2f1ecabc502e3e6daa6b8b14">IMP::core::CentroidOfRefined::apply_indexes()</a>, <a href="classIMP_1_1core_1_1CentroidOfRefined.html#a98f230b962e9bdc78ff0cd8a88262669">IMP::core::CentroidOfRefined::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1CentroidOfRefined.html#ad04634358bd6e25a30c7ac73e6b1ca9d">IMP::core::CentroidOfRefined::do_get_outputs()</a>, <a href="classIMP_1_1core_1_1ChildrenRefiner.html#afe91028902021ac8df4b80ad2fa54d07">IMP::core::ChildrenRefiner::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1ClosePairsFinder.html#a496d0a48861b5eda84f2860df60eafb6">IMP::core::ClosePairsFinder::get_close_pairs()</a>, <a href="classIMP_1_1core_1_1ClosePairsFinder.html#a4d6d67a76a843aa3d03276ffc1e8a909">IMP::core::ClosePairsFinder::get_close_pairs()</a>, <a href="classIMP_1_1core_1_1ClosePairsPairScore.html#a9ffa318803895c0eddeed26a1d90a136">IMP::core::ClosePairsPairScore::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1CoinFlipPairPredicate.html#a214ad5d5f2ee406fcd7faeb96f1e37e5">IMP::core::CoinFlipPairPredicate::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1CoinFlipQuadPredicate.html#ac8e2ef5399a70a272afcefececa0dd25">IMP::core::CoinFlipQuadPredicate::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1CoinFlipSingletonPredicate.html#a0c1e6586bc5001ecd3825f22a7bc0f15">IMP::core::CoinFlipSingletonPredicate::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1CoinFlipSingletonPredicate.html#a0fba9cc42ca7ad1853fb34690267c6b2">IMP::core::CoinFlipSingletonPredicate::get_value()</a>, <a href="classIMP_1_1core_1_1CoinFlipSingletonPredicate.html#a6a035570b259887ae76e82589e78eb5c">IMP::core::CoinFlipSingletonPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1CoinFlipTripletPredicate.html#a32e08547a110cc9f272511c24f9d7e74">IMP::core::CoinFlipTripletPredicate::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1ConjugateGradients.html#a29627a663e934b8c6d67850771ae7e21">IMP::core::ConjugateGradients::get_score()</a>, <a href="classIMP_1_1core_1_1ConjugateGradients.html#a7b66cc06c4eed4394398188e839c2387">IMP::core::ConjugateGradients::line_search()</a>, <a href="classIMP_1_1core_1_1ConstantPairPredicate.html#a1fd8ed83b3dc362c40cda6565b84ce85">IMP::core::ConstantPairPredicate::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1ConstantQuadPredicate.html#aa7bfc5fc5b37fc54b8b64de1add071d5">IMP::core::ConstantQuadPredicate::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1ConstantSingletonPredicate.html#acca07750d9840f52e22b49547f6d4418">IMP::core::ConstantSingletonPredicate::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1ConstantSingletonPredicate.html#ad67894d82f52fd060c840e65c44c4409">IMP::core::ConstantSingletonPredicate::get_value()</a>, <a href="classIMP_1_1core_1_1ConstantSingletonPredicate.html#a06f8c07a0ff02a80e264c44f9143c264">IMP::core::ConstantSingletonPredicate::get_value_index()</a>, <a href="classIMP_1_1core_1_1ConstantTripletPredicate.html#a39b8e9fd479ae7f80935f7ab8f7e14ca">IMP::core::ConstantTripletPredicate::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1Cover.html#ac2d49f1fd16f20fd1225483fe19e6e53">IMP::core::Cover::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1CoverRefined.html#afe0c430053195537421b9f5f3be433db">IMP::core::CoverRefined::apply_indexes()</a>, <a href="classIMP_1_1core_1_1CoverRefined.html#ac8093b20bf4415549a275b15b0504ef0">IMP::core::CoverRefined::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1CoverRefined.html#ae2ceba8c4a8d4f342c55bf4e63ff1f2d">IMP::core::CoverRefined::do_get_outputs()</a>, <a href="classIMP_1_1core_1_1DerivativesFromRefined.html#ae0507498d1d954720230b21103987cb0">IMP::core::DerivativesFromRefined::apply_indexes()</a>, <a href="classIMP_1_1core_1_1DerivativesFromRefined.html#a10636b33468e5c72e21ce7567781e288">IMP::core::DerivativesFromRefined::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1DerivativesFromRefined.html#a824136ecb4b046ac246ce79149e72bd2">IMP::core::DerivativesFromRefined::do_get_outputs()</a>, <a href="classIMP_1_1core_1_1DerivativesToRefined.html#ac913d70f2591ee438ac8e4926d4db32c">IMP::core::DerivativesToRefined::apply_indexes()</a>, <a href="classIMP_1_1core_1_1DerivativesToRefined.html#a9dbf014826795d90d055982bf1e07c51">IMP::core::DerivativesToRefined::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1DerivativesToRefined.html#ae56c30905324ad0e97b9770b03704448">IMP::core::DerivativesToRefined::do_get_outputs()</a>, <a href="classIMP_1_1core_1_1DistancePairScore.html#a71740d22e71f6d713b37c5690f83b9a6">IMP::core::DistancePairScore::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1FixedRefiner.html#a3bb442e598984ba0e8560ce196706dd1">IMP::core::FixedRefiner::FixedRefiner()</a>, <a href="classIMP_1_1core_1_1FixedRefiner.html#a71409c5169fd02437048f3a65057b912">IMP::core::FixedRefiner::FixedRefiner()</a>, <a href="classIMP_1_1core_1_1FixedRefiner.html#a05bf207d25fd1e0646bf7bd9f608180f">IMP::core::FixedRefiner::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1GenericAttributeSingletonScore.html#a0a6f908b5d70da7b5b49923e82d5e8f4">IMP::core::GenericAttributeSingletonScore::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1GenericAttributeSingletonScore.html#ac08553a44f5431458ef1726cbf5fa412">IMP::core::GenericAttributeSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1core_1_1GenericAttributeSingletonScore.html#a1110467dc8c2d176d244a4fe7740afe5">IMP::core::GenericAttributeSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1core_1_1GenericAttributeSingletonScore.html#a7b88a951501e6ac69f59247148fc6721">IMP::core::GenericAttributeSingletonScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1core_1_1GenericAttributeSingletonScore.html#a33c00df5d2c0813886a637d5de0ed529">IMP::core::GenericAttributeSingletonScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1core_1_1GenericBoundingBox3DSingletonScore.html#ad29972b4e5dca87ab4ab0718baaf8a62">IMP::core::GenericBoundingBox3DSingletonScore::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1GenericBoundingBox3DSingletonScore.html#a04625a228cade49bf22f3bb30475f4b8">IMP::core::GenericBoundingBox3DSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1core_1_1GenericBoundingBox3DSingletonScore.html#a0393df9fd8e034fcfe47e3e7bb7ec113">IMP::core::GenericBoundingBox3DSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1core_1_1GenericBoundingBox3DSingletonScore.html#a690cd1988db7fbf97811be8722822054">IMP::core::GenericBoundingBox3DSingletonScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1core_1_1GenericBoundingBox3DSingletonScore.html#a08383123609392bff2dd3cc6869631d4">IMP::core::GenericBoundingBox3DSingletonScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1core_1_1GenericBoundingSphere3DSingletonScore.html#a08314347092d3377bbbf21fc73badfeb">IMP::core::GenericBoundingSphere3DSingletonScore::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1GenericBoundingSphere3DSingletonScore.html#ab712e8cbd70c00f776eacf8ef02fc37e">IMP::core::GenericBoundingSphere3DSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1core_1_1GenericBoundingSphere3DSingletonScore.html#a49ec02d56efc9f7e949680934aadf0a5">IMP::core::GenericBoundingSphere3DSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1core_1_1GenericBoundingSphere3DSingletonScore.html#a1754cfe7b3d7f3ce30ea5c9c7cbeaaa7">IMP::core::GenericBoundingSphere3DSingletonScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1core_1_1GenericBoundingSphere3DSingletonScore.html#af209e14f62168fe09fef7e3e4ec2ff5a">IMP::core::GenericBoundingSphere3DSingletonScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1core_1_1GenericDistanceToSingletonScore.html#abe951740eed5618b81c10acb148d7d90">IMP::core::GenericDistanceToSingletonScore::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1GenericDistanceToSingletonScore.html#a1f787d0844c9a36fae2da0215afab271">IMP::core::GenericDistanceToSingletonScore::evaluate_if_good_indexes()</a>, <a href="classIMP_1_1core_1_1GenericDistanceToSingletonScore.html#a1db4302e9f5afde1e643da0b6863fac7">IMP::core::GenericDistanceToSingletonScore::evaluate_indexes()</a>, <a href="classIMP_1_1core_1_1GenericDistanceToSingletonScore.html#ac812e2e81f059642613603217b99d42a">IMP::core::GenericDistanceToSingletonScore::evaluate_indexes_delta()</a>, <a href="classIMP_1_1core_1_1GenericDistanceToSingletonScore.html#a0063febf20d887a0f353146daed7e14a">IMP::core::GenericDistanceToSingletonScore::evaluate_indexes_scores()</a>, <a href="classIMP_1_1core_1_1GridClosePairsFinder.html#a225d46ec6e2d652085bf7482534e876a">IMP::core::GridClosePairsFinder::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1GridClosePairsFinder.html#adb27193de7ef63f08562aca372fe9ebf">IMP::core::GridClosePairsFinder::get_close_pairs()</a>, <a href="classIMP_1_1core_1_1GridClosePairsFinder.html#a562c0d5780f2d63841aab1d8bd3044f6">IMP::core::GridClosePairsFinder::get_close_pairs()</a>, <a 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href="classIMP_1_1core_1_1TableRefiner.html#a03a464dc0f8a50aaf2571b1a190619c7">IMP::core::TableRefiner::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1TableRefiner.html#a1b5c10798a6f72040ebf6b9e70b0bfd7">IMP::core::TableRefiner::set_particle()</a>, <a href="classIMP_1_1core_1_1Transform.html#a9fb0c18ddace5e1860339ed56c0e89b0">IMP::core::Transform::apply_indexes()</a>, <a href="classIMP_1_1core_1_1Transform.html#abc15040c376fac0584ef1b672cb90202">IMP::core::Transform::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1Transform.html#a077c38f8515aa5f29afcfced5e9c7813">IMP::core::Transform::do_get_outputs()</a>, <a href="classIMP_1_1core_1_1TransformationAndReflectionSymmetry.html#a5cb7a7e6c98f4d3125720c4b534c7c0d">IMP::core::TransformationAndReflectionSymmetry::apply_indexes()</a>, <a href="classIMP_1_1core_1_1TransformationAndReflectionSymmetry.html#a7f2dd4f0f0c96736a3b688d4cd0bafbc">IMP::core::TransformationAndReflectionSymmetry::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1TransformationAndReflectionSymmetry.html#ace515e2c0a7939303f48bc35e9f8a673">IMP::core::TransformationAndReflectionSymmetry::do_get_outputs()</a>, <a href="classIMP_1_1core_1_1TransformationSymmetry.html#ab4507bf24c5a36b8bd7a0aed2b787a40">IMP::core::TransformationSymmetry::apply_indexes()</a>, <a href="classIMP_1_1core_1_1TransformationSymmetry.html#aaaf113636089a1fc82dbd8ab17fe241d">IMP::core::TransformationSymmetry::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1TransformationSymmetry.html#aef54d4aac2ea82c8afa4e7d9749507e4">IMP::core::TransformationSymmetry::do_get_outputs()</a>, <a href="classIMP_1_1core_1_1TransformedDistancePairScore.html#aac45b19a8752f8b2c77b07c8254eb4be">IMP::core::TransformedDistancePairScore::do_get_inputs()</a>, <a href="classIMP_1_1core_1_1TypedPairScore.html#a716161cd98212d11c5c3e059525f91f8">IMP::core::TypedPairScore::do_get_inputs()</a>, <a 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href="classIMP_1_1spb_1_1TransformationSymmetry.html#ad3220adc7af95bfcb96960a1ed7f802b">IMP::spb::TransformationSymmetry::apply_indexes()</a>, <a href="classIMP_1_1spb_1_1TransformationSymmetry.html#abcf369e819f6086116904fd75b4a0000">IMP::spb::TransformationSymmetry::do_get_inputs()</a>, <a href="classIMP_1_1spb_1_1TransformationSymmetry.html#a793d87375210d7b312238f6926783f4c">IMP::spb::TransformationSymmetry::do_get_outputs()</a>, <a href="classIMP_1_1spb_1_1TwoStateGoModelRestraint.html#a777d991ba45adb75ca10e02de5000f6a">IMP::spb::TwoStateGoModelRestraint::set_parameters()</a>, <a href="classIMP_1_1spb_1_1TwoStateGoModelRestraint.html#a86411f5aaf5aabbd595385cc1cc079f0">IMP::spb::TwoStateGoModelRestraint::TwoStateGoModelRestraint()</a>, <a href="classIMP_1_1statistics_1_1ParticleEmbedding.html#a33b5c1fa395bd49c9ae4d2b6b429190c">IMP::statistics::ParticleEmbedding::ParticleEmbedding()</a>, <a href="classIMP_1_1symmetry_1_1BallMover.html#aa31ed479ef4b404d06981ac681f99667">IMP::symmetry::BallMover::BallMover()</a>, <a href="classIMP_1_1symmetry_1_1RigidBodyMover.html#ad9dca2981893121c227c5bc4f46b74fe">IMP::symmetry::RigidBodyMover::RigidBodyMover()</a>, <a href="classIMP_1_1symmetry_1_1RigidBodyMover.html#a46b76b01c2cd25d8b05ad691ca14bbbc">IMP::symmetry::RigidBodyMover::get_particles()</a>, <a href="classIMP_1_1symmetry_1_1RigidBodyMover.html#ac2903b33221154299bb495fe40cf441b">IMP::symmetry::RigidBodyMover::get_rigid_bodies()</a>, <a href="namespaceIMP.html#ac49fedd9ea52d5339c003cc00c1b906e">IMP::write_particles_to_buffer()</a>, <a href="namespaceIMP.html#a45908f291844b3e8a7749269e9199b74">IMP::read_particles_from_buffer()</a>, <a href="namespaceIMP.html#aabc6b814ba85ea74a1b3f9f0ce8c06cf">IMP::get_indexes()</a>, <a href="namespaceIMP.html#a282964e47bdd3107ef2e3ef72df66001">IMP::get_particles()</a>, <a href="namespaceIMP.html#ab756ae75c8588c7ba606e4ec2bc4ab57">IMP::get_random_numbers_normal()</a>, <a href="namespaceIMP.html#a8db8fe945488db02b181b74a5a5ec378">IMP::get_random_numbers_uniform()</a>, <a href="namespaceIMP_1_1algebra.html#a45f138d8d70f63b404c8ffc9e9b2896e">IMP::algebra::get_principal_components()</a>, <a href="namespaceIMP_1_1atom.html#a27cddb5d82fc586eee446fa630c58fc2">IMP::atom::write_multimodel_pdb()</a>, <a href="namespaceIMP_1_1atom.html#a1b00eeb0093e23eb053c3686e71dbee3">IMP::atom::read_psipred()</a>, <a href="namespaceIMP_1_1atom.html#a64f18ad8ce0534736253b21f84c7c308">IMP::atom::create_excluded_volume_restraint()</a>, <a href="namespaceIMP_1_1atom.html#a1b72819ad85249bfe290fe31b4084e9e">IMP::atom::create_rigid_body()</a>, <a href="namespaceIMP_1_1atom.html#acf2a8c9e18db10d978cbdb97c654eaf4">IMP::atom::get_component_placement_score()</a>, <a href="namespaceIMP_1_1atom.html#ac1ac30470fc07d7436876b1e1f7accab">IMP::atom::get_pairwise_rmsd_score()</a>, <a href="namespaceIMP_1_1atom.html#ad664639ebfb7a53a52704685bbe1a803">IMP::atom::get_placement_score()</a>, <a href="namespaceIMP_1_1atom.html#a4dca993f5bd4a70bb5c5cbd09176819f">IMP::atom::get_radius_of_gyration()</a>, <a href="namespaceIMP_1_1atom.html#aa8c6ee981db76d88d7661bb4dd6fb63b">IMP::atom::get_rmsd()</a>, <a href="namespaceIMP_1_1atom.html#a6548fc0fb1b2329ba9bb38511610953c">IMP::atom::get_rmsd_transforming_first()</a>, <a href="namespaceIMP_1_1atom.html#a6eb0ed1c738a5d6b223b3628b09533f6">IMP::atom::setup_as_approximation()</a>, <a href="namespaceIMP_1_1atom.html#a26d5bf29f960fc1cc1816a3d9fae4da5">IMP::atom::setup_coarse_secondary_structure_residue()</a>, <a href="namespaceIMP_1_1atom.html#a886a95c9c35244e6120f8484f501bdb9">IMP::atom::setup_coarse_secondary_structure_residues()</a>, <a href="namespaceIMP_1_1bayesianem.html#a0b6f78cede979bad023144902501dc73">IMP::bayesianem::gem_score_cc()</a>, <a href="namespaceIMP_1_1bayesianem.html#a1716313a64108d274e678e8114ed0f7a">IMP::bayesianem::get_percentage_closer_than()</a>, <a href="namespaceIMP_1_1bayesianem.html#a682f5694efb808a931e527bff3fa3911">IMP::bayesianem::get_rmsd_excluding_higher_than()</a>, <a href="namespaceIMP_1_1bayesianem.html#a5bd594b8cc8998209495d30a4fdedb35">IMP::bayesianem::get_rmsd_of_best_population()</a>, <a href="namespaceIMP_1_1bayesianem.html#a881f7a5b123adbd240145f76a35cf4c9">IMP::bayesianem::NormalizePCA()</a>, <a href="namespaceIMP_1_1cnmultifit.html#a957e7710eb8a161975d25f3549824df8">IMP::cnmultifit::cn_symm_score()</a>, <a href="namespaceIMP_1_1cnmultifit.html#a6067aedfd378547038d133f84bb820e3">IMP::cnmultifit::fit_cn_assembly()</a>, <a href="namespaceIMP_1_1cnmultifit.html#a4438e6a4266c8a34503f504f861e890a">IMP::cnmultifit::generate_cn_transformations()</a>, <a href="namespaceIMP_1_1cnmultifit.html#ae902a3b7629959005fa3c503903dc95d">IMP::cnmultifit::generate_translations_along_symm_axis()</a>, <a href="namespaceIMP_1_1cnmultifit.html#a6955cc359b815de543af54b62dcaf87d">IMP::cnmultifit::get_cn_rmsd()</a>, <a href="namespaceIMP_1_1cnmultifit.html#a326d661ede67dfeb87070ee6447ad678">IMP::cnmultifit::symmetry_local_fitting()</a>, <a href="namespaceIMP_1_1cnmultifit.html#a4a6654fa258c0a93903370ff327d4199">IMP::cnmultifit::transform_cn_assembly()</a>, <a href="namespaceIMP_1_1container.html#ac8965a95934fc142a9797c44fdc03d88">IMP::container::get_slack_estimate()</a>, <a href="namespaceIMP_1_1container.html#a10c42d60066d5eeb4b9cd5fa4a6d72d9">IMP::container::get_slack_estimate()</a>, <a href="namespaceIMP_1_1core.html#ae0adf8c625b9410b8fbcf490f7d46d9e">IMP::core::assign_blame()</a>, <a href="namespaceIMP_1_1core.html#aec2608fca14a0c657e461ed34b9f7317">IMP::core::create_blame_geometries()</a>, <a href="namespaceIMP_1_1core.html#a0ba3b6f5fba01f4ecf8a3b8f18a311f2">IMP::core::get_bounding_box()</a>, <a href="namespaceIMP_1_1core.html#a46250a46a10465f03487ad0670586394">IMP::core::get_centroid()</a>, <a href="namespaceIMP_1_1core.html#ac28cbff46cedec4186ab8e63a3c3b41b">IMP::core::get_enclosing_sphere()</a>, <a href="namespaceIMP_1_1core.html#a345d1856d74f6a0768a145c96920e04d">IMP::core::get_initial_reference_frame()</a>, <a href="namespaceIMP_1_1core.html#ae8f9b0b21c300bd80d9c3507fa5a24c0">IMP::core::get_initial_reference_frame()</a>, <a href="namespaceIMP_1_1core.html#a25735ab61a19f9813d051462afd24b2f">IMP::core::set_enclosing_radius()</a>, <a href="namespaceIMP_1_1core.html#a9f00e88e92a88b5ef349978fe737df7d">IMP::core::set_enclosing_sphere()</a>, <a href="namespaceIMP_1_1domino.html#a32c0b82e732879cbf0d77bbea28541bb">IMP::domino::get_interaction_graph()</a>, <a href="namespaceIMP_1_1domino.html#a541325fed96c13d825cbd4aa9dd7c5eb">IMP::domino::write_merge_tree()</a>, <a href="namespaceIMP_1_1domino.html#aca9cd1b21d36f9766400b55396ae3239">IMP::domino::read_merge_tree()</a>, <a href="namespaceIMP_1_1domino.html#ab5fc791399c0d6c76e1bea5d4b3da6ca">IMP::domino::get_index()</a>, <a href="namespaceIMP_1_1domino.html#a4c8c50c718ab2dcabacc4b2e41aba522">IMP::domino::get_partial_index()</a>, <a href="namespaceIMP_1_1domino.html#aa29c2ec35739c08db3a13ffe4ec38088">IMP::domino::get_possible_interactions()</a>, <a href="namespaceIMP_1_1em.html#a7e08fd743778d6b18b8e759bea705454">IMP::em::bayesem3d_get_density_from_particle()</a>, <a href="namespaceIMP_1_1em.html#ae027b772ce1eeb542809f08605b47679">IMP::em::bayesem3d_get_normalized_intensities()</a>, <a href="namespaceIMP_1_1em.html#a247c0133e66b108ee7d36e98cea961c9">IMP::em::bayesem3d_get_score_and_derivative()</a>, <a href="namespaceIMP_1_1em.html#a3f5170ae051deffd9fd3b3c6064f403b">IMP::em::compute_fitting_score()</a>, <a href="namespaceIMP_1_1em.html#a4350b15571abb634d2285ce9114a5725">IMP::em::compute_fitting_scores()</a>, <a href="namespaceIMP_1_1em.html#a5a49f58c2b493fe460df2a1f42aed80d">IMP::em::get_number_of_particles_outside_of_the_density()</a>, <a href="namespaceIMP_1_1em.html#a55a883a182ff619b805f5bbcb5297c2e">IMP::em::get_numbers_of_particles_outside_of_the_density()</a>, <a href="namespaceIMP_1_1em.html#a6ac62bc20e89bf2c6e8f8f6bb5cbca5a">IMP::em::get_percentage_of_voxels_covered_by_particles()</a>, <a href="namespaceIMP_1_1em.html#a2092ec68df3aaeeef8daee59353d0327">IMP::em::local_rigid_fitting_grid_search()</a>, <a href="namespaceIMP_1_1em.html#a12121a1c9d4ec3f58b959b1b8c136ecb">IMP::em::particles2binarized_density()</a>, <a href="namespaceIMP_1_1em.html#af47d3d5898cb50aecaf7b8cf5a40d167">IMP::em::particles2density()</a>, <a href="namespaceIMP_1_1em.html#a4c18a8d1e939db80e5767b8b3e9c040f">IMP::em::particles2surface()</a>, <a href="namespaceIMP_1_1em2d.html#ac7fc9ca9b6ac50bc5de57a157882766f">IMP::em2d::create_evenly_distributed_projections()</a>, <a href="namespaceIMP_1_1em2d.html#ab15ba9866050315bb0248dd27f0ef0bb">IMP::em2d::do_project_particles()</a>, <a href="namespaceIMP_1_1em2d.html#ae2eeaa84aab84eb5254470522964d4de">IMP::em2d::get_enclosing_image_size()</a>, <a href="namespaceIMP_1_1em2d.html#a060e62f5acd6d4c6dc09f1f2c7b1528b">IMP::em2d::get_projection()</a>, <a href="namespaceIMP_1_1em2d.html#a65e066ed72e099282a5714fbd2333989">IMP::em2d::get_projections()</a>, <a href="namespaceIMP_1_1em2d.html#aa167999977d5c4f4e0486534693a86da">IMP::em2d::get_projections()</a>, <a href="namespaceIMP_1_1example.html#a9aa2ea9cadf531860b3041ded1973637">IMP::example::create_chain_restraint()</a>, <a href="namespaceIMP_1_1example.html#a3664740d13bae6e46e99912a842c5160">IMP::example::create_excluded_volume()</a>, <a href="namespaceIMP_1_1example.html#af40da724913bdb102f043359fdf966f5">IMP::example::create_serial_mover()</a>, <a href="namespaceIMP_1_1example.html#af8c9f5150402309a3284c9fb93e55efa">IMP::example::get_number_of_incidences()</a>, <a href="namespaceIMP_1_1example.html#aa485f4a9129b84b2b1296b4e150edb51">IMP::example::optimize_assembly()</a>, <a href="namespaceIMP_1_1example.html#ae4f0f8060682cb190fcc18eb72322b62">IMP::example::optimize_balls()</a>, <a href="namespaceIMP_1_1kinematics.html#a849442176d35434ec22fc45351b429f4">IMP::kinematics::add_missing_bonds()</a>, <a href="namespaceIMP_1_1kinematics.html#a1917c6e073639123db3b09d24d8b6dc6">IMP::kinematics::create_bond()</a>, <a href="namespaceIMP_1_1kinematics.html#a1d074d177f3e9b19fef1233c4c928f77">IMP::kinematics::find_atom()</a>, <a href="namespaceIMP_1_1kinematics.html#aecb446da0c7ec323296acebe02e5c644">IMP::kinematics::find_residue()</a>, <a href="namespaceIMP_1_1kinematics.html#a43aefa0b49fa5b99d235cbcf1170d685">IMP::kinematics::get_ca_atom()</a>, <a href="namespaceIMP_1_1kinematics.html#ac4ae6c45f2d494aaa704ded2a20170ef">IMP::kinematics::read_angle_file()</a>, <a href="namespaceIMP_1_1kinematics.html#aa5b40e0b8704ecf11f90c12b0af8cbe8">IMP::kinematics::read_connect_chains_file()</a>, <a href="namespaceIMP_1_1multifit.html#a0ba5b604076ef3a7ee623203283c3ab6">IMP::multifit::get_actual_radius_of_gyration()</a>, <a href="namespaceIMP_1_1multifit.html#a173eff7add1e1652a69ce9c1365ddf2f">IMP::multifit::get_anchor_indices_matching_secondary_structure()</a>, <a href="namespaceIMP_1_1multifit.html#afdf294ea4f4b41a0fa4da41f6c95e32c">IMP::multifit::pca_based_rigid_fitting()</a>, <a href="namespaceIMP_1_1multifit.html#ad3f92bb765e32aee3d6f1c0d15366d5a">IMP::multifit::write_connolly_surface()</a>, <a href="namespaceIMP_1_1npctransport.html#a57e19bdcf2152f8ac61b92eea2f3b577">IMP::npctransport::add_hierarchies_with_sites()</a>, <a href="namespaceIMP_1_1npctransport.html#a219f900a3b5e5ad3289d2d09356df1eb">IMP::npctransport::add_hierarchies_with_sites()</a>, <a href="namespaceIMP_1_1npctransport.html#a5c9e777a69706ccc7d158f6dcfe50950">IMP::npctransport::get_non_optimizable_particles()</a>, <a href="namespaceIMP_1_1npctransport.html#aa2114c9f9168cf02dccc106844de85ec">IMP::npctransport::get_optimizable_particles()</a>, <a href="namespaceIMP_1_1npctransport.html#aca539801adb3226e34f7e8c7598dd0b8">IMP::npctransport::get_particle_indexes()</a>, <a href="namespaceIMP_1_1npctransport.html#adb310505fe5a5592a8dc7c13922e4f79">IMP::npctransport::link_hierarchies_with_sites()</a>, <a href="namespaceIMP_1_1npctransport.html#a03670f5844c2eaf98f64d0aed46f6255">IMP::npctransport::write_geometry()</a>, <a href="namespaceIMP_1_1pmi.html#a136fbe0c4b8cf1f652b8786ae448bc24">IMP::pmi::create_elastic_network()</a>, <a href="namespaceIMP_1_1pmi.html#a02135ed357a72ea565d8546ac8e93dda">IMP::pmi::get_bipartite_minimum_sphere_distance()</a>, <a href="namespaceIMP_1_1pmi.html#aae907accf543c88fa551e5772304e3e8">IMP::pmi::get_list_of_bipartite_minimum_sphere_distance()</a>, <a href="namespaceIMP_1_1pmi1.html#a2995df7ccbc9bebba29bf2f879e92fc7">IMP::pmi1::create_elastic_network()</a>, <a href="namespaceIMP_1_1pmi1.html#a0133266ed81510145b9715105103cd8a">IMP::pmi1::get_bipartite_minimum_sphere_distance()</a>, <a href="namespaceIMP_1_1pmi1.html#a6a9484ab3e8e6cbe2b750ae8635ff74a">IMP::pmi1::get_list_of_bipartite_minimum_sphere_distance()</a>, <a href="namespaceIMP_1_1rmf.html#adbc5eb9278e61f0a4449eb181cbd2a74">IMP::rmf::add_hierarchies()</a>, <a href="namespaceIMP_1_1rmf.html#a9f63044bfe82f715e14e819e1ae3a2f4">IMP::rmf::add_hierarchies()</a>, <a href="namespaceIMP_1_1rmf.html#a5bc1f4e588466260be12aba4bac30255">IMP::rmf::link_hierarchies()</a>, <a href="namespaceIMP_1_1rmf.html#a3ec708eaea5f9a236c558f0759ff0e3e">IMP::rmf::add_particles()</a>, <a href="namespaceIMP_1_1rmf.html#a3d3bf9a9a6ceb4aaaae7d699f2243573">IMP::rmf::add_particles()</a>, <a href="namespaceIMP_1_1rmf.html#a5736b0372c4c5f8344d093882d883702">IMP::rmf::link_particles()</a>, <a href="namespaceIMP_1_1saxs.html#a9dd5a67ebe96a9ce98c53ab08f9d93ef">IMP::saxs::compute_max_distance()</a>, <a href="namespaceIMP_1_1saxs.html#ac62b03b218a730a56a730b06a14bfffd">IMP::saxs::compute_max_distance()</a>, <a href="namespaceIMP_1_1saxs.html#a3088d29b90d6cefe75a9cf2bd68f340b">IMP::saxs::compute_profile()</a>, <a href="namespaceIMP_1_1saxs.html#a8e68a6a5c9b97f0e39107df27c649055">IMP::saxs::get_coordinates()</a>, <a href="namespaceIMP_1_1saxs.html#ae26123273b31cf5c08fd365df7b056e1">IMP::saxs::get_form_factors()</a>, <a href="namespaceIMP_1_1saxs.html#a770cbee09c575c3e143146e040bc7128">IMP::saxs::radius_of_gyration()</a>, <a href="namespaceIMP_1_1saxs.html#a48a6e99f77380532e66b861ecd6ff64c">IMP::saxs::read_files()</a>, <a href="namespaceIMP_1_1saxs.html#abd840b58460b2d3c4874fe738272f80b">IMP::saxs::read_pdb()</a>, <a href="namespaceIMP_1_1spb.html#ac2f1c4f7d0477ff1f40bdd383b9dc914">IMP::spb::add_BallMover()</a>, <a href="namespaceIMP_1_1spb.html#ac82266395d7d5fcf26defd3c2f2f9f06">IMP::spb::add_link()</a>, <a href="namespaceIMP_1_1spb.html#a2e319d74f871dffac11765e34a748794">IMP::spb::add_link()</a>, <a href="namespaceIMP_1_1spb.html#ac8ec6f7f84c9684326f06ce1e0f9e74e">IMP::spb::add_PbcBoxedMover()</a>, <a href="namespaceIMP_1_1spb.html#aec465b74f8f98da4682c157f396f8a7f">IMP::spb::add_PbcBoxedRigidBodyMover()</a>, <a href="namespaceIMP_1_1spb.html#a238100618f48d22ed7acd619702caea9">IMP::spb::add_SPBexcluded_volume()</a>, <a href="namespaceIMP_1_1spb.html#a06b534d7a1f9697f71f4a75366ba0a93">IMP::spb::add_symmetry_restraint()</a>, <a href="namespaceIMP_1_1spb.html#abeff346a43c51e4d81a56567357880a1">IMP::spb::create_merged_protein()</a>, <a href="namespaceIMP_1_1spb.html#a76fc05e5b9a81702e8c5a6d560695b08">IMP::spb::do_bipartite_mindist()</a>, <a href="namespaceIMP_1_1spb.html#a034798d478f68b2f5cab9cb68ac983d4">IMP::spb::do_bipartite_mindist()</a>, <a href="namespaceIMP_1_1spb.html#ae9d0b23db782452a116f737439adcd0f">IMP::spb::em2d_restraint()</a>, <a href="namespaceIMP_1_1spb.html#a381a514f0f058cbd0c02028c3f2654ca">IMP::spb::em2d_restraint()</a>, <a href="namespaceIMP_1_1spb.html#a8a576f8cb8828bb3f7bf1853ed9e9f21">IMP::spb::fret_restraint()</a>, <a href="namespaceIMP_1_1spb.html#acfc148835c56484d4e992d107aa55bee">IMP::spb::fret_restraint()</a>, <a href="namespaceIMP_1_1spb.html#abdbc7bac876d7baf8c690b92ed9d5208">IMP::spb::fret_restraint()</a>, <a href="namespaceIMP_1_1spb.html#a767148a9e5c40841aa2c91221389e67e">IMP::spb::get_rigid_bodies()</a>, <a href="namespaceIMP_1_1spb.html#a58a94cfc6958d85d112e235f74068ac1">IMP::spb::load_restart()</a>, <a href="namespaceIMP_1_1spb.html#a2271ff41d487482a3029eb6e6ccd06cb">IMP::spb::recenter_rb()</a>, <a href="namespaceIMP_1_1spb.html#a7c113921b584fd1fce234cdb478f354b">IMP::spb::spb_assemble_restraints()</a>, <a href="namespaceIMP_1_1spb.html#adc86ba90554da52601fc2e10c42cf016">IMP::spb::y2h_restraint()</a>, <a href="namespaceIMP_1_1spb.html#ab5e2abcde6e2dd7c9578b1f952808e38">IMP::spb::y2h_restraint()</a>, <a href="namespaceIMP_1_1spb.html#ac4ef731aae34f16b158cc7ab451ccd38">IMP::spb::y2h_restraint()</a>, <a href="namespaceIMP_1_1spb.html#ab16e77716acf17384a5092aa7ae86294">IMP::spb::y2h_restraint()</a></td></tr>
65 </table>
66 # IMP.algebra # {#argument_index_algebra}
67 <table><tr>
68 <th>Class</th><th>Users</th></tr>
69 <tr><td>@ref IMP::algebra::BoundingBoxD</td><td><a href="classIMP_1_1algebra_1_1BoundingBoxD.html#ac93f335b7c79748991ec968e7209b28f">IMP::algebra::BoundingBoxD::get_contains()</a>, <a href="classIMP_1_1algebra_1_1BoundingBoxD.html#a2469d780b50d800679f17bdc0b536541">IMP::algebra::BoundingBoxD::operator+()</a>, <a href="classIMP_1_1algebra_1_1BoundingBoxD.html#aa8092895377c9aca82b78050456b33c9">IMP::algebra::BoundingBoxD::operator+=()</a>, <a href="classIMP_1_1algebra_1_1DefaultEmbeddingD.html#a75841ace50c634c2ffa23e4e5d458564">IMP::algebra::DefaultEmbeddingD::initialize_from_box()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#aba328c5e51d34efea9057707ac80695c">IMP::algebra::GridD::voxels_begin()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#ad206879a1a9b301229b3034dbe3c87c5">IMP::algebra::GridD::voxels_end()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#a17f80a5eac1f7d71b66f49334a8f9d93">IMP::algebra::GridD::voxels_begin()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#a63d86b3db27639e5117b86f0964dd7e9">IMP::algebra::GridD::voxels_end()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#a0e73f5094989644138b2df7a923e59f5">IMP::algebra::GridD::indexes_begin()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#aa18ee2704ae69eff7db20ca04098fedf">IMP::algebra::GridD::indexes_end()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#a91df12851f5e94fb5d1eaa17228b74a6">IMP::algebra::GridD::extended_indexes_begin()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#ab8d1e94d9e10cc7d56abf46cdbb71dd6">IMP::algebra::GridD::extended_indexes_end()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#a3e65b1bbbceeb84c5bed65fb4506a2fa">IMP::algebra::GridD::get_indexes()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#a7a7210fd159af13e5af33db938498adc">IMP::algebra::GridD::get_extended_indexes()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#a97ccb184c448edc82741a0b8126ec750">IMP::algebra::GridD::GridD()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#aa575da807c4f8427657289c1725587c2">IMP::algebra::GridD::GridD()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#ab96be5a02e7d8a1729e6b47e8f6b93da">IMP::algebra::GridD::GridD()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#ab560837a0b4afe66e89bfc0d628deaa8">IMP::algebra::GridD::set_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#aa0ae0da722e8d9f7f7111424309f58f9">IMP::algebra::LogEmbeddingD::initialize_from_box()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#a11cfe0991d05693602b83f0a601a9c26">IMP::algebra::LogEmbeddingD::LogEmbeddingD()</a>, <a href="classIMP_1_1core_1_1GenericBoundingBox3DSingletonScore.html#a4c822d5e5d8b3895b3f820b6cad91f42">IMP::core::GenericBoundingBox3DSingletonScore::GenericBoundingBox3DSingletonScore()</a>, <a href="classIMP_1_1core_1_1MCCGSampler.html#ad2439bf720e48f108c5250f2ad6fd84c">IMP::core::MCCGSampler::set_bounding_box()</a>, <a href="classIMP_1_1display_1_1BoundingBoxGeometry.html#a09bd7874b00fda0019a13c52054fec6b">IMP::display::BoundingBoxGeometry::BoundingBoxGeometry()</a>, <a href="classIMP_1_1display_1_1BoundingBoxGeometry.html#abffcb4633c7da35860a1a7f3f97f35b0">IMP::display::BoundingBoxGeometry::BoundingBoxGeometry()</a>, <a href="classIMP_1_1display_1_1BoundingBoxGeometry.html#a6f4bacf190fc76a5ecdc2459bfed9891">IMP::display::BoundingBoxGeometry::BoundingBoxGeometry()</a>, <a href="classIMP_1_1display_1_1BoundingBoxGeometry.html#ae5b0e15df553dc00f20635f7f1b3f7fd">IMP::display::BoundingBoxGeometry::BoundingBoxGeometry()</a>, <a href="classIMP_1_1display_1_1BoundingBoxGeometry.html#aac5c637efa72beefcc9cc51b6ca71eb7">IMP::display::BoundingBoxGeometry::set_geometry()</a>, <a href="classIMP_1_1example_1_1ExampleSingletonModifier.html#ae16321e35f3831e87c4dbbaaa26badc9">IMP::example::ExampleSingletonModifier::ExampleSingletonModifier()</a>, <a href="classIMP_1_1statistics_1_1HistogramD.html#a7598b6d1cd28f41e56929ec813bed28d">IMP::statistics::HistogramD::HistogramD()</a>, <a href="namespaceIMP_1_1algebra.html#aa93b951ad9978ca2264245e0178777fc">IMP::algebra::get_random_vector_in()</a>, <a href="namespaceIMP_1_1algebra.html#a1d68a09215054f5656feb5c310a9e9e0">IMP::algebra::get_random_vector_on()</a>, <a href="namespaceIMP_1_1algebra.html#ac8c32603c6e50a2178b34e5b7cd5f4a7">IMP::algebra::get_grid_interior_cover_by_spacing()</a>, <a href="namespaceIMP_1_1algebra.html#a17aeb2742e60928cf687ef786530d44c">IMP::algebra::get_edges()</a>, <a href="namespaceIMP_1_1algebra.html#ab00c98290b98833acf41b7cdfaa1a701">IMP::algebra::get_interiors_intersect()</a>, <a href="namespaceIMP_1_1algebra.html#a7d107e54c2f6c82ac6af484a62dba718">IMP::algebra::get_intersection()</a>, <a href="namespaceIMP_1_1algebra.html#a06143c1eada26a19c52b0727f8ab2028">IMP::algebra::get_maximum_length()</a>, <a href="namespaceIMP_1_1algebra.html#aec3bea2d24fbbf621216822517ca1593">IMP::algebra::get_transformed()</a>, <a href="namespaceIMP_1_1algebra.html#a5884c6b32a247dd314db4c33b92508b8">IMP::algebra::get_union()</a>, <a href="namespaceIMP_1_1algebra.html#ae9bb408f4492a9ce063d095b02cd4cd1">IMP::algebra::get_vertices()</a>, <a href="namespaceIMP_1_1algebra.html#a94f280e1b578da3b5875fb157cfc7c68">IMP::algebra::get_volume()</a>, <a href="namespaceIMP_1_1core.html#a2d189bddcf9e654a50e9ce934a9a4ac6">IMP::core::create_bounding_box_3d_singleton_score()</a>, <a href="namespaceIMP_1_1display.html#a788545ff045770aea75e72b5568aba1d">IMP::display::create_geometry()</a>, <a href="namespaceIMP_1_1em.html#a11f40ffc07e7b3d9dde0711015f3e97e">IMP::em::create_density_header()</a></td></tr>
70 <tr><td>@ref IMP::algebra::Cone3D</td><td><a href="classIMP_1_1algebra_1_1Cone3D.html#a42215f5c82c6b41689887aee272d6f29">IMP::algebra::Cone3D::get_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1Cone3D.html#a9408590e3b4ed9bea9901e0cc53f1039">IMP::algebra::Cone3D::get_cone_3d_geometry()</a>, <a href="classIMP_1_1algebra_1_1Cone3D.html#a65a8552f8446684eba1acb5a97edd9c2">IMP::algebra::Cone3D::get_surface_area()</a>, <a href="classIMP_1_1algebra_1_1Cone3D.html#a024adad21c3b01de7558343ad0520532">IMP::algebra::Cone3D::get_volume()</a>, <a href="classIMP_1_1algebra_1_1Cone3D.html#a8ef5b67cbfb8740ffc1efe1d2c28ab9e">IMP::algebra::Cone3D::set_cone_3d_geometry()</a>, <a href="namespaceIMP_1_1algebra.html#a87c353d6dce6da5d919b552792b88c46">IMP::algebra::get_uniform_surface_cover()</a></td></tr>
71 <tr><td>@ref IMP::algebra::Cylinder3D</td><td><a href="classIMP_1_1algebra_1_1Cylinder3D.html#a2c0e1a36a0080caf666ff5e8657c44ea">IMP::algebra::Cylinder3D::get_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1Cylinder3D.html#a1f598fc535a050c3979cd2726732a552">IMP::algebra::Cylinder3D::get_cylinder_3d_geometry()</a>, <a href="classIMP_1_1algebra_1_1Cylinder3D.html#a16c33aab2de593af8b93d80f4c76f74e">IMP::algebra::Cylinder3D::get_surface_area()</a>, <a href="classIMP_1_1algebra_1_1Cylinder3D.html#a8a6dda8bdf445ff3c166165eddc7e2e5">IMP::algebra::Cylinder3D::get_volume()</a>, <a href="classIMP_1_1algebra_1_1Cylinder3D.html#a286efcbeac664dac18d23afae3232bb7">IMP::algebra::Cylinder3D::set_cylinder_3d_geometry()</a>, <a href="classIMP_1_1display_1_1CylinderGeometry.html#ae1b4a1736ef8057c5ce389bc4310e7ef">IMP::display::CylinderGeometry::CylinderGeometry()</a>, <a href="classIMP_1_1display_1_1CylinderGeometry.html#ab08ceebc8704d641be302119db1ebb73">IMP::display::CylinderGeometry::CylinderGeometry()</a>, <a href="classIMP_1_1display_1_1CylinderGeometry.html#af38ad28d6d178422d8db293d14b7d646">IMP::display::CylinderGeometry::CylinderGeometry()</a>, <a href="classIMP_1_1display_1_1CylinderGeometry.html#a31190a41e1a7354c221761274eaf5f34">IMP::display::CylinderGeometry::CylinderGeometry()</a>, <a href="classIMP_1_1display_1_1CylinderGeometry.html#abf3c1eee4096e672e2f5ed468c766e0f">IMP::display::CylinderGeometry::set_geometry()</a>, <a href="namespaceIMP_1_1algebra.html#a0c132a833a6f30793378bbed6dfb8f65">IMP::algebra::get_random_vector_in()</a>, <a href="namespaceIMP_1_1algebra.html#a991a576bd3cb05927a2cf4b0089f9d56">IMP::algebra::get_uniform_surface_cover()</a>, <a href="namespaceIMP_1_1algebra.html#af754ef2df6fa5f3ba1a211458399a8b5">IMP::algebra::get_grid_surface_cover()</a>, <a href="namespaceIMP_1_1display.html#a418acde3993b51a25f3ba4311f4c9b74">IMP::display::create_geometry()</a></td></tr>
72 <tr><td>@ref IMP::algebra::DenseGridStorageD</td><td><a href="classIMP_1_1algebra_1_1DenseGridStorageD.html#ab208fed96240a99ad591add590f90ed2">IMP::algebra::DenseGridStorageD::copy_from()</a>, <a href="classIMP_1_1algebra_1_1DenseGridStorageD.html#aae130f31cd621b14e73d06497b671ddb">IMP::algebra::DenseGridStorageD::DenseGridStorageD()</a>, <a href="classIMP_1_1algebra_1_1DenseGridStorageD.html#a5cd0208038b5008c73248047c91f38a7">IMP::algebra::DenseGridStorageD::operator=()</a></td></tr>
73 <tr><td>@ref IMP::algebra::Ellipsoid3D</td><td><a href="classIMP_1_1algebra_1_1Ellipsoid3D.html#a51e51989d370ac6d1f72605ea2b55659">IMP::algebra::Ellipsoid3D::get_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1Ellipsoid3D.html#a2fd68925f46292fc3f90454f7a34bded">IMP::algebra::Ellipsoid3D::get_ellipsoid_3d_geometry()</a>, <a href="classIMP_1_1algebra_1_1Ellipsoid3D.html#a5cea431932512ba0f6c5e54fd129deba">IMP::algebra::Ellipsoid3D::get_surface_area()</a>, <a href="classIMP_1_1algebra_1_1Ellipsoid3D.html#a7a64fb811faa2d387a26960c723bb772">IMP::algebra::Ellipsoid3D::get_volume()</a>, <a href="classIMP_1_1algebra_1_1Ellipsoid3D.html#a00d1a28d190859480cc3a8f1c01aef0e">IMP::algebra::Ellipsoid3D::set_ellipsoid_3d_geometry()</a>, <a href="classIMP_1_1display_1_1EllipsoidGeometry.html#ac975d8291f2dce584758a7fa4c0ac3e5">IMP::display::EllipsoidGeometry::EllipsoidGeometry()</a>, <a href="classIMP_1_1display_1_1EllipsoidGeometry.html#a8b23de125510a349978b1b789743ea33">IMP::display::EllipsoidGeometry::EllipsoidGeometry()</a>, <a href="classIMP_1_1display_1_1EllipsoidGeometry.html#a880be80c539c27f6e16c0a38a9fa9c9c">IMP::display::EllipsoidGeometry::EllipsoidGeometry()</a>, <a href="classIMP_1_1display_1_1EllipsoidGeometry.html#ae80469cfe57e39a43311da048a65b785">IMP::display::EllipsoidGeometry::EllipsoidGeometry()</a>, <a href="classIMP_1_1display_1_1EllipsoidGeometry.html#a06dbe9b339d4fdb16b7f76b095ff4cf7">IMP::display::EllipsoidGeometry::set_geometry()</a>, <a href="namespaceIMP_1_1display.html#acbb9389b216a0e7f8c4d9794075ccbf8">IMP::display::create_geometry()</a></td></tr>
74 <tr><td>@ref IMP::algebra::ExtendedGridIndexD</td><td><a href="classIMP_1_1algebra_1_1BoundedGridRangeD.html#a406ec057e7a1bee2dd04eb234e8756fc">IMP::algebra::BoundedGridRangeD::indexes_begin()</a>, <a href="classIMP_1_1algebra_1_1BoundedGridRangeD.html#a43156c09951cce2f2519378f32681b54">IMP::algebra::BoundedGridRangeD::indexes_end()</a>, <a href="classIMP_1_1algebra_1_1BoundedGridRangeD.html#a962bbb90a0676e27b1707dbb9b2c0386">IMP::algebra::BoundedGridRangeD::extended_indexes_begin()</a>, <a href="classIMP_1_1algebra_1_1BoundedGridRangeD.html#af6ebb547d959a0ef5b0c2f0ec24c8f43">IMP::algebra::BoundedGridRangeD::extended_indexes_end()</a>, <a href="classIMP_1_1algebra_1_1BoundedGridRangeD.html#abfd54359550894c029defa77ead61ab8">IMP::algebra::BoundedGridRangeD::get_indexes()</a>, <a href="classIMP_1_1algebra_1_1BoundedGridRangeD.html#a737ab039ddae4cf86fe92044c15424e6">IMP::algebra::BoundedGridRangeD::get_extended_indexes()</a>, <a href="classIMP_1_1algebra_1_1BoundedGridRangeD.html#a4aae88234ef495bca2bfd9baf28b8ce3">IMP::algebra::BoundedGridRangeD::get_has_index()</a>, <a href="classIMP_1_1algebra_1_1BoundedGridRangeD.html#acf1f33b1c1d7957330f442f15d656ac9">IMP::algebra::BoundedGridRangeD::get_index()</a>, <a href="classIMP_1_1algebra_1_1DefaultEmbeddingD.html#a42f36edf378dc3cb21d8b8320b2262d9">IMP::algebra::DefaultEmbeddingD::get_center()</a>, <a href="classIMP_1_1algebra_1_1DefaultEmbeddingD.html#aa939cc38c61633c05ba8f512671c9922">IMP::algebra::DefaultEmbeddingD::get_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1ExtendedGridIndexD.html#a86a4c3b004691c387e506c2b811e071c">IMP::algebra::ExtendedGridIndexD::compare()</a>, <a href="classIMP_1_1algebra_1_1ExtendedGridIndexD.html#a90a201d5f614a5a06afdad11b40ce16f">IMP::algebra::ExtendedGridIndexD::IMP_COMPARISONS()</a>, <a href="classIMP_1_1algebra_1_1ExtendedGridIndexD.html#a4aba51011654e969e574224831b909be">IMP::algebra::ExtendedGridIndexD::IMP_HASHABLE_INLINE()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#a6f4d8f177ef76a4b4f05dbc3e26489f1">IMP::algebra::LogEmbeddingD::get_center()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#afcefc82a3dc1a028efd0ef7a76ae3f62">IMP::algebra::LogEmbeddingD::get_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1SparseGridStorageD.html#a08248411df29a888727eb1fbe06c2538">IMP::algebra::SparseGridStorageD::indexes_begin()</a>, <a href="classIMP_1_1algebra_1_1SparseGridStorageD.html#a9ba25e899fa8d084b868bb334e482945">IMP::algebra::SparseGridStorageD::indexes_end()</a>, <a href="classIMP_1_1algebra_1_1SparseGridStorageD.html#a9943a6836e190dd7f3f1bff9c550ed8b">IMP::algebra::SparseGridStorageD::get_indexes()</a>, <a href="classIMP_1_1algebra_1_1SparseGridStorageD.html#ab3283a6eb40d179b0648b804a95ef499">IMP::algebra::SparseGridStorageD::add_voxel()</a>, <a href="classIMP_1_1algebra_1_1SparseGridStorageD.html#a053acf2aeafd935e97726038903032b6">IMP::algebra::SparseGridStorageD::get_has_index()</a>, <a href="classIMP_1_1algebra_1_1SparseGridStorageD.html#abcf4643d745ad8f61ac711026cb9a5cb">IMP::algebra::SparseGridStorageD::get_index()</a>, <a href="classIMP_1_1algebra_1_1UnboundedGridRangeD.html#adfa1746ee9fc9f43027330471032f67d">IMP::algebra::UnboundedGridRangeD::extended_indexes_begin()</a>, <a href="classIMP_1_1algebra_1_1UnboundedGridRangeD.html#a2902667d16ac2e28ebe7b9f7cbb5be27">IMP::algebra::UnboundedGridRangeD::extended_indexes_end()</a>, <a href="classIMP_1_1algebra_1_1UnboundedGridRangeD.html#ae36705377d9f2caf5c06984d1ce8bfaa">IMP::algebra::UnboundedGridRangeD::get_extended_indexes()</a>, <a href="classIMP_1_1algebra_1_1UnboundedGridRangeD.html#aa2c6004fc6e1985df04a8a4ee3e77c33">IMP::algebra::UnboundedGridRangeD::get_has_index()</a></td></tr>
75 <tr><td>@ref IMP::algebra::Gaussian3D</td><td><a href="classIMP_1_1core_1_1Gaussian.html#a2485c4d8d99ba29b1a408e698f0db2ac">IMP::core::Gaussian::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1Gaussian.html#a9c7aaccfc3793025edac3d2eaa275b71">IMP::core::Gaussian::set_gaussian()</a>, <a href="classIMP_1_1core_1_1Gaussian.html#a0b69d1b1dbe516bac468d716d1373427">IMP::core::Gaussian::setup_particle()</a>, <a href="classIMP_1_1core_1_1Gaussian.html#a03345ca51aeba0893a3280bbb2435ee6">IMP::core::Gaussian::setup_particle()</a>, <a href="namespaceIMP_1_1algebra.html#a4883e8de2c04d91ad0b0d336564dc4a4">IMP::algebra::get_covariance()</a></td></tr>
76 <tr><td>@ref IMP::algebra::GridD</td><td><a href="classIMP_1_1display_1_1IsosurfaceGeometry.html#aee4743136bd5d0a62b41fd956ab1d7da">IMP::display::IsosurfaceGeometry::IsosurfaceGeometry()</a>, <a href="namespaceIMP_1_1algebra.html#a9ed792e2cc65d410fdcce57c0850eb92">IMP::algebra::get_bounding_box()</a>, <a href="namespaceIMP_1_1algebra.html#adb4e0a724bc2f1f9c54e3ebc9437c260">IMP::algebra::get_linearly_interpolated()</a>, <a href="namespaceIMP_1_1algebra.html#a32242a25f36a56f9acc877f4841b3c24">IMP::algebra::get_trilinearly_interpolated()</a>, <a href="namespaceIMP_1_1em.html#ae63d1d8a3cfad97be2846c51d1a03203">IMP::em::create_density_map()</a></td></tr>
77 <tr><td>@ref IMP::algebra::GridIndexD</td><td><a href="classIMP_1_1algebra_1_1DefaultEmbeddingD.html#a584a87ad7db962f804e65beb46356e8a">IMP::algebra::DefaultEmbeddingD::get_center()</a>, <a href="classIMP_1_1algebra_1_1DefaultEmbeddingD.html#a2ef44b764283d6da46c20bfbf17dbff7">IMP::algebra::DefaultEmbeddingD::get_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1DenseGridStorageD.html#a85058347da34147a6b5f84c6426c4186">IMP::algebra::DenseGridStorageD::at()</a>, <a href="classIMP_1_1algebra_1_1DenseGridStorageD.html#a694d33906f3ba67e60e0ea60d8a17a26">IMP::algebra::DenseGridStorageD::at()</a>, <a href="classIMP_1_1algebra_1_1DenseGridStorageD.html#ad933d82953ca758bf6dc392ddfac821b">IMP::algebra::DenseGridStorageD::operator[]()</a>, <a href="classIMP_1_1algebra_1_1DenseGridStorageD.html#a4df3d9da366d98183e66457bc64d14c6">IMP::algebra::DenseGridStorageD::operator[]()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#a1f513a99898cd34a8f760b887b4f9220">IMP::algebra::GridD::get_extended_index()</a>, <a href="classIMP_1_1algebra_1_1GridIndexD.html#a7395cf092160a16c034f2463a0d201d2">IMP::algebra::GridIndexD::compare()</a>, <a href="classIMP_1_1algebra_1_1GridIndexD.html#a2bb1616e7c972fb3a4f972cc6f048fdd">IMP::algebra::GridIndexD::IMP_COMPARISONS()</a>, <a href="classIMP_1_1algebra_1_1GridIndexD.html#a415a95740bb325aff1fd8fc142dfec4b">IMP::algebra::GridIndexD::IMP_HASHABLE_INLINE()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#a5cb83dd94de983716f6591c717d1b47a">IMP::algebra::LogEmbeddingD::get_center()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#a19437cca74047a689ad5622534007858">IMP::algebra::LogEmbeddingD::get_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1SparseGridStorageD.html#abed2b815720c9ede48da08042f7fc746">IMP::algebra::SparseGridStorageD::at()</a>, <a href="classIMP_1_1algebra_1_1SparseGridStorageD.html#a37c00e0b555991fdea311958456f5859">IMP::algebra::SparseGridStorageD::at()</a>, <a href="classIMP_1_1algebra_1_1SparseGridStorageD.html#afcd504ad60ecde44a739a6f87da87c37">IMP::algebra::SparseGridStorageD::operator[]()</a>, <a href="classIMP_1_1algebra_1_1SparseGridStorageD.html#aa3df25129d9c6875e71f1029274be1e4">IMP::algebra::SparseGridStorageD::operator[]()</a>, <a href="classIMP_1_1algebra_1_1SparseGridStorageD.html#a6f314f928557c11837214335428533f0">IMP::algebra::SparseGridStorageD::remove_voxel()</a></td></tr>
78 <tr><td>@ref IMP::algebra::Line3D</td><td><a href="classIMP_1_1algebra_1_1Line3D.html#a43cfe2dada35bf7f0765ac32a62b0b0c">IMP::algebra::Line3D::get_reciprocal_product()</a>, <a href="classIMP_1_1algebra_1_1Line3D.html#a0ddee92213d742382802d0fe52ca8e44">IMP::algebra::Line3D::get_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1Line3D.html#afc6ba02a46de817baba50c58eab655e8">IMP::algebra::Line3D::get_line_3d_geometry()</a>, <a href="namespaceIMP_1_1algebra.html#a3b3d323c48102eb90b501b0bab217bbe">IMP::algebra::get_angle()</a>, <a href="namespaceIMP_1_1algebra.html#acf82e7318469cc77db87a30cc98ef67f">IMP::algebra::get_distance()</a>, <a href="namespaceIMP_1_1algebra.html#ac02176c89a2b318dac48b35e11b90343">IMP::algebra::get_distance()</a>, <a href="namespaceIMP_1_1algebra.html#a77d0b01755739146b53216fecabcb899">IMP::algebra::get_projected()</a>, <a href="namespaceIMP_1_1algebra.html#ae4a0378baab9f9cb01c824f2ec6abc51">IMP::algebra::get_projected()</a>, <a href="namespaceIMP_1_1algebra.html#aba7bf2d5c4d78a8bcd21d63ced9c30ad">IMP::algebra::get_segment_connecting_first_to_second()</a>, <a href="namespaceIMP_1_1algebra.html#a151019bab90b6cdc2f1755c6b7a92bdc">IMP::algebra::get_transformed()</a>, <a href="namespaceIMP_1_1algebra.html#a3734de20720549f27949b55fe2166e34">IMP::algebra::set_line_3d_geometry()</a></td></tr>
79 <tr><td>@ref IMP::algebra::Plane3D</td><td><a href="classIMP_1_1algebra_1_1Plane3D.html#a2ce4dc9bc8335a283d1993a24ed1130e">IMP::algebra::Plane3D::get_area()</a>, <a href="classIMP_1_1algebra_1_1Plane3D.html#aedce7034965a145fc52252f640761b26">IMP::algebra::Plane3D::get_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1Plane3D.html#ade3bebd378b15acf3e134236ccf4a894">IMP::algebra::Plane3D::get_plane_3d_geometry()</a>, <a href="classIMP_1_1algebra_1_1Plane3D.html#a6e8806b130e7420d2a33e532c4ecfdcf">IMP::algebra::Plane3D::set_plane_3d_geometry()</a>, <a href="classIMP_1_1algebra_1_1Reflection3D.html#a03378aadd6106ab2f6b3bd04db45c605">IMP::algebra::Reflection3D::Reflection3D()</a>, <a href="classIMP_1_1algebra_1_1SpherePatch3D.html#ae2287e153d7407b77aa454e4e838fa65">IMP::algebra::SpherePatch3D::SpherePatch3D()</a>, <a href="classIMP_1_1display_1_1FilterGeometry.html#a48ddb9438d24ddbc71317779b7010caa">IMP::display::FilterGeometry::FilterGeometry()</a>, <a href="classIMP_1_1display_1_1PlaneGeometry.html#a14117c198d70a7eb81b96e2f336800f8">IMP::display::PlaneGeometry::PlaneGeometry()</a>, <a href="namespaceIMP_1_1algebra.html#a1bcf2debc9b22076e1fb66f9ac3d0991">IMP::algebra::get_distance()</a>, <a href="namespaceIMP_1_1algebra.html#a2ef88c55248b535ca69a39e67fd935bd">IMP::algebra::get_reflected()</a></td></tr>
80 <tr><td>@ref IMP::algebra::PrincipalComponentAnalysisD</td><td><a href="classIMP_1_1algebra_1_1PrincipalComponentAnalysisD.html#a4d8d20acb063e51daa4bc67e3f0ecc68">IMP::algebra::PrincipalComponentAnalysisD::compare()</a>, <a href="namespaceIMP_1_1algebra.html#aea2393b6f73c8eb830dfbe6996cafdc5">IMP::algebra::get_alignments_from_first_to_second()</a>, <a href="namespaceIMP_1_1multifit.html#a2ded6207f6b3f25048701821adf3bea7">IMP::multifit::write_markers()</a></td></tr>
81 <tr><td>@ref IMP::algebra::ReferenceFrame3D</td><td><a href="classIMP_1_1algebra_1_1Ellipsoid3D.html#a4e9bc6c671de9b3e82ecd7680e567a28">IMP::algebra::Ellipsoid3D::Ellipsoid3D()</a>, <a href="classIMP_1_1algebra_1_1Gaussian3D.html#a552489afb6a4079a4bfd4dbd17fab338">IMP::algebra::Gaussian3D::Gaussian3D()</a>, <a href="classIMP_1_1algebra_1_1ReferenceFrame3D.html#af4e8c0e2c90dffb8a059a866ada3f7e4">IMP::algebra::ReferenceFrame3D::get_global_reference_frame()</a>, <a href="classIMP_1_1algebra_1_1ReferenceFrame3D.html#ac4adf03ce952d182320a9a99709cb728">IMP::algebra::ReferenceFrame3D::get_local_reference_frame()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#a6cb67f5f077f0ee3a9197641ee0ac74a">IMP::core::RigidBody::add_member_internal()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#ae4c23d1cee5717182c900c9686963f85">IMP::core::RigidBody::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#a9f4a8f119d07286c0b233f98c2a5eab8">IMP::core::RigidBody::set_reference_frame()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#a16aa0a44a153cc3efe7e7fb54191248e">IMP::core::RigidBody::set_reference_frame_lazy()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#a568f76829966c6cdc02e10b93a30251b">IMP::core::RigidBody::setup_particle()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#a500ea9f86fa983526bff173076a42677">IMP::core::RigidBody::setup_particle()</a>, <a href="classIMP_1_1core_1_1Surface.html#af44678ab712043cdd43861183d2f1d8a">IMP::core::Surface::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1Surface.html#afbd39b286d5a68edf1248a602af7f18c">IMP::core::Surface::setup_particle()</a>, <a href="classIMP_1_1core_1_1Surface.html#a72a0ed69bd2ab51b3d11d95a126dd65b">IMP::core::Surface::setup_particle()</a>, <a href="classIMP_1_1core_1_1Surface.html#a9233fc3470e1ddf45699ee96c1699867">IMP::core::Surface::set_reference_frame()</a>, <a href="classIMP_1_1display_1_1ReferenceFrameGeometry.html#a525a097acac17a27ed993e7142ec35a3">IMP::display::ReferenceFrameGeometry::ReferenceFrameGeometry()</a>, <a href="classIMP_1_1display_1_1ReferenceFrameGeometry.html#a431e05df3b0c309759e12b8049948402">IMP::display::ReferenceFrameGeometry::ReferenceFrameGeometry()</a>, <a href="classIMP_1_1display_1_1ReferenceFrameGeometry.html#a7525a19a4c0cd13b906ed83124a89a33">IMP::display::ReferenceFrameGeometry::ReferenceFrameGeometry()</a>, <a href="classIMP_1_1display_1_1ReferenceFrameGeometry.html#af3a77034f7e8360e3c5b9c2a32c15ca6">IMP::display::ReferenceFrameGeometry::ReferenceFrameGeometry()</a>, <a href="classIMP_1_1display_1_1ReferenceFrameGeometry.html#a754864fc968d2e3ae69d23236d5c4501">IMP::display::ReferenceFrameGeometry::set_geometry()</a>, <a href="classIMP_1_1kinematics_1_1KinematicForest.html#a879e819eda0a9d2851e6ac8c654b8355">IMP::kinematics::KinematicForest::set_reference_frame_safe()</a>, <a href="namespaceIMP_1_1algebra.html#a2e7851e2cdd810e68bb3235699c0f5ba">IMP::algebra::get_transformation_from_first_to_second()</a>, <a href="namespaceIMP_1_1algebra.html#ad1ae16d9089296d2d7f458c2d667e587">IMP::algebra::get_transformed()</a>, <a href="namespaceIMP_1_1display.html#a7e059bdeb2a7290b1260cab6923bdd29">IMP::display::create_geometry()</a></td></tr>
82 <tr><td>@ref IMP::algebra::Reflection3D</td><td><a href="classIMP_1_1core_1_1TransformationAndReflectionSymmetry.html#a9dabd7d0f4cdaeeed13f806dbe89a09c">IMP::core::TransformationAndReflectionSymmetry::TransformationAndReflectionSymmetry()</a></td></tr>
83 <tr><td>@ref IMP::algebra::Rotation2D</td><td><a href="classIMP_1_1algebra_1_1Transformation2D.html#ae38299503ccbbfc00f6601c73c934524">IMP::algebra::Transformation2D::Transformation2D()</a>, <a href="namespaceIMP_1_1algebra.html#a4ace4e3f3bb2f5d5fd442360945370a3">IMP::algebra::compose()</a>, <a href="namespaceIMP_1_1algebra.html#ae3383dcf150f2e7d76498fecbc55dde9">IMP::algebra::get_rotation_about_point()</a></td></tr>
84 <tr><td>@ref IMP::algebra::Rotation3D</td><td><a href="classIMP_1_1algebra_1_1Ellipsoid3D.html#a5dad9047d0e92873b41b9153cc768ca9">IMP::algebra::Ellipsoid3D::Ellipsoid3D()</a>, <a href="classIMP_1_1algebra_1_1Rotation3D.html#afc684796571469465e420137494c09c7">IMP::algebra::Rotation3D::copy_cache()</a>, <a href="classIMP_1_1algebra_1_1Rotation3D.html#a291747d669f67987bca04174ecafc0c1">IMP::algebra::Rotation3D::Rotation3D()</a>, <a href="classIMP_1_1algebra_1_1Rotation3D.html#add6b45584377d72708fa41d93cf0e912">IMP::algebra::Rotation3D::operator*()</a>, <a href="classIMP_1_1algebra_1_1Rotation3D.html#a1f4eed6fc383b00ae8c5430c42190d39">IMP::algebra::Rotation3D::operator/()</a>, <a href="classIMP_1_1algebra_1_1Rotation3D.html#a754ca1baec7553d4487fa6bd532bf372">IMP::algebra::Rotation3D::operator/=()</a>, <a href="classIMP_1_1algebra_1_1Rotation3D.html#a2c5853c7c473d87926900b9a6136749e">IMP::algebra::Rotation3D::operator=()</a>, <a href="classIMP_1_1algebra_1_1Transformation3D.html#a0f2df89b87c067870907e1cf5103e036">IMP::algebra::Transformation3D::Transformation3D()</a>, <a href="classIMP_1_1core_1_1NonRigidMember.html#ade46fb3f9d4031dc92a335054d6cbd50">IMP::core::NonRigidMember::add_to_internal_rotational_derivatives()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#a91be8fde5bc2268a05b278e4b09ffd14">IMP::core::RigidBody::add_to_derivatives()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#adb1dbd74e7b5480c0827d699aac15be2">IMP::core::RigidBody::add_to_rotational_derivatives()</a>, <a href="classIMP_1_1em2d_1_1ProjectionParameters.html#a79fdaffbae5ee9fbecf3e457085f5db8">IMP::em2d::ProjectionParameters::set_rotation()</a>, <a href="classIMP_1_1em2d_1_1RegistrationResult.html#ad0d2a9e3362a2e5d70c02d7a9573f0d1">IMP::em2d::RegistrationResult::RegistrationResult()</a>, <a href="classIMP_1_1em2d_1_1RegistrationResult.html#a996ceea30768ec25b24b6c306415039e">IMP::em2d::RegistrationResult::set_rotation()</a>, <a href="classIMP_1_1npctransport_1_1BodyStatisticsOptimizerState.html#a2d8cf252039037ded2e301940b821139">IMP::npctransport::BodyStatisticsOptimizerState::add_orientation()</a>, <a href="namespaceIMP_1_1algebra.html#a9ff9afb5d3b97dc0f5a1af70a0a6dde8">IMP::algebra::get_fixed_xyz_from_rotation()</a>, <a href="namespaceIMP_1_1algebra.html#a216ec1243a72a2c3f9ddf6bd8bc22ece">IMP::algebra::compose()</a>, <a href="namespaceIMP_1_1algebra.html#aeaccab75a3705673bac9a5d4c08d1fd7">IMP::algebra::compose_adjoint()</a>, <a href="namespaceIMP_1_1algebra.html#a502cf3dd86afae125f6caf9a0f9763f5">IMP::algebra::compose_adjoint()</a>, <a href="namespaceIMP_1_1algebra.html#a691fe5fa25816b65206ae26096c72213">IMP::algebra::get_axis_and_angle()</a>, <a href="namespaceIMP_1_1algebra.html#a55e80fed63202bf78ee2234003ddbd0f">IMP::algebra::get_distance()</a>, <a href="namespaceIMP_1_1algebra.html#ad8184a18160d6fd07ec0a23356bcb3ff">IMP::algebra::get_gradient_of_composed_with_respect_to_first()</a>, <a href="namespaceIMP_1_1algebra.html#ab95ea53d5fa3ea57e1847cd24d9f1046">IMP::algebra::get_gradient_of_composed_with_respect_to_second()</a>, <a href="namespaceIMP_1_1algebra.html#aad56f25091896ce8e87f8e5f1098bf79">IMP::algebra::get_interpolated()</a>, <a href="namespaceIMP_1_1algebra.html#a7fa0a30c71127a92245cefc71613bb0f">IMP::algebra::get_jacobian_of_composed_wrt_first()</a>, <a href="namespaceIMP_1_1algebra.html#ab2f433fffe772a43eab54d008444f27e">IMP::algebra::get_jacobian_of_composed_wrt_second()</a>, <a href="namespaceIMP_1_1algebra.html#abd23e8a25dda2d4acf8c00db35e2537f">IMP::algebra::get_random_rotation_3d()</a>, <a href="namespaceIMP_1_1algebra.html#a07063149bf0d6fd24bd5a1116d6b5115">IMP::algebra::get_rotation_about_point()</a>, <a href="namespaceIMP_1_1em2d.html#ab15ba9866050315bb0248dd27f0ef0bb">IMP::em2d::do_project_particles()</a>, <a href="namespaceIMP_1_1em2d.html#a33ff594b9223f368d44b25a7da4c349e">IMP::em2d::do_project_vectors()</a>, <a href="namespaceIMP_1_1em2d.html#a3cc89c1d22ffa4f91512f49072542be6">IMP::em2d::do_project_vectors()</a>, <a href="namespaceIMP_1_1em2d.html#ad5dd142cfbb44bbea471ab17f9d8ff77">IMP::em2d::get_unique_index()</a></td></tr>
85 <tr><td>@ref IMP::algebra::Segment3D</td><td><a href="classIMP_1_1algebra_1_1Cone3D.html#a54ff89422998af39f072dd3f3723e772">IMP::algebra::Cone3D::Cone3D()</a>, <a href="classIMP_1_1algebra_1_1Cylinder3D.html#ad34db39ba5b3bbfffd6e8dbb5c5f1d60">IMP::algebra::Cylinder3D::Cylinder3D()</a>, <a href="classIMP_1_1algebra_1_1Line3D.html#a448a5b70799cc482486c08a07d016869">IMP::algebra::Line3D::Line3D()</a>, <a href="classIMP_1_1algebra_1_1Segment3D.html#abd21d39499ca4acd3616d7a9355b90fd">IMP::algebra::Segment3D::get_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1Segment3D.html#af5c43b376efc839be7570ffa3ee7825b">IMP::algebra::Segment3D::get_segment_3d_geometry()</a>, <a href="classIMP_1_1display_1_1SegmentGeometry.html#aacb32ca6ae044acacb1a67263de8ad27">IMP::display::SegmentGeometry::SegmentGeometry()</a>, <a href="classIMP_1_1display_1_1SegmentGeometry.html#a0eda17f53f2e8cef8ae21c615f3e1b2b">IMP::display::SegmentGeometry::SegmentGeometry()</a>, <a href="classIMP_1_1display_1_1SegmentGeometry.html#a0722985d583856076e2251d4cb85f380">IMP::display::SegmentGeometry::SegmentGeometry()</a>, <a href="classIMP_1_1display_1_1SegmentGeometry.html#a2bcd2eb9aa948125500f86b9dbf99344">IMP::display::SegmentGeometry::SegmentGeometry()</a>, <a href="classIMP_1_1display_1_1SegmentGeometry.html#a91092ed036516a4474cd0d7143a5cd2a">IMP::display::SegmentGeometry::set_geometry()</a>, <a href="namespaceIMP_1_1algebra.html#a242c09659e380bd7d7c1dbc779863023">IMP::algebra::get_shortest_segment()</a>, <a href="namespaceIMP_1_1algebra.html#afacab5ba739f7028d32cd34be05a10c7">IMP::algebra::get_shortest_segment()</a>, <a href="namespaceIMP_1_1algebra.html#a7f7687e40a5b27f12babf9730ff8d80c">IMP::algebra::get_distance()</a>, <a href="namespaceIMP_1_1algebra.html#a27ea6a618c778638a2a0198aeb9fbd7c">IMP::algebra::get_distance()</a>, <a href="namespaceIMP_1_1algebra.html#ae4a0378baab9f9cb01c824f2ec6abc51">IMP::algebra::get_projected()</a>, <a href="namespaceIMP_1_1algebra.html#ac5577591de549991f08c38744447c953">IMP::algebra::get_relative_projection_on_segment()</a>, <a href="namespaceIMP_1_1algebra.html#ad4acc0a53f732829a51ec021d4bb604d">IMP::algebra::set_segment_3d_geometry()</a>, <a href="namespaceIMP_1_1display.html#a071ef8e162f88294b235de620e423d2c">IMP::display::create_geometry()</a></td></tr>
86 <tr><td>@ref IMP::algebra::SphereD</td><td><a href="classIMP_1_1algebra_1_1SphereD.html#a77963d4ae201c1d27518495e9c13275d">IMP::algebra::SphereD::get_contains()</a>, <a href="namespaceIMP_1_1algebra.html#a2d16674563f8d6b2ec19ca4ac4141f35">IMP::algebra::get_random_vector_in()</a>, <a href="namespaceIMP_1_1algebra.html#a13112e2dae882f9c03a368a64986c198">IMP::algebra::get_random_vector_in()</a>, <a href="namespaceIMP_1_1algebra.html#a5cee60da7af2c8bdb9939983e71b4c40">IMP::algebra::get_random_vector_on()</a>, <a href="namespaceIMP_1_1algebra.html#ad574480bc92f3b796036c52057f02c53">IMP::algebra::get_uniform_surface_cover()</a>, <a href="namespaceIMP_1_1algebra.html#a089e7a683da477067cf9083066239c2a">IMP::algebra::get_uniform_upper_hemisphere_cover()</a>, <a href="namespaceIMP_1_1algebra.html#a847f07074743af85946a6b46cd2a296f">IMP::algebra::get_distance()</a>, <a href="namespaceIMP_1_1algebra.html#a9538f0814e3bdb8494ad2083acea5f20">IMP::algebra::get_interiors_intersect()</a>, <a href="namespaceIMP_1_1algebra.html#a79e54ebe8fa9974a1401ba40be75d732">IMP::algebra::get_power_distance()</a>, <a href="namespaceIMP_1_1algebra.html#a707b6892f5273351caf839871b84b04a">IMP::algebra::get_vector_geometry()</a></td></tr>
87 <tr><td>@ref IMP::algebra::SpherePatch3D</td><td><a href="classIMP_1_1algebra_1_1SpherePatch3D.html#a96d364ca0c2621089adcfe22945de30b">IMP::algebra::SpherePatch3D::get_area()</a>, <a href="classIMP_1_1algebra_1_1SpherePatch3D.html#ae5375e21b4c4a14ecf4278d36cab2387">IMP::algebra::SpherePatch3D::get_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1SpherePatch3D.html#ab64eeda4f1106781fd57c3635e593b12">IMP::algebra::SpherePatch3D::get_sphere_patch_3d_geometry()</a>, <a href="classIMP_1_1algebra_1_1SpherePatch3D.html#a45d61d6b1d79f6f08aaa5e7540b25001">IMP::algebra::SpherePatch3D::set_sphere_patch_3d_geometry()</a>, <a href="namespaceIMP_1_1algebra.html#a72ff2a60e8a826fcc1914fba3552f359">IMP::algebra::get_uniform_surface_cover()</a></td></tr>
88 <tr><td>@ref IMP::algebra::Torus3D</td><td><a href="classIMP_1_1algebra_1_1Torus3D.html#aaaa8ffb3b19028f35539da46be602814">IMP::algebra::Torus3D::get_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1Torus3D.html#a52583cc4f6079095374c4cf242aacb0b">IMP::algebra::Torus3D::get_surface_area()</a>, <a href="classIMP_1_1algebra_1_1Torus3D.html#a87d58fbd0252feffafd1fe4cb8b3ff0e">IMP::algebra::Torus3D::get_torus_3d_geometry()</a>, <a href="classIMP_1_1algebra_1_1Torus3D.html#a138c34153dc211ac2e43aca8dd2988d9">IMP::algebra::Torus3D::get_volume()</a>, <a href="classIMP_1_1algebra_1_1Torus3D.html#aabbf662b635d6bfb8a745d77b9a543a0">IMP::algebra::Torus3D::set_torus_3d_geometry()</a></td></tr>
89 <tr><td>@ref IMP::algebra::Transformation2D</td><td><a href="classIMP_1_1algebra_1_1Transformation2D.html#a522e638b36bb208b63a4cff80481b2fd">IMP::algebra::Transformation2D::operator*()</a>, <a href="classIMP_1_1algebra_1_1Transformation2D.html#afaf5b30d6215c311e8d00ad6f2ae28ab">IMP::algebra::Transformation2D::operator*=()</a>, <a href="classIMP_1_1algebra_1_1Transformation2D.html#aeea8a543dd04a6a6c4eb1b646eee47ed">IMP::algebra::Transformation2D::operator/()</a>, <a href="classIMP_1_1algebra_1_1Transformation2D.html#aa4796bb23d7e3855e14f3603323f8260">IMP::algebra::Transformation2D::operator/=()</a>, <a href="classIMP_1_1em2d_1_1RegistrationResult.html#ae9ab15bdd1f3d4e782063f8b0d7f1923">IMP::em2d::RegistrationResult::add_in_plane_transformation()</a>, <a href="namespaceIMP_1_1algebra.html#a5d83cbee6a0e0af8738adf030f364f6d">IMP::algebra::compose()</a>, <a href="namespaceIMP_1_1algebra.html#a95b9c2466fd2ba29cddff88efc887aff">IMP::algebra::get_transformation_3d()</a>, <a href="namespaceIMP_1_1em2d.html#a0701b9da59d031b6bb82fbb493d824b1">IMP::em2d::get_transformed()</a></td></tr>
90 <tr><td>@ref IMP::algebra::Transformation3D</td><td><a href="classIMP_1_1algebra_1_1ReferenceFrame3D.html#a2784d26ef83ccd5b34f1f2752d0940fc">IMP::algebra::ReferenceFrame3D::ReferenceFrame3D()</a>, <a href="classIMP_1_1algebra_1_1Transformation3D.html#a3d4eb9fcd2303c38d71935e133c909ea">IMP::algebra::Transformation3D::operator*()</a>, <a href="classIMP_1_1algebra_1_1Transformation3D.html#a07bc275d62927745a4eb2df457bbaf12">IMP::algebra::Transformation3D::operator*=()</a>, <a href="classIMP_1_1algebra_1_1Transformation3D.html#ad527f26807df0a9fe8a5aca648d91b4c">IMP::algebra::Transformation3D::operator/()</a>, <a href="classIMP_1_1algebra_1_1Transformation3D.html#afe442ff46864a4e9fde422dc62d30047">IMP::algebra::Transformation3D::operator/=()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#aed2dde23e30fbcf168f174798fa911d1">IMP::core::RigidBody::pull_back_body_member_adjoints()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#a76e5fbad51df6a7b03992147afa7951d">IMP::core::RigidBody::pull_back_member_adjoints()</a>, <a href="classIMP_1_1core_1_1RigidBodyMember.html#a20d2d7d753660ff877180065eacfdad8">IMP::core::RigidBodyMember::set_internal_transformation()</a>, <a href="classIMP_1_1core_1_1Transform.html#a82c43f463be9cd6645ebad7030c7a3a1">IMP::core::Transform::Transform()</a>, <a href="classIMP_1_1core_1_1TransformationAndReflectionSymmetry.html#a9dabd7d0f4cdaeeed13f806dbe89a09c">IMP::core::TransformationAndReflectionSymmetry::TransformationAndReflectionSymmetry()</a>, <a href="classIMP_1_1core_1_1TransformationSymmetry.html#a1d253ea2704fc7d13430962c7ae9b90a">IMP::core::TransformationSymmetry::TransformationSymmetry()</a>, <a href="classIMP_1_1core_1_1TransformationSymmetry.html#a0dffda61b5cba0755a6b4841b6f5e593">IMP::core::TransformationSymmetry::set_transformation()</a>, <a href="classIMP_1_1core_1_1TransformedDistancePairScore.html#a18d9ea122d7eb647fbd53c3a17cb110c">IMP::core::TransformedDistancePairScore::TransformedDistancePairScore()</a>, <a href="classIMP_1_1core_1_1TransformedDistancePairScore.html#aef34c0fb45006291f5f984f1d4e84669">IMP::core::TransformedDistancePairScore::set_transformation()</a>, <a href="classIMP_1_1em_1_1DensityMap.html#a136741fcac5174f8af99e7aac939e9f9">IMP::em::DensityMap::get_transformed()</a>, <a href="classIMP_1_1em_1_1DensityMap.html#afea835c4ddafaf25568cc64c66bcc3f1">IMP::em::DensityMap::get_transformed()</a>, <a href="classIMP_1_1em_1_1DensityMap.html#a8fde3a97a69c15d1dfce64e6757e369e">IMP::em::DensityMap::get_transformed_into()</a>, <a href="classIMP_1_1em_1_1EnvelopeScore.html#afa6a3d84c3a17c1c6f993f7d8bb2eb05">IMP::em::EnvelopeScore::is_penetrating()</a>, <a href="classIMP_1_1em_1_1EnvelopeScore.html#a5dab57fdb2e5667acac468f5d00ab04c">IMP::em::EnvelopeScore::score()</a>, <a href="classIMP_1_1em_1_1FittingSolutions.html#a29fe60f4c55c1b2c278382c0a6b91dd5">IMP::em::FittingSolutions::add_solution()</a>, <a href="classIMP_1_1em_1_1FittingSolutions.html#a352dad9206bc06891bf050b04e2c3985">IMP::em::FittingSolutions::multiply()</a>, <a href="classIMP_1_1kinematics_1_1Joint.html#a39e9a4cc8ba86e14a84109bdab62a12a">IMP::kinematics::Joint::set_transformation_child_to_parent_no_checks()</a>, <a href="classIMP_1_1kinematics_1_1KinematicForest.html#a7e6c2352a1bf031b30d5f2e463e07b76">IMP::kinematics::KinematicForest::apply_transform_safely()</a>, <a href="classIMP_1_1kinematics_1_1KinematicForest.html#ae44ea8f250039804adc64a7e977eadf0">IMP::kinematics::KinematicForest::transform_safe()</a>, <a href="classIMP_1_1kinematics_1_1TransformationJoint.html#ac2ae8dc832dc667fdf4ed898160c99e5">IMP::kinematics::TransformationJoint::set_transformation_child_to_parent()</a>, <a href="classIMP_1_1multifit_1_1FittingSolutionRecord.html#a630272d692c4a3ca1667619ab555ddb7">IMP::multifit::FittingSolutionRecord::set_dock_transformation()</a>, <a href="classIMP_1_1multifit_1_1FittingSolutionRecord.html#a5691631ad5cb65972c19a04120ded5be">IMP::multifit::FittingSolutionRecord::set_fit_transformation()</a>, <a href="classIMP_1_1spb_1_1DistanceRMSDMetric.html#a0a0bf383cc7420e3f6d389ff6dbb251f">IMP::spb::DistanceRMSDMetric::get_transformation()</a>, <a href="classIMP_1_1spb_1_1PbcBoxedMover.html#a809ab75d13edfc108f6b6beb6db3be37">IMP::spb::PbcBoxedMover::get_transformation()</a>, <a href="classIMP_1_1spb_1_1PbcBoxedRigidBodyMover.html#a0fdb29cf211306df2a0812f2141cc091">IMP::spb::PbcBoxedRigidBodyMover::get_transformation()</a>, <a href="classIMP_1_1spb_1_1TransformationSymmetry.html#abbd918cd369d5b315141934b20ac0868">IMP::spb::TransformationSymmetry::TransformationSymmetry()</a>, <a href="namespaceIMP_1_1algebra.html#af2121b116324f67ee007e4aef258555c">IMP::algebra::compose()</a>, <a href="namespaceIMP_1_1algebra.html#aee0ec0159d4e39827517da06b6e354a5">IMP::algebra::compose_adjoint()</a>, <a href="namespaceIMP_1_1algebra.html#a7ba58ded833da82158e5830aa9ffb6b2">IMP::algebra::compose_adjoint()</a>, <a href="namespaceIMP_1_1algebra.html#a4a5934ef70db58630906eaaf2ff5bae8">IMP::algebra::get_rmsd_transforming_first()</a>, <a href="namespaceIMP_1_1algebra.html#ad1ae16d9089296d2d7f458c2d667e587">IMP::algebra::get_transformed()</a>, <a href="namespaceIMP_1_1algebra.html#aec3bea2d24fbbf621216822517ca1593">IMP::algebra::get_transformed()</a>, <a href="namespaceIMP_1_1algebra.html#a151019bab90b6cdc2f1755c6b7a92bdc">IMP::algebra::get_transformed()</a>, <a href="namespaceIMP_1_1algebra.html#a6fd63b261e533e6e344228afadfca32f">IMP::algebra::get_weighted_rmsd_transforming_first()</a>, <a href="namespaceIMP_1_1atom.html#a6548fc0fb1b2329ba9bb38511610953c">IMP::atom::get_rmsd_transforming_first()</a>, <a href="namespaceIMP_1_1atom.html#a603f2b73d6e22b3a9128e0398bc6e082">IMP::atom::get_rmsd_transforming_first()</a>, <a href="namespaceIMP_1_1atom.html#adf218eed76f556ada452b525acd835ee">IMP::atom::transform()</a>, <a href="namespaceIMP_1_1cnmultifit.html#a3733609ff3265bd070779045acf03fca">IMP::cnmultifit::build_cn_dens_assembly()</a>, <a href="namespaceIMP_1_1cnmultifit.html#a4a6654fa258c0a93903370ff327d4199">IMP::cnmultifit::transform_cn_assembly()</a>, <a href="namespaceIMP_1_1core.html#a556f7cad1de8ed389d05b4d7acbeb4d0">IMP::core::transform()</a>, <a href="namespaceIMP_1_1core.html#a4c5298df54cae6b0e4419852390281be">IMP::core::transform()</a>, <a href="namespaceIMP_1_1em.html#a5a49f58c2b493fe460df2a1f42aed80d">IMP::em::get_number_of_particles_outside_of_the_density()</a>, <a href="namespaceIMP_1_1em.html#a6ac62bc20e89bf2c6e8f8f6bb5cbca5a">IMP::em::get_percentage_of_voxels_covered_by_particles()</a>, <a href="namespaceIMP_1_1em.html#abd0e642dde82199ac2b181e297526241">IMP::em::get_transformed_into2()</a></td></tr>
91 <tr><td>@ref IMP::algebra::Triangle3D</td><td><a href="classIMP_1_1display_1_1TriangleGeometry.html#a035a07939f07970172cd8e8349277f90">IMP::display::TriangleGeometry::TriangleGeometry()</a>, <a href="classIMP_1_1display_1_1TriangleGeometry.html#a8880501417b489547a254c4c2003cf3d">IMP::display::TriangleGeometry::TriangleGeometry()</a>, <a href="classIMP_1_1display_1_1TriangleGeometry.html#a6a039b1098c7111bafe6a715fdbdc6ba">IMP::display::TriangleGeometry::TriangleGeometry()</a>, <a href="classIMP_1_1display_1_1TriangleGeometry.html#a33df56da0761fbdde97e8e938c13b96a">IMP::display::TriangleGeometry::TriangleGeometry()</a>, <a href="classIMP_1_1display_1_1TriangleGeometry.html#a9c7b1a40aaf76f2d29c5c38be25ce8d4">IMP::display::TriangleGeometry::set_geometry()</a>, <a href="namespaceIMP_1_1algebra.html#a40b9b1290fa21102bda8255d8eb3c4d8">IMP::algebra::get_transformation_from_first_triangle_to_second()</a>, <a href="namespaceIMP_1_1display.html#a54a071369efd0709c091051cd6355e67">IMP::display::create_geometry()</a></td></tr>
92 <tr><td>@ref IMP::algebra::UnitSimplexD</td><td><a href="namespaceIMP_1_1algebra.html#a98110c41b03335f1cd92afd6b31dc072">IMP::algebra::get_random_vector_on()</a>, <a href="namespaceIMP_1_1algebra.html#aa4da44bccd16cdd03d99be6dba3c9bb1">IMP::algebra::get_embedded_from_increasing()</a>, <a href="namespaceIMP_1_1algebra.html#ad15dcdb7389932d61124924f60e2249c">IMP::algebra::get_increasing_from_embedded()</a>, <a href="namespaceIMP_1_1algebra.html#aa359f8016971b4ea9ae8642f51490a9c">IMP::algebra::get_projected()</a>, <a href="namespaceIMP_1_1algebra.html#a8de5b9c2c7304487d384942301cdfde3">IMP::algebra::get_triangle_3d()</a>, <a href="namespaceIMP_1_1algebra.html#ab92aec57b46d729379791cdda2d5d9b6">IMP::algebra::get_vertices()</a></td></tr>
93 <tr><td>@ref IMP::algebra::VectorBaseD</td><td><a href="classIMP_1_1algebra_1_1VectorBaseD.html#a6d175c10b69919d25d4bf5675a1cdaa1">IMP::algebra::VectorBaseD::check_compatible_vector()</a>, <a href="classIMP_1_1algebra_1_1VectorBaseD.html#a19b24b188ccfe587839d8b422e2bad70">IMP::algebra::VectorBaseD::get_scalar_product()</a></td></tr>
94 <tr><td>@ref IMP::algebra::VectorD</td><td><a href="classIMP_1_1algebra_1_1BoundingBoxD.html#a7850dae79dc4afd896372a3a3156e027">IMP::algebra::BoundingBoxD::BoundingBoxD()</a>, <a href="classIMP_1_1algebra_1_1BoundingBoxD.html#af4deddc06a6067f120d36d48d8cc5ecd">IMP::algebra::BoundingBoxD::BoundingBoxD()</a>, <a href="classIMP_1_1algebra_1_1BoundingBoxD.html#a612cedf52eea6d53f4ce2d5e219541b7">IMP::algebra::BoundingBoxD::BoundingBoxD()</a>, <a href="classIMP_1_1algebra_1_1BoundingBoxD.html#a79a46310633b3f17c6ba14b06f25492f">IMP::algebra::BoundingBoxD::get_contains()</a>, <a href="classIMP_1_1algebra_1_1BoundingBoxD.html#abe7e39f1ee5d58dae32272ee29e51f0b">IMP::algebra::BoundingBoxD::operator+=()</a>, <a href="classIMP_1_1algebra_1_1DefaultEmbeddingD.html#a9b5bbdb991053c94930f1a13f08555df">IMP::algebra::DefaultEmbeddingD::get_elementwise_product()</a>, <a href="classIMP_1_1algebra_1_1DefaultEmbeddingD.html#a8d2e2913eb8be64456c599b7cf91ce2a">IMP::algebra::DefaultEmbeddingD::DefaultEmbeddingD()</a>, <a href="classIMP_1_1algebra_1_1DefaultEmbeddingD.html#a7c5f5633d6495ade19fa00cca4dccff5">IMP::algebra::DefaultEmbeddingD::get_extended_index()</a>, <a href="classIMP_1_1algebra_1_1DefaultEmbeddingD.html#ae4437a1c4ca95b4abbf58c9531209d02">IMP::algebra::DefaultEmbeddingD::get_index()</a>, <a href="classIMP_1_1algebra_1_1DefaultEmbeddingD.html#a2bac26324f8cff64d5c484aa94d5bde9">IMP::algebra::DefaultEmbeddingD::set_origin()</a>, <a href="classIMP_1_1algebra_1_1DefaultEmbeddingD.html#a0f1379242a9846c0eda7c219fe08b937">IMP::algebra::DefaultEmbeddingD::set_unit_cell()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#a81b743c5cc601b32b1eb1b31874afeb6">IMP::algebra::GridD::get_nearest_index()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#a0e464be5a75232f1392a54c3bd9711eb">IMP::algebra::GridD::get_nearest_extended_index()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#ab96be5a02e7d8a1729e6b47e8f6b93da">IMP::algebra::GridD::GridD()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#adb32bd20c18445dd15609b6d71ab6eff">IMP::algebra::GridD::GridD()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#a1331afb93fdf474e352ce38076a1dd56">IMP::algebra::GridD::GridD()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#a24ba706b342d7dc7e3c5cb42ed64fccf">IMP::algebra::GridD::add_voxel()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#a6ed148a6870b552c9a0ece4fbade160f">IMP::algebra::GridD::at()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#adb7e2e9c0cb96a26c31683ac51541273">IMP::algebra::GridD::at()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#a4253e432b3e29c9717dec9cdc29ba314">IMP::algebra::GridD::operator[]()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#adf5b3de175047e40a340c7acdb47b7d9">IMP::algebra::GridD::operator[]()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#a16239837f79a0844a742d9282646b83e">IMP::algebra::LogEmbeddingD::LogEmbeddingD()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#a11cfe0991d05693602b83f0a601a9c26">IMP::algebra::LogEmbeddingD::LogEmbeddingD()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#a8d697bdd7ff524e64906160bd1cea582">IMP::algebra::LogEmbeddingD::LogEmbeddingD()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#a333cca1384be415a4beb6423dc4e6273">IMP::algebra::LogEmbeddingD::get_extended_index()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#a09613ab4444befc995178b6b8a416358">IMP::algebra::LogEmbeddingD::get_index()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#ad08277a3eeb3b3e7e1c7e78420efc7ea">IMP::algebra::LogEmbeddingD::set_origin()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#a49a414e862bc4b3722e1c4e09bb2ff32">IMP::algebra::LogEmbeddingD::set_unit_cell()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#a789d0401da99b97b26b6f1d685a42a1e">IMP::algebra::LogEmbeddingD::set_unit_cell()</a>, <a href="classIMP_1_1algebra_1_1NearestNeighborD.html#aa7bdb458b64d199dc003b10a6a25d951">IMP::algebra::NearestNeighborD::NearestNeighborD()</a>, <a href="classIMP_1_1algebra_1_1NearestNeighborD.html#ae8e3cd61ac7781993d837de4bb875b41">IMP::algebra::NearestNeighborD::get_in_ball()</a>, <a href="classIMP_1_1algebra_1_1NearestNeighborD.html#a4b167c84313976e55534a4324732673e">IMP::algebra::NearestNeighborD::get_nearest_neighbor()</a>, <a href="classIMP_1_1algebra_1_1NearestNeighborD.html#a7beece69ce6579d62acad7e1bb8fed83">IMP::algebra::NearestNeighborD::get_nearest_neighbors()</a>, <a href="classIMP_1_1algebra_1_1PrincipalComponentAnalysisD.html#a446bf7701bd38a6e6aa307aa4031e419">IMP::algebra::PrincipalComponentAnalysisD::PrincipalComponentAnalysisD()</a>, <a href="classIMP_1_1algebra_1_1PrincipalComponentAnalysisD.html#acda30c2ce2059cbc07177515cafa9397">IMP::algebra::PrincipalComponentAnalysisD::set_centroid()</a>, <a href="classIMP_1_1algebra_1_1Rotation3D.html#a7f9a88f4c31d4d8f2115beeda2a979a8">IMP::algebra::Rotation3D::Rotation3D()</a>, <a href="classIMP_1_1algebra_1_1SphereD.html#abd5763e637b98958069b7ba8806fd209">IMP::algebra::SphereD::SphereD()</a>, <a href="classIMP_1_1algebra_1_1SphereD.html#a9c5b271fe56058daa14d41b4463994e1">IMP::algebra::SphereD::get_contains()</a>, <a href="classIMP_1_1algebra_1_1UnitSimplexBaseD.html#a5cfd4528d5d55177a1fa777a4976dfb4">IMP::algebra::UnitSimplexBaseD::get_contains()</a>, <a href="classIMP_1_1algebra_1_1VectorD.html#a6a954f4fa6f2c313b4bb83672fc48f32">IMP::algebra::VectorD::VectorD()</a>, <a href="classIMP_1_1algebra_1_1VectorD.html#ac4af6defcf88fe29cefed14a2f3a28cb">IMP::algebra::VectorD::operator*()</a>, <a href="classIMP_1_1algebra_1_1VectorD.html#a441606f948618b1faa1372da374647b2">IMP::algebra::VectorD::operator+()</a>, <a href="classIMP_1_1algebra_1_1VectorD.html#abf2def3932df79b1c577d4eaba27b5da">IMP::algebra::VectorD::operator+=()</a>, <a href="classIMP_1_1algebra_1_1VectorD.html#a35f40a1bd09bdb4cf1c48c7b189be911">IMP::algebra::VectorD::operator-()</a>, <a href="classIMP_1_1algebra_1_1VectorD.html#ad2e8dd83e90954e1b9bfa24d2ecff466">IMP::algebra::VectorD::operator-=()</a>, <a href="classIMP_1_1example_1_1ExampleTemplateClassD.html#aa93938fc836a0c96102da8f1530e1e6c">IMP::example::ExampleTemplateClassD::ExampleTemplateClassD()</a>, <a href="classIMP_1_1multifit_1_1GeometricHash.html#a8dbc8daec12deaf6fad60f92ed5837e2">IMP::multifit::GeometricHash::GeometricHash()</a>, <a href="classIMP_1_1multifit_1_1GeometricHash.html#a55cdc6df5f5b89e3c5f8f42e4a1b749d">IMP::multifit::GeometricHash::add()</a>, <a href="classIMP_1_1multifit_1_1GeometricHash.html#a66c9f0b496a518db3e5dcc57a52e0618">IMP::multifit::GeometricHash::bucket()</a>, <a href="classIMP_1_1multifit_1_1GeometricHash.html#afe9af3b97de330452c7586379948501d">IMP::multifit::GeometricHash::neighbors()</a>, <a href="classIMP_1_1multifit_1_1GeometricHash.html#a6c2ba8256d11954e48844f26d8a09ff4">IMP::multifit::GeometricHash::neighbors()</a>, <a href="classIMP_1_1multifit_1_1GeometricHash.html#a4a243f10f4650280f7873c0e2e5f5d4a">IMP::multifit::GeometricHash::neighbors()</a>, <a href="classIMP_1_1multifit_1_1GeometricHash.html#adb8e5c95a478e0bbe3d809319c83b1b9">IMP::multifit::GeometricHash::neighbors()</a>, <a href="classIMP_1_1multifit_1_1GeometricHash.html#ad836b61873521a48bf1a0211f2d139f2">IMP::multifit::GeometricHash::neighbors_data()</a>, <a href="classIMP_1_1multifit_1_1GeometricHash.html#a3846d3f77b57a015b3294005fd1fa6e5">IMP::multifit::GeometricHash::cube_inside_sphere_rec()</a>, <a href="classIMP_1_1multifit_1_1GeometricHash.html#ae094fb3a173684802c426d64a8e88c6d">IMP::multifit::GeometricHash::to_bucket()</a>, <a href="classIMP_1_1multifit_1_1GeometricHash.html#ab715cee46df8e90e95c9981a8b7d6a9e">IMP::multifit::GeometricHash::inf_distance()</a>, <a href="classIMP_1_1spb_1_1TiltSingletonScore.html#a342433901f7f30ddc1d221ea9a2ea5c7">IMP::spb::TiltSingletonScore::TiltSingletonScore()</a>, <a href="classIMP_1_1statistics_1_1HistogramD.html#a592798e458c9acaded04b9ed7a9a95d7">IMP::statistics::HistogramD::add()</a>, <a href="classIMP_1_1statistics_1_1HistogramD.html#aa8f8a40723844f8f480074771dc3f0d2">IMP::statistics::HistogramD::get_standard_deviation()</a>, <a href="namespaceIMP_1_1algebra.html#a964a6d360e228da939368f3621f6aab9">IMP::algebra::get_l2_norm()</a>, <a href="namespaceIMP_1_1algebra.html#a7574f7e7033de011d30e6c1a22a034f4">IMP::algebra::get_l1_norm()</a>, <a href="namespaceIMP_1_1algebra.html#aab0012e9e00266f181f4ec0ab7f01444">IMP::algebra::get_linf_norm()</a>, <a href="namespaceIMP_1_1algebra.html#aa040b3bcfec950a979371f3e19b14058">IMP::algebra::compare()</a>, <a href="namespaceIMP_1_1algebra.html#a01d00ac6807479bb970254b3e188bcc6">IMP::algebra::get_distance()</a>, <a href="namespaceIMP_1_1algebra.html#af800ee8500d39c126da5897ca6f8ebaa">IMP::algebra::get_elementwise_product()</a>, <a href="namespaceIMP_1_1algebra.html#a019cfab4b720c4002cd8ca3085176778">IMP::algebra::get_elementwise_product()</a>, <a href="namespaceIMP_1_1algebra.html#aa4da44bccd16cdd03d99be6dba3c9bb1">IMP::algebra::get_embedded_from_increasing()</a>, <a href="namespaceIMP_1_1algebra.html#ad15dcdb7389932d61124924f60e2249c">IMP::algebra::get_increasing_from_embedded()</a>, <a href="namespaceIMP_1_1algebra.html#adb4e0a724bc2f1f9c54e3ebc9437c260">IMP::algebra::get_linearly_interpolated()</a>, <a href="namespaceIMP_1_1algebra.html#a45f138d8d70f63b404c8ffc9e9b2896e">IMP::algebra::get_principal_components()</a>, <a href="namespaceIMP_1_1algebra.html#aa359f8016971b4ea9ae8642f51490a9c">IMP::algebra::get_projected()</a>, <a href="namespaceIMP_1_1algebra.html#a3003fd1a5254db165a8600f2979e7146">IMP::algebra::get_rotation_from_vector4d()</a>, <a href="namespaceIMP_1_1algebra.html#af6c0ba059d657cbc42dad97dfb6cc490">IMP::algebra::get_squared_distance()</a>, <a href="namespaceIMP_1_1algebra.html#afdc2e1d2d13e716a0d8b2b315187e13e">IMP::algebra::operator*()</a></td></tr>
95 </table>
96 # IMP.atom # {#argument_index_atom}
97 <table><tr>
98 <th>Class</th><th>Users</th></tr>
99 <tr><td>@ref IMP::atom::AngularVelocity</td><td><a href="classIMP_1_1atom_1_1AngularVelocity.html#a0c0a1b0bb984aa424ee4a4d35f3b01ef">IMP::atom::AngularVelocity::IMP_DECORATOR_METHODS()</a>, <a href="classIMP_1_1atom_1_1AngularVelocity.html#a12cf8ad5cf55cb685f71561427aa690d">IMP::atom::AngularVelocity::IMP_DECORATOR_SETUP_0()</a>, <a href="classIMP_1_1atom_1_1AngularVelocity.html#a497dddb1030251caf4f8f9652f2badf6">IMP::atom::AngularVelocity::IMP_DECORATOR_SETUP_1()</a></td></tr>
100 <tr><td>@ref IMP::atom::Atom</td><td><a href="classIMP_1_1atom_1_1Atom.html#a129e3c38ccce94e7468e7cb504a040a3">IMP::atom::Atom::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Atom.html#a8673b3453596560cdbe50d3dbf4815a0">IMP::atom::Atom::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Atom.html#aa05431b15bea7b5c936623226d4501c1">IMP::atom::Atom::setup_particle()</a>, <a href="classIMP_1_1atom_1_1CHARMMParameters.html#ac05940015eac5733ba23c5dd1c405cb7">IMP::atom::CHARMMParameters::get_force_field_atom_type()</a>, <a href="classIMP_1_1atom_1_1ForceFieldParameters.html#a7ab2b4cd229510811991b7e5b72760a0">IMP::atom::ForceFieldParameters::get_epsilon()</a>, <a href="classIMP_1_1atom_1_1ForceFieldParameters.html#aa18ecbbff837742ea4cf8ae2c1e144f6">IMP::atom::ForceFieldParameters::get_radius()</a>, <a href="classIMP_1_1atom_1_1ForceFieldParameters.html#a8f1bb071899906abd71171f38b934ba1">IMP::atom::ForceFieldParameters::get_force_field_atom_type()</a>, <a href="classIMP_1_1kinematics_1_1ProteinKinematics.html#a28d16f8a623da30f013632758da625bb">IMP::kinematics::ProteinKinematics::mark_rotatable_angle()</a>, <a href="classIMP_1_1score__functor_1_1OrientedSoap.html#ad88beca24508ce2d57b8fae69f8034bb">IMP::score_functor::OrientedSoap::score_doublets()</a>, <a href="namespaceIMP_1_1atom.html#a1b9a562a6a9548c3e85047d8fe53183d">IMP::atom::get_residue()</a>, <a href="namespaceIMP_1_1pmi.html#a92ba20c3853f0f1b366f4fece0a7b387">IMP::pmi::get_dihedral_angle()</a>, <a href="namespaceIMP_1_1pmi1.html#a82af7f80d3f8f96a55a9dbaca7999cae">IMP::pmi1::get_dihedral_angle()</a></td></tr>
101 <tr><td>@ref IMP::atom::AtomType</td><td><a href="classIMP_1_1atom_1_1Atom.html#a2b24077e12488f4f1370697fc0776755">IMP::atom::Atom::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Atom.html#a8dfcc4758811f77db0c3cac0dc0ed992">IMP::atom::Atom::set_atom_type()</a>, <a href="classIMP_1_1atom_1_1Atom.html#ae77d0503f22ce6b6902900807ee92829">IMP::atom::Atom::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Atom.html#a0001e1b21f8f133618a3dd12482eb910">IMP::atom::Atom::setup_particle()</a>, <a href="classIMP_1_1atom_1_1CHARMMResidueTopologyBase.html#a91fff9329d2a36aa42719d443fb5fc35">IMP::atom::CHARMMResidueTopologyBase::get_atom()</a>, <a href="classIMP_1_1atom_1_1ForceFieldParameters_1_1Bond.html#a23a3cef96fb2868431d501bb9811df0a">IMP::atom::ForceFieldParameters::Bond::Bond()</a>, <a href="classIMP_1_1atom_1_1Selection.html#a1aa9fab76bf21cfdab1e7b25751a094a">IMP::atom::Selection::Selection()</a>, <a href="classIMP_1_1atom_1_1Selection.html#aa8af1e705fed866dd406011e8e6b2937">IMP::atom::Selection::set_atom_type()</a>, <a href="classIMP_1_1rotamer_1_1ResidueRotamer.html#ada53a356af89839596eb5148c15de6d8">IMP::rotamer::ResidueRotamer::get_atom_exists()</a>, <a href="classIMP_1_1rotamer_1_1ResidueRotamer.html#aa3b628cc432c926a0a90b6065eeb0592">IMP::rotamer::ResidueRotamer::get_coordinates()</a>, <a href="classIMP_1_1rotamer_1_1ResidueRotamer.html#a4e6c416e3801b8584c2e712a7a397cf5">IMP::rotamer::ResidueRotamer::get_number_of_cases()</a>, <a href="classIMP_1_1rotamer_1_1ResidueRotamer.html#a4303f70f6f7cea1ef5fbbf126b88abeb">IMP::rotamer::ResidueRotamer::add_coordinates()</a>, <a href="classIMP_1_1rotamer_1_1ResidueRotamer.html#aa7af13636acbba99ebef5cca6754265c">IMP::rotamer::ResidueRotamer::get_coordinates()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#ae5a59dd0ebd0d5590db3d2127444204e">IMP::saxs::FormFactorTable::get_carbon_atom_type()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#adc7d132da89b412ddc3bed43094c29a5">IMP::saxs::FormFactorTable::get_nitrogen_atom_type()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#a01b57170c71bbaa7edc35ce486805ac6">IMP::saxs::FormFactorTable::get_oxygen_atom_type()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#a3453246d72667c72492393cb9e7b00e1">IMP::saxs::FormFactorTable::get_sulfur_atom_type()</a>, <a href="namespaceIMP_1_1atom.html#a899927712a6b9ae00aa8875407f5311a">IMP::atom::get_atom()</a>, <a href="namespaceIMP_1_1atom.html#a75d5d735a5ea9dcfc3289baae0dd51fe">IMP::atom::get_element_for_atom_type()</a></td></tr>
102 <tr><td>@ref IMP::atom::Bond</td><td><a href="classIMP_1_1atom_1_1BondGeometry.html#a02bf784b049c0439f004cbd1a70cd490">IMP::atom::BondGeometry::BondGeometry()</a>, <a href="group__bond.html#ga1c817f9827d6115fe10530ca349098fa">IMP::atom::create_bond()</a>, <a href="group__bond.html#ga53d105256db430c876b1a83c5a2786a4">IMP::atom::destroy_bond()</a></td></tr>
103 <tr><td>@ref IMP::atom::Bonded</td><td><a href="group__bond.html#gad928d4afc3de5646070a1a55499772d3">IMP::atom::create_bond()</a>, <a href="group__bond.html#ga1c817f9827d6115fe10530ca349098fa">IMP::atom::create_bond()</a>, <a href="group__bond.html#ga4434a119a32491177223b0fe0d6f7d6d">IMP::atom::create_custom_bond()</a>, <a href="group__bond.html#gaf75358e1a709b3b9cf2153bf741b5efa">IMP::atom::get_bond()</a></td></tr>
104 <tr><td>@ref IMP::atom::BrownianDynamics</td><td><a href="namespaceIMP_1_1atom.html#a0e5dbe5aa039ab94bb0bdd9cb18bf91e">IMP::atom::get_maximum_time_step_estimate()</a></td></tr>
105 <tr><td>@ref IMP::atom::CHARMMAtomTopology</td><td><a href="classIMP_1_1atom_1_1CHARMMAtomTopology.html#ad1fb27edcbf97c268c4f0db85b45f7b2">IMP::atom::CHARMMAtomTopology::CHARMMAtomTopology()</a>, <a href="classIMP_1_1atom_1_1CHARMMResidueTopologyBase.html#a010e65c13afaec4e7740704393aca2b1">IMP::atom::CHARMMResidueTopologyBase::add_atom()</a></td></tr>
106 <tr><td>@ref IMP::atom::CHARMMBondEndpoint</td><td><a href="classIMP_1_1atom_1_1CHARMMConnection.html#a9625d8ee87f5a2d67148cf1c47a12e95">IMP::atom::CHARMMConnection::CHARMMConnection()</a>, <a href="classIMP_1_1atom_1_1CHARMMInternalCoordinate.html#a6dea63854f3357e4abf39965864726c8">IMP::atom::CHARMMInternalCoordinate::CHARMMInternalCoordinate()</a></td></tr>
107 <tr><td>@ref IMP::atom::CHARMMConnection</td><td><a href="classIMP_1_1atom_1_1CHARMMResidueTopologyBase.html#a9347ca0463be92c325e6a102f1a55c91">IMP::atom::CHARMMResidueTopologyBase::add_angle()</a>, <a href="classIMP_1_1atom_1_1CHARMMResidueTopologyBase.html#af6451fe6bbacb79b49b9cd547fde5f05">IMP::atom::CHARMMResidueTopologyBase::add_bond()</a>, <a href="classIMP_1_1atom_1_1CHARMMResidueTopologyBase.html#a736a8348838b728ca24de82ebad1355a">IMP::atom::CHARMMResidueTopologyBase::add_dihedral()</a>, <a href="classIMP_1_1atom_1_1CHARMMResidueTopologyBase.html#aad7ed56d6b1421d1ee7fdd526e546533">IMP::atom::CHARMMResidueTopologyBase::add_improper()</a></td></tr>
108 <tr><td>@ref IMP::atom::CHARMMIdealResidueTopology</td><td><a href="classIMP_1_1atom_1_1CHARMMParameters.html#a532d6c3f6529759fccff26616f0f7e27">IMP::atom::CHARMMParameters::add_residue_topology()</a>, <a href="classIMP_1_1atom_1_1CHARMMResidueTopology.html#adf36f0b3ed6504c273e75a78dd024e70">IMP::atom::CHARMMResidueTopology::CHARMMResidueTopology()</a></td></tr>
109 <tr><td>@ref IMP::atom::CHARMMInternalCoordinate</td><td><a href="classIMP_1_1atom_1_1CHARMMResidueTopologyBase.html#a9142afbbc65ceebb6c471f4ae8825c91">IMP::atom::CHARMMResidueTopologyBase::add_internal_coordinate()</a></td></tr>
110 <tr><td>@ref IMP::atom::CHARMMParameters</td><td><a href="classIMP_1_1atom_1_1CHARMMSegmentTopology.html#a61807dec0e56f4a375bc9e6b6f62d574">IMP::atom::CHARMMSegmentTopology::apply_default_patches()</a>, <a href="classIMP_1_1atom_1_1CHARMMTopology.html#aa10f457dd2b70f950ea875a3f271ae86">IMP::atom::CHARMMTopology::CHARMMTopology()</a></td></tr>
111 <tr><td>@ref IMP::atom::CHARMMPatch</td><td><a href="classIMP_1_1atom_1_1CHARMMParameters.html#ad47e2ffd1893d14ac6b120b12213b9aa">IMP::atom::CHARMMParameters::add_patch()</a></td></tr>
112 <tr><td>@ref IMP::atom::CHARMMResidueTopology</td><td><a href="classIMP_1_1atom_1_1CHARMMBondEndpoint.html#a78501b3f4e2e1f8f67ac507253244ade">IMP::atom::CHARMMBondEndpoint::CHARMMBondEndpoint()</a>, <a href="classIMP_1_1atom_1_1CHARMMBondEndpoint.html#a5271a836eccdc72f7763d32a0af46573">IMP::atom::CHARMMBondEndpoint::get_atom()</a>, <a href="classIMP_1_1atom_1_1CHARMMConnection.html#adf29f3ca8131dfa961d939a35ce4af60">IMP::atom::CHARMMConnection::get_atoms()</a>, <a href="classIMP_1_1atom_1_1CHARMMPatch.html#a3e11ae77d0d6eade9acbe77caf143b92">IMP::atom::CHARMMPatch::apply()</a>, <a href="classIMP_1_1atom_1_1CHARMMPatch.html#ac0f0e4636e87cb7aa2dc2da9de0fca2d">IMP::atom::CHARMMPatch::apply()</a>, <a href="classIMP_1_1atom_1_1CHARMMSegmentTopology.html#a44a86531107d85bdafc879df3e68c987">IMP::atom::CHARMMSegmentTopology::remove_residue()</a>, <a href="classIMP_1_1atom_1_1CHARMMSegmentTopology.html#ab93a919188ee694d37ed07f146fc5e20">IMP::atom::CHARMMSegmentTopology::add_residue()</a></td></tr>
113 <tr><td>@ref IMP::atom::CHARMMResidueTopologyBase</td><td><a href="classIMP_1_1atom_1_1CHARMMParameters.html#a0e017ab02dc3673cfa7cd48fb6e4686d">IMP::atom::CHARMMParameters::parse_atom_line()</a>, <a href="classIMP_1_1atom_1_1CHARMMParameters.html#aa0c19662e8ac391cdce1666af3b810eb">IMP::atom::CHARMMParameters::parse_bond_line()</a></td></tr>
114 <tr><td>@ref IMP::atom::CHARMMSegmentTopology</td><td><a href="classIMP_1_1atom_1_1CHARMMTopology.html#a26bc410f529a0f187d78db52d401a7ad">IMP::atom::CHARMMTopology::remove_segment()</a>, <a href="classIMP_1_1atom_1_1CHARMMTopology.html#aa24e0702d81ced734eba1ec5533a411f">IMP::atom::CHARMMTopology::add_segment()</a></td></tr>
115 <tr><td>@ref IMP::atom::CHARMMTopology</td><td><a href="classIMP_1_1atom_1_1CHARMMStereochemistryRestraint.html#aa053a5423e162bc45edb28ed4777bf57">IMP::atom::CHARMMStereochemistryRestraint::CHARMMStereochemistryRestraint()</a>, <a href="classIMP_1_1atom_1_1CHARMMStereochemistryRestraint.html#ae55a4983c41e935a811d933ba32a60c8">IMP::atom::CHARMMStereochemistryRestraint::CHARMMStereochemistryRestraint()</a></td></tr>
116 <tr><td>@ref IMP::atom::CenterOfMass</td><td><a href="classIMP_1_1atom_1_1CenterOfMass.html#a7a1789c85c3f0d71008c1a5d4c4fe914">IMP::atom::CenterOfMass::teardown_particle()</a></td></tr>
117 <tr><td>@ref IMP::atom::Chain</td><td><a href="classIMP_1_1atom_1_1Chain.html#a177a82bf81cb3793fc3d07e1a670e841">IMP::atom::Chain::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Chain.html#a1a39ce6772b2575cbe7cf3478c504f1e">IMP::atom::Chain::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Chain.html#ab65be1b3500bbf38bc1223075d66db16">IMP::atom::Chain::setup_particle()</a>, <a href="namespaceIMP_1_1atom.html#af12315103e56599289223816dc3b3aeb">IMP::atom::create_simplified_along_backbone()</a></td></tr>
118 <tr><td>@ref IMP::atom::ChainType</td><td><a href="classIMP_1_1atom_1_1Chain.html#a909409d14e1fd0c5e9e66858b9091cfc">IMP::atom::Chain::set_chain_type()</a></td></tr>
119 <tr><td>@ref IMP::atom::Domain</td><td><a href="classIMP_1_1atom_1_1Domain.html#a819670ecca8da38947c51a89c4a03b76">IMP::atom::Domain::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Domain.html#a5584f87cb8159c5de3b8c59e40d73a5e">IMP::atom::Domain::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Domain.html#a3a0129647c98c031a50340344fc708f2">IMP::atom::Domain::setup_particle()</a></td></tr>
120 <tr><td>@ref IMP::atom::ForceFieldParameters</td><td><a href="namespaceIMP_1_1atom.html#a0b3af7559bf1bed6ecdfe98701fab423">IMP::atom::add_bonds()</a>, <a href="namespaceIMP_1_1atom.html#ad6e74dd86fdc8480090199a6cdc8bf55">IMP::atom::add_radii()</a></td></tr>
121 <tr><td>@ref IMP::atom::Fragment</td><td><a href="classIMP_1_1atom_1_1Fragment.html#a687ca04e39b23144786cc5d835b84218">IMP::atom::Fragment::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Fragment.html#a51312f05a7e6f3637e687541fbe4852d">IMP::atom::Fragment::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Fragment.html#a666570dc72f118be1ddf31cfcd960661">IMP::atom::Fragment::setup_particle()</a></td></tr>
122 <tr><td>@ref IMP::atom::Hierarchy</td><td><a href="classIMP_1_1atom_1_1BondGraph.html#a93e77475a24d5f08f9568e11befa2224">IMP::atom::BondGraph::BondGraph()</a>, <a href="classIMP_1_1atom_1_1CHARMMBondEndpoint.html#a5271a836eccdc72f7763d32a0af46573">IMP::atom::CHARMMBondEndpoint::get_atom()</a>, <a href="classIMP_1_1atom_1_1CHARMMConnection.html#adf29f3ca8131dfa961d939a35ce4af60">IMP::atom::CHARMMConnection::get_atoms()</a>, <a href="classIMP_1_1atom_1_1CHARMMParameters.html#aab56534fc18ba3715778af3f2aea8073">IMP::atom::CHARMMParameters::create_topology()</a>, <a href="classIMP_1_1atom_1_1CHARMMStereochemistryRestraint.html#aa053a5423e162bc45edb28ed4777bf57">IMP::atom::CHARMMStereochemistryRestraint::CHARMMStereochemistryRestraint()</a>, <a href="classIMP_1_1atom_1_1CHARMMStereochemistryRestraint.html#ae55a4983c41e935a811d933ba32a60c8">IMP::atom::CHARMMStereochemistryRestraint::CHARMMStereochemistryRestraint()</a>, <a href="classIMP_1_1atom_1_1CHARMMTopology.html#aab1206d77a4f09ece75f44e668185915">IMP::atom::CHARMMTopology::map_residue_topology_to_hierarchy()</a>, <a href="classIMP_1_1atom_1_1CHARMMTopology.html#aa7c8c6a2a0e48500776a56be1029a7a8">IMP::atom::CHARMMTopology::add_atom_types()</a>, <a href="classIMP_1_1atom_1_1CHARMMTopology.html#a403b30e23e492dc1da0514bd8f5dd149">IMP::atom::CHARMMTopology::add_bonds()</a>, <a href="classIMP_1_1atom_1_1CHARMMTopology.html#aeba76e2f28c02ab70dc1a4b2148e02e4">IMP::atom::CHARMMTopology::add_charges()</a>, <a href="classIMP_1_1atom_1_1CHARMMTopology.html#a4018c73156fe2bdd6257cd861b9acf16">IMP::atom::CHARMMTopology::add_coordinates()</a>, <a href="classIMP_1_1atom_1_1CHARMMTopology.html#af33d6daa29a776882987d0ee4c4c7507">IMP::atom::CHARMMTopology::add_dihedrals()</a>, <a href="classIMP_1_1atom_1_1CHARMMTopology.html#a8093b89059a159c3c31f4d583843aa36">IMP::atom::CHARMMTopology::add_impropers()</a>, <a href="classIMP_1_1atom_1_1CHARMMTopology.html#ae9806eee2eb64e7742e679c0a3217fe3">IMP::atom::CHARMMTopology::add_missing_atoms()</a>, <a href="classIMP_1_1atom_1_1CHARMMTopology.html#a1aef3017da939dbaec3a4f88ab5853bd">IMP::atom::CHARMMTopology::setup_hierarchy()</a>, <a href="classIMP_1_1atom_1_1ForceFieldParameters.html#a8ec3c7e77ae87b988c803bfc2f375772">IMP::atom::ForceFieldParameters::add_bonds()</a>, <a href="classIMP_1_1atom_1_1ForceFieldParameters.html#ad37b61f76545a6e4e6aa67783bfe7f1b">IMP::atom::ForceFieldParameters::add_radii()</a>, <a href="classIMP_1_1atom_1_1ForceFieldParameters.html#a797d6ab508017979fb7d5ab6dbeae578">IMP::atom::ForceFieldParameters::add_well_depths()</a>, <a href="classIMP_1_1atom_1_1Hierarchy.html#a6a8c2cba388bf79adef66c28a7c78a57">IMP::atom::Hierarchy::add_child()</a>, <a href="classIMP_1_1atom_1_1Hierarchy.html#ad75a34753bf156665572134c16cec886">IMP::atom::Hierarchy::create_clone()</a>, <a href="classIMP_1_1atom_1_1Hierarchy.html#abbbefbfaf89bcb6b38a4ec0378c9766a">IMP::atom::Hierarchy::create_clone_one()</a>, <a href="classIMP_1_1atom_1_1Hierarchy.html#a6b0f7ef3e58cd7e8ebca949c2478e6d6">IMP::atom::Hierarchy::destroy()</a>, <a href="classIMP_1_1atom_1_1Hierarchy.html#a0b2a97a5d1d9906dd31d60a8ba588e5a">IMP::atom::Hierarchy::get_bounding_box()</a>, <a href="classIMP_1_1atom_1_1Hierarchy.html#a9ab80a6441e9d05b4779b90aff226012">IMP::atom::Hierarchy::get_bounding_sphere()</a>, <a href="classIMP_1_1atom_1_1Hierarchy.html#a95fbed1f1a06037900159c8dc6767b35">IMP::atom::Hierarchy::get_by_type()</a>, <a href="classIMP_1_1atom_1_1Hierarchy.html#a234db3ebe46ca02a1f2742c535ab3180">IMP::atom::Hierarchy::get_internal_bonds()</a>, <a href="classIMP_1_1atom_1_1Hierarchy.html#ab9cd7eaeb2f192503ebbe0c0b04e4cde">IMP::atom::Hierarchy::get_is_heterogen()</a>, <a href="classIMP_1_1atom_1_1Hierarchy.html#a88d34e2044a5fbfbb25069331da1b527">IMP::atom::Hierarchy::get_leaves()</a>, <a href="classIMP_1_1atom_1_1Hierarchy.html#a86187ce8981c3d096033da90bbbdd0af">IMP::atom::Hierarchy::get_residue()</a>, <a href="classIMP_1_1atom_1_1Hierarchy.html#aa1160975ada3565969069b9709de38b0">IMP::atom::Hierarchy::get_root()</a>, <a href="classIMP_1_1atom_1_1Hierarchy.html#a5dea58cb3af1bb760fbd42ade7a9ce3e">IMP::atom::Hierarchy::show()</a>, <a href="classIMP_1_1atom_1_1ProteinLigandRestraint.html#ae938de2b2aa36558d19a335b0e33787c">IMP::atom::ProteinLigandRestraint::initialize()</a>, <a href="classIMP_1_1atom_1_1ProteinLigandRestraint.html#ae7c1888332ceda6b47560b590cc8dbea">IMP::atom::ProteinLigandRestraint::ProteinLigandRestraint()</a>, <a href="classIMP_1_1atom_1_1ProteinLigandRestraint.html#abc3c5536068dfa6656755334f3430c77">IMP::atom::ProteinLigandRestraint::ProteinLigandRestraint()</a>, <a href="classIMP_1_1atom_1_1Selection.html#a1aa9fab76bf21cfdab1e7b25751a094a">IMP::atom::Selection::Selection()</a>, <a href="classIMP_1_1atom_1_1Selection.html#ab37f62060b5266fbc0f233534ebf41a8">IMP::atom::Selection::Selection()</a>, <a href="classIMP_1_1kinematics_1_1KinematicForest.html#a3b814e2d09d66914a410a7304e30f5ff">IMP::kinematics::KinematicForest::KinematicForest()</a>, <a href="classIMP_1_1kinematics_1_1ProteinKinematics.html#a52c69182a55e364dfbba34880d19f4cb">IMP::kinematics::ProteinKinematics::ProteinKinematics()</a>, <a href="classIMP_1_1kinematics_1_1ProteinKinematics.html#a4d8caa494b87d0d8c85885e1e17a790a">IMP::kinematics::ProteinKinematics::ProteinKinematics()</a>, <a href="classIMP_1_1kinematics_1_1ProteinKinematics.html#a75272db07d39d0512dc8785a64592f7a">IMP::kinematics::ProteinKinematics::ProteinKinematics()</a>, <a href="classIMP_1_1kinematics_1_1ProteinKinematics.html#aeecb67f9f8f67c05f5b8273bcbcd231e">IMP::kinematics::ProteinKinematics::ProteinKinematics()</a>, <a href="classIMP_1_1multifit_1_1Ensemble.html#aaccff3f8521198b49310efcaf86f5ea9">IMP::multifit::Ensemble::add_component_and_fits()</a>, <a href="classIMP_1_1multifit_1_1FFTFitting.html#a136cac955ee735ec87b1238b82aa67ac">IMP::multifit::FFTFitting::do_global_fitting()</a>, <a href="classIMP_1_1multifit_1_1FFTFitting.html#ae47864b146f9cf99c92495967e611d01">IMP::multifit::FFTFitting::do_local_fitting()</a>, <a href="classIMP_1_1multifit_1_1FFTFitting.html#ab18f1bb918cf5b1f45d22d800a80fad4">IMP::multifit::FFTFitting::prepare_probe()</a>, <a href="classIMP_1_1multifit_1_1MergeTreeBuilder.html#ae22a43002fc2abd6556fdc73b5c6166a">IMP::multifit::MergeTreeBuilder::increase_edge()</a>, <a href="classIMP_1_1npctransport_1_1FGChain.html#ab83a13508a81b6943ac2d26d56a1b267">IMP::npctransport::FGChain::set_root()</a>, <a href="classIMP_1_1rotamer_1_1RotamerCalculator.html#a7b2c4dcc21cd3cf6cee2430993a1e756">IMP::rotamer::RotamerCalculator::transform()</a>, <a href="namespaceIMP_1_1atom.html#a830fbd488be01d4f14b53cb840ab7ce9">IMP::atom::add_dope_score_data()</a>, <a href="namespaceIMP_1_1atom.html#a1b4c863b0fefde1c1d95cdf6fed794a8">IMP::atom::create_simplified_along_backbone()</a>, <a href="namespaceIMP_1_1atom.html#ab8f5c1d19389bcbe4c5bee4728069bee">IMP::atom::get_residue_indexes()</a>, <a href="namespaceIMP_1_1atom.html#a7bc45846fa709afb3ea73f2e9a3ad923">IMP::atom::get_residue_type()</a>, <a href="namespaceIMP_1_1atom.html#af4a6c11848aec861d0ef55068cf6261a">IMP::atom::get_atom_type()</a>, <a href="namespaceIMP_1_1atom.html#a4b530a5d405a84e423361b2ba7f93cff">IMP::atom::get_domain_name()</a>, <a href="namespaceIMP_1_1atom.html#ae740b8ef38083ec8033617ac85e91477">IMP::atom::add_loop_statistical_score_data()</a>, <a href="namespaceIMP_1_1atom.html#abfcacb973482471e99c5fb1ca306f20b">IMP::atom::write_mol2()</a>, <a href="namespaceIMP_1_1atom.html#a0176b83aca48c8580d80b88f6d91ef6f">IMP::atom::read_pdb()</a>, <a href="namespaceIMP_1_1atom.html#a948fb97a18c5b5d08144b058d2b39ec6">IMP::atom::add_protein_ligand_score_data()</a>, <a href="namespaceIMP_1_1atom.html#aeb911633eea643d7307e2dbe8e7684a5">IMP::atom::show_molecular_hierarchy()</a>, <a href="namespaceIMP_1_1atom.html#a0b3af7559bf1bed6ecdfe98701fab423">IMP::atom::add_bonds()</a>, <a href="namespaceIMP_1_1atom.html#ad6e74dd86fdc8480090199a6cdc8bf55">IMP::atom::add_radii()</a>, <a href="namespaceIMP_1_1atom.html#a70ac55d293e6851c67b45d7fd55a3163">IMP::atom::create_compatible_rigid_body()</a>, <a href="namespaceIMP_1_1atom.html#a40da5b3553d98acf020078b4e435b12a">IMP::atom::create_rigid_body()</a>, <a href="namespaceIMP_1_1atom.html#a1ec0bdeff49fc6221a7c4e370ba68279">IMP::atom::create_simplified_assembly_from_volume()</a>, <a href="namespaceIMP_1_1atom.html#ad36632c4fe1304975ff1afce38816295">IMP::atom::create_simplified_from_volume()</a>, <a href="namespaceIMP_1_1atom.html#a13fb268fe2be9e83bbd9a1a2197499ef">IMP::atom::get_chain()</a>, <a href="namespaceIMP_1_1atom.html#a46482205ec4626a8fb4800a6bce46af7">IMP::atom::get_chain_id()</a>, <a href="namespaceIMP_1_1atom.html#a8f2e62640647e36570c22b0328283a9c">IMP::atom::get_charmm_untyped_atoms()</a>, <a href="namespaceIMP_1_1atom.html#aa9d8e71ec12f5e1011ed0f457c70ec3a">IMP::atom::get_copy_index()</a>, <a href="namespaceIMP_1_1atom.html#a3ad3ffc63b7488509170066bcd021c4c">IMP::atom::get_hierarchy_tree()</a>, <a href="namespaceIMP_1_1atom.html#a3e2c48e16f6245ccf46936fe4ed5837b">IMP::atom::get_molecule_name()</a>, <a href="namespaceIMP_1_1atom.html#a48aba7ec117050a9a4d05f11266fa56d">IMP::atom::get_representation()</a>, <a href="namespaceIMP_1_1atom.html#a0413486542eba96a7d75081dff43a096">IMP::atom::get_resolution()</a>, <a href="namespaceIMP_1_1atom.html#a230e74d4b499e3e9ada75e78e93c1af8">IMP::atom::get_state_index()</a>, <a href="namespaceIMP_1_1atom.html#ab986bb0421e989ecdf45675e06e143fd">IMP::atom::remove_charmm_untyped_atoms()</a>, <a href="namespaceIMP_1_1atom.html#a86c2aff722129fb074c5e32484dd31aa">IMP::atom::setup_as_approximation()</a>, <a href="namespaceIMP_1_1atom.html#ac52c25104f859e6b56e168c3fc1e4307">IMP::atom::show_with_representations()</a>, <a href="namespaceIMP_1_1atom.html#adf218eed76f556ada452b525acd835ee">IMP::atom::transform()</a>, <a href="namespaceIMP_1_1multifit.html#af83b1866a4b7bb6747eea98bd9bb28e1">IMP::multifit::fft_based_rigid_fitting()</a>, <a href="namespaceIMP_1_1multifit.html#a72317593e3aff9f9e43e2e4f92481f47">IMP::multifit::get_close_to_point()</a>, <a href="namespaceIMP_1_1multifit.html#ad9a90449965866bc3f547eb9e2193399">IMP::multifit::get_points_close_to_molecule()</a>, <a href="namespaceIMP_1_1multifit.html#a602f75b13bf7afebbc5fbfb3ab89e1e9">IMP::multifit::get_points_far_from_molecule()</a>, <a href="namespaceIMP_1_1multifit.html#aedc64c26eefe139ef34e5cce89d13a51">IMP::multifit::molecule2anchors()</a>, <a href="namespaceIMP_1_1npctransport.html#a96dbb54aa78a3ae2f795b3525565044d">IMP::npctransport::add_hierarchy_with_sites()</a>, <a href="namespaceIMP_1_1npctransport.html#ac5025684e81bdc014b287d20e18373d9">IMP::npctransport::create_fg_chain()</a>, <a href="namespaceIMP_1_1npctransport.html#ab096cc50c7e35bf530e712d1bd321809">IMP::npctransport::get_fg_chain()</a>, <a href="namespaceIMP_1_1pmi.html#a2a36ae0688c03337fb7d4dcad3d47e65">IMP::pmi::get_is_canonical()</a>, <a href="namespaceIMP_1_1pmi.html#a29784187f69b015fd2d9ae278d862188">IMP::pmi::get_molecule_name_and_copy()</a>, <a href="namespaceIMP_1_1rmf.html#afb3c4144b9161813668b971b21295c8e">IMP::rmf::add_hierarchy()</a>, <a href="namespaceIMP_1_1spb.html#a5cf4889f38b10df0422f43533e1efa71">IMP::spb::add_diameter_rgyr_restraint()</a>, <a href="namespaceIMP_1_1spb.html#a6a49d172ebb893d6a3b0de6234cb318e">IMP::spb::add_GFP_restraint()</a>, <a href="namespaceIMP_1_1spb.html#ac82266395d7d5fcf26defd3c2f2f9f06">IMP::spb::add_link()</a>, <a href="namespaceIMP_1_1spb.html#a2e319d74f871dffac11765e34a748794">IMP::spb::add_link()</a>, <a href="namespaceIMP_1_1spb.html#a1d50546bf0502a542c492062c8f0f42b">IMP::spb::add_restrain_coiledcoil_to_cterm()</a>, <a href="namespaceIMP_1_1spb.html#ada54561155757e22856d4066515ecca0">IMP::spb::add_restrain_protein_length()</a>, <a href="namespaceIMP_1_1spb.html#ac09f34c6ac78e8632549a693c32154e7">IMP::spb::add_stay_close_restraint()</a>, <a href="namespaceIMP_1_1spb.html#a575f993823c11b8c6d9b11c1fcd089f0">IMP::spb::add_stay_close_restraint()</a>, <a href="namespaceIMP_1_1spb.html#aaf1e29ff21dfe105c06b225967d4849e">IMP::spb::add_stay_on_plane_restraint()</a>, <a href="namespaceIMP_1_1spb.html#a69efcfb24ba7b76acf747b54f9c8ce75">IMP::spb::add_tilt()</a>, <a href="namespaceIMP_1_1spb.html#adc86ba90554da52601fc2e10c42cf016">IMP::spb::y2h_restraint()</a>, <a href="namespaceIMP_1_1spb.html#ab5e2abcde6e2dd7c9578b1f952808e38">IMP::spb::y2h_restraint()</a>, <a href="namespaceIMP_1_1spb.html#ac4ef731aae34f16b158cc7ab451ccd38">IMP::spb::y2h_restraint()</a>, <a href="namespaceIMP_1_1spb.html#ab16e77716acf17384a5092aa7ae86294">IMP::spb::y2h_restraint()</a></td></tr>
123 <tr><td>@ref IMP::atom::LennardJones</td><td><a href="classIMP_1_1atom_1_1LennardJonesPairScore.html#ac927946f510789b92834bc6603dd2f20">IMP::atom::LennardJonesPairScore::get_factors()</a></td></tr>
124 <tr><td>@ref IMP::atom::LinearVelocity</td><td><a href="classIMP_1_1atom_1_1LinearVelocity.html#ac885de7b2294784c501d5a2f0c2c664a">IMP::atom::LinearVelocity::IMP_DECORATOR_METHODS()</a>, <a href="classIMP_1_1atom_1_1LinearVelocity.html#a39631423d559c083b38a3699c55ae9ac">IMP::atom::LinearVelocity::IMP_DECORATOR_SETUP_0()</a>, <a href="classIMP_1_1atom_1_1LinearVelocity.html#acff9254e2b6337366b5a63e8a51f2f24">IMP::atom::LinearVelocity::IMP_DECORATOR_SETUP_1()</a></td></tr>
125 <tr><td>@ref IMP::atom::Mass</td><td><a href="classIMP_1_1atom_1_1Mass.html#a7b0fde3167a1649f8f0f2bedada95c28">IMP::atom::Mass::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Mass.html#aed7e8decd2da73941a27bb4d8fa22fcb">IMP::atom::Mass::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Mass.html#a4b111729975b621a095fe54baa1b0e52">IMP::atom::Mass::setup_particle()</a></td></tr>
126 <tr><td>@ref IMP::atom::Mol2Selector</td><td><a href="namespaceIMP_1_1atom.html#a63d0f55dbe0f5805915a028a15bf1b1f">IMP::atom::read_mol2()</a></td></tr>
127 <tr><td>@ref IMP::atom::Molecule</td><td><a href="classIMP_1_1atom_1_1Molecule.html#a648f9ce0abc36479ca2b763261591ba5">IMP::atom::Molecule::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Molecule.html#aae69a4fd98b352878b7c4922bb79767f">IMP::atom::Molecule::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Molecule.html#ac719cd07adab9dac805eebb8d2fe51c9">IMP::atom::Molecule::setup_particle()</a>, <a href="namespaceIMP_1_1spb.html#a23e14d249f701c421fd66833c044539a">IMP::spb::add_internal_restraint()</a>, <a href="namespaceIMP_1_1spb.html#ac5d9e593d188cd0afbeb276881d82996">IMP::spb::add_my_connectivity()</a></td></tr>
128 <tr><td>@ref IMP::atom::PDBSelector</td><td><a href="classIMP_1_1atom_1_1AndPDBSelector.html#ae53bc29f8e73c1dd5f716f8107d3fb36">IMP::atom::AndPDBSelector::AndPDBSelector()</a>, <a href="classIMP_1_1atom_1_1NotPDBSelector.html#a325e5301ba51b57e4e7f4b04659c4a47">IMP::atom::NotPDBSelector::NotPDBSelector()</a>, <a href="classIMP_1_1atom_1_1OrPDBSelector.html#a796cbfff392c6c35a3632f6da515aa0d">IMP::atom::OrPDBSelector::OrPDBSelector()</a>, <a href="classIMP_1_1atom_1_1XorPDBSelector.html#a79e2e09a59541eb7cac5ebfb5f4ab2c8">IMP::atom::XorPDBSelector::XorPDBSelector()</a>, <a href="namespaceIMP_1_1atom.html#ae3392202746ce0960f27d6acb66c3523">IMP::atom::read_pdb()</a>, <a href="namespaceIMP_1_1atom.html#a4383e2b7c2330222eaba39867aa4b12d">IMP::atom::read_multimodel_pdb()</a>, <a href="namespaceIMP_1_1atom.html#a2efb72426efcdea0d7566faa78d793ae">IMP::atom::read_mmcif()</a>, <a href="namespaceIMP_1_1atom.html#a8dd513ff4e39c4c40c56e11f2d23da94">IMP::atom::read_multimodel_mmcif()</a>, <a href="namespaceIMP_1_1atom.html#ae2befbe269f1b12d6ccfd31fff5d4673">IMP::atom::read_multimodel_pdb_or_mmcif()</a>, <a href="namespaceIMP_1_1atom.html#afa75d21223f20565d1cc585ec7ebc9af">IMP::atom::read_pdb_or_mmcif()</a></td></tr>
129 <tr><td>@ref IMP::atom::Representation</td><td><a href="classIMP_1_1atom_1_1Representation.html#a66f5f23a4f44938ca35bdbefa9458a74">IMP::atom::Representation::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Representation.html#af24e26b69812ec688ef7265f8f5c0bc1">IMP::atom::Representation::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Representation.html#a4d969beb1d0fef460d6c8b10ad894838">IMP::atom::Representation::setup_particle()</a></td></tr>
130 <tr><td>@ref IMP::atom::Residue</td><td><a href="classIMP_1_1atom_1_1ForceFieldParameters.html#acc61a54cee5f3f8746ee722c8611c357">IMP::atom::ForceFieldParameters::add_bonds()</a>, <a href="classIMP_1_1atom_1_1ForceFieldParameters.html#a3aad1834ad554e00e510ff9d6229929c">IMP::atom::ForceFieldParameters::add_bonds()</a>, <a href="classIMP_1_1atom_1_1Residue.html#a620dc5f061ea1c5605c0b745afa12f14">IMP::atom::Residue::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Residue.html#a8f192aba52a14ffc0c9e0ee30b948e0b">IMP::atom::Residue::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Residue.html#ace3fac09ee49d5c1c13f4dde0d291783">IMP::atom::Residue::setup_particle()</a>, <a href="classIMP_1_1kinematics_1_1ProteinKinematics.html#abdd347a82ed349b9ae068ed6c1261434">IMP::kinematics::ProteinKinematics::add_dihedral_joint()</a>, <a href="classIMP_1_1kinematics_1_1ProteinKinematics.html#a6c5a65323c8646424869e05b66a063b0">IMP::kinematics::ProteinKinematics::add_dihedral_joints()</a>, <a href="classIMP_1_1kinematics_1_1ProteinKinematics.html#aec77aae9528482853d752645611830d0">IMP::kinematics::ProteinKinematics::get_chi1_joint()</a>, <a href="classIMP_1_1kinematics_1_1ProteinKinematics.html#a297106a361a557f6005bc4913e124f8a">IMP::kinematics::ProteinKinematics::get_chi2_joint()</a>, <a href="classIMP_1_1kinematics_1_1ProteinKinematics.html#a75a2449d9d48411cd4a1b4b0c1547b82">IMP::kinematics::ProteinKinematics::get_chi3_joint()</a>, <a href="classIMP_1_1kinematics_1_1ProteinKinematics.html#a40623eb6c48ec11e7769328d1e04be66">IMP::kinematics::ProteinKinematics::get_chi4_joint()</a>, <a href="classIMP_1_1kinematics_1_1ProteinKinematics.html#a696922070461ecdb785fa0d94a97c927">IMP::kinematics::ProteinKinematics::get_chi5_joint()</a>, <a href="classIMP_1_1kinematics_1_1ProteinKinematics.html#a181d087b1a248cfca6d9174bce650a82">IMP::kinematics::ProteinKinematics::get_joint()</a>, <a href="classIMP_1_1kinematics_1_1ProteinKinematics.html#ae04568da36217aeff08f590a0b2de28d">IMP::kinematics::ProteinKinematics::get_other_joint()</a>, <a href="classIMP_1_1kinematics_1_1ProteinKinematics.html#a15a55c6976ebd2c8409a882aaaf8c3e9">IMP::kinematics::ProteinKinematics::get_phi()</a>, <a href="classIMP_1_1kinematics_1_1ProteinKinematics.html#a175fe14ea73c95932e547b64dcd6c032">IMP::kinematics::ProteinKinematics::get_phi_joint()</a>, <a href="classIMP_1_1kinematics_1_1ProteinKinematics.html#aba4a7bd581a53c247d9dbace7a037aef">IMP::kinematics::ProteinKinematics::get_psi()</a>, <a href="classIMP_1_1kinematics_1_1ProteinKinematics.html#a3bfc396bdc667f1d73df79025a3e9292">IMP::kinematics::ProteinKinematics::get_psi_joint()</a>, <a href="classIMP_1_1kinematics_1_1ProteinKinematics.html#ae56d73b6d4c39ced40bf4ae1acd5e119">IMP::kinematics::ProteinKinematics::set_phi()</a>, <a href="classIMP_1_1kinematics_1_1ProteinKinematics.html#ad30580ddbd4d671934281b358161e935">IMP::kinematics::ProteinKinematics::set_psi()</a>, <a href="classIMP_1_1rotamer_1_1ResidueRotamer.html#a07539b639bd491e81d4b86e87405df8c">IMP::rotamer::ResidueRotamer::set_coordinates()</a>, <a href="classIMP_1_1rotamer_1_1RotamerCalculator.html#a87f7878daf288370734d78479eaea929">IMP::rotamer::RotamerCalculator::get_rotamer()</a>, <a href="namespaceIMP_1_1atom.html#a899927712a6b9ae00aa8875407f5311a">IMP::atom::get_atom()</a>, <a href="namespaceIMP_1_1atom.html#a30ce58af4f3485274c3c59c7170d6698">IMP::atom::get_chi_dihedral_atoms()</a>, <a href="namespaceIMP_1_1atom.html#a49d8d008661379b8938d7bfbd324b262">IMP::atom::get_chi_dihedral_particle_indexes()</a>, <a href="namespaceIMP_1_1atom.html#a2cadcc607aa4c1f8b1ec4c0c8d493312">IMP::atom::get_next_residue()</a>, <a href="namespaceIMP_1_1atom.html#a5ceb85645196ab77765e0ffad9866330">IMP::atom::get_omega_dihedral_atoms()</a>, <a href="namespaceIMP_1_1atom.html#a6ef3ab3e84fd5ab0e83ce40fdc675455">IMP::atom::get_phi_dihedral_atoms()</a>, <a href="namespaceIMP_1_1atom.html#ad329e5c66a8de2f49304492c5a690d90">IMP::atom::get_previous_residue()</a>, <a href="namespaceIMP_1_1atom.html#a1c15e940e47a1a8f5872029fcb93c601">IMP::atom::get_psi_dihedral_atoms()</a></td></tr>
131 <tr><td>@ref IMP::atom::ResidueType</td><td><a href="classIMP_1_1atom_1_1CHARMMIdealResidueTopology.html#a53ca62b5ccb300cee4346944619ebbba">IMP::atom::CHARMMIdealResidueTopology::CHARMMIdealResidueTopology()</a>, <a href="classIMP_1_1atom_1_1CHARMMParameters.html#a93c5e6fbf6e839294e91ec2a179f74af">IMP::atom::CHARMMParameters::get_residue_topology()</a>, <a href="classIMP_1_1atom_1_1CHARMMParameters.html#a0e017ab02dc3673cfa7cd48fb6e4686d">IMP::atom::CHARMMParameters::parse_atom_line()</a>, <a href="classIMP_1_1atom_1_1CHARMMParameters.html#aa0c19662e8ac391cdce1666af3b810eb">IMP::atom::CHARMMParameters::parse_bond_line()</a>, <a href="classIMP_1_1atom_1_1CHARMMResidueTopology.html#acd586e0463d6dddd9399956945c4e5cc">IMP::atom::CHARMMResidueTopology::CHARMMResidueTopology()</a>, <a href="classIMP_1_1atom_1_1Residue.html#a7ae7541583930e1473396598c7b937a6">IMP::atom::Residue::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Residue.html#aa47d3e8ac5a0f07fc67eea29c60b2792">IMP::atom::Residue::set_residue_type()</a>, <a href="classIMP_1_1atom_1_1Residue.html#aa8472267328ddc075dba74e16e71900b">IMP::atom::Residue::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Residue.html#ad00f788c4a62ba2039b3d0e19696c627">IMP::atom::Residue::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Residue.html#a301e9b56ab80581166b286745560443a">IMP::atom::Residue::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Residue.html#a432006d0924f45aeaf4d0a313948865a">IMP::atom::Residue::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Residue.html#a649753abdd11818384bfb4322b273205">IMP::atom::Residue::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Residue.html#a85df62736aed4cce5b488a36fb78adb5">IMP::atom::Residue::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Selection.html#a1aa9fab76bf21cfdab1e7b25751a094a">IMP::atom::Selection::Selection()</a>, <a href="classIMP_1_1atom_1_1Selection.html#a68024499c221b617df3ee27d6460b4d6">IMP::atom::Selection::set_residue_type()</a>, <a href="classIMP_1_1rotamer_1_1ResidueRotamer.html#ad8f9411effe5a159c0619e8135993d9a">IMP::rotamer::ResidueRotamer::ResidueRotamer()</a>, <a href="classIMP_1_1rotamer_1_1RotamerLibrary.html#a917624d3ba6e635f360c999efe4ce0f7">IMP::rotamer::RotamerLibrary::get_rotamers()</a>, <a href="classIMP_1_1rotamer_1_1RotamerLibrary.html#a17b121526a2716bca70671c76dc56fc5">IMP::rotamer::RotamerLibrary::get_rotamers_fast()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#ae5a59dd0ebd0d5590db3d2127444204e">IMP::saxs::FormFactorTable::get_carbon_atom_type()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#a9d89b134eb2b325d8146583edd8dd38e">IMP::saxs::FormFactorTable::get_dummy_form_factor()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#a49a2f6d3990a37730dc181888846b9f9">IMP::saxs::FormFactorTable::get_form_factor()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#adc7d132da89b412ddc3bed43094c29a5">IMP::saxs::FormFactorTable::get_nitrogen_atom_type()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#a01b57170c71bbaa7edc35ce486805ac6">IMP::saxs::FormFactorTable::get_oxygen_atom_type()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#a3453246d72667c72492393cb9e7b00e1">IMP::saxs::FormFactorTable::get_sulfur_atom_type()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#a173cb42739782091ecd27e3b760a20ed">IMP::saxs::FormFactorTable::get_vacuum_form_factor()</a>, <a href="namespaceIMP_1_1atom.html#a3982cc0d820dfdeb89abf056f3338754">IMP::atom::get_volume_from_residue_type()</a>, <a href="namespaceIMP_1_1atom.html#ad62901c76275a45e34aed68c76548508">IMP::atom::get_chi_dihedral_atom_types()</a>, <a href="namespaceIMP_1_1atom.html#a7236ea7f2911d16543c5af18f46f0f5c">IMP::atom::get_mass()</a>, <a href="namespaceIMP_1_1atom.html#a6bf9912d67e4c9d6a134930015a928de">IMP::atom::get_one_letter_code()</a></td></tr>
132 <tr><td>@ref IMP::atom::SecondaryStructureResidue</td><td><a href="namespaceIMP_1_1atom.html#a3164dab692507ddc3602d0a179f642c6">IMP::atom::get_secondary_structure_match_score()</a></td></tr>
133 <tr><td>@ref IMP::atom::Selection</td><td><a href="classIMP_1_1atom_1_1Selection.html#a79306b9477cdce20dc3589eb1b5040bf">IMP::atom::Selection::set_difference()</a>, <a href="classIMP_1_1atom_1_1Selection.html#ab230edcc56bbc2163dcb2d8bb1a822f2">IMP::atom::Selection::set_intersection()</a>, <a href="classIMP_1_1atom_1_1Selection.html#adab4f65a622a2a377c6805ac3341049c">IMP::atom::Selection::set_symmetric_difference()</a>, <a href="classIMP_1_1atom_1_1Selection.html#a63be78e2118e882d1fb047b20b085368">IMP::atom::Selection::set_union()</a>, <a href="classIMP_1_1atom_1_1SelectionGeometry.html#afbe413545c59b4ed65283124b438d359">IMP::atom::SelectionGeometry::SelectionGeometry()</a>, <a href="namespaceIMP_1_1atom.html#a73e18e3fed07044ae62a1fb2954b5784">IMP::atom::write_pdb()</a>, <a href="namespaceIMP_1_1atom.html#a6eee9382831652975bf689feeab8d508">IMP::atom::write_pdb_of_c_alphas()</a>, <a href="namespaceIMP_1_1atom.html#aed5950befd1610327f1bc9bc737de49f">IMP::atom::create_cover()</a>, <a href="namespaceIMP_1_1atom.html#abc59e05e0e702438730b01f225858438">IMP::atom::create_distance_restraint()</a>, <a href="namespaceIMP_1_1atom.html#a2e83759163a5032a2f429eae3e86f0cd">IMP::atom::create_internal_connectivity_restraint()</a>, <a href="namespaceIMP_1_1atom.html#aced8686a48e1011e90376a302cc3155d">IMP::atom::create_internal_connectivity_restraint()</a>, <a href="namespaceIMP_1_1atom.html#af5b0cc808be9672d3996baeb2f9210fd">IMP::atom::get_leaves()</a>, <a href="namespaceIMP_1_1atom.html#ae122a232c9f291d3f5f4d218c06652e4">IMP::atom::get_mass()</a>, <a href="namespaceIMP_1_1atom.html#a8ac4a06cec8ed51c3f992851dbaf25b8">IMP::atom::get_radius_of_gyration()</a>, <a href="namespaceIMP_1_1atom.html#a9793120929ce62d48d46e06575e19721">IMP::atom::get_rmsd()</a>, <a href="namespaceIMP_1_1atom.html#a603f2b73d6e22b3a9128e0398bc6e082">IMP::atom::get_rmsd_transforming_first()</a>, <a href="namespaceIMP_1_1atom.html#a1ffa9eaea1cc4ecd2d9e3a10b2dd50b2">IMP::atom::get_surface_area()</a>, <a href="namespaceIMP_1_1atom.html#a72ceba6f0fb3a05221086170a55f4d46">IMP::atom::get_transformation_aligning_first_to_second()</a>, <a href="namespaceIMP_1_1atom.html#ada8d754330898011ea1435fa0e693136">IMP::atom::get_volume()</a>, <a href="namespaceIMP_1_1bayesianem.html#ad37a96ab85d8d8ca91478886426b89fa">IMP::bayesianem::get_rmsd_of_best_population()</a>, <a href="namespaceIMP_1_1bayesianem.html#a2b1cbbee53f6277e776c525a0ea8ff09">IMP::bayesianem::get_transformation_aligning_first_to_second()</a></td></tr>
134 <tr><td>@ref IMP::atom::Simulator</td><td><a href="classIMP_1_1npctransport_1_1ParticleTransportStatisticsOptimizerState.html#a8e9618751dbd77f8f62232e40c95af61">IMP::npctransport::ParticleTransportStatisticsOptimizerState::ParticleTransportStatisticsOptimizerState()</a>, <a href="classIMP_1_1npctransport_1_1ParticleTransportStatisticsOptimizerState.html#a131fb76848a857a11cc966986b256a0c">IMP::npctransport::ParticleTransportStatisticsOptimizerState::set_owner()</a>, <a href="classIMP_1_1rmf_1_1SaveOptimizerState.html#aaf387b770701f90b639953345671c103">IMP::rmf::SaveOptimizerState::set_simulator()</a></td></tr>
135 <tr><td>@ref IMP::atom::SmoothingFunction</td><td><a href="classIMP_1_1atom_1_1CoulombPairScore.html#a9fefe76aa6517db64b15098e4a08000e">IMP::atom::CoulombPairScore::CoulombPairScore()</a>, <a href="classIMP_1_1atom_1_1LennardJonesPairScore.html#a125aef6ff287967f6aee1177254bf0e1">IMP::atom::LennardJonesPairScore::LennardJonesPairScore()</a></td></tr>
136 <tr><td>@ref IMP::atom::State</td><td><a href="classIMP_1_1atom_1_1State.html#ac6a1554b2b0a64e2aca3a03692baffba">IMP::atom::State::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1State.html#a7ab84b565ba352fa722735edc0db873f">IMP::atom::State::setup_particle()</a>, <a href="classIMP_1_1atom_1_1State.html#a81848e10ddf84cdf61ab74770229ab65">IMP::atom::State::setup_particle()</a></td></tr>
137 </table>
138 # IMP.cnmultifit # {#argument_index_cnmultifit}
139 <table><tr>
140 <th>Class</th><th>Users</th></tr>
141 <tr><td>@ref IMP::cnmultifit::AlignSymmetric</td><td><a href="namespaceIMP_1_1cnmultifit.html#a6067aedfd378547038d133f84bb820e3">IMP::cnmultifit::fit_cn_assembly()</a></td></tr>
142 <tr><td>@ref IMP::cnmultifit::CnSymmAxisDetector</td><td><a href="namespaceIMP_1_1cnmultifit.html#a1b5327db66abe2f5bc1712f1013a4436">IMP::cnmultifit::fit_cn_assembly()</a></td></tr>
143 <tr><td>@ref IMP::cnmultifit::MolCnSymmAxisDetector</td><td><a href="namespaceIMP_1_1cnmultifit.html#a1b5327db66abe2f5bc1712f1013a4436">IMP::cnmultifit::fit_cn_assembly()</a></td></tr>
144 </table>
145 # IMP.container # {#argument_index_container}
146 <table><tr>
147 <th>Class</th><th>Users</th></tr>
148 <tr><td>@ref IMP::container::ClosePairContainer</td><td><a href="namespaceIMP_1_1container.html#ac8965a95934fc142a9797c44fdc03d88">IMP::container::get_slack_estimate()</a>, <a href="namespaceIMP_1_1container.html#a10c42d60066d5eeb4b9cd5fa4a6d72d9">IMP::container::get_slack_estimate()</a></td></tr>
149 <tr><td>@ref IMP::container::ConsecutivePairContainer</td><td><a href="classIMP_1_1container_1_1ConsecutivePairFilter.html#a2e0d4f04b8080a9c0d77a9a0e1a68ba5">IMP::container::ConsecutivePairFilter::ConsecutivePairFilter()</a></td></tr>
150 <tr><td>@ref IMP::container::ListSingletonContainer</td><td><a href="namespaceIMP_1_1spb.html#a4f4e29033718c00197737912b750ef5b">IMP::spb::add_bayesian_layer_restraint()</a>, <a href="namespaceIMP_1_1spb.html#a89c91f69eb459a1a6ef9a2da1c9d885a">IMP::spb::add_layer_restraint()</a>, <a href="namespaceIMP_1_1spb.html#ae8957e05a946a61598e363e00de9763c">IMP::spb::create_GFP()</a>, <a href="namespaceIMP_1_1spb.html#ae9d935784a933409cd306c7c046cfff6">IMP::spb::create_representation()</a>, <a href="namespaceIMP_1_1spb.html#a7c113921b584fd1fce234cdb478f354b">IMP::spb::spb_assemble_restraints()</a></td></tr>
151 </table>
152 # IMP.core # {#argument_index_core}
153 <table><tr>
154 <th>Class</th><th>Users</th></tr>
155 <tr><td>@ref IMP::core::BinormalTerm</td><td><a href="classIMP_1_1core_1_1MultipleBinormalRestraint.html#a5d2e581b729662bc10e2dad4bc688203">IMP::core::MultipleBinormalRestraint::add_term()</a></td></tr>
156 <tr><td>@ref IMP::core::ClosePairsFinder</td><td><a href="classIMP_1_1container_1_1ClosePairContainer.html#a19f52fd2b6c1f34261b304f5870ac9ca">IMP::container::ClosePairContainer::ClosePairContainer()</a>, <a href="classIMP_1_1core_1_1RigidClosePairsFinder.html#a7b77f4659d0ba5ebf6656168aaad0af9">IMP::core::RigidClosePairsFinder::RigidClosePairsFinder()</a></td></tr>
157 <tr><td>@ref IMP::core::ClusterProvenance</td><td><a href="classIMP_1_1core_1_1ClusterProvenance.html#af79f110e64dbd4abb1fc4654735a1518">IMP::core::ClusterProvenance::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1ClusterProvenance.html#a5b750ffcdf47f2a97db99091a3aca15c">IMP::core::ClusterProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1ClusterProvenance.html#a8bcfa300fc8ea8a70f93105572b0afe1">IMP::core::ClusterProvenance::setup_particle()</a></td></tr>
158 <tr><td>@ref IMP::core::CombineProvenance</td><td><a href="classIMP_1_1core_1_1CombineProvenance.html#aeeab03ecbd191225dcf1218b503c71e8">IMP::core::CombineProvenance::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1CombineProvenance.html#a108e878f8abbef6d9ef5013d5df15c97">IMP::core::CombineProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1CombineProvenance.html#a03cf92b0778a2a99ecfe40102e480b2b">IMP::core::CombineProvenance::setup_particle()</a></td></tr>
159 <tr><td>@ref IMP::core::DataObject</td><td><a href="classIMP_1_1core_1_1DataObject.html#a21902b043155f25d342ab159bcbd55bd">IMP::core::DataObject::IMP_OBJECT_METHODS()</a></td></tr>
160 <tr><td>@ref IMP::core::Direction</td><td><a href="classIMP_1_1core_1_1DirectionMover.html#aef113faaac68f5369251134fe2f113d4">IMP::core::DirectionMover::DirectionMover()</a>, <a href="namespaceIMP_1_1core.html#afd0ee355a8489289443d4de259d3b71e">IMP::core::get_angle()</a></td></tr>
161 <tr><td>@ref IMP::core::DistancePairScore</td><td><a href="namespaceIMP_1_1spb.html#a034798d478f68b2f5cab9cb68ac983d4">IMP::spb::do_bipartite_mindist()</a></td></tr>
162 <tr><td>@ref IMP::core::FilterProvenance</td><td><a href="classIMP_1_1core_1_1FilterProvenance.html#a571e0a23391146e0ea38af90053c91a6">IMP::core::FilterProvenance::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1FilterProvenance.html#af157b1d08abda33e13e8b9833e2776b9">IMP::core::FilterProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1FilterProvenance.html#a22a1ef6b2b9d09e5f0e3892787974995">IMP::core::FilterProvenance::setup_particle()</a></td></tr>
163 <tr><td>@ref IMP::core::Hierarchy</td><td><a href="classIMP_1_1atom_1_1Hierarchy.html#a776a2d762c4245a3aa0da74e0b51cf09">IMP::atom::Hierarchy::Hierarchy()</a>, <a href="classIMP_1_1atom_1_1HierarchyGeometry.html#ad9ff1e203d46f1a116dc32de72f50acf">IMP::atom::HierarchyGeometry::HierarchyGeometry()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#adc79064f4b0e3857aa00c9416bcf7d48">IMP::core::Hierarchy::add_child()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#af755f5483b8fdab8c227d07220e96cc7">IMP::core::Hierarchy::add_child_at()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#ad99b4f19345b28138ee910b6af438426">IMP::core::Hierarchy::remove_child()</a>, <a href="classIMP_1_1core_1_1HierarchyVisitor.html#aa45442c4bff64f5fea3fcc547783f412">IMP::core::HierarchyVisitor::operator()()</a>, <a href="classIMP_1_1core_1_1ModifierVisitor.html#ae7529eda6952ce1e036e8e018cf3fa84">IMP::core::ModifierVisitor::operator()()</a>, <a href="namespaceIMP_1_1core.html#a24d4c4b06793bcadc5962885098ed400">IMP::core::get_all_descendants()</a>, <a href="namespaceIMP_1_1core.html#a65ebb1067e86f517214ff78f111ad622">IMP::core::get_internal()</a>, <a href="namespaceIMP_1_1core.html#a8743287de001c73866a23377c8bd466f">IMP::core::get_leaves()</a>, <a href="namespaceIMP_1_1core.html#a4c078026c66398b7ae77eeb6f13ddcd0">IMP::core::get_root()</a>, <a href="group__hierarchy.html#ga346251f63e1305b2bd2b0599f1d8d761">IMP::core::show()</a>, <a href="namespaceIMP_1_1multifit.html#a3e058408a3879546f50897a4e8f9253b">IMP::multifit::add_surface_index()</a></td></tr>
164 <tr><td>@ref IMP::core::HierarchyTraits</td><td><a href="classIMP_1_1core_1_1ChildrenRefiner.html#ac93f559610e5324ee059430e86e4b7c0">IMP::core::ChildrenRefiner::ChildrenRefiner()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#a1e0991bcc14d8b2a81f64694682e3101">IMP::core::Hierarchy::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#adda6afa7704ddbed3d665dae79922201">IMP::core::Hierarchy::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#ace96e58edb213b68108a369df5d182f1">IMP::core::Hierarchy::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#a5ad401d6e66517fdbe9813c5abf93421">IMP::core::Hierarchy::Hierarchy()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#a7c88d2bfea245adc2f9b22ca302bc666">IMP::core::Hierarchy::Hierarchy()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#aa257f3f243db94bb9f9c6c42ad7e8680">IMP::core::Hierarchy::get_is_setup()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#adc0113e58530d49717664c8e668e26ee">IMP::core::Hierarchy::get_is_setup()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#aa66644bbb2c9feefcc49e439d5623f78">IMP::core::Hierarchy::setup_particle()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#a4cce2b68f4e46377b8f09d39813bef54">IMP::core::Hierarchy::setup_particle()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#a0f07a9befe64a751b3bb0422696b3e17">IMP::core::Hierarchy::setup_particle()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#ad3309b0bfcb19888094814f4d3310a63">IMP::core::Hierarchy::setup_particle()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#a34cd5c036aac3d8cd71c18dae9e6595c">IMP::core::Hierarchy::setup_particle()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#aaabcf56ef3c97a5ca142745e55ab1483">IMP::core::Hierarchy::setup_particle()</a>, <a href="classIMP_1_1core_1_1HierarchyTraits.html#a963da285babd3bf204ce3d25c632dd15">IMP::core::HierarchyTraits::operator==()</a>, <a href="classIMP_1_1core_1_1LeavesRefiner.html#ab054bc5b90fd5c7a2906d93f39e7b412">IMP::core::LeavesRefiner::LeavesRefiner()</a></td></tr>
165 <tr><td>@ref IMP::core::IncrementalScoringFunction</td><td><a href="classIMP_1_1core_1_1MonteCarlo.html#ad373e9c68d7c1b64424f454a9f6755a2">IMP::core::MonteCarlo::set_incremental_scoring_function()</a></td></tr>
166 <tr><td>@ref IMP::core::IsCollisionPairPredicate</td><td><a href="classIMP_1_1core_1_1IsCollisionPairPredicate.html#a996b7777db7f4b01ca37f2586d2fc0c5">IMP::core::IsCollisionPairPredicate::IMP_PAIR_PREDICATE_METHODS()</a></td></tr>
167 <tr><td>@ref IMP::core::MonteCarlo</td><td><a href="classIMP_1_1core_1_1MCCGSampler.html#a3bbeae34bab083c8ae1aaf5a636a4c90">IMP::core::MCCGSampler::set_up_movers()</a></td></tr>
168 <tr><td>@ref IMP::core::MonteCarloMover</td><td><a href="classIMP_1_1core_1_1MonteCarlo.html#aef0c0e787d5720c79b492b7418da7ecd">IMP::core::MonteCarlo::remove_mover()</a>, <a href="classIMP_1_1core_1_1MonteCarlo.html#a4da70b551db763688cf1e25a42a6bca3">IMP::core::MonteCarlo::add_mover()</a></td></tr>
169 <tr><td>@ref IMP::core::Provenance</td><td><a href="classIMP_1_1core_1_1Provenance.html#a9aac89f86b0c4db19c335908fd118919">IMP::core::Provenance::set_previous()</a>, <a href="classIMP_1_1core_1_1Provenanced.html#ac25129fa1cc8e69c4d3701eaa47a8fa9">IMP::core::Provenanced::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1Provenanced.html#ad673bbc3c3472dc1a27217940fd719cd">IMP::core::Provenanced::setup_particle()</a>, <a href="classIMP_1_1core_1_1Provenanced.html#a3aea98306c09aee470fc1f540f5ea7e0">IMP::core::Provenanced::setup_particle()</a>, <a href="classIMP_1_1core_1_1Provenanced.html#a44c831cbcd9d363d716e4357d5d440cc">IMP::core::Provenanced::set_provenance()</a>, <a href="namespaceIMP_1_1core.html#a25de2b4c4ee9212c60a8963a0df5c55e">IMP::core::add_provenance()</a>, <a href="namespaceIMP_1_1core.html#ab7597523d0b09bc8fa288b7261cedb69">IMP::core::create_clone()</a></td></tr>
170 <tr><td>@ref IMP::core::RigidBody</td><td><a href="classIMP_1_1core_1_1RigidBody.html#a31cf63db783589db090984512e76bc09">IMP::core::RigidBody::teardown_particle()</a>, <a href="classIMP_1_1core_1_1RigidBodyDerivativeGeometry.html#aedb8aae145938a6e43f5d1704ae8d538">IMP::core::RigidBodyDerivativeGeometry::RigidBodyDerivativeGeometry()</a>, <a href="classIMP_1_1core_1_1RigidBodyFrameGeometry.html#aad20ba7053ff132800b3aae9c59ddfc9">IMP::core::RigidBodyFrameGeometry::RigidBodyFrameGeometry()</a>, <a href="classIMP_1_1core_1_1RigidBodyHierarchyGeometry.html#ae2b3ffa55b43543636f37d5b0f3087ac">IMP::core::RigidBodyHierarchyGeometry::RigidBodyHierarchyGeometry()</a>, <a href="classIMP_1_1em2d_1_1RelativePositionMover.html#af7912452d781bfdc25f904b717101676">IMP::em2d::RelativePositionMover::RelativePositionMover()</a>, <a href="classIMP_1_1em2d_1_1RelativePositionMover.html#a2045622f5bc5c6c61b42f5f27748c4f9">IMP::em2d::RelativePositionMover::add_internal_transformations()</a>, <a href="classIMP_1_1em2d_1_1RigidBodiesImageFitRestraint.html#adc029e547932f000de091deb35097fe4">IMP::em2d::RigidBodiesImageFitRestraint::get_number_of_masks()</a>, <a href="classIMP_1_1em2d_1_1RigidBodiesImageFitRestraint.html#a9ecd59712114458c5d440bb7e01870f1">IMP::em2d::RigidBodiesImageFitRestraint::set_orientations()</a>, <a href="classIMP_1_1em2d_1_1RigidBodiesImageFitRestraint.html#ad421603f6b2c67d918d5262140c50095">IMP::em2d::RigidBodiesImageFitRestraint::get_rigid_body_index()</a>, <a href="classIMP_1_1kinematics_1_1BondAngleRevoluteJoint.html#a16ba2ca9dff457daf656a6336e46f56a">IMP::kinematics::BondAngleRevoluteJoint::BondAngleRevoluteJoint()</a>, <a href="classIMP_1_1kinematics_1_1CompositeJoint.html#a06ea6091af7ff36c08a5d5eb5dfd780e">IMP::kinematics::CompositeJoint::CompositeJoint()</a>, <a href="classIMP_1_1kinematics_1_1DihedralAngleRevoluteJoint.html#a518c71ba70ed25ad87aae3cb9dbab4ff">IMP::kinematics::DihedralAngleRevoluteJoint::DihedralAngleRevoluteJoint()</a>, <a href="classIMP_1_1kinematics_1_1Joint.html#a7e1a407b470b3ee5e785583430b0a5e6">IMP::kinematics::Joint::Joint()</a>, <a href="classIMP_1_1kinematics_1_1KinematicForest.html#a4f4f75ae4464f9238edbd4f9f53da211">IMP::kinematics::KinematicForest::add_edge()</a>, <a href="classIMP_1_1kinematics_1_1KinematicForest.html#ab7e7b80fe79c36af1bca159df73f7f97">IMP::kinematics::KinematicForest::get_coordinates_safe()</a>, <a href="classIMP_1_1kinematics_1_1KinematicForest.html#a35103e7f5bb31a571e30965ec39e3ae3">IMP::kinematics::KinematicForest::get_is_member()</a>, <a href="classIMP_1_1kinematics_1_1KinematicForest.html#ae9aea73c759c2ceeb7c88c46553fdc47">IMP::kinematics::KinematicForest::get_reference_frame_safe()</a>, <a href="classIMP_1_1kinematics_1_1KinematicForest.html#ab9ffe60cb86e0edc2ee54cbd36c98199">IMP::kinematics::KinematicForest::set_coordinates_safe()</a>, <a href="classIMP_1_1kinematics_1_1KinematicForest.html#a879e819eda0a9d2851e6ac8c654b8355">IMP::kinematics::KinematicForest::set_reference_frame_safe()</a>, <a href="classIMP_1_1kinematics_1_1PrismaticJoint.html#a69b32641f0207229ec1fd26b6d399546">IMP::kinematics::PrismaticJoint::PrismaticJoint()</a>, <a href="classIMP_1_1kinematics_1_1PrismaticJoint.html#ae1c2a772c0581223f7a8ed3dc5fdfd8a">IMP::kinematics::PrismaticJoint::PrismaticJoint()</a>, <a href="classIMP_1_1kinematics_1_1RevoluteJoint.html#a531e935921d67d59df7b1b09f6c258fe">IMP::kinematics::RevoluteJoint::RevoluteJoint()</a>, <a href="classIMP_1_1kinematics_1_1TransformationJoint.html#af215277d41c031829b1fae9c7e5ba73b">IMP::kinematics::TransformationJoint::TransformationJoint()</a>, <a href="classIMP_1_1multifit_1_1ComplementarityRestraint.html#ad6aba49b9073b20c3338cd1542ae9500">IMP::multifit::ComplementarityRestraint::get_grid_object()</a>, <a href="classIMP_1_1spb_1_1PbcBoxedRigidBodyMover.html#a71a75e5182b952b8fb0b4a4e5ca49eeb">IMP::spb::PbcBoxedRigidBodyMover::PbcBoxedRigidBodyMover()</a>, <a href="classIMP_1_1spb_1_1RigidBodyNewMover.html#af43951b1f208f16ca904dd5bb845f30f">IMP::spb::RigidBodyNewMover::RigidBodyNewMover()</a>, <a href="classIMP_1_1symmetry_1_1RigidBodyMover.html#ad9dca2981893121c227c5bc4f46b74fe">IMP::symmetry::RigidBodyMover::RigidBodyMover()</a>, <a href="namespaceIMP_1_1core.html#ad2e0faca3653d6acca9edc09af19ef99">IMP::core::show_rigid_body_hierarchy()</a>, <a href="namespaceIMP_1_1core.html#a4c5298df54cae6b0e4419852390281be">IMP::core::transform()</a>, <a href="namespaceIMP_1_1em.html#ab8beedad8915dcd1aa22b5ba75a61439">IMP::em::compute_fitting_scores()</a>, <a href="namespaceIMP_1_1multifit.html#a3359231b0601df5803958afcd8d93184">IMP::multifit::create_hit_map()</a>, <a href="namespaceIMP_1_1multifit.html#a8273d850c0ab1cd53983c9f169af3cd6">IMP::multifit::create_weighted_excluded_volume_restraint()</a>, <a href="namespaceIMP_1_1multifit.html#a45c8385d6183240ec7216ae97374c7a9">IMP::multifit::pca_based_rigid_fitting()</a>, <a href="namespaceIMP_1_1spb.html#a2271ff41d487482a3029eb6e6ccd06cb">IMP::spb::recenter_rb()</a></td></tr>
171 <tr><td>@ref IMP::core::RigidMember</td><td><a href="classIMP_1_1core_1_1RigidBody.html#aba355d51adad0c18053680d1b0b20fa1">IMP::core::RigidBody::get_coordinates()</a>, <a href="namespaceIMP_1_1core.html#af5b47e4ca263d6c156fb5936223c8a29">IMP::core::get_root_rigid_body()</a></td></tr>
172 <tr><td>@ref IMP::core::SampleProvenance</td><td><a href="classIMP_1_1core_1_1SampleProvenance.html#a9c6f4ff751d1f2b38f989a820f370382">IMP::core::SampleProvenance::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1SampleProvenance.html#a2162a2c167f1a332b3c6c71d2da8ebc2">IMP::core::SampleProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1SampleProvenance.html#af02b0b8650e58bf9aae34b7b61557283">IMP::core::SampleProvenance::setup_particle()</a></td></tr>
173 <tr><td>@ref IMP::core::ScriptProvenance</td><td><a href="classIMP_1_1core_1_1ScriptProvenance.html#a928bc3f1109d45319251e7438aa1dcca">IMP::core::ScriptProvenance::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1ScriptProvenance.html#a50f3d03183437ba64252c917645b79ae">IMP::core::ScriptProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1ScriptProvenance.html#a248401f9e74c426ff1b66c0c724da23a">IMP::core::ScriptProvenance::setup_particle()</a></td></tr>
174 <tr><td>@ref IMP::core::SoftSpherePairScore</td><td><a href="classIMP_1_1core_1_1ExcludedVolumeRestraint.html#a3901b13b7a361386dfe813d43384b05e">IMP::core::ExcludedVolumeRestraint::ExcludedVolumeRestraint()</a></td></tr>
175 <tr><td>@ref IMP::core::SoftwareProvenance</td><td><a href="classIMP_1_1core_1_1SoftwareProvenance.html#a6ca8a5fcb8f7555b42b7d27a40fa31f6">IMP::core::SoftwareProvenance::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1SoftwareProvenance.html#a0fdc3df205b116a9ec891ba68fdf9a48">IMP::core::SoftwareProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1SoftwareProvenance.html#a3f5dd1f507dd6187510c00565573593a">IMP::core::SoftwareProvenance::setup_particle()</a></td></tr>
176 <tr><td>@ref IMP::core::SphereDistancePairScore</td><td><a href="namespaceIMP_1_1spb.html#a76fc05e5b9a81702e8c5a6d560695b08">IMP::spb::do_bipartite_mindist()</a></td></tr>
177 <tr><td>@ref IMP::core::StructureProvenance</td><td><a href="classIMP_1_1core_1_1StructureProvenance.html#a64da17ce1ec4f996cffbd142876438bb">IMP::core::StructureProvenance::do_setup_particle()</a>, <a href="classIMP_1_1core_1_1StructureProvenance.html#a5905f04f65df6b6ecb322e533bf0ecd0">IMP::core::StructureProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1StructureProvenance.html#aaf11a4f9558d13560cbc87ea306ebf8a">IMP::core::StructureProvenance::setup_particle()</a></td></tr>
178 <tr><td>@ref IMP::core::Surface</td><td><a href="classIMP_1_1core_1_1LateralSurfaceConstraint.html#a15da8840351877dad1a931c7736397b4">IMP::core::LateralSurfaceConstraint::LateralSurfaceConstraint()</a>, <a href="classIMP_1_1core_1_1SurfaceGeometry.html#a7b8e83983dd9f018d5d16e90afc56c0d">IMP::core::SurfaceGeometry::SurfaceGeometry()</a>, <a href="classIMP_1_1core_1_1SurfaceGeometry.html#af8a9caf61f550b77dd0774b156ff95b5">IMP::core::SurfaceGeometry::SurfaceGeometry()</a>, <a href="classIMP_1_1core_1_1SurfaceGeometry.html#a39e6f171cd1bab6badb5a5b7309e6532">IMP::core::SurfaceGeometry::set_geometry()</a>, <a href="classIMP_1_1core_1_1SurfaceGeometryConstraint.html#abb639e04c8072f2afb272fb392d4e9fe">IMP::core::SurfaceGeometryConstraint::SurfaceGeometryConstraint()</a>, <a href="classIMP_1_1core_1_1SurfaceMover.html#a09dbf120da0f834b79a2a5067e6de3c3">IMP::core::SurfaceMover::SurfaceMover()</a>, <a href="namespaceIMP_1_1core.html#a1713078e0a0ce8c3fb525af366bb71a5">IMP::core::create_geometry()</a>, <a href="namespaceIMP_1_1core.html#aa4af8ca0fe605b70667023285eccf34d">IMP::core::get_constrained_surface_geometry()</a>, <a href="namespaceIMP_1_1core.html#a75ddddcaa7bc977a250b60f266cd39ec">IMP::core::get_depth()</a>, <a href="namespaceIMP_1_1core.html#a871feee8cd80fe860602685979bbb5f2">IMP::core::get_depth()</a>, <a href="namespaceIMP_1_1core.html#af9c67a7fc68dd22fa3f7e685ff7e77b9">IMP::core::get_distance()</a>, <a href="namespaceIMP_1_1core.html#a6392a6cdb5d044f09949dd87846de2fa">IMP::core::get_distance()</a>, <a href="namespaceIMP_1_1core.html#aca45b7f82466b871a7a2772559b2e121">IMP::core::get_height()</a>, <a href="namespaceIMP_1_1core.html#a2de8a0a4e81ff897fdf4a8741be335e1">IMP::core::get_height()</a></td></tr>
179 <tr><td>@ref IMP::core::SurfaceGeometry</td><td><a href="classIMP_1_1core_1_1SurfaceGeometryConstraint.html#abb639e04c8072f2afb272fb392d4e9fe">IMP::core::SurfaceGeometryConstraint::SurfaceGeometryConstraint()</a></td></tr>
180 <tr><td>@ref IMP::core::TableRefiner</td><td><a href="classIMP_1_1spb_1_1RigidBodyPackingScore.html#af9450aec17ade4688cbcfcf7981772af">IMP::spb::RigidBodyPackingScore::RigidBodyPackingScore()</a></td></tr>
181 <tr><td>@ref IMP::core::TransformationSymmetry</td><td><a href="classIMP_1_1core_1_1TransformationSymmetryMover.html#af2ceb2b3911ae2406e06502d5d0153a0">IMP::core::TransformationSymmetryMover::TransformationSymmetryMover()</a></td></tr>
182 <tr><td>@ref IMP::core::XYZ</td><td><a href="classIMP_1_1atom_1_1Angle.html#abf8e9da4ebd4f545e4bce03ac6f0dc50">IMP::atom::Angle::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Angle.html#ac05c3945ed23762560f6d065d2626981">IMP::atom::Angle::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Angle.html#a85dc3dea18311ca858192b5a8e1087d7">IMP::atom::Angle::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Dihedral.html#a0ec428430e4eddddd8844339e2fea103">IMP::atom::Dihedral::do_setup_particle()</a>, <a href="classIMP_1_1atom_1_1Dihedral.html#a7fd379c8d46a632cbe59b22f2a9043e5">IMP::atom::Dihedral::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Dihedral.html#aba8bf926754ed9a62e899e93f951b96c">IMP::atom::Dihedral::setup_particle()</a>, <a href="classIMP_1_1core_1_1LateralSurfaceConstraint.html#a15da8840351877dad1a931c7736397b4">IMP::core::LateralSurfaceConstraint::LateralSurfaceConstraint()</a>, <a href="classIMP_1_1core_1_1XYZ.html#abdf4dcafcd415cddf90e0b7565f89f62">IMP::core::XYZ::get_vector_to()</a>, <a href="classIMP_1_1core_1_1XYZDerivativeGeometry.html#a348f6ac949c5a28e305b377e86d78d70">IMP::core::XYZDerivativeGeometry::XYZDerivativeGeometry()</a>, <a href="classIMP_1_1kinematics_1_1BondAngleRevoluteJoint.html#a16ba2ca9dff457daf656a6336e46f56a">IMP::kinematics::BondAngleRevoluteJoint::BondAngleRevoluteJoint()</a>, <a href="classIMP_1_1kinematics_1_1BondAngleRevoluteJoint.html#a879f42c6e5b39ca8e849f6283deb98e5">IMP::kinematics::BondAngleRevoluteJoint::get_perpendicular_vector()</a>, <a href="classIMP_1_1kinematics_1_1CCDLoopClosure.html#aae25b8faa1131674a8f7c775cede7388">IMP::kinematics::CCDLoopClosure::CCDLoopClosure()</a>, <a href="classIMP_1_1kinematics_1_1DihedralAngleRevoluteJoint.html#a518c71ba70ed25ad87aae3cb9dbab4ff">IMP::kinematics::DihedralAngleRevoluteJoint::DihedralAngleRevoluteJoint()</a>, <a href="classIMP_1_1kinematics_1_1PrismaticJoint.html#a69b32641f0207229ec1fd26b6d399546">IMP::kinematics::PrismaticJoint::PrismaticJoint()</a>, <a href="namespaceIMP_1_1core.html#a871feee8cd80fe860602685979bbb5f2">IMP::core::get_depth()</a>, <a href="namespaceIMP_1_1core.html#a8586c04d2d9396490dc9cc71f7899141">IMP::core::get_dihedral()</a>, <a href="namespaceIMP_1_1core.html#a6392a6cdb5d044f09949dd87846de2fa">IMP::core::get_distance()</a>, <a href="namespaceIMP_1_1core.html#af2049fdca8aae38e86549cfdeff1d1fc">IMP::core::get_distance()</a>, <a href="namespaceIMP_1_1core.html#a2de8a0a4e81ff897fdf4a8741be335e1">IMP::core::get_height()</a>, <a href="namespaceIMP_1_1core.html#ab188fc0fd41b9715232fe9c23b11bfdf">IMP::core::get_vector_geometry()</a>, <a href="namespaceIMP_1_1core.html#aa284a594e40d97aa3e915a3da70a4d3d">IMP::core::set_vector_geometry()</a>, <a href="namespaceIMP_1_1core.html#a556f7cad1de8ed389d05b4d7acbeb4d0">IMP::core::transform()</a></td></tr>
183 <tr><td>@ref IMP::core::XYZR</td><td><a href="classIMP_1_1core_1_1XYZRGeometry.html#a7e4091e42fc2eea3a7a2e4098037f845">IMP::core::XYZRGeometry::XYZRGeometry()</a>, <a href="namespaceIMP_1_1core.html#a75ddddcaa7bc977a250b60f266cd39ec">IMP::core::get_depth()</a>, <a href="namespaceIMP_1_1core.html#ad65d79ddb3c6e1db815d57f73c8f18ea">IMP::core::get_distance()</a>, <a href="namespaceIMP_1_1core.html#af9c67a7fc68dd22fa3f7e685ff7e77b9">IMP::core::get_distance()</a>, <a href="namespaceIMP_1_1core.html#aca45b7f82466b871a7a2772559b2e121">IMP::core::get_height()</a>, <a href="namespaceIMP_1_1core.html#a25735ab61a19f9813d051462afd24b2f">IMP::core::set_enclosing_radius()</a>, <a href="namespaceIMP_1_1core.html#a9f00e88e92a88b5ef349978fe737df7d">IMP::core::set_enclosing_sphere()</a></td></tr>
184 </table>
185 # IMP.display # {#argument_index_display}
186 <table><tr>
187 <th>Class</th><th>Users</th></tr>
188 <tr><td>@ref IMP::display::BoundingBoxGeometry</td><td><a href="classIMP_1_1display_1_1GeometryProcessor.html#a5f2b7edfdeef5ca64a4000c048e5e45d">IMP::display::GeometryProcessor::handle_bounding_box()</a></td></tr>
189 <tr><td>@ref IMP::display::Color</td><td><a href="classIMP_1_1core_1_1SurfaceGeometry.html#af8a9caf61f550b77dd0774b156ff95b5">IMP::core::SurfaceGeometry::SurfaceGeometry()</a>, <a href="classIMP_1_1display_1_1BoundingBoxGeometry.html#abffcb4633c7da35860a1a7f3f97f35b0">IMP::display::BoundingBoxGeometry::BoundingBoxGeometry()</a>, <a href="classIMP_1_1display_1_1BoundingBoxGeometry.html#a6f4bacf190fc76a5ecdc2459bfed9891">IMP::display::BoundingBoxGeometry::BoundingBoxGeometry()</a>, <a href="classIMP_1_1display_1_1Color.html#a2ac3767f2e1dfdd2d5168a5ff34388c5">IMP::display::Color::compare()</a>, <a href="classIMP_1_1display_1_1Colored.html#a37d69f63a128fa2fbf0413f41b97bb05">IMP::display::Colored::do_setup_particle()</a>, <a href="classIMP_1_1display_1_1Colored.html#a496c82c2b609ba9e97936aa5c1ca1423">IMP::display::Colored::set_color()</a>, <a href="classIMP_1_1display_1_1Colored.html#a1f682cba5427be0068b38d6c126da974">IMP::display::Colored::setup_particle()</a>, <a href="classIMP_1_1display_1_1Colored.html#ac7a6985811693a52c964d64d650a881c">IMP::display::Colored::setup_particle()</a>, <a href="classIMP_1_1display_1_1CylinderGeometry.html#ab08ceebc8704d641be302119db1ebb73">IMP::display::CylinderGeometry::CylinderGeometry()</a>, <a href="classIMP_1_1display_1_1CylinderGeometry.html#af38ad28d6d178422d8db293d14b7d646">IMP::display::CylinderGeometry::CylinderGeometry()</a>, <a href="classIMP_1_1display_1_1EllipsoidGeometry.html#a8b23de125510a349978b1b789743ea33">IMP::display::EllipsoidGeometry::EllipsoidGeometry()</a>, <a href="classIMP_1_1display_1_1EllipsoidGeometry.html#a880be80c539c27f6e16c0a38a9fa9c9c">IMP::display::EllipsoidGeometry::EllipsoidGeometry()</a>, <a href="classIMP_1_1display_1_1FilterGeometry.html#ace71488df43cbc6136b3e4805fb86256">IMP::display::FilterGeometry::handle_cylinder()</a>, <a href="classIMP_1_1display_1_1FilterGeometry.html#a385bb7f540f28e4be780764ec4dbbac3">IMP::display::FilterGeometry::handle_point()</a>, <a href="classIMP_1_1display_1_1FilterGeometry.html#a43fffd6a9d69c4ce15e6f1290772ec5d">IMP::display::FilterGeometry::handle_segment()</a>, <a href="classIMP_1_1display_1_1FilterGeometry.html#ac60a266887c09160d1949ddbb8cb17c4">IMP::display::FilterGeometry::handle_sphere()</a>, <a href="classIMP_1_1display_1_1Geometry.html#ab56604ac628c5536a5277797a3f586e5">IMP::display::Geometry::Geometry()</a>, <a href="classIMP_1_1display_1_1Geometry.html#a5e68da46ed42586463a05eaa006c9533">IMP::display::Geometry::set_color()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#a5cb9e1aa859508c2b54013ee5bdcadfd">IMP::display::GeometryProcessor::handle_anything()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#a5f2b7edfdeef5ca64a4000c048e5e45d">IMP::display::GeometryProcessor::handle_bounding_box()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#adfa4f37b2300fd8c0443515ad00c8416">IMP::display::GeometryProcessor::handle_cylinder()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#aeb1a54db3c67211bbe8c32922354d7af">IMP::display::GeometryProcessor::handle_ellipsoid()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#a354c0c4086663725556733b3aeecd7e0">IMP::display::GeometryProcessor::handle_label()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#a89102436eae74971a1a982d63cfc5b4e">IMP::display::GeometryProcessor::handle_point()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#acc01161a988e1c3ced6c32c6b500f16b">IMP::display::GeometryProcessor::handle_polygon()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#a14360b2b0fc05eb9ae45018f30d5ca5e">IMP::display::GeometryProcessor::handle_segment()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#acbee35eb67b6659899f44b2218127ef1">IMP::display::GeometryProcessor::handle_sphere()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#a53e8793ca9ccb036c3f234967a492fd6">IMP::display::GeometryProcessor::handle_surface_mesh()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#a835b0ea8d9b35735917b0eb9efd9afba">IMP::display::GeometryProcessor::handle_triangle()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#a883ab2186aa243200cee7ce65b7c92c4">IMP::display::GeometryProcessor::handle_geometry_internal()</a>, <a href="classIMP_1_1display_1_1GeometrySet.html#abc566fc8470c8cc0059a8fe9fd78baf2">IMP::display::GeometrySet::GeometrySet()</a>, <a href="classIMP_1_1display_1_1GeometrySet.html#a3f808d88d9832770e804ce07813806fa">IMP::display::GeometrySet::GeometrySet()</a>, <a href="classIMP_1_1display_1_1PairsGeometry.html#a1a82af0664dd2d3206b5e4f4aeb0ca5d">IMP::display::PairsGeometry::PairsGeometry()</a>, <a href="classIMP_1_1display_1_1PointGeometry.html#a6fded29c99e011a7d7735e845f745ad7">IMP::display::PointGeometry::PointGeometry()</a>, <a href="classIMP_1_1display_1_1PointGeometry.html#affe821e4562c888981f6cc674f6f6144">IMP::display::PointGeometry::PointGeometry()</a>, <a href="classIMP_1_1display_1_1PolygonGeometry.html#acd5cc1ee58451042ac360b2302916b6a">IMP::display::PolygonGeometry::PolygonGeometry()</a>, <a href="classIMP_1_1display_1_1PolygonGeometry.html#ac357ffc56fb03894e549a5e5d9a20b7e">IMP::display::PolygonGeometry::PolygonGeometry()</a>, <a href="classIMP_1_1display_1_1PymolWriter.html#adf65270d7a6288b6bb1207ffac5af062">IMP::display::PymolWriter::handle_cylinder()</a>, <a href="classIMP_1_1display_1_1PymolWriter.html#a37b5143f0b5ae311db1fe45bb88384f9">IMP::display::PymolWriter::handle_label()</a>, <a href="classIMP_1_1display_1_1PymolWriter.html#adc29c2e61c29bc42a26c0f2b5f097b0c">IMP::display::PymolWriter::handle_point()</a>, <a href="classIMP_1_1display_1_1PymolWriter.html#a2e7061f9395e31948fd871ebf750bd5c">IMP::display::PymolWriter::handle_polygon()</a>, <a href="classIMP_1_1display_1_1PymolWriter.html#a4993e607662088fb6667987a24714db4">IMP::display::PymolWriter::handle_segment()</a>, <a href="classIMP_1_1display_1_1PymolWriter.html#a35b2b860e0325a6beb3ac0d49e83c490">IMP::display::PymolWriter::handle_sphere()</a>, <a href="classIMP_1_1display_1_1PymolWriter.html#a9e0e77ab73c48a55efac2081eb4b710e">IMP::display::PymolWriter::handle_surface()</a>, <a href="classIMP_1_1display_1_1PymolWriter.html#a3a6fd19e9d1e8b25ee0de69b99dd769a">IMP::display::PymolWriter::handle_triangle()</a>, <a href="classIMP_1_1display_1_1ReferenceFrameGeometry.html#a431e05df3b0c309759e12b8049948402">IMP::display::ReferenceFrameGeometry::ReferenceFrameGeometry()</a>, <a href="classIMP_1_1display_1_1ReferenceFrameGeometry.html#a7525a19a4c0cd13b906ed83124a89a33">IMP::display::ReferenceFrameGeometry::ReferenceFrameGeometry()</a>, <a href="classIMP_1_1display_1_1SegmentGeometry.html#a0eda17f53f2e8cef8ae21c615f3e1b2b">IMP::display::SegmentGeometry::SegmentGeometry()</a>, <a href="classIMP_1_1display_1_1SegmentGeometry.html#a0722985d583856076e2251d4cb85f380">IMP::display::SegmentGeometry::SegmentGeometry()</a>, <a href="classIMP_1_1display_1_1SingletonsGeometry.html#a6bfeea07e40dfd0843f9174ed55189a4">IMP::display::SingletonsGeometry::SingletonsGeometry()</a>, <a href="classIMP_1_1display_1_1SphereGeometry.html#ad3f60723035bcb75f0b0fa499678c5de">IMP::display::SphereGeometry::SphereGeometry()</a>, <a href="classIMP_1_1display_1_1SphereGeometry.html#a4667a4de9e70e142a3b0d3bb7a102996">IMP::display::SphereGeometry::SphereGeometry()</a>, <a href="classIMP_1_1display_1_1TriangleGeometry.html#a8880501417b489547a254c4c2003cf3d">IMP::display::TriangleGeometry::TriangleGeometry()</a>, <a href="classIMP_1_1display_1_1TriangleGeometry.html#a6a039b1098c7111bafe6a715fdbdc6ba">IMP::display::TriangleGeometry::TriangleGeometry()</a>, <a href="classIMP_1_1npctransport_1_1ParticleFactory.html#aba74e71f6c9b9937152ffb044859b3d4">IMP::npctransport::ParticleFactory::ParticleFactory()</a>, <a href="classIMP_1_1npctransport_1_1SimulationData.html#ab8e251c849477123d14c6b67d96716be">IMP::npctransport::SimulationData::create_floaters()</a>, <a href="namespaceIMP_1_1display.html#ada2a3156a15dd0217840bfc8675724d8">IMP::display::get_interpolated_rgb()</a>, <a href="namespaceIMP_1_1npctransport.html#ac5025684e81bdc014b287d20e18373d9">IMP::npctransport::create_fg_chain()</a>, <a href="namespaceIMP_1_1spb.html#af9854762e7ddee17e6b588f2a8502c20">IMP::spb::create_coiled_coil()</a>, <a href="namespaceIMP_1_1spb.html#a78b1fb512e1db9c6362bb36df94293be">IMP::spb::create_protein()</a>, <a href="namespaceIMP_1_1spb.html#a994bd0fe39346bf4f08cbc6693a230f3">IMP::spb::create_protein()</a></td></tr>
190 <tr><td>@ref IMP::display::CylinderGeometry</td><td><a href="classIMP_1_1display_1_1FilterGeometry.html#ace71488df43cbc6136b3e4805fb86256">IMP::display::FilterGeometry::handle_cylinder()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#adfa4f37b2300fd8c0443515ad00c8416">IMP::display::GeometryProcessor::handle_cylinder()</a>, <a href="classIMP_1_1display_1_1PymolWriter.html#adf65270d7a6288b6bb1207ffac5af062">IMP::display::PymolWriter::handle_cylinder()</a></td></tr>
191 <tr><td>@ref IMP::display::EllipsoidGeometry</td><td><a href="classIMP_1_1display_1_1GeometryProcessor.html#aeb1a54db3c67211bbe8c32922354d7af">IMP::display::GeometryProcessor::handle_ellipsoid()</a></td></tr>
192 <tr><td>@ref IMP::display::Geometry</td><td><a href="classIMP_1_1display_1_1FilterGeometry.html#ae62eb73dfa5a06f67362a8753ec3238a">IMP::display::FilterGeometry::add_geometry()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#a5cb9e1aa859508c2b54013ee5bdcadfd">IMP::display::GeometryProcessor::handle_anything()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#a2ec53ebfd26f0e83e5260de90a16e0de">IMP::display::GeometryProcessor::handle_geometry()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#a883ab2186aa243200cee7ce65b7c92c4">IMP::display::GeometryProcessor::handle_geometry_internal()</a>, <a href="classIMP_1_1display_1_1WriteOptimizerState.html#a585eefb24f1e1b12baf0ddc9daa7728f">IMP::display::WriteOptimizerState::add_geometry()</a>, <a href="classIMP_1_1display_1_1WriteOptimizerState.html#a7ebf99fba15e4baccdcd33931c76519a">IMP::display::WriteOptimizerState::remove_geometry()</a>, <a href="classIMP_1_1display_1_1Writer.html#ad844e55168736fe8a629eeef6a7ccb40">IMP::display::Writer::add_geometry()</a>, <a href="namespaceIMP_1_1rmf.html#ac527cf5f24b42ec60119b3ff253781ba">IMP::rmf::add_geometry()</a></td></tr>
193 <tr><td>@ref IMP::display::LabelGeometry</td><td><a href="classIMP_1_1display_1_1GeometryProcessor.html#a354c0c4086663725556733b3aeecd7e0">IMP::display::GeometryProcessor::handle_label()</a>, <a href="classIMP_1_1display_1_1PymolWriter.html#a37b5143f0b5ae311db1fe45bb88384f9">IMP::display::PymolWriter::handle_label()</a></td></tr>
194 <tr><td>@ref IMP::display::PointGeometry</td><td><a href="classIMP_1_1display_1_1FilterGeometry.html#a385bb7f540f28e4be780764ec4dbbac3">IMP::display::FilterGeometry::handle_point()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#a89102436eae74971a1a982d63cfc5b4e">IMP::display::GeometryProcessor::handle_point()</a>, <a href="classIMP_1_1display_1_1PymolWriter.html#adc29c2e61c29bc42a26c0f2b5f097b0c">IMP::display::PymolWriter::handle_point()</a></td></tr>
195 <tr><td>@ref IMP::display::PolygonGeometry</td><td><a href="classIMP_1_1display_1_1GeometryProcessor.html#acc01161a988e1c3ced6c32c6b500f16b">IMP::display::GeometryProcessor::handle_polygon()</a>, <a href="classIMP_1_1display_1_1PymolWriter.html#a2e7061f9395e31948fd871ebf750bd5c">IMP::display::PymolWriter::handle_polygon()</a></td></tr>
196 <tr><td>@ref IMP::display::SegmentGeometry</td><td><a href="classIMP_1_1display_1_1FilterGeometry.html#a43fffd6a9d69c4ce15e6f1290772ec5d">IMP::display::FilterGeometry::handle_segment()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#a14360b2b0fc05eb9ae45018f30d5ca5e">IMP::display::GeometryProcessor::handle_segment()</a>, <a href="classIMP_1_1display_1_1PymolWriter.html#a4993e607662088fb6667987a24714db4">IMP::display::PymolWriter::handle_segment()</a></td></tr>
197 <tr><td>@ref IMP::display::SphereGeometry</td><td><a href="classIMP_1_1display_1_1FilterGeometry.html#ac60a266887c09160d1949ddbb8cb17c4">IMP::display::FilterGeometry::handle_sphere()</a>, <a href="classIMP_1_1display_1_1GeometryProcessor.html#acbee35eb67b6659899f44b2218127ef1">IMP::display::GeometryProcessor::handle_sphere()</a>, <a href="classIMP_1_1display_1_1PymolWriter.html#a35b2b860e0325a6beb3ac0d49e83c490">IMP::display::PymolWriter::handle_sphere()</a></td></tr>
198 <tr><td>@ref IMP::display::SurfaceMeshGeometry</td><td><a href="classIMP_1_1display_1_1GeometryProcessor.html#a53e8793ca9ccb036c3f234967a492fd6">IMP::display::GeometryProcessor::handle_surface_mesh()</a>, <a href="classIMP_1_1display_1_1PymolWriter.html#a9e0e77ab73c48a55efac2081eb4b710e">IMP::display::PymolWriter::handle_surface()</a></td></tr>
199 <tr><td>@ref IMP::display::TriangleGeometry</td><td><a href="classIMP_1_1display_1_1GeometryProcessor.html#a835b0ea8d9b35735917b0eb9efd9afba">IMP::display::GeometryProcessor::handle_triangle()</a>, <a href="classIMP_1_1display_1_1PymolWriter.html#a3a6fd19e9d1e8b25ee0de69b99dd769a">IMP::display::PymolWriter::handle_triangle()</a></td></tr>
200 <tr><td>@ref IMP::display::Writer</td><td><a href="classIMP_1_1display_1_1WriterAdaptor.html#a5c8ef5befd08eefeb081e6bb41204bb3">IMP::display::WriterAdaptor::WriterAdaptor()</a>, <a href="namespaceIMP_1_1npctransport.html#a03670f5844c2eaf98f64d0aed46f6255">IMP::npctransport::write_geometry()</a></td></tr>
201 <tr><td>@ref IMP::display::WriterAdaptor</td><td><a href="classIMP_1_1display_1_1WriteOptimizerState.html#a51ae42814a3cf03a8d4003bc94508de7">IMP::display::WriteOptimizerState::WriteOptimizerState()</a>, <a href="classIMP_1_1display_1_1WriteOptimizerState.html#a6b064de0f80556707f5c7626de74a26f">IMP::display::WriteOptimizerState::write()</a></td></tr>
202 </table>
203 # IMP.domino # {#argument_index_domino}
204 <table><tr>
205 <th>Class</th><th>Users</th></tr>
206 <tr><td>@ref IMP::domino::Assignment</td><td><a href="classIMP_1_1domino_1_1AssignmentContainer.html#a205dd896cae1e38d153254a34cf57b5d">IMP::domino::AssignmentContainer::add_assignment()</a>, <a href="classIMP_1_1domino_1_1CappedAssignmentContainer.html#a5ed14b8e7c62b1c853891c15d817dfcf">IMP::domino::CappedAssignmentContainer::add_assignment()</a>, <a href="classIMP_1_1domino_1_1HeapAssignmentContainer.html#a2b659623be5f37ba9f2290d6a4045b2d">IMP::domino::HeapAssignmentContainer::add_assignment()</a>, <a href="classIMP_1_1domino_1_1ListAssignmentContainer.html#ad8fd70ea8e018c656dd47a130fd711cf">IMP::domino::ListAssignmentContainer::add_assignment()</a>, <a href="classIMP_1_1domino_1_1Order.html#acebb05321bf90fe7e6d4bc27b37902df">IMP::domino::Order::get_list_ordered()</a>, <a href="classIMP_1_1domino_1_1PackedAssignmentContainer.html#ab4ce677fc222f2284de6a49fa901f0a7">IMP::domino::PackedAssignmentContainer::add_assignment()</a>, <a href="classIMP_1_1domino_1_1RangeViewAssignmentContainer.html#a24c95a9c8decf80d6d9daa9b0e6116a3">IMP::domino::RangeViewAssignmentContainer::add_assignment()</a>, <a href="classIMP_1_1domino_1_1ReadAssignmentContainer.html#a123c10790ce5474a09ccd4c89b1aba1d">IMP::domino::ReadAssignmentContainer::add_assignment()</a>, <a href="classIMP_1_1domino_1_1ReadHDF5AssignmentContainer.html#abb640818153942e00d0e9740f31c5d9f">IMP::domino::ReadHDF5AssignmentContainer::add_assignment()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#a900c1be619f7302ade5f53c08b86f8b8">IMP::domino::RestraintCache::get_score()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#a277af62358d51335e22c3c5419ced30a">IMP::domino::RestraintCache::get_score()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#a7cb8d67a4032980ccdbbb2393c4a8aad">IMP::domino::RestraintCache::load_last_score()</a>, <a href="classIMP_1_1domino_1_1SampleAssignmentContainer.html#ab9dfb0061d501d144f0fac3d16cbb908">IMP::domino::SampleAssignmentContainer::add_assignment()</a>, <a href="classIMP_1_1domino_1_1Slice.html#ab3c699a06268f2fa405c296149c4515b">IMP::domino::Slice::get_sliced()</a>, <a href="classIMP_1_1domino_1_1SubsetFilter.html#ae6ac39cf0c88e5f67f47ab75a255252d">IMP::domino::SubsetFilter::get_is_ok()</a>, <a href="classIMP_1_1domino_1_1SubsetFilter.html#a98bb346a18334bae9a8028d7f99851a2">IMP::domino::SubsetFilter::get_next_state()</a>, <a href="classIMP_1_1domino_1_1WriteAssignmentContainer.html#a9823c664b05000244a86680fdfce4393">IMP::domino::WriteAssignmentContainer::add_assignment()</a>, <a href="classIMP_1_1domino_1_1WriteHDF5AssignmentContainer.html#a2bc4307eff9201b71e24bd6c3c376b57">IMP::domino::WriteHDF5AssignmentContainer::add_assignment()</a>, <a href="classIMP_1_1em2d_1_1DistanceFilter.html#a862db6bdd0cccc956f3a1c5e186d6594">IMP::em2d::DistanceFilter::get_is_ok()</a>, <a href="namespaceIMP_1_1domino.html#a0c08cfa3955a23464c5f59c15f95a4ae">IMP::domino::load_particle_states()</a>, <a href="namespaceIMP_1_1domino.html#a3a112fd41a97e8e93dbff8be3dfb8bb6">IMP::domino::get_distance_if_smaller_than()</a>, <a href="namespaceIMP_1_1domino.html#a3247d32b900c4633e5c58cd7032d043b">IMP::domino::get_embedding()</a>, <a href="namespaceIMP_1_1domino.html#a419db1b5a46dd7eefe31fd0279087c94">IMP::domino::swap()</a></td></tr>
207 <tr><td>@ref IMP::domino::AssignmentContainer</td><td><a href="classIMP_1_1domino_1_1AssignmentsTable.html#a82165fe3c39a0a5bd1005826f5121c26">IMP::domino::AssignmentsTable::load_assignments()</a>, <a href="classIMP_1_1domino_1_1BranchAndBoundAssignmentsTable.html#a9165b72d63a07e7e68728a8017628e6e">IMP::domino::BranchAndBoundAssignmentsTable::load_assignments()</a>, <a href="classIMP_1_1domino_1_1CappedAssignmentContainer.html#a981ac5833c29ad4c1a881b3a89a84710">IMP::domino::CappedAssignmentContainer::CappedAssignmentContainer()</a>, <a href="classIMP_1_1domino_1_1DominoSampler.html#a317227a05c7903a41070a939a8ee079b">IMP::domino::DominoSampler::load_vertex_assignments()</a>, <a href="classIMP_1_1domino_1_1DominoSampler.html#a32961043b9b12602d60b6a50a1014aa8">IMP::domino::DominoSampler::load_vertex_assignments()</a>, <a href="classIMP_1_1domino_1_1ListAssignmentsTable.html#aa0422fdbb973a84ae9dfd12c08b3979d">IMP::domino::ListAssignmentsTable::load_assignments()</a>, <a href="classIMP_1_1domino_1_1ListAssignmentsTable.html#a15fa28a76023dd8fa328b452d2245908">IMP::domino::ListAssignmentsTable::set_assignments()</a>, <a href="classIMP_1_1domino_1_1RangeViewAssignmentContainer.html#a7de21afe06173ad8218f45a82cf21e15">IMP::domino::RangeViewAssignmentContainer::RangeViewAssignmentContainer()</a>, <a href="classIMP_1_1domino_1_1RecursiveAssignmentsTable.html#a90514e1adc6368f99d345b59668a803a">IMP::domino::RecursiveAssignmentsTable::load_assignments()</a>, <a href="classIMP_1_1domino_1_1SimpleAssignmentsTable.html#a23b9149da5312b4e120a36f3d4949bc9">IMP::domino::SimpleAssignmentsTable::load_assignments()</a>, <a href="namespaceIMP_1_1domino.html#a4570cce69f194985e23b710c3b5e18b4">IMP::domino::load_leaf_assignments()</a>, <a href="namespaceIMP_1_1domino.html#a200c71a273844cc32fd32f6a5eafa0aa">IMP::domino::load_merged_assignments()</a>, <a href="namespaceIMP_1_1domino.html#a3305fe8f61d81cba57e9f6896024b263">IMP::domino::load_merged_assignments_random_order()</a></td></tr>
208 <tr><td>@ref IMP::domino::AssignmentsTable</td><td><a href="classIMP_1_1domino_1_1DiscreteSampler.html#aad5f8f5ee7e3e9b17f247917235ab62b">IMP::domino::DiscreteSampler::set_assignments_table()</a>, <a href="namespaceIMP_1_1domino.html#a4570cce69f194985e23b710c3b5e18b4">IMP::domino::load_leaf_assignments()</a></td></tr>
209 <tr><td>@ref IMP::domino::Order</td><td><a href="namespaceIMP_1_1domino.html#adf25d025631b32526e9e794ae0be804a">IMP::domino::swap()</a></td></tr>
210 <tr><td>@ref IMP::domino::ParticleStates</td><td><a href="classIMP_1_1domino_1_1CompoundStates.html#a43d16cc20bd7c0c107341a1395319ca7">IMP::domino::CompoundStates::CompoundStates()</a>, <a href="classIMP_1_1domino_1_1DiscreteSampler.html#af01fe0f3283adc61bdb94b716afca5cd">IMP::domino::DiscreteSampler::set_particle_states()</a>, <a href="classIMP_1_1domino_1_1ParticleStatesTable.html#a9ad869bd5d88c52e03c4395d8ab36e9e">IMP::domino::ParticleStatesTable::set_particle_states()</a>, <a href="classIMP_1_1domino_1_1PermutationStates.html#a95308fa6fbdd565f52c7d58d4fdbaee8">IMP::domino::PermutationStates::PermutationStates()</a></td></tr>
211 <tr><td>@ref IMP::domino::ParticleStatesTable</td><td><a href="classIMP_1_1domino_1_1BranchAndBoundAssignmentsTable.html#a4c39de9b95b22e5efe0804df01b95ee7">IMP::domino::BranchAndBoundAssignmentsTable::BranchAndBoundAssignmentsTable()</a>, <a href="classIMP_1_1domino_1_1BranchAndBoundSampler.html#a8246e854a8ba9054935a9c75cb9c3a5b">IMP::domino::BranchAndBoundSampler::BranchAndBoundSampler()</a>, <a href="classIMP_1_1domino_1_1DiscreteSampler.html#ae87fc3c189ff87dbc93ba9959da79e4f">IMP::domino::DiscreteSampler::set_particle_states_table()</a>, <a href="classIMP_1_1domino_1_1DiscreteSampler.html#aea4170286d84da9b510356cb25bd0636">IMP::domino::DiscreteSampler::get_subset_filter_tables_to_use()</a>, <a href="classIMP_1_1domino_1_1DiscreteSampler.html#a721fbf1b3bf0780e90966a0453f547d4">IMP::domino::DiscreteSampler::DiscreteSampler()</a>, <a href="classIMP_1_1domino_1_1DisjointSetsSubsetFilterTable.html#a6d219703856338684fecf5d96cdd599c">IMP::domino::DisjointSetsSubsetFilterTable::DisjointSetsSubsetFilterTable()</a>, <a href="classIMP_1_1domino_1_1DominoSampler.html#a383966690daeef40257e5f33c3a76ada">IMP::domino::DominoSampler::DominoSampler()</a>, <a href="classIMP_1_1domino_1_1EqualitySubsetFilterTable.html#a4e777dc82d3cac03bffe26eddb42e129">IMP::domino::EqualitySubsetFilterTable::EqualitySubsetFilterTable()</a>, <a href="classIMP_1_1domino_1_1EquivalenceAndExclusionSubsetFilterTable.html#a2354750aa4ca41885dd8726639902dc4">IMP::domino::EquivalenceAndExclusionSubsetFilterTable::EquivalenceAndExclusionSubsetFilterTable()</a>, <a href="classIMP_1_1domino_1_1EquivalenceSubsetFilterTable.html#a90d1efcd9ae9d2bbc3d14662893a8d28">IMP::domino::EquivalenceSubsetFilterTable::EquivalenceSubsetFilterTable()</a>, <a href="classIMP_1_1domino_1_1ExclusionSubsetFilterTable.html#a7a840667473246f7a134eba28011636e">IMP::domino::ExclusionSubsetFilterTable::ExclusionSubsetFilterTable()</a>, <a href="classIMP_1_1domino_1_1ListSubsetFilterTable.html#a43f47a195717a826c88ad066c1553656">IMP::domino::ListSubsetFilterTable::ListSubsetFilterTable()</a>, <a href="classIMP_1_1domino_1_1ParticlesAdaptor.html#a7de81f47fe87067fd633f6d442055117">IMP::domino::ParticlesAdaptor::ParticlesAdaptor()</a>, <a href="classIMP_1_1domino_1_1RecursiveAssignmentsTable.html#a0809f8c142a88c80dbd62f57197e795d">IMP::domino::RecursiveAssignmentsTable::RecursiveAssignmentsTable()</a>, <a href="classIMP_1_1domino_1_1RecursiveStates.html#a64d119281ac852e97227186e68b69c0c">IMP::domino::RecursiveStates::RecursiveStates()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#aa442ea37df1d8b970993d4ce57c6e68a">IMP::domino::RestraintCache::RestraintCache()</a>, <a href="classIMP_1_1domino_1_1RestraintScoreSubsetFilterTable.html#a27a72d5b2d3000fa72df9c45755db866">IMP::domino::RestraintScoreSubsetFilterTable::RestraintScoreSubsetFilterTable()</a>, <a href="classIMP_1_1domino_1_1SimpleAssignmentsTable.html#a327026ad51858f3eb8800617576fea85">IMP::domino::SimpleAssignmentsTable::SimpleAssignmentsTable()</a>, <a href="classIMP_1_1em2d_1_1DistanceFilter.html#a0fdd72792f673c8b7d590b5abe80b3fa">IMP::em2d::DistanceFilter::DistanceFilter()</a>, <a href="classIMP_1_1em2d_1_1DistanceFilterTable.html#a8edc09e71c701c228c5a37783130a2de">IMP::em2d::DistanceFilterTable::DistanceFilterTable()</a>, <a href="namespaceIMP_1_1domino.html#a7745ea629841a6a4475211ba0a134b44">IMP::domino::get_interaction_graph()</a>, <a href="namespaceIMP_1_1domino.html#a52b8de54766ce0eeaece21adff2c9bd1">IMP::domino::get_merge_tree()</a>, <a href="namespaceIMP_1_1domino.html#a0c08cfa3955a23464c5f59c15f95a4ae">IMP::domino::load_particle_states()</a>, <a href="namespaceIMP_1_1domino.html#ab0efd3e3db335ea082bf9b7567011958">IMP::domino::get_restraints()</a>, <a href="namespaceIMP_1_1domino.html#a3a112fd41a97e8e93dbff8be3dfb8bb6">IMP::domino::get_distance_if_smaller_than()</a>, <a href="namespaceIMP_1_1domino.html#a3247d32b900c4633e5c58cd7032d043b">IMP::domino::get_embedding()</a>, <a href="namespaceIMP_1_1domino.html#abd8a69ba2cc2b8fea2f49c99189d8711">IMP::domino::get_nearest_assignment()</a>, <a href="namespaceIMP_1_1domino.html#aa29c2ec35739c08db3a13ffe4ec38088">IMP::domino::get_possible_interactions()</a>, <a href="namespaceIMP_1_1domino.html#ab0eb2c05d5eb0c9e64fba8c85011ad01">IMP::domino::get_restraint_graph()</a>, <a href="namespaceIMP_1_1domino.html#a7b094ee7dac304dfc212772818a9ba04">IMP::domino::get_state_clusters()</a></td></tr>
212 <tr><td>@ref IMP::domino::RestraintCache</td><td><a href="classIMP_1_1domino_1_1HeapAssignmentContainer.html#ae441675fd3cc83cc810db7fcfc9928e9">IMP::domino::HeapAssignmentContainer::HeapAssignmentContainer()</a>, <a href="classIMP_1_1domino_1_1MinimumRestraintScoreSubsetFilterTable.html#a8af4401981928e337a9e624884c15937">IMP::domino::MinimumRestraintScoreSubsetFilterTable::MinimumRestraintScoreSubsetFilterTable()</a>, <a href="classIMP_1_1domino_1_1RestraintScoreSubsetFilterTable.html#afea31f7827234768b9e719e4db0545d2">IMP::domino::RestraintScoreSubsetFilterTable::RestraintScoreSubsetFilterTable()</a></td></tr>
213 <tr><td>@ref IMP::domino::Slice</td><td><a href="namespaceIMP_1_1domino.html#a52a530f6cadbd362b3c42b9210ef5dae">IMP::domino::swap()</a></td></tr>
214 <tr><td>@ref IMP::domino::Subset</td><td><a href="classIMP_1_1domino_1_1AssignmentsTable.html#a82165fe3c39a0a5bd1005826f5121c26">IMP::domino::AssignmentsTable::load_assignments()</a>, <a href="classIMP_1_1domino_1_1BranchAndBoundAssignmentsTable.html#a9165b72d63a07e7e68728a8017628e6e">IMP::domino::BranchAndBoundAssignmentsTable::load_assignments()</a>, <a href="classIMP_1_1domino_1_1BranchAndBoundSampler.html#ae6043ff455cc1079a594cb25d74f117b">IMP::domino::BranchAndBoundSampler::do_get_sample_assignments()</a>, <a href="classIMP_1_1domino_1_1DiscreteSampler.html#a127213eff7a87b103e692c4f2d82d133">IMP::domino::DiscreteSampler::do_get_sample_assignments()</a>, <a href="classIMP_1_1domino_1_1DiscreteSampler.html#a4174eb43930468fea7d113da69c51656">IMP::domino::DiscreteSampler::get_sample_assignments()</a>, <a href="classIMP_1_1domino_1_1DominoSampler.html#a342ed03b6bd9bb5818c747921d86abb0">IMP::domino::DominoSampler::do_get_sample_assignments()</a>, <a href="classIMP_1_1domino_1_1EqualitySubsetFilterTable.html#a006a9c15d84fd63aa3ec114ce4652823">IMP::domino::EqualitySubsetFilterTable::get_strength()</a>, <a href="classIMP_1_1domino_1_1EqualitySubsetFilterTable.html#a0e41d167243f8bb91c8ebdf1e68fa66b">IMP::domino::EqualitySubsetFilterTable::get_subset_filter()</a>, <a href="classIMP_1_1domino_1_1EquivalenceAndExclusionSubsetFilterTable.html#afe157522e3913cddcd3977c40d458018">IMP::domino::EquivalenceAndExclusionSubsetFilterTable::get_strength()</a>, <a href="classIMP_1_1domino_1_1EquivalenceAndExclusionSubsetFilterTable.html#a313e21c2ac19d8a2520391cc7a728692">IMP::domino::EquivalenceAndExclusionSubsetFilterTable::get_subset_filter()</a>, <a href="classIMP_1_1domino_1_1EquivalenceSubsetFilterTable.html#afd7e5705543d7ac7071d4222578de781">IMP::domino::EquivalenceSubsetFilterTable::get_strength()</a>, <a href="classIMP_1_1domino_1_1EquivalenceSubsetFilterTable.html#a88463fb614a2dcb2b155e62b77d64a23">IMP::domino::EquivalenceSubsetFilterTable::get_subset_filter()</a>, <a href="classIMP_1_1domino_1_1ExclusionSubsetFilterTable.html#a2afbe186f5948675dd1c217efe8a4dbd">IMP::domino::ExclusionSubsetFilterTable::get_strength()</a>, <a href="classIMP_1_1domino_1_1ExclusionSubsetFilterTable.html#ab21a7dbe5fd65a957b80d37cecb05e10">IMP::domino::ExclusionSubsetFilterTable::get_subset_filter()</a>, <a href="classIMP_1_1domino_1_1HeapAssignmentContainer.html#ae441675fd3cc83cc810db7fcfc9928e9">IMP::domino::HeapAssignmentContainer::HeapAssignmentContainer()</a>, <a href="classIMP_1_1domino_1_1ListAssignmentsTable.html#aa0422fdbb973a84ae9dfd12c08b3979d">IMP::domino::ListAssignmentsTable::load_assignments()</a>, <a href="classIMP_1_1domino_1_1ListAssignmentsTable.html#a15fa28a76023dd8fa328b452d2245908">IMP::domino::ListAssignmentsTable::set_assignments()</a>, <a href="classIMP_1_1domino_1_1ListSubsetFilterTable.html#a9c1103c9929bdfc78a2b084bf1c1ef47">IMP::domino::ListSubsetFilterTable::get_strength()</a>, <a href="classIMP_1_1domino_1_1ListSubsetFilterTable.html#a324e1729565ebd6513a5357b3f8ca424">IMP::domino::ListSubsetFilterTable::get_subset_filter()</a>, <a href="classIMP_1_1domino_1_1MinimumRestraintScoreSubsetFilterTable.html#a8c9292deeb5be59528a670cc22f5004c">IMP::domino::MinimumRestraintScoreSubsetFilterTable::get_restraints()</a>, <a href="classIMP_1_1domino_1_1MinimumRestraintScoreSubsetFilterTable.html#a952953b0b75eec4bdbace3a90ad0ff6b">IMP::domino::MinimumRestraintScoreSubsetFilterTable::get_strength()</a>, <a href="classIMP_1_1domino_1_1MinimumRestraintScoreSubsetFilterTable.html#a04cfce4e5e82589e9a958780ec276853">IMP::domino::MinimumRestraintScoreSubsetFilterTable::get_subset_filter()</a>, <a href="classIMP_1_1domino_1_1Order.html#af3c283658a88922d49dea1706bf5dade">IMP::domino::Order::Order()</a>, <a href="classIMP_1_1domino_1_1PairListSubsetFilterTable.html#af0147ea4d258ecf4720c652fcd8f5943">IMP::domino::PairListSubsetFilterTable::fill()</a>, <a href="classIMP_1_1domino_1_1PairListSubsetFilterTable.html#af8a8fefbfe5e695a47eecd0865b1240d">IMP::domino::PairListSubsetFilterTable::get_strength()</a>, <a href="classIMP_1_1domino_1_1PairListSubsetFilterTable.html#abca0f6c8d5df498eed912ef7ccfa1268">IMP::domino::PairListSubsetFilterTable::get_subset_filter()</a>, <a href="classIMP_1_1domino_1_1ProbabilisticSubsetFilterTable.html#ab41b77ad7948c43f0d47996997c445fa">IMP::domino::ProbabilisticSubsetFilterTable::get_strength()</a>, <a href="classIMP_1_1domino_1_1ProbabilisticSubsetFilterTable.html#ad96b79309670a8ed32b79f69c2ac15de">IMP::domino::ProbabilisticSubsetFilterTable::get_subset_filter()</a>, <a href="classIMP_1_1domino_1_1ReadAssignmentContainer.html#a64260a4cc0a37ec54ca79c7f5638801f">IMP::domino::ReadAssignmentContainer::ReadAssignmentContainer()</a>, <a href="classIMP_1_1domino_1_1ReadHDF5AssignmentContainer.html#a036c1db5a3e3dfe65ef9a28edc610de4">IMP::domino::ReadHDF5AssignmentContainer::ReadHDF5AssignmentContainer()</a>, <a href="classIMP_1_1domino_1_1RecursiveAssignmentsTable.html#a90514e1adc6368f99d345b59668a803a">IMP::domino::RecursiveAssignmentsTable::load_assignments()</a>, <a href="classIMP_1_1domino_1_1RecursiveStates.html#a64d119281ac852e97227186e68b69c0c">IMP::domino::RecursiveStates::RecursiveStates()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#ab63563966e52189ed4944e938c148660">IMP::domino::RestraintCache::add_restraint_internal()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#afec39699a2c73dfbe5176b6564c02124">IMP::domino::RestraintCache::add_restraint_set_child_internal()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#ae7e20f6f1ca49677a51ed9bd7b1884e0">IMP::domino::RestraintCache::add_restraint_set_internal()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#aaf2bd6854f707db56461daa2ba29fe12">IMP::domino::RestraintCache::get_restraints()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#a277af62358d51335e22c3c5419ced30a">IMP::domino::RestraintCache::get_score()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#a15f1f5513308176b4eaccc9e411277f2">IMP::domino::RestraintCache::get_slice()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#a7cb8d67a4032980ccdbbb2393c4a8aad">IMP::domino::RestraintCache::load_last_score()</a>, <a href="classIMP_1_1domino_1_1RestraintScoreSubsetFilterTable.html#a6270ec3bab499836ff25bd78049318cf">IMP::domino::RestraintScoreSubsetFilterTable::get_strength()</a>, <a href="classIMP_1_1domino_1_1RestraintScoreSubsetFilterTable.html#afe6c067399f81400198864d011a90efb">IMP::domino::RestraintScoreSubsetFilterTable::get_subset_filter()</a>, <a href="classIMP_1_1domino_1_1SimpleAssignmentsTable.html#a23b9149da5312b4e120a36f3d4949bc9">IMP::domino::SimpleAssignmentsTable::load_assignments()</a>, <a href="classIMP_1_1domino_1_1Slice.html#aea927878d3695d75c661a75968659d17">IMP::domino::Slice::get_slice()</a>, <a href="classIMP_1_1domino_1_1Slice.html#a70118528acacd6664939fe4131de82e7">IMP::domino::Slice::Slice()</a>, <a href="classIMP_1_1domino_1_1Slice.html#a2f4e028d276be06d17293141b9a472c1">IMP::domino::Slice::get_sliced()</a>, <a href="classIMP_1_1domino_1_1Subset.html#ae3aa0ebb6ac23b03606b5c5156ea6b12">IMP::domino::Subset::get_contains()</a>, <a href="classIMP_1_1domino_1_1SubsetFilterTable.html#abaa42cb0bed9f3c8fcfa4c3ac3e0162b">IMP::domino::SubsetFilterTable::get_strength()</a>, <a href="classIMP_1_1domino_1_1SubsetFilterTable.html#ac455bb060804addf2274c8304a2aa5fd">IMP::domino::SubsetFilterTable::get_subset_filter()</a>, <a href="classIMP_1_1domino_1_1WriteAssignmentContainer.html#aa38651e93740676aadac20cc808c6314">IMP::domino::WriteAssignmentContainer::WriteAssignmentContainer()</a>, <a href="classIMP_1_1domino_1_1WriteHDF5AssignmentContainer.html#a5d18c778ada3f85a22eb699e18ece884">IMP::domino::WriteHDF5AssignmentContainer::WriteHDF5AssignmentContainer()</a>, <a href="classIMP_1_1domino_1_1WriteHDF5AssignmentContainer.html#a6e731107ef281e262906e58a5f945ee8">IMP::domino::WriteHDF5AssignmentContainer::WriteHDF5AssignmentContainer()</a>, <a href="classIMP_1_1em2d_1_1DistanceFilter.html#a0fdd72792f673c8b7d590b5abe80b3fa">IMP::em2d::DistanceFilter::DistanceFilter()</a>, <a href="classIMP_1_1em2d_1_1DistanceFilterTable.html#a8edc09e71c701c228c5a37783130a2de">IMP::em2d::DistanceFilterTable::DistanceFilterTable()</a>, <a href="classIMP_1_1em2d_1_1DistanceFilterTable.html#ab98d30cb579fdd0e2c5be13f5d73b2f8">IMP::em2d::DistanceFilterTable::get_strength()</a>, <a href="classIMP_1_1em2d_1_1DistanceFilterTable.html#adca029b4278e5e58f6e1142ba85cc2bc">IMP::em2d::DistanceFilterTable::get_subset_filter()</a>, <a href="classIMP_1_1example_1_1ExampleSubsetFilterTable.html#a0853fa5682f067893c15062765eed42c">IMP::example::ExampleSubsetFilterTable::get_indexes()</a>, <a href="classIMP_1_1example_1_1ExampleSubsetFilterTable.html#ab89d74a7a5ae94bce6c6d0301b0482ef">IMP::example::ExampleSubsetFilterTable::get_strength()</a>, <a href="classIMP_1_1example_1_1ExampleSubsetFilterTable.html#a8fe7c10211739dd503ff88579ad18434">IMP::example::ExampleSubsetFilterTable::get_subset_filter()</a>, <a href="namespaceIMP_1_1domino.html#a36895b9e0319ed81ff55feca2b07d596">IMP::domino::get_is_merge_tree()</a>, <a href="namespaceIMP_1_1domino.html#a0c08cfa3955a23464c5f59c15f95a4ae">IMP::domino::load_particle_states()</a>, <a href="namespaceIMP_1_1domino.html#ab0efd3e3db335ea082bf9b7567011958">IMP::domino::get_restraints()</a>, <a href="namespaceIMP_1_1domino.html#a1e91ca287b91fd6144aeeff14960c14a">IMP::domino::get_difference()</a>, <a href="namespaceIMP_1_1domino.html#a3a112fd41a97e8e93dbff8be3dfb8bb6">IMP::domino::get_distance_if_smaller_than()</a>, <a href="namespaceIMP_1_1domino.html#a3247d32b900c4633e5c58cd7032d043b">IMP::domino::get_embedding()</a>, <a href="namespaceIMP_1_1domino.html#ab5fc791399c0d6c76e1bea5d4b3da6ca">IMP::domino::get_index()</a>, <a href="namespaceIMP_1_1domino.html#a399d7344a0696fbab4a6ca6c2796157b">IMP::domino::get_intersection()</a>, <a href="namespaceIMP_1_1domino.html#abd8a69ba2cc2b8fea2f49c99189d8711">IMP::domino::get_nearest_assignment()</a>, <a href="namespaceIMP_1_1domino.html#a0f43ef4b4efed8a9481e65694ce3fadb">IMP::domino::get_order()</a>, <a href="namespaceIMP_1_1domino.html#a4c8c50c718ab2dcabacc4b2e41aba522">IMP::domino::get_partial_index()</a>, <a href="namespaceIMP_1_1domino.html#a619c0aea6816fda8b69b08cf5e57876d">IMP::domino::get_slice()</a>, <a href="namespaceIMP_1_1domino.html#a7b094ee7dac304dfc212772818a9ba04">IMP::domino::get_state_clusters()</a>, <a href="namespaceIMP_1_1domino.html#adc940e96eb944fe259a8fba40830a251">IMP::domino::get_union()</a>, <a href="namespaceIMP_1_1domino.html#a4570cce69f194985e23b710c3b5e18b4">IMP::domino::load_leaf_assignments()</a>, <a href="namespaceIMP_1_1domino.html#a200c71a273844cc32fd32f6a5eafa0aa">IMP::domino::load_merged_assignments()</a>, <a href="namespaceIMP_1_1domino.html#a3305fe8f61d81cba57e9f6896024b263">IMP::domino::load_merged_assignments_random_order()</a>, <a href="namespaceIMP_1_1domino.html#a517fc7420fdb629c2f09280f36e898d3">IMP::domino::swap()</a></td></tr>
215 <tr><td>@ref IMP::domino::SubsetFilterTable</td><td><a href="classIMP_1_1domino_1_1DiscreteSampler.html#aea4629b51fe360838144aa20d647c9c4">IMP::domino::DiscreteSampler::remove_subset_filter_table()</a>, <a href="classIMP_1_1domino_1_1DiscreteSampler.html#a69a5fd252f550161d778f1a3c0654fa7">IMP::domino::DiscreteSampler::add_subset_filter_table()</a></td></tr>
216 </table>
217 # IMP.em # {#argument_index_em}
218 <table><tr>
219 <th>Class</th><th>Users</th></tr>
220 <tr><td>@ref IMP::em::DensityHeader</td><td><a href="classIMP_1_1em_1_1DensityMap.html#abf9a162f4619e31c0a3cbc021d7cb7b0">IMP::em::DensityMap::DensityMap()</a>, <a href="classIMP_1_1em_1_1DistanceMask.html#aae2e7c52f4bf9bc869986b8eda1f8bb6">IMP::em::DistanceMask::DistanceMask()</a>, <a href="classIMP_1_1em_1_1EMReaderWriter.html#a2adec96c33055a0eab6a8b6e5ec157f5">IMP::em::EMReaderWriter::read()</a>, <a href="classIMP_1_1em_1_1EMReaderWriter.html#a7cd4eef722dc6cbfbc353e19e1f3aaa3">IMP::em::EMReaderWriter::write()</a>, <a href="classIMP_1_1em_1_1MRCReaderWriter.html#addccce7ae3fd97389d0b055c2c142117">IMP::em::MRCReaderWriter::read()</a>, <a href="classIMP_1_1em_1_1MRCReaderWriter.html#af313f416ceca587f7d6d0b3ae510adfc">IMP::em::MRCReaderWriter::write()</a>, <a href="classIMP_1_1em_1_1MapReaderWriter.html#a4e5943c96cad40f104d1076dc05ad197">IMP::em::MapReaderWriter::read()</a>, <a href="classIMP_1_1em_1_1MapReaderWriter.html#af7410c2a895560c6bdcae982f28e5655">IMP::em::MapReaderWriter::write()</a>, <a href="classIMP_1_1em_1_1RadiusDependentDistanceMask.html#af3e62f683eda2980a136e62790edfbe8">IMP::em::RadiusDependentDistanceMask::RadiusDependentDistanceMask()</a>, <a href="classIMP_1_1em_1_1SampledDensityMap.html#a99c7f42f73230ec27c4ab0f664b3dc95">IMP::em::SampledDensityMap::SampledDensityMap()</a>, <a href="classIMP_1_1em_1_1SpiderMapReaderWriter.html#aa73bc0929bf35db8b546d109f7e8d0c1">IMP::em::SpiderMapReaderWriter::read()</a>, <a href="classIMP_1_1em_1_1SpiderMapReaderWriter.html#a6a4605a4c76247437791dc46e4ab2d41">IMP::em::SpiderMapReaderWriter::write()</a>, <a href="classIMP_1_1em_1_1SurfaceShellDensityMap.html#a906367559e2670491fe3f54dca3ced4d">IMP::em::SurfaceShellDensityMap::SurfaceShellDensityMap()</a>, <a href="classIMP_1_1em_1_1XplorReaderWriter.html#a22433b0ad5ba114ffd892fac4544e437">IMP::em::XplorReaderWriter::read()</a>, <a href="classIMP_1_1em_1_1XplorReaderWriter.html#ab65670ab3e1fea1f9d6a36903cb5e33b">IMP::em::XplorReaderWriter::write()</a>, <a href="namespaceIMP_1_1cnmultifit.html#a3733609ff3265bd070779045acf03fca">IMP::cnmultifit::build_cn_dens_assembly()</a>, <a href="namespaceIMP_1_1em.html#a59459b7c51d60c2f2a3c9b6491cb1455">IMP::em::DensityHeader_to_ImageHeader()</a>, <a href="namespaceIMP_1_1em.html#ab7f8287dfcc5d61b20445c3c683c3e12">IMP::em::ImageHeader_to_DensityHeader()</a></td></tr>
221 <tr><td>@ref IMP::em::DensityMap</td><td><a href="classIMP_1_1cnmultifit_1_1AlignSymmetric.html#afcbb4fa0d636862512fb346809db119a">IMP::cnmultifit::AlignSymmetric::AlignSymmetric()</a>, <a href="classIMP_1_1cnmultifit_1_1CnSymmAxisDetector.html#a0dbacc4bb1c3edd576f297c1616e32ef">IMP::cnmultifit::CnSymmAxisDetector::CnSymmAxisDetector()</a>, <a href="classIMP_1_1em_1_1CoarseCC.html#af20504f32c33f8f6261b004a8e9db8dd">IMP::em::CoarseCC::calc_score()</a>, <a href="classIMP_1_1em_1_1CoarseCC.html#a8a788b503910e0ea75300da9089887e3">IMP::em::CoarseCC::cross_correlation_coefficient()</a>, <a href="classIMP_1_1em_1_1CoarseCC.html#abc28b2cd26b083a5b172fb330d2bd246">IMP::em::CoarseCC::local_cross_correlation_coefficient()</a>, <a href="classIMP_1_1em_1_1CoarseCCatIntervals.html#a4d120a2d38fe2f32674507fada921712">IMP::em::CoarseCCatIntervals::evaluate()</a>, <a href="classIMP_1_1em_1_1CoarseConvolution.html#af95d23ee56098360e25659d575c7aca3">IMP::em::CoarseConvolution::convolution()</a>, <a href="classIMP_1_1em_1_1DensityFillingRestraint.html#a0656eecc49cff09bae195f12553ebd95">IMP::em::DensityFillingRestraint::DensityFillingRestraint()</a>, <a href="classIMP_1_1em_1_1DensityMap.html#a0f672a08c4e0c77954f1a4aef2b01538">IMP::em::DensityMap::add()</a>, <a href="classIMP_1_1em_1_1DensityMap.html#a8fdd76efff4b4d2fe640f05fc66a3749">IMP::em::DensityMap::copy_map()</a>, <a href="classIMP_1_1em_1_1DensityMap.html#ad8b6d7f1edcab290e04d6056faf2434c">IMP::em::DensityMap::pick_max()</a>, <a href="classIMP_1_1em_1_1DensityMap.html#aa1bf0fe2dd98afc7cd94e0f441ff38f2">IMP::em::DensityMap::same_dimensions()</a>, <a href="classIMP_1_1em_1_1DensityMap.html#ab6f89d974d50aadf45b16f1879a01326">IMP::em::DensityMap::same_origin()</a>, <a href="classIMP_1_1em_1_1DensityMap.html#afeca80ac2ffc08fc0769e037cca55a31">IMP::em::DensityMap::same_voxel_size()</a>, <a href="classIMP_1_1em_1_1DensityMap.html#aec381e89f990536e40c6d68fc3a6eebe">IMP::em::DensityMap::add_to_map()</a>, <a href="classIMP_1_1em_1_1DensityMap.html#a54fa7df010fd43d4d0d13f71fa77b03d">IMP::em::DensityMap::get_binarized_interior()</a>, <a href="classIMP_1_1em_1_1DensityMap.html#adbf6a76c82d8de409004cc3f304d9333">IMP::em::DensityMap::get_density()</a>, <a href="classIMP_1_1em_1_1DensityMap.html#a08ef3f70aec3b1d6e01a2e72149e4902">IMP::em::DensityMap::get_resampled()</a>, <a href="classIMP_1_1em_1_1DensityMap.html#a136741fcac5174f8af99e7aac939e9f9">IMP::em::DensityMap::get_transformed()</a>, <a href="classIMP_1_1em_1_1DensityMap.html#afea835c4ddafaf25568cc64c66bcc3f1">IMP::em::DensityMap::get_transformed()</a>, <a href="classIMP_1_1em_1_1DensityMap.html#a8fde3a97a69c15d1dfce64e6757e369e">IMP::em::DensityMap::get_transformed_into()</a>, <a href="classIMP_1_1em_1_1DensityMap.html#a0301a7f2fa5fccda297495bd7fe71b9b">IMP::em::DensityMap::write_map()</a>, <a href="classIMP_1_1em_1_1DensityMap.html#a618403f050529bb7bc82752b2af3c157">IMP::em::DensityMap::write_map()</a>, <a href="classIMP_1_1em_1_1EnvelopeFitRestraint.html#a53d60213da33d49c6c013e48d1e5b04f">IMP::em::EnvelopeFitRestraint::EnvelopeFitRestraint()</a>, <a href="classIMP_1_1em_1_1EnvelopePenetrationRestraint.html#a7e2e5b60bd73875222e250e7a0aefa87">IMP::em::EnvelopePenetrationRestraint::EnvelopePenetrationRestraint()</a>, <a href="classIMP_1_1em_1_1FitRestraint.html#a586e135631bd2bf9fea7e22988e5d23e">IMP::em::FitRestraint::FitRestraint()</a>, <a href="classIMP_1_1em_1_1FitRestraintBayesEM3D.html#a3ff6005e532b6ffc891b6e5b83c2aab2">IMP::em::FitRestraintBayesEM3D::FitRestraintBayesEM3D()</a>, <a href="classIMP_1_1em_1_1HighDensityEmbedding.html#a15ad76f739395c5555e9ade9bbed66ed">IMP::em::HighDensityEmbedding::HighDensityEmbedding()</a>, <a href="classIMP_1_1em_1_1MapDistanceTransform.html#a3e85e6e9693a3b1047ff17f40e906d05">IMP::em::MapDistanceTransform::MapDistanceTransform()</a>, <a href="classIMP_1_1em_1_1PCAAligner.html#a983b2f7a93a890f6103b18c7cf725e00">IMP::em::PCAAligner::PCAAligner()</a>, <a href="classIMP_1_1em_1_1PCAFitRestraint.html#a4df8c7271acc2675c17249a9755544c3">IMP::em::PCAFitRestraint::PCAFitRestraint()</a>, <a href="classIMP_1_1multifit_1_1DensityDataPoints.html#a51782d49c5e98b159037c274f4e0e99c">IMP::multifit::DensityDataPoints::DensityDataPoints()</a>, <a href="classIMP_1_1multifit_1_1DensityDataPoints.html#ab0e076ff29e061cafed9b70b181b089c">IMP::multifit::DensityDataPoints::set_density()</a>, <a href="classIMP_1_1multifit_1_1FFTFitting.html#a136cac955ee735ec87b1238b82aa67ac">IMP::multifit::FFTFitting::do_global_fitting()</a>, <a href="classIMP_1_1multifit_1_1FFTFitting.html#ae47864b146f9cf99c92495967e611d01">IMP::multifit::FFTFitting::do_local_fitting()</a>, <a href="classIMP_1_1multifit_1_1FFTFitting.html#aaeb4a52a506bcee42b2cacb393fbaa43">IMP::multifit::FFTFitting::copy_density_data()</a>, <a href="classIMP_1_1multifit_1_1FFTFitting.html#a37d65339d5125709922ec82eba2ce9ed">IMP::multifit::FFTFitting::crop_margin()</a>, <a href="classIMP_1_1multifit_1_1FFTFitting.html#ab063459cb69df88446f638fded7d95da">IMP::multifit::FFTFitting::prepare_lowres_map()</a>, <a href="classIMP_1_1multifit_1_1FFTFitting.html#aced49e5f2dae277cdcc74732c76c4aca">IMP::multifit::FFTFitting::prepare_poslist()</a>, <a href="classIMP_1_1multifit_1_1FFTFitting.html#a91969e61ffab79ed9b4f9cd5d222ef37">IMP::multifit::FFTFitting::prepare_poslist_flipped()</a>, <a href="classIMP_1_1multifit_1_1ProteomicsEMAlignmentAtomic.html#a88d1ed53c74d930ee8bd5d6d07a95112">IMP::multifit::ProteomicsEMAlignmentAtomic::set_density_map()</a>, <a href="namespaceIMP_1_1bayesianem.html#aac1c7654b58f288053040fd246060d07">IMP::bayesianem::get_masked_map()</a>, <a href="namespaceIMP_1_1bayesianem.html#a125ec55be9d5ada5559c3411936afec4">IMP::bayesianem::get_overlap_binned()</a>, <a href="namespaceIMP_1_1bayesianem.html#a42d5ce91141cec17eaa4a5338756f55c">IMP::bayesianem::get_overlap_fast()</a>, <a href="namespaceIMP_1_1bayesianem.html#a07e08b6a53f777d0e35e7b6ff6024ee7">IMP::bayesianem::get_sub_map()</a>, <a href="namespaceIMP_1_1cnmultifit.html#a3733609ff3265bd070779045acf03fca">IMP::cnmultifit::build_cn_dens_assembly()</a>, <a href="namespaceIMP_1_1cnmultifit.html#a6067aedfd378547038d133f84bb820e3">IMP::cnmultifit::fit_cn_assembly()</a>, <a href="namespaceIMP_1_1cnmultifit.html#a1b5327db66abe2f5bc1712f1013a4436">IMP::cnmultifit::fit_cn_assembly()</a>, <a href="namespaceIMP_1_1cnmultifit.html#a326d661ede67dfeb87070ee6447ad678">IMP::cnmultifit::symmetry_local_fitting()</a>, <a href="namespaceIMP_1_1em.html#a6e4fd1709fe2bbb486a3e70d4dfe0f27">IMP::em::approximate_molecular_mass()</a>, <a href="namespaceIMP_1_1em.html#a97f77317e298df3b4573ca3907c66638">IMP::em::bayesem3d_get_cross_correlation_coefficient()</a>, <a href="namespaceIMP_1_1em.html#a7c137733471276a4bec62dd3614c3849">IMP::em::bayesem3d_get_cumulative_sum()</a>, <a href="namespaceIMP_1_1em.html#ac260890ecbfef938c627e3fecc89aacb">IMP::em::bayesem3d_get_cumulative_sum_with_reference()</a>, <a href="namespaceIMP_1_1em.html#a7e08fd743778d6b18b8e759bea705454">IMP::em::bayesem3d_get_density_from_particle()</a>, <a href="namespaceIMP_1_1em.html#aea9d3382eae88ebccecf5d47768eeb72">IMP::em::bayesem3d_get_distinct_and_counts()</a>, <a href="namespaceIMP_1_1em.html#a0fd16ec8233e9e763b995827b7496ffd">IMP::em::bayesem3d_get_em_density_squared()</a>, <a href="namespaceIMP_1_1em.html#ae027b772ce1eeb542809f08605b47679">IMP::em::bayesem3d_get_normalized_intensities()</a>, <a href="namespaceIMP_1_1em.html#a247c0133e66b108ee7d36e98cea961c9">IMP::em::bayesem3d_get_score_and_derivative()</a>, <a href="namespaceIMP_1_1em.html#a1c88424c8b24a5802ef048175e22787b">IMP::em::binarize()</a>, <a href="namespaceIMP_1_1em.html#a3f5170ae051deffd9fd3b3c6064f403b">IMP::em::compute_fitting_score()</a>, <a href="namespaceIMP_1_1em.html#a4350b15571abb634d2285ce9114a5725">IMP::em::compute_fitting_scores()</a>, <a href="namespaceIMP_1_1em.html#ab8beedad8915dcd1aa22b5ba75a61439">IMP::em::compute_fitting_scores()</a>, <a href="namespaceIMP_1_1em.html#a8505c0c435a33d043c98f29ade4fc2ee">IMP::em::convolute()</a>, <a href="namespaceIMP_1_1em.html#aa873c569e58e5c5d66dac1c0420f3e6c">IMP::em::create_density_map()</a>, <a href="namespaceIMP_1_1em.html#ad7c905f64de2740109026908aaa1e952">IMP::em::density2particles()</a>, <a href="namespaceIMP_1_1em.html#a5cbea21ee3c92fa5008bea0e8a6fc612">IMP::em::density2vectors()</a>, <a href="namespaceIMP_1_1em.html#a820db29914536321043260f19e89fca1">IMP::em::get_bounding_box()</a>, <a href="namespaceIMP_1_1em.html#a58f523ec7b9df988f0c9ef3caae1b6a0">IMP::em::get_bounding_box()</a>, <a href="namespaceIMP_1_1em.html#a31277ed67fe1b97b72bab4454be1e5af">IMP::em::get_coarse_cc_coefficient()</a>, <a href="namespaceIMP_1_1em.html#a8b478cdb42f4ae609c02907320cd5be1">IMP::em::get_coarse_cc_local_coefficient()</a>, <a href="namespaceIMP_1_1em.html#a29fc47f6607faab06b83b42ab6511aba">IMP::em::get_coarse_cc_score()</a>, <a href="namespaceIMP_1_1em.html#a9c72b01f6d6bbe0c84a0779fc08b809c">IMP::em::get_grid()</a>, <a href="namespaceIMP_1_1em.html#a65ce4b02f4593b0de63eb19d4441e56e">IMP::em::get_interiors_intersect()</a>, <a href="namespaceIMP_1_1em.html#a1a9e2f7c4a8e6a32405eca965626d554">IMP::em::get_molecular_mass_at_threshold()</a>, <a href="namespaceIMP_1_1em.html#a5a49f58c2b493fe460df2a1f42aed80d">IMP::em::get_number_of_particles_outside_of_the_density()</a>, <a href="namespaceIMP_1_1em.html#a55a883a182ff619b805f5bbcb5297c2e">IMP::em::get_numbers_of_particles_outside_of_the_density()</a>, <a href="namespaceIMP_1_1em.html#a6ac62bc20e89bf2c6e8f8f6bb5cbca5a">IMP::em::get_percentage_of_voxels_covered_by_particles()</a>, <a href="namespaceIMP_1_1em.html#a8dfa355f085d452c5636987d4f8ab956">IMP::em::get_segment()</a>, <a href="namespaceIMP_1_1em.html#aa92d0be9d42aa9d9b7a20796baacbf3b">IMP::em::get_segment()</a>, <a href="namespaceIMP_1_1em.html#a94fc09c5491718e3e0e61b2c4ff04f8f">IMP::em::get_segment_by_masking()</a>, <a href="namespaceIMP_1_1em.html#a0b1f187c3b53af89037d40912cc10aef">IMP::em::get_sum()</a>, <a href="namespaceIMP_1_1em.html#a7be03879088ecc74f54b40e68ba7a99c">IMP::em::get_threshold_for_approximate_mass()</a>, <a href="namespaceIMP_1_1em.html#ac70c499fce515b0328e43e6084fe92dc">IMP::em::get_threshold_for_approximate_volume()</a>, <a href="namespaceIMP_1_1em.html#a3078e4c77b9e81fa61b8222934185d1e">IMP::em::get_threshold_map()</a>, <a href="namespaceIMP_1_1em.html#abd0e642dde82199ac2b181e297526241">IMP::em::get_transformed_into2()</a>, <a href="namespaceIMP_1_1em.html#a402ab2b7809cc5ce708092b3c2c1a297">IMP::em::get_volume_at_threshold()</a>, <a href="namespaceIMP_1_1em.html#a7ca59d2a3aa688060c280efa250d80a7">IMP::em::interpolate_map()</a>, <a href="namespaceIMP_1_1em.html#a300a1ede18ac26749a961beca4c971e3">IMP::em::local_rigid_fitting()</a>, <a href="namespaceIMP_1_1em.html#a46543f4001a8c31276003433db00f776">IMP::em::local_rigid_fitting_around_point()</a>, <a href="namespaceIMP_1_1em.html#a729f3b19106724e0dbc8c7e98336ff64">IMP::em::local_rigid_fitting_around_points()</a>, <a href="namespaceIMP_1_1em.html#a2092ec68df3aaeeef8daee59353d0327">IMP::em::local_rigid_fitting_grid_search()</a>, <a href="namespaceIMP_1_1em.html#ae6c068669daa6977fb4a6e9800d79b44">IMP::em::mask_and_norm()</a>, <a href="namespaceIMP_1_1em.html#a0337abc873be82054e0b4061912cf0dc">IMP::em::multiply()</a>, <a href="namespaceIMP_1_1multifit.html#a3ae2f2b63f2b07f548e4fd095871d9b8">IMP::multifit::create_coarse_molecule_from_density()</a>, <a href="namespaceIMP_1_1multifit.html#a3359231b0601df5803958afcd8d93184">IMP::multifit::create_hit_map()</a>, <a href="namespaceIMP_1_1multifit.html#af83b1866a4b7bb6747eea98bd9bb28e1">IMP::multifit::fft_based_rigid_fitting()</a>, <a href="namespaceIMP_1_1multifit.html#af5cfce601c0bc38d4fd668dec337b3f4">IMP::multifit::get_anchors_for_density()</a>, <a href="namespaceIMP_1_1multifit.html#aebdba0d523d4730ee0031629b70b8ea1">IMP::multifit::get_connected_components()</a>, <a href="namespaceIMP_1_1multifit.html#a6945fa68efec8cd7f189ebd51b7af727">IMP::multifit::get_segment_maximum()</a>, <a href="namespaceIMP_1_1multifit.html#aeb628c3804ee3d8aa7df59051b0ad1d2">IMP::multifit::get_segmentation()</a>, <a href="namespaceIMP_1_1multifit.html#a45c8385d6183240ec7216ae97374c7a9">IMP::multifit::pca_based_rigid_fitting()</a>, <a href="namespaceIMP_1_1multifit.html#afdf294ea4f4b41a0fa4da41f6c95e32c">IMP::multifit::pca_based_rigid_fitting()</a>, <a href="namespaceIMP_1_1multifit.html#a8528245410468cfc40ab674d0ef64d70">IMP::multifit::remove_background()</a>, <a href="namespaceIMP_1_1multifit.html#a8009ecb4c53812a36bf544ed7e9fe9a0">IMP::multifit::write_segment_as_mrc()</a>, <a href="namespaceIMP_1_1multifit.html#ac66c9128b0009595989bc520e3e6dcd3">IMP::multifit::write_segments_as_mrc()</a></td></tr>
222 <tr><td>@ref IMP::em::FittingSolutions</td><td><a href="namespaceIMP_1_1multifit.html#a04303e2e87f1a25c6e4fdf2ca2e73453">IMP::multifit::convert_em_to_multifit_format()</a></td></tr>
223 <tr><td>@ref IMP::em::ImageHeader</td><td><a href="classIMP_1_1em2d_1_1ImageReaderWriter.html#a5e44ebd2e762bc482741d31eb2f61ae5">IMP::em2d::ImageReaderWriter::read()</a>, <a href="classIMP_1_1em2d_1_1ImageReaderWriter.html#adbd764fa1dacf7cf79ec44670f49b6a4">IMP::em2d::ImageReaderWriter::read_from_floats()</a>, <a href="classIMP_1_1em2d_1_1ImageReaderWriter.html#ad5d892bb53865c0995d9226d3d7dadfe">IMP::em2d::ImageReaderWriter::read_from_ints()</a>, <a href="classIMP_1_1em2d_1_1ImageReaderWriter.html#aae799f91ac40249ea85441d1154ad0f1">IMP::em2d::ImageReaderWriter::write()</a>, <a href="classIMP_1_1em2d_1_1ImageReaderWriter.html#a59263b05b2204f8a045cadb975604e72">IMP::em2d::ImageReaderWriter::write_to_floats()</a>, <a href="classIMP_1_1em2d_1_1ImageReaderWriter.html#acdc118dbb9ccf187f29072010f4e71d6">IMP::em2d::ImageReaderWriter::write_to_ints()</a>, <a href="classIMP_1_1em2d_1_1JPGImageReaderWriter.html#ada85593d93e916c209685881c7a4fcd5">IMP::em2d::JPGImageReaderWriter::read()</a>, <a href="classIMP_1_1em2d_1_1JPGImageReaderWriter.html#abe4ea8ee65e316e0642cfd0dadd2aaaa">IMP::em2d::JPGImageReaderWriter::read_from_floats()</a>, <a href="classIMP_1_1em2d_1_1JPGImageReaderWriter.html#a3dd656c0f71e7189264c6d57aad86aab">IMP::em2d::JPGImageReaderWriter::read_from_ints()</a>, <a href="classIMP_1_1em2d_1_1JPGImageReaderWriter.html#a0cf20b7c7d484849803dd81af78b3070">IMP::em2d::JPGImageReaderWriter::write()</a>, <a href="classIMP_1_1em2d_1_1JPGImageReaderWriter.html#a5a9cd9610c937d6f353c5340ffb557e3">IMP::em2d::JPGImageReaderWriter::write_to_floats()</a>, <a href="classIMP_1_1em2d_1_1JPGImageReaderWriter.html#a87bc26efc426f5621fb1b703e50289ca">IMP::em2d::JPGImageReaderWriter::write_to_ints()</a>, <a href="classIMP_1_1em2d_1_1RegistrationResult.html#afd9d889f9b8de4e3a3d7d42fa965f41d">IMP::em2d::RegistrationResult::read_from_image()</a>, <a href="classIMP_1_1em2d_1_1RegistrationResult.html#a51e23a3b0f9c050a741b597e2e4448ab">IMP::em2d::RegistrationResult::set_in_image()</a>, <a href="classIMP_1_1em2d_1_1SpiderImageReaderWriter.html#a7d98a6bb47da11f23cf28541af4d3840">IMP::em2d::SpiderImageReaderWriter::read()</a>, <a href="classIMP_1_1em2d_1_1SpiderImageReaderWriter.html#a8f6626f64c73a13c6205432c79396e55">IMP::em2d::SpiderImageReaderWriter::read_from_floats()</a>, <a href="classIMP_1_1em2d_1_1SpiderImageReaderWriter.html#a53e49da7099624ced8586b8aed6a10e0">IMP::em2d::SpiderImageReaderWriter::read_from_ints()</a>, <a href="classIMP_1_1em2d_1_1SpiderImageReaderWriter.html#a111a790b326496d7c87883071043cb09">IMP::em2d::SpiderImageReaderWriter::write()</a>, <a href="classIMP_1_1em2d_1_1SpiderImageReaderWriter.html#a82c2bce1a8a4751a51ca44470733ca03">IMP::em2d::SpiderImageReaderWriter::write_to_floats()</a>, <a href="classIMP_1_1em2d_1_1SpiderImageReaderWriter.html#aaf4a3d2aa39b23806bf5ac24fce657c2">IMP::em2d::SpiderImageReaderWriter::write_to_ints()</a>, <a href="classIMP_1_1em2d_1_1TIFFImageReaderWriter.html#a78eff1cda352c26b9e0155ac080866f1">IMP::em2d::TIFFImageReaderWriter::read()</a>, <a href="classIMP_1_1em2d_1_1TIFFImageReaderWriter.html#a4b60fcfe1dfa744e1b5f468ceae86cd4">IMP::em2d::TIFFImageReaderWriter::read_from_floats()</a>, <a href="classIMP_1_1em2d_1_1TIFFImageReaderWriter.html#a13d4d4bfbd95cff976ef099e68f6ddf6">IMP::em2d::TIFFImageReaderWriter::read_from_ints()</a>, <a href="classIMP_1_1em2d_1_1TIFFImageReaderWriter.html#aea18b2d98bb9115f1cbdef6101bb3b7d">IMP::em2d::TIFFImageReaderWriter::write()</a>, <a href="classIMP_1_1em2d_1_1TIFFImageReaderWriter.html#a819d72ed5ecdbf153adda9421be6314d">IMP::em2d::TIFFImageReaderWriter::write_to_floats()</a>, <a href="classIMP_1_1em2d_1_1TIFFImageReaderWriter.html#a9c3bf9fbc299b23e4f09b5dca61eb458">IMP::em2d::TIFFImageReaderWriter::write_to_ints()</a>, <a href="namespaceIMP_1_1em.html#a59459b7c51d60c2f2a3c9b6491cb1455">IMP::em::DensityHeader_to_ImageHeader()</a>, <a href="namespaceIMP_1_1em.html#ab7f8287dfcc5d61b20445c3c683c3e12">IMP::em::ImageHeader_to_DensityHeader()</a></td></tr>
224 <tr><td>@ref IMP::em::KernelParameters</td><td><a href="classIMP_1_1em2d_1_1ProjectionMask.html#aaabd9546d6461c424ed619a26f08b2be">IMP::em2d::ProjectionMask::ProjectionMask()</a>, <a href="classIMP_1_1em2d_1_1ProjectionMask.html#ae4919afad95b6343f92834b60ae84503">IMP::em2d::ProjectionMask::create()</a>, <a href="namespaceIMP_1_1em.html#acf93458d53bb786095f8fcfc32782929">IMP::em::bayesem3d_get_value()</a>, <a href="namespaceIMP_1_1em.html#a7cc0ae516db501ad39635d0066092094">IMP::em::bayesem3d_get_value_no_deriv()</a></td></tr>
225 <tr><td>@ref IMP::em::MapDistanceTransform</td><td><a href="classIMP_1_1em_1_1EnvelopeScore.html#afeceacd6778085f40838b7fe1758907e">IMP::em::EnvelopeScore::EnvelopeScore()</a></td></tr>
226 <tr><td>@ref IMP::em::MapReaderWriter</td><td><a href="classIMP_1_1em_1_1DensityMap.html#aa7ad31965184a36215f80816a2749662">IMP::em::DensityMap::read_map()</a>, <a href="classIMP_1_1em_1_1DensityMap.html#a0301a7f2fa5fccda297495bd7fe71b9b">IMP::em::DensityMap::write_map()</a></td></tr>
227 <tr><td>@ref IMP::em::SampledDensityMap</td><td><a href="classIMP_1_1em_1_1CoarseCC.html#af20504f32c33f8f6261b004a8e9db8dd">IMP::em::CoarseCC::calc_score()</a>, <a href="classIMP_1_1em_1_1CoarseCCatIntervals.html#a4d120a2d38fe2f32674507fada921712">IMP::em::CoarseCCatIntervals::evaluate()</a>, <a href="namespaceIMP_1_1em.html#a29fc47f6607faab06b83b42ab6511aba">IMP::em::get_coarse_cc_score()</a></td></tr>
228 <tr><td>@ref IMP::em::SurfaceShellDensityMap</td><td><a href="namespaceIMP_1_1em.html#a84a15c16174944d980061dc91958793b">IMP::em::calculate_intersection_score()</a></td></tr>
229 </table>
230 # IMP.em2d # {#argument_index_em2d}
231 <table><tr>
232 <th>Class</th><th>Users</th></tr>
233 <tr><td>@ref IMP::em2d::ClusterSet</td><td><a href="classIMP_1_1em2d_1_1AverageDistanceLinkage.html#a9e4a72284ae366295907143152ca8cb1">IMP::em2d::AverageDistanceLinkage::operator()()</a>, <a href="classIMP_1_1em2d_1_1CompleteLinkage.html#a63235ad1a6acdcb8e7c0b76e42279fd9">IMP::em2d::CompleteLinkage::operator()()</a>, <a href="classIMP_1_1em2d_1_1SingleLinkage.html#a49ba34ff3b564943003feb4950656f1c">IMP::em2d::SingleLinkage::operator()()</a></td></tr>
234 <tr><td>@ref IMP::em2d::Em2DRestraintParameters</td><td><a href="classIMP_1_1em2d_1_1Em2DRestraint.html#a3351edb9bbe8eab5297df9396542effd">IMP::em2d::Em2DRestraint::setup()</a>, <a href="classIMP_1_1em2d_1_1ProjectionFinder.html#aff42f0cb55360eba23aca76e71cc25fd">IMP::em2d::ProjectionFinder::setup()</a></td></tr>
235 <tr><td>@ref IMP::em2d::Image</td><td><a href="classIMP_1_1em2d_1_1ChiSquaredScore.html#a347b3892b7bd2c64baa1cd6b96cf62b7">IMP::em2d::ChiSquaredScore::get_private_score()</a>, <a href="classIMP_1_1em2d_1_1ChiSquaredScore.html#a1fe1b42f7da351ead5b18ac99200940b">IMP::em2d::ChiSquaredScore::set_variance_imag_private()</a>, <a href="classIMP_1_1em2d_1_1EM2DScore.html#a45ecaef07f5671a0f22ba92d60af757d">IMP::em2d::EM2DScore::get_private_score()</a>, <a href="classIMP_1_1em2d_1_1Fine2DRegistrationRestraint.html#a04ddb2aa50708a968d1f2064831afdfe">IMP::em2d::Fine2DRegistrationRestraint::set_subject_image()</a>, <a href="classIMP_1_1em2d_1_1Image.html#a8f60a2fc69d0e0ea1502ed2448b42376">IMP::em2d::Image::set_size()</a>, <a href="classIMP_1_1em2d_1_1MeanAbsoluteDifference.html#a1a8d2ddf225f88452205035cbfc010c4">IMP::em2d::MeanAbsoluteDifference::get_private_score()</a>, <a href="classIMP_1_1em2d_1_1RigidBodiesImageFitRestraint.html#af061f3bf53dde9fec3da4b4432220b84">IMP::em2d::RigidBodiesImageFitRestraint::RigidBodiesImageFitRestraint()</a>, <a href="classIMP_1_1em2d_1_1ScoreFunction.html#a7111cef1cdadc7b3245e8621b7b46fb0">IMP::em2d::ScoreFunction::get_score()</a>, <a href="classIMP_1_1em2d_1_1ScoreFunction.html#afb6049939c1645c590a5b4e0911578ac">IMP::em2d::ScoreFunction::set_variance_image()</a>, <a href="classIMP_1_1em2d_1_1ScoreFunction.html#a936827b9594e03838640cf7f0fc04155">IMP::em2d::ScoreFunction::get_private_score()</a>, <a href="classIMP_1_1em2d_1_1ScoreFunction.html#a75e086aa82705e1efa5501d2b264f200">IMP::em2d::ScoreFunction::set_variance_image_private()</a>, <a href="namespaceIMP_1_1em2d.html#a06c274b3934ad8569f1ed6f97248dc2a">IMP::em2d::add_noise()</a>, <a href="namespaceIMP_1_1em2d.html#a6fbd3f388210a4942c4ac54c95b88fd8">IMP::em2d::apply_diffusion_filter()</a>, <a href="namespaceIMP_1_1em2d.html#a90402327da81d37eb865301ff37fbb19">IMP::em2d::apply_mean_outside_mask()</a>, <a href="namespaceIMP_1_1em2d.html#a258020f16ff0205998ee972aa2656499">IMP::em2d::apply_variance_filter()</a>, <a href="namespaceIMP_1_1em2d.html#af9e50eaa31332e8e42eb3ee0d2b8872e">IMP::em2d::crop()</a>, <a href="namespaceIMP_1_1em2d.html#aec931bf7254087acda23ffca83c40d2b">IMP::em2d::do_combined_fill_holes_and_threshold()</a>, <a href="namespaceIMP_1_1em2d.html#ac225b565975f40a59970616e9b25cc7f">IMP::em2d::do_extend_borders()</a>, <a href="namespaceIMP_1_1em2d.html#a8dbdd9fda0c62746f8d306f171e72939">IMP::em2d::do_fill_holes()</a>, <a href="namespaceIMP_1_1em2d.html#a8ca0f5601724287c85b00fb71ddecc44">IMP::em2d::do_normalize()</a>, <a href="namespaceIMP_1_1em2d.html#aac8b25edf0a90e063935009e934ff14a">IMP::em2d::do_remove_small_objects()</a>, <a href="namespaceIMP_1_1em2d.html#a1d4044443138ae1ad3c60ba33afd6e5e">IMP::em2d::do_resample_polar()</a>, <a href="namespaceIMP_1_1em2d.html#a64eb9b75ba5371ca0b73ad4bb455b6f7">IMP::em2d::do_segmentation()</a>, <a href="namespaceIMP_1_1em2d.html#a5fa6302882e4cc2ddc39262f434058e6">IMP::em2d::do_subtract_images()</a>, <a href="namespaceIMP_1_1em2d.html#a185b28584381f8d779db94c0f91f9db0">IMP::em2d::get_autocorrelation2d()</a>, <a href="namespaceIMP_1_1em2d.html#a47326ad3deacabc6aa0fc68818c453ea">IMP::em2d::get_correlation2d()</a>, <a href="namespaceIMP_1_1em2d.html#af22f5cc59992f1a392b914e6b57a0ecc">IMP::em2d::get_cross_correlation_coefficient()</a>, <a href="namespaceIMP_1_1em2d.html#a4f87a85f1ee35aa0a6dc6f0c859df0b0">IMP::em2d::get_histogram()</a>, <a href="namespaceIMP_1_1em2d.html#a060e62f5acd6d4c6dc09f1f2c7b1528b">IMP::em2d::get_projection()</a></td></tr>
236 <tr><td>@ref IMP::em2d::ImageReaderWriter</td><td><a href="classIMP_1_1em2d_1_1Image.html#a051c8ca01c41487d6d638a3867854283">IMP::em2d::Image::Image()</a>, <a href="classIMP_1_1em2d_1_1Image.html#a3711206f3d3632ed50f56194528574d5">IMP::em2d::Image::read()</a>, <a href="classIMP_1_1em2d_1_1Image.html#a0d4c7013411e8712825ea2bf38188bc5">IMP::em2d::Image::write()</a>, <a href="classIMP_1_1em2d_1_1ProjectingOptions.html#a02c2425aa3903fa5ec263dd65320101b">IMP::em2d::ProjectingOptions::ProjectingOptions()</a>, <a href="namespaceIMP_1_1em2d.html#a9b93ce77266955bd99874dbb269fc87c">IMP::em2d::read_images()</a>, <a href="namespaceIMP_1_1em2d.html#a3c4762ec4e3272cd645d012e24b464b3">IMP::em2d::save_images()</a></td></tr>
237 <tr><td>@ref IMP::em2d::PolarResamplingParameters</td><td><a href="namespaceIMP_1_1em2d.html#aad3c7e6514aadaa236e5e354ceff8856">IMP::em2d::do_resample_polar()</a>, <a href="namespaceIMP_1_1em2d.html#a1d4044443138ae1ad3c60ba33afd6e5e">IMP::em2d::do_resample_polar()</a></td></tr>
238 <tr><td>@ref IMP::em2d::ProjectingOptions</td><td><a href="namespaceIMP_1_1em2d.html#ac7fc9ca9b6ac50bc5de57a157882766f">IMP::em2d::create_evenly_distributed_projections()</a>, <a href="namespaceIMP_1_1em2d.html#ab15ba9866050315bb0248dd27f0ef0bb">IMP::em2d::do_project_particles()</a>, <a href="namespaceIMP_1_1em2d.html#a060e62f5acd6d4c6dc09f1f2c7b1528b">IMP::em2d::get_projection()</a>, <a href="namespaceIMP_1_1em2d.html#a65e066ed72e099282a5714fbd2333989">IMP::em2d::get_projections()</a>, <a href="namespaceIMP_1_1em2d.html#aa167999977d5c4f4e0486534693a86da">IMP::em2d::get_projections()</a></td></tr>
239 <tr><td>@ref IMP::em2d::ProjectingParameters</td><td><a href="classIMP_1_1em2d_1_1Fine2DRegistrationRestraint.html#ab1ee83011c2b01795ca1901bef283926">IMP::em2d::Fine2DRegistrationRestraint::setup()</a>, <a href="classIMP_1_1em2d_1_1RigidBodiesImageFitRestraint.html#a477b51eb69d95e8a70cc7d42d392327c">IMP::em2d::RigidBodiesImageFitRestraint::set_projecting_parameters()</a></td></tr>
240 <tr><td>@ref IMP::em2d::RegistrationResult</td><td><a href="namespaceIMP_1_1em2d.html#a060e62f5acd6d4c6dc09f1f2c7b1528b">IMP::em2d::get_projection()</a>, <a href="namespaceIMP_1_1em2d.html#a57a725bb5e94995d20b75abe96d9cfbd">IMP::em2d::get_rotation_error()</a>, <a href="namespaceIMP_1_1em2d.html#ad612906ea96b2c6f162c97b654309c7f">IMP::em2d::get_shift_error()</a></td></tr>
241 <tr><td>@ref IMP::em2d::ScoreFunction</td><td><a href="classIMP_1_1em2d_1_1Em2DRestraint.html#a3351edb9bbe8eab5297df9396542effd">IMP::em2d::Em2DRestraint::setup()</a>, <a href="classIMP_1_1em2d_1_1Fine2DRegistrationRestraint.html#ab1ee83011c2b01795ca1901bef283926">IMP::em2d::Fine2DRegistrationRestraint::setup()</a>, <a href="classIMP_1_1em2d_1_1ProjectionFinder.html#aff42f0cb55360eba23aca76e71cc25fd">IMP::em2d::ProjectionFinder::setup()</a>, <a href="classIMP_1_1em2d_1_1RigidBodiesImageFitRestraint.html#af061f3bf53dde9fec3da4b4432220b84">IMP::em2d::RigidBodiesImageFitRestraint::RigidBodiesImageFitRestraint()</a></td></tr>
242 <tr><td>@ref IMP::em2d::SegmentationParameters</td><td><a href="namespaceIMP_1_1em2d.html#a90292cd68858d8e90c4e99c2826739bb">IMP::em2d::do_segmentation()</a>, <a href="namespaceIMP_1_1em2d.html#a64eb9b75ba5371ca0b73ad4bb455b6f7">IMP::em2d::do_segmentation()</a></td></tr>
243 </table>
244 # IMP.isd # {#argument_index_isd}
245 <table><tr>
246 <th>Class</th><th>Users</th></tr>
247 <tr><td>@ref IMP::isd::BivariateFunction</td><td><a href="classIMP_1_1isd_1_1GaussianProcessInterpolation.html#a311544e5a8ddbf811c9d98d8ddffa248">IMP::isd::GaussianProcessInterpolation::GaussianProcessInterpolation()</a></td></tr>
248 <tr><td>@ref IMP::isd::CrossLinkData</td><td><a href="classIMP_1_1isd_1_1CysteineCrossLinkRestraint.html#add9b9dde6bf243b14dc3abac501e4d24">IMP::isd::CysteineCrossLinkRestraint::CysteineCrossLinkRestraint()</a>, <a href="classIMP_1_1isd_1_1CysteineCrossLinkRestraint.html#a5a9d77f313f04238dffb52b016ddac66">IMP::isd::CysteineCrossLinkRestraint::CysteineCrossLinkRestraint()</a></td></tr>
249 <tr><td>@ref IMP::isd::CysteineCrossLinkData</td><td><a href="classIMP_1_1isd_1_1CysteineCrossLinkRestraint.html#a5a9d77f313f04238dffb52b016ddac66">IMP::isd::CysteineCrossLinkRestraint::CysteineCrossLinkRestraint()</a></td></tr>
250 <tr><td>@ref IMP::isd::FretData</td><td><a href="classIMP_1_1isd_1_1FretRestraint.html#a903a8d2d1fa7852c47f20a40acb840d6">IMP::isd::FretRestraint::FretRestraint()</a></td></tr>
251 <tr><td>@ref IMP::isd::GaussianProcessInterpolation</td><td><a href="classIMP_1_1isd_1_1GaussianProcessInterpolationRestraint.html#a0f80da67a5f7bf01537ad983178e1e0f">IMP::isd::GaussianProcessInterpolationRestraint::GaussianProcessInterpolationRestraint()</a></td></tr>
252 <tr><td>@ref IMP::isd::Scale</td><td><a href="classIMP_1_1isd_1_1NormalSigmaPCRestraint.html#aeeccf541c974339fe969a11ecd3bd7b8">IMP::isd::NormalSigmaPCRestraint::NormalSigmaPCRestraint()</a></td></tr>
253 <tr><td>@ref IMP::isd::UnivariateFunction</td><td><a href="classIMP_1_1isd_1_1GaussianProcessInterpolation.html#a311544e5a8ddbf811c9d98d8ddffa248">IMP::isd::GaussianProcessInterpolation::GaussianProcessInterpolation()</a></td></tr>
254 </table>
255 # IMP.kinematics # {#argument_index_kinematics}
256 <table><tr>
257 <th>Class</th><th>Users</th></tr>
258 <tr><td>@ref IMP::kinematics::DOFValues</td><td><a href="classIMP_1_1kinematics_1_1DOFValues.html#a5258006aa5c63f22f4eec17a295e60a7">IMP::kinematics::DOFValues::get_distance()</a>, <a href="classIMP_1_1kinematics_1_1DOFValues.html#a15eb4c9914d5b5b15a9d2161277c3c41">IMP::kinematics::DOFValues::get_distance()</a>, <a href="classIMP_1_1kinematics_1_1DOFValues.html#a09f54814051e678e83b772f49b43249c">IMP::kinematics::DOFValues::get_distance2()</a>, <a href="classIMP_1_1kinematics_1_1DOFValues.html#ad4e437dadc69f4c867c824213f39ec83">IMP::kinematics::DOFValues::get_distance2()</a>, <a href="classIMP_1_1kinematics_1_1DOFsSampler.html#a91b1e5f356122a2a6b026988035c327e">IMP::kinematics::DOFsSampler::apply()</a>, <a href="classIMP_1_1kinematics_1_1DirectionalDOF.html#a5a44c86fbf765b4371007564b14e33ea">IMP::kinematics::DirectionalDOF::set_end_points()</a>, <a href="classIMP_1_1kinematics_1_1FibrilSampler.html#ab99f720493e680f4932248de583120b5">IMP::kinematics::FibrilSampler::apply()</a>, <a href="classIMP_1_1kinematics_1_1LocalPlanner.html#ae1a5e3af8bdac8533a6cf66ff496456e">IMP::kinematics::LocalPlanner::is_valid()</a>, <a href="classIMP_1_1kinematics_1_1LocalPlanner.html#aa3e2c3f33045da082ccbc0c57cf98fae">IMP::kinematics::LocalPlanner::plan()</a>, <a href="classIMP_1_1kinematics_1_1PathLocalPlanner.html#a67f80137a9768983eb7c54911f00e158">IMP::kinematics::PathLocalPlanner::plan()</a>, <a href="classIMP_1_1kinematics_1_1RRT.html#ae0a8a14fbcb0eb68a6a50e3a4e04cd72">IMP::kinematics::RRT::add_nodes()</a>, <a href="classIMP_1_1kinematics_1_1RRT.html#a5068d0aa8c1a96b967a8f59e4800811f">IMP::kinematics::RRT::get_q_near()</a>, <a href="classIMP_1_1kinematics_1_1RRT_1_1RRTNode.html#adbd4de04681704f91459900d988a6bdd">IMP::kinematics::RRT::RRTNode::RRTNode()</a>, <a href="classIMP_1_1kinematics_1_1UniformBackboneSampler.html#a8c5a804a7742a32683f26a85bda7512c">IMP::kinematics::UniformBackboneSampler::apply()</a></td></tr>
259 <tr><td>@ref IMP::kinematics::DOFsSampler</td><td><a href="classIMP_1_1kinematics_1_1LocalPlanner.html#a6116efc0a31bfccbfb862257eaef3b6b">IMP::kinematics::LocalPlanner::LocalPlanner()</a>, <a href="classIMP_1_1kinematics_1_1PathLocalPlanner.html#a3c709f8a11cecb83e42fa72ced88bf5d">IMP::kinematics::PathLocalPlanner::PathLocalPlanner()</a>, <a href="classIMP_1_1kinematics_1_1RRT.html#abb76ef6b539bc20f536babaf3aad119e">IMP::kinematics::RRT::RRT()</a></td></tr>
260 <tr><td>@ref IMP::kinematics::DirectionalDOF</td><td><a href="classIMP_1_1kinematics_1_1PathLocalPlanner.html#a3c709f8a11cecb83e42fa72ced88bf5d">IMP::kinematics::PathLocalPlanner::PathLocalPlanner()</a></td></tr>
261 <tr><td>@ref IMP::kinematics::Joint</td><td><a href="classIMP_1_1kinematics_1_1CompositeJoint.html#a5c53ae6c3e1d44be15e303bb88dc624b">IMP::kinematics::CompositeJoint::add_downstream_joint()</a>, <a href="classIMP_1_1kinematics_1_1CompositeJoint.html#a16faab96024055e41874f66e7e64819a">IMP::kinematics::CompositeJoint::add_upstream_joint()</a>, <a href="classIMP_1_1kinematics_1_1KinematicForest.html#aa327ed003021277f339df961628efb2f">IMP::kinematics::KinematicForest::add_edge()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#a5fa4f049cb6720ea45e9a7eab37fae0f">IMP::kinematics::KinematicNode::do_setup_particle()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#ab124f751588f8c4f28f24efe321bddea">IMP::kinematics::KinematicNode::setup_particle()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#abcf21ca959f72e4e59d0517f8997cfa1">IMP::kinematics::KinematicNode::setup_particle()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#af34e2ec4aa0e829b7164b370f8ff87f3">IMP::kinematics::KinematicNode::setup_particle()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#a42c150181046d83c51d8799f14326c96">IMP::kinematics::KinematicNode::setup_particle()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#ae89ff1d8121a770643723f6b11d59016">IMP::kinematics::KinematicNode::add_out_joint()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#af6fbf6325f2d75517cc9c6199f6e1c98">IMP::kinematics::KinematicNode::set_in_joint()</a></td></tr>
262 <tr><td>@ref IMP::kinematics::KinematicForest</td><td><a href="classIMP_1_1kinematics_1_1Joint.html#a55f61a87ca11cf493e0465e9136af62f">IMP::kinematics::Joint::set_owner_kf()</a>, <a href="classIMP_1_1kinematics_1_1KinematicForestScoreState.html#ae6edcf80a922ef61286a58c348fb341c">IMP::kinematics::KinematicForestScoreState::KinematicForestScoreState()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#a5fa4f049cb6720ea45e9a7eab37fae0f">IMP::kinematics::KinematicNode::do_setup_particle()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#abfb20ad6959f6bd74156061302f47700">IMP::kinematics::KinematicNode::setup_particle()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#abc4cd7cbbcd2fc955adf9b53e6f0026c">IMP::kinematics::KinematicNode::setup_particle()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#ab124f751588f8c4f28f24efe321bddea">IMP::kinematics::KinematicNode::setup_particle()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#abcf21ca959f72e4e59d0517f8997cfa1">IMP::kinematics::KinematicNode::setup_particle()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#af34e2ec4aa0e829b7164b370f8ff87f3">IMP::kinematics::KinematicNode::setup_particle()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#a42c150181046d83c51d8799f14326c96">IMP::kinematics::KinematicNode::setup_particle()</a></td></tr>
263 <tr><td>@ref IMP::kinematics::LocalPlanner</td><td><a href="classIMP_1_1kinematics_1_1RRT.html#abb76ef6b539bc20f536babaf3aad119e">IMP::kinematics::RRT::RRT()</a></td></tr>
264 <tr><td>@ref IMP::kinematics::RRT::RRTNode</td><td><a href="classIMP_1_1kinematics_1_1RRT.html#ae0a8a14fbcb0eb68a6a50e3a4e04cd72">IMP::kinematics::RRT::add_nodes()</a>, <a href="classIMP_1_1kinematics_1_1RRT_1_1RRTNode.html#a7ae4d37384f00ee2eb31854946d38e49">IMP::kinematics::RRT::RRTNode::add_edge()</a>, <a href="classIMP_1_1kinematics_1_1RRT_1_1RRTNode.html#a297cb88bb8ebbb28f005c4a3496bfb44">IMP::kinematics::RRT::RRTNode::is_edge()</a></td></tr>
265 </table>
266 # IMP.misc # {#argument_index_misc}
267 <table><tr>
268 <th>Class</th><th>Users</th></tr>
269 <tr><td>@ref IMP::misc::CustomXYZR</td><td><a href="namespaceIMP_1_1misc.html#a65ae63767baf9a8606e74158c6ef2ade">IMP::misc::get_distance()</a>, <a href="namespaceIMP_1_1misc.html#a4754647ec2a9fab5886f7c0ff31c27a0">IMP::misc::get_sphere_d_geometry()</a>, <a href="namespaceIMP_1_1misc.html#a1cca898df2ee830b5c161c85f0a1dd81">IMP::misc::set_sphere_d_geometry()</a></td></tr>
270 <tr><td>@ref IMP::misc::LogPairScore</td><td><a href="classIMP_1_1misc_1_1LogPairScore.html#a959fd9c4aaa38c637a9fc8ad23201e65">IMP::misc::LogPairScore::IMP_PAIR_SCORE_METHODS()</a></td></tr>
271 </table>
272 # IMP.multi_state # {#argument_index_multi_state}
273 <table><tr>
274 <th>Class</th><th>Users</th></tr>
275 <tr><td>@ref IMP::multi_state::MultiStateModel</td><td><a href="classIMP_1_1multi__state_1_1CompareMultiStateModels.html#a84ecdc2f6511970ebdec76591f111034">IMP::multi_state::CompareMultiStateModels::operator()()</a>, <a href="classIMP_1_1multi__state_1_1EnsembleGenerator.html#a81d07bf2f1bcf1a8e2d65e0323d2b1fa">IMP::multi_state::EnsembleGenerator::get_score()</a>, <a href="classIMP_1_1multi__state_1_1MultiStateModelScore.html#a2b494cabfb945524b92cfee90f7605fa">IMP::multi_state::MultiStateModelScore::get_fit_parameters()</a>, <a href="classIMP_1_1multi__state_1_1MultiStateModelScore.html#a4c812ba169d4396e2fb92769cd46fe84">IMP::multi_state::MultiStateModelScore::get_score()</a>, <a href="classIMP_1_1multi__state_1_1MultiStateModelScore.html#a21eda43b8139229847b4c6dba839e047">IMP::multi_state::MultiStateModelScore::get_score()</a>, <a href="classIMP_1_1multi__state_1_1MultiStateModelScore.html#a243e6455a808839d9d4e20ffc9507823">IMP::multi_state::MultiStateModelScore::write_fit_file()</a>, <a href="classIMP_1_1multi__state_1_1SAXSMultiStateModelScore.html#ac186d743882728f4cab89e5a2bf46f75">IMP::multi_state::SAXSMultiStateModelScore::get_fit_parameters()</a>, <a href="classIMP_1_1multi__state_1_1SAXSMultiStateModelScore.html#a0a4d78fca89143d35ae9b2424b35b20e">IMP::multi_state::SAXSMultiStateModelScore::get_score()</a>, <a href="classIMP_1_1multi__state_1_1SAXSMultiStateModelScore.html#afe8c069e501f0b2c681ffabb57d3ec1e">IMP::multi_state::SAXSMultiStateModelScore::get_score()</a>, <a href="classIMP_1_1multi__state_1_1SAXSMultiStateModelScore.html#ad93630fdd0313f364f10778a5a1c4138">IMP::multi_state::SAXSMultiStateModelScore::write_fit_file()</a></td></tr>
276 <tr><td>@ref IMP::multi_state::MultiStateModelScore</td><td><a href="classIMP_1_1multi__state_1_1EnsembleGenerator.html#a516826c95231987ba20f174ae861d6fd">IMP::multi_state::EnsembleGenerator::EnsembleGenerator()</a></td></tr>
277 </table>
278 # IMP.multifit # {#argument_index_multifit}
279 <table><tr>
280 <th>Class</th><th>Users</th></tr>
281 <tr><td>@ref IMP::multifit::AnchorsData</td><td><a href="classIMP_1_1multifit_1_1ProteinsAnchorsSamplingSpace.html#a897a2e3f157111ff53f6b1f94687c217">IMP::multifit::ProteinsAnchorsSamplingSpace::set_anchors()</a>, <a href="namespaceIMP_1_1multifit.html#a173eff7add1e1652a69ce9c1365ddf2f">IMP::multifit::get_anchor_indices_matching_secondary_structure()</a>, <a href="namespaceIMP_1_1multifit.html#ae4ba0e88472d3177de3ea67a7583d5c0">IMP::multifit::write_cmm()</a>, <a href="namespaceIMP_1_1multifit.html#ae2e18c9a8f1e3e81cf1a561a93e235c0">IMP::multifit::write_txt()</a></td></tr>
282 <tr><td>@ref IMP::multifit::AssemblyHeader</td><td><a href="classIMP_1_1multifit_1_1SettingsData.html#aaa24862022bf887ad2291a4e9e488a48">IMP::multifit::SettingsData::set_assembly_header()</a></td></tr>
283 <tr><td>@ref IMP::multifit::ComponentHeader</td><td><a href="classIMP_1_1multifit_1_1SettingsData.html#a991309d896089e3fd7ec4f9b70ad0ecb">IMP::multifit::SettingsData::add_component_header()</a>, <a href="classIMP_1_1multifit_1_1SettingsData.html#a6c99c0e9881422ed66c90ffd42a6d9e4">IMP::multifit::SettingsData::remove_component_header()</a></td></tr>
284 <tr><td>@ref IMP::multifit::DataPointsAssignment</td><td><a href="namespaceIMP_1_1multifit.html#a6945fa68efec8cd7f189ebd51b7af727">IMP::multifit::get_segment_maximum()</a>, <a href="namespaceIMP_1_1multifit.html#ab1ebb302ab2e310015f0f643bcef86f7">IMP::multifit::get_segment_maximum()</a>, <a href="namespaceIMP_1_1multifit.html#a1ab8b06464f3c9727f0a710d4f1e2f0a">IMP::multifit::write_chimera()</a>, <a href="namespaceIMP_1_1multifit.html#a3f44dc59f3fb41dfdd084270d6a10a61">IMP::multifit::write_pdb()</a>, <a href="namespaceIMP_1_1multifit.html#a8009ecb4c53812a36bf544ed7e9fe9a0">IMP::multifit::write_segment_as_mrc()</a>, <a href="namespaceIMP_1_1multifit.html#afa9365426346e3cbf57346e724da4691">IMP::multifit::write_segment_as_pdb()</a>, <a href="namespaceIMP_1_1multifit.html#ac66c9128b0009595989bc520e3e6dcd3">IMP::multifit::write_segments_as_mrc()</a>, <a href="namespaceIMP_1_1multifit.html#a52c63362745917843277eb7ba97d76d5">IMP::multifit::write_segments_as_pdb()</a></td></tr>
285 <tr><td>@ref IMP::multifit::ProteinsAnchorsSamplingSpace</td><td><a href="classIMP_1_1multifit_1_1Ensemble.html#ac3c46ee809eda56b27ed47c510d6b70b">IMP::multifit::Ensemble::Ensemble()</a>, <a href="classIMP_1_1multifit_1_1ProteomicsEMAlignmentAtomic.html#a5951962f4133ac2a456960ced4511253">IMP::multifit::ProteomicsEMAlignmentAtomic::ProteomicsEMAlignmentAtomic()</a>, <a href="namespaceIMP_1_1multifit.html#a1cc01cbbbb1cf9bb7f226524e0616e12">IMP::multifit::get_part_of_sampling_space()</a>, <a href="namespaceIMP_1_1multifit.html#a990fc248adf46233d96011ab77130eec">IMP::multifit::load_ensemble()</a>, <a href="namespaceIMP_1_1multifit.html#a11b1f20be441ca935aedaf5947b01cb6">IMP::multifit::write_protein_anchors_mapping()</a></td></tr>
286 <tr><td>@ref IMP::multifit::ProteomicsData</td><td><a href="classIMP_1_1multifit_1_1ProteinsAnchorsSamplingSpace.html#a5611298f4d66c2966344bb6f37783df5">IMP::multifit::ProteinsAnchorsSamplingSpace::ProteinsAnchorsSamplingSpace()</a>, <a href="namespaceIMP_1_1multifit.html#aac05dae9e06cb11ef27e820cf54be014">IMP::multifit::get_partial_proteomics_data()</a>, <a href="namespaceIMP_1_1multifit.html#adbd924144aee36a0b6dd9789ca164da8">IMP::multifit::read_protein_anchors_mapping()</a></td></tr>
287 <tr><td>@ref IMP::multifit::SettingsData</td><td><a href="classIMP_1_1multifit_1_1Ensemble.html#ac3c46ee809eda56b27ed47c510d6b70b">IMP::multifit::Ensemble::Ensemble()</a>, <a href="classIMP_1_1multifit_1_1ProteomicsEMAlignmentAtomic.html#a5951962f4133ac2a456960ced4511253">IMP::multifit::ProteomicsEMAlignmentAtomic::ProteomicsEMAlignmentAtomic()</a>, <a href="namespaceIMP_1_1multifit.html#a3746dc39094e607667c55bde5aca85e6">IMP::multifit::get_partial_assembly_setting_data()</a>, <a href="namespaceIMP_1_1multifit.html#a990fc248adf46233d96011ab77130eec">IMP::multifit::load_ensemble()</a>, <a href="namespaceIMP_1_1multifit.html#aa9401684ce59f4d47aaa1e519e1d574b">IMP::multifit::write_settings()</a></td></tr>
288 </table>
289 # IMP.npctransport # {#argument_index_npctransport}
290 <table><tr>
291 <th>Class</th><th>Users</th></tr>
292 <tr><td>@ref IMP::npctransport::FGChain</td><td><a href="classIMP_1_1npctransport_1_1Scoring.html#a19aa8517aaaf627dd0752f45d0bddf4a">IMP::npctransport::Scoring::add_chain_restraints()</a>, <a href="classIMP_1_1npctransport_1_1Statistics.html#a0cf5a8c74dd00ea5d832a9240e09a92b">IMP::npctransport::Statistics::add_fg_chain_stats()</a></td></tr>
293 <tr><td>@ref IMP::npctransport::Scoring</td><td><a href="classIMP_1_1npctransport_1_1FGChain.html#ad22487450a50d3fcec1b5f61d76036b4">IMP::npctransport::FGChain::update_bonds_restraint()</a>, <a href="classIMP_1_1npctransport_1_1FGChain.html#a7df6739cdd5f325888858ec1ca32439e">IMP::npctransport::FGChain::get_chain_restraints()</a></td></tr>
294 <tr><td>@ref IMP::npctransport::SimulationData</td><td><a href="classIMP_1_1npctransport_1_1ParticleFactory.html#aba74e71f6c9b9937152ffb044859b3d4">IMP::npctransport::ParticleFactory::ParticleFactory()</a>, <a href="classIMP_1_1npctransport_1_1Scoring.html#a59c9139729570e2ead12d7129256eb6f">IMP::npctransport::Scoring::Scoring()</a>, <a href="classIMP_1_1npctransport_1_1Statistics.html#ad8fa946acbb73598c6510378be2bff8e">IMP::npctransport::Statistics::Statistics()</a>, <a href="namespaceIMP_1_1npctransport.html#a6ccdfe974fc27d12b30cfa5eac2a2297">IMP::npctransport::copy_FGs_coordinates()</a>, <a href="namespaceIMP_1_1npctransport.html#ac5025684e81bdc014b287d20e18373d9">IMP::npctransport::create_fg_chain()</a>, <a href="namespaceIMP_1_1npctransport.html#acf2b03b3939c022ec65e8402c3016dbf">IMP::npctransport::do_main_loop()</a>, <a href="namespaceIMP_1_1npctransport.html#ac3ab0c2e603459987e3d2b830f9542a2">IMP::npctransport::inflate_floater()</a>, <a href="namespaceIMP_1_1npctransport.html#a2e1017a2f94fda8e6e05bda62dc2b6c4">IMP::npctransport::initialize_positions()</a>, <a href="namespaceIMP_1_1npctransport.html#a6208eea9bbe3ff93c959efd27ad0e27b">IMP::npctransport::remove_Nup42()</a>, <a href="namespaceIMP_1_1npctransport.html#a22d9fcba42fae7e2c499b42c0682d420">IMP::npctransport::reset_box_size()</a></td></tr>
295 <tr><td>@ref IMP::npctransport::SlabWithCylindricalPore</td><td><a href="classIMP_1_1npctransport_1_1AnchorToCylidnricalPorePairScore.html#a1f82abf93180b5708bb77465c4a40382">IMP::npctransport::AnchorToCylidnricalPorePairScore::AnchorToCylidnricalPorePairScore()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithCylindricalPorePairScore.html#a77eb2891252ad5ceec130ed962f7ab8c">IMP::npctransport::SlabWithCylindricalPorePairScore::get_displacement_direction()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithCylindricalPorePairScore.html#aef5d246d897659dc304b4b9aa683dd43">IMP::npctransport::SlabWithCylindricalPorePairScore::get_displacement_magnitude()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithCylindricalPorePairScore.html#a70ab2db413613a8cd1d8ea6d47cd9410">IMP::npctransport::SlabWithCylindricalPorePairScore::update_cached_slab_params()</a></td></tr>
296 <tr><td>@ref IMP::npctransport::SlabWithToroidalPore</td><td><a href="classIMP_1_1npctransport_1_1SlabWithToroidalPorePairScore.html#aec5461fbfbf8ad7721efd50daddc1b71">IMP::npctransport::SlabWithToroidalPorePairScore::update_cached_slab_params()</a></td></tr>
297 <tr><td>@ref IMP::npctransport::Statistics</td><td><a href="classIMP_1_1npctransport_1_1BipartitePairsStatisticsOptimizerState.html#a6ca3e1a26cccb7556a39a9073f685610">IMP::npctransport::BipartitePairsStatisticsOptimizerState::BipartitePairsStatisticsOptimizerState()</a>, <a href="classIMP_1_1npctransport_1_1BodyStatisticsOptimizerState.html#a2f2eb382d62edd4e6ee40b6efee5d54b">IMP::npctransport::BodyStatisticsOptimizerState::BodyStatisticsOptimizerState()</a>, <a href="classIMP_1_1npctransport_1_1GlobalStatisticsOptimizerState.html#ab3af708699123e6ebe45fdb283e9d3dc">IMP::npctransport::GlobalStatisticsOptimizerState::GlobalStatisticsOptimizerState()</a>, <a href="classIMP_1_1npctransport_1_1ParticleTransportStatisticsOptimizerState.html#a8e9618751dbd77f8f62232e40c95af61">IMP::npctransport::ParticleTransportStatisticsOptimizerState::ParticleTransportStatisticsOptimizerState()</a></td></tr>
298 </table>
299 # IMP.rotamer # {#argument_index_rotamer}
300 <table><tr>
301 <th>Class</th><th>Users</th></tr>
302 <tr><td>@ref IMP::rotamer::RotamerLibrary</td><td><a href="classIMP_1_1rotamer_1_1RotamerCalculator.html#ae6d0ae1fea1b6f90e0ac4f4698f9e0a9">IMP::rotamer::RotamerCalculator::RotamerCalculator()</a></td></tr>
303 </table>
304 # IMP.saxs # {#argument_index_saxs}
305 <table><tr>
306 <th>Class</th><th>Users</th></tr>
307 <tr><td>@ref IMP::saxs::DeltaDistributionFunction</td><td><a href="classIMP_1_1saxs_1_1DerivativeCalculator.html#a87546c6807ef081645bb5f42eb3ca3a9">IMP::saxs::DerivativeCalculator::compute_intensity_derivatives()</a></td></tr>
308 <tr><td>@ref IMP::saxs::DerivativeCalculator</td><td><a href="classIMP_1_1saxs_1_1RigidBodiesProfileHandler.html#a67d3fe4fac308624da7c39df74702ba5">IMP::saxs::RigidBodiesProfileHandler::compute_derivatives()</a></td></tr>
309 <tr><td>@ref IMP::saxs::FormFactorTable</td><td><a href="classIMP_1_1saxs_1_1Profile.html#a8a1d10d7b06c24dbc9cc3b70d7b56a92">IMP::saxs::Profile::set_ff_table()</a>, <a href="namespaceIMP_1_1saxs.html#a3088d29b90d6cefe75a9cf2bd68f340b">IMP::saxs::compute_profile()</a>, <a href="namespaceIMP_1_1saxs.html#ae26123273b31cf5c08fd365df7b056e1">IMP::saxs::get_form_factors()</a></td></tr>
310 <tr><td>@ref IMP::saxs::Profile</td><td><a href="classIMP_1_1multi__state_1_1SAXSMultiStateModelScore.html#ac3b3741c8d85d21dded7b8eadcc9c653">IMP::multi_state::SAXSMultiStateModelScore::SAXSMultiStateModelScore()</a>, <a href="classIMP_1_1multi__state_1_1SAXSMultiStateModelScore.html#a907a51273a0711bee143f3194199ce1f">IMP::multi_state::SAXSMultiStateModelScore::resample()</a>, <a href="classIMP_1_1saxs_1_1ChiFreeScore.html#afc9b3d54c486f90baad3208bdfeeac32">IMP::saxs::ChiFreeScore::compute_offset()</a>, <a href="classIMP_1_1saxs_1_1ChiFreeScore.html#a1ed7895c98acedde2c7ebc70bc1bfca0">IMP::saxs::ChiFreeScore::compute_scale_factor()</a>, <a href="classIMP_1_1saxs_1_1ChiFreeScore.html#a9b05b53eeabda292f4e959f886aa591b">IMP::saxs::ChiFreeScore::compute_score()</a>, <a href="classIMP_1_1saxs_1_1ChiScore.html#a67bbdc721bbe32b1fa043856fe2a3d02">IMP::saxs::ChiScore::compute_offset()</a>, <a href="classIMP_1_1saxs_1_1ChiScore.html#ac5a13ba273d5591d0ab82ca22fecf04a">IMP::saxs::ChiScore::compute_scale_factor()</a>, <a href="classIMP_1_1saxs_1_1ChiScore.html#ae07f553da50575740b7e5ed509859bac">IMP::saxs::ChiScore::compute_score()</a>, <a href="classIMP_1_1saxs_1_1ChiScoreLog.html#a6fe658d1f117966cd1839cd299c502a3">IMP::saxs::ChiScoreLog::compute_offset()</a>, <a href="classIMP_1_1saxs_1_1ChiScoreLog.html#a916c72515914f42624a95b9dc42e7dde">IMP::saxs::ChiScoreLog::compute_scale_factor()</a>, <a href="classIMP_1_1saxs_1_1ChiScoreLog.html#a5ebada1e0629d162f6e4b43c340783c2">IMP::saxs::ChiScoreLog::compute_score()</a>, <a href="classIMP_1_1saxs_1_1ChiScoreLog.html#ad586fa8712228048a998f1d9a338bad4">IMP::saxs::ChiScoreLog::compute_score()</a>, <a href="classIMP_1_1saxs_1_1DerivativeCalculator.html#a6d74d86a67d1ba3aefceccb71578c63f">IMP::saxs::DerivativeCalculator::DerivativeCalculator()</a>, <a href="classIMP_1_1saxs_1_1DerivativeCalculator.html#a163a8ac0c3dafe0b32ea60875dca5d24">IMP::saxs::DerivativeCalculator::compute_chisquare_derivative()</a>, <a href="classIMP_1_1saxs_1_1DerivativeCalculator.html#a561de457d223a06aa56a8651e790858f">IMP::saxs::DerivativeCalculator::compute_chisquare_derivative()</a>, <a href="classIMP_1_1saxs_1_1DerivativeCalculator.html#a7a526c03bc0cdf2f25eb7295ffc185ce">IMP::saxs::DerivativeCalculator::compute_gaussian_effect_size()</a>, <a href="classIMP_1_1saxs_1_1DerivativeCalculator.html#a9ebc76cc8dbdb3d16457bc4870f76a5e">IMP::saxs::DerivativeCalculator::precompute_derivative_helpers()</a>, <a href="classIMP_1_1saxs_1_1DerivativeCalculator.html#a0ae3d95128ec4d29148f83c5bbe7548d">IMP::saxs::DerivativeCalculator::compute_sinc_cos()</a>, <a href="classIMP_1_1saxs_1_1Profile.html#af2d065b52f2c154fedd4dbfa84d046ab">IMP::saxs::Profile::add()</a>, <a href="classIMP_1_1saxs_1_1Profile.html#a13596be5f2149e65e6a457041e49e478">IMP::saxs::Profile::add()</a>, <a href="classIMP_1_1saxs_1_1Profile.html#ac8f8e0caded8f8dec4df955c341b3e2e">IMP::saxs::Profile::add_partial_profiles()</a>, <a href="classIMP_1_1saxs_1_1Profile.html#a03e96bef7c9652e7dddee5e588e2532f">IMP::saxs::Profile::add_partial_profiles()</a>, <a href="classIMP_1_1saxs_1_1Profile.html#aad86fc9975dd25aadd81a698410918ac">IMP::saxs::Profile::copy_errors()</a>, <a href="classIMP_1_1saxs_1_1Profile.html#ab89bf550f73ed2bdc93addcf0b62d23d">IMP::saxs::Profile::downsample()</a>, <a href="classIMP_1_1saxs_1_1Profile.html#a7894872bb7d93b30adb9951bff99735a">IMP::saxs::Profile::resample()</a>, <a href="classIMP_1_1saxs_1_1ProfileClustering.html#a74b8bf812ba281d1a66569d18b71a2f5">IMP::saxs::ProfileClustering::ProfileClustering()</a>, <a href="classIMP_1_1saxs_1_1ProfileClustering.html#af249c9c0d39a244466a3bb0eb175084e">IMP::saxs::ProfileClustering::ProfileClustering()</a>, <a href="classIMP_1_1saxs_1_1ProfileFitter.html#a344f7cdb6981bb1b9d568a9a8927987b">IMP::saxs::ProfileFitter::ProfileFitter()</a>, <a href="classIMP_1_1saxs_1_1ProfileFitter.html#aa2b22f8b8ce22da520317058a8c75c36">IMP::saxs::ProfileFitter::ProfileFitter()</a>, <a href="classIMP_1_1saxs_1_1ProfileFitter.html#a224cf0e4fd31d2d7fe08a27d6b7c5bbd">IMP::saxs::ProfileFitter::compute_offset()</a>, <a href="classIMP_1_1saxs_1_1ProfileFitter.html#a04886872e631bfbd3d9d31f374c0c194">IMP::saxs::ProfileFitter::compute_scale_factor()</a>, <a href="classIMP_1_1saxs_1_1ProfileFitter.html#a3ac45584df4d5b3f05cea7065a7e51a2">IMP::saxs::ProfileFitter::compute_score()</a>, <a href="classIMP_1_1saxs_1_1ProfileFitter.html#afaa5cad2558d184e54d2255880ab156e">IMP::saxs::ProfileFitter::fit_profile()</a>, <a href="classIMP_1_1saxs_1_1ProfileFitter.html#a66edb60e5085c5f369a4e786ef0aa4e4">IMP::saxs::ProfileFitter::resample()</a>, <a href="classIMP_1_1saxs_1_1ProfileFitter.html#a999f7782299af184c844e55b6331d358">IMP::saxs::ProfileFitter::write_SAXS_fit_file()</a>, <a href="classIMP_1_1saxs_1_1ProfileFitter.html#aac32d65c66c88a72e95c19661698ed90">IMP::saxs::ProfileFitter::search_fit_parameters()</a>, <a href="classIMP_1_1saxs_1_1RadiusOfGyrationRestraint.html#a9b5742b6241cf0f196b45dec658bc5d1">IMP::saxs::RadiusOfGyrationRestraint::RadiusOfGyrationRestraint()</a>, <a href="classIMP_1_1saxs_1_1RatioVolatilityScore.html#ad7d3e363ae302ff0224a58c9b6cf731a">IMP::saxs::RatioVolatilityScore::compute_offset()</a>, <a href="classIMP_1_1saxs_1_1RatioVolatilityScore.html#a5de4fb24262bc131250a2ee400e0ca7c">IMP::saxs::RatioVolatilityScore::compute_scale_factor()</a>, <a href="classIMP_1_1saxs_1_1RatioVolatilityScore.html#a0726dc59f2141150ba74cdab844a8d14">IMP::saxs::RatioVolatilityScore::compute_score()</a>, <a href="classIMP_1_1saxs_1_1Restraint.html#ad11e61724397d0366af159ff0eda0ab6">IMP::saxs::Restraint::Restraint()</a>, <a href="classIMP_1_1saxs_1_1RigidBodiesProfileHandler.html#a67d3fe4fac308624da7c39df74702ba5">IMP::saxs::RigidBodiesProfileHandler::compute_derivatives()</a>, <a href="classIMP_1_1saxs_1_1RigidBodiesProfileHandler.html#ac0113e2be22d5d7c176ff06c81da89e3">IMP::saxs::RigidBodiesProfileHandler::compute_profile()</a>, <a href="classIMP_1_1saxs_1_1WeightedProfileFitter.html#aaf22d8d5fe1016714188b0e67c8dea51">IMP::saxs::WeightedProfileFitter::WeightedProfileFitter()</a></td></tr>
311 <tr><td>@ref IMP::saxs::RadialDistributionFunction</td><td><a href="classIMP_1_1saxs_1_1Profile.html#a1c170e6a2d3867d31fb0a6104093cd33">IMP::saxs::Profile::distribution_2_profile()</a>, <a href="classIMP_1_1saxs_1_1Profile.html#a76a8fa45603a71e8e2e2e468bb5cb59d">IMP::saxs::Profile::profile_2_distribution()</a>, <a href="classIMP_1_1saxs_1_1Profile.html#a9dd95cf18dd18cd346ab6185dad2004e">IMP::saxs::Profile::squared_distribution_2_profile()</a>, <a href="classIMP_1_1saxs_1_1Profile.html#a4ec6bd16b5ad105ca2264d6b4b41e810">IMP::saxs::Profile::squared_distributions_2_partial_profiles()</a>, <a href="classIMP_1_1saxs_1_1RadialDistributionFunction.html#aeb53667c6c8b782418cc9189c9bd0a12">IMP::saxs::RadialDistributionFunction::add()</a>, <a href="classIMP_1_1saxs_1_1RadialDistributionFunction.html#aa3db96b43586768ea44f52b91803545e">IMP::saxs::RadialDistributionFunction::fit()</a>, <a href="classIMP_1_1saxs_1_1RadialDistributionFunction.html#a9c67650585b9ad2d0a9d43546fe5b66a">IMP::saxs::RadialDistributionFunction::R_factor_score()</a>, <a href="classIMP_1_1saxs_1_1RadialDistributionFunction.html#a2a28e47456ae50eb04e601cfd416c840">IMP::saxs::RadialDistributionFunction::write_fit_file()</a></td></tr>
312 <tr><td>@ref IMP::saxs::WeightedFitParameters</td><td><a href="classIMP_1_1multi__state_1_1EnsembleGenerator.html#a95551cfa5651934563304e4ffe349862">IMP::multi_state::EnsembleGenerator::get_weights_average_and_std()</a>, <a href="classIMP_1_1multi__state_1_1EnsembleGenerator.html#abddfbe8fed489debf83ef02a1f280e10">IMP::multi_state::EnsembleGenerator::output()</a>, <a href="classIMP_1_1multi__state_1_1EnsembleGenerator.html#aa7c2c2078b9edcb6aebdfb55ea043f03">IMP::multi_state::EnsembleGenerator::rescore()</a>, <a href="classIMP_1_1multi__state_1_1MultiStateModelScore.html#a243e6455a808839d9d4e20ffc9507823">IMP::multi_state::MultiStateModelScore::write_fit_file()</a>, <a href="classIMP_1_1multi__state_1_1SAXSMultiStateModelScore.html#a2cf47e187b3358559966682e6ff34e85">IMP::multi_state::SAXSMultiStateModelScore::set_average_c1_c2()</a>, <a href="classIMP_1_1multi__state_1_1SAXSMultiStateModelScore.html#ad93630fdd0313f364f10778a5a1c4138">IMP::multi_state::SAXSMultiStateModelScore::write_fit_file()</a>, <a href="classIMP_1_1saxs_1_1WeightedProfileFitter.html#a489c79b2bdb91a7aed83289c5dcee477">IMP::saxs::WeightedProfileFitter::write_fit_file()</a></td></tr>
313 <tr><td>@ref IMP::saxs::WeightedProfileFitter</td><td><a href="classIMP_1_1multi__state_1_1SAXSMultiStateModelScore.html#a2ba264185bccf493b2f7094c5821d8de">IMP::multi_state::SAXSMultiStateModelScore::set_average_c1_c2()</a></td></tr>
314 </table>
315 # IMP.statistics # {#argument_index_statistics}
316 <table><tr>
317 <th>Class</th><th>Users</th></tr>
318 <tr><td>@ref IMP::statistics::Embedding</td><td><a href="classIMP_1_1statistics_1_1EuclideanMetric.html#a5d5bcbea89a38c0c4cdb29b2a6aad159">IMP::statistics::EuclideanMetric::EuclideanMetric()</a>, <a href="classIMP_1_1statistics_1_1RecursivePartitionalClusteringEmbedding.html#ad2e702ad3bd288cff7f34307c124456c">IMP::statistics::RecursivePartitionalClusteringEmbedding::RecursivePartitionalClusteringEmbedding()</a>, <a href="namespaceIMP_1_1statistics.html#a2ccc84a060553c450d17b18bce708436">IMP::statistics::create_bin_based_clustering()</a>, <a href="namespaceIMP_1_1statistics.html#a19eae7a22f877948e0582872cb42e760">IMP::statistics::create_centrality_clustering()</a>, <a href="namespaceIMP_1_1statistics.html#ad6ac98231fe5e79078029b821e5d2417">IMP::statistics::create_connectivity_clustering()</a>, <a href="namespaceIMP_1_1statistics.html#a84d813a09204387c1b2af83e6fb5e014">IMP::statistics::create_lloyds_kmeans()</a>, <a href="namespaceIMP_1_1statistics.html#ac31b5cbb1a3c6722e837341ce0ee872d">IMP::statistics::get_centroids()</a>, <a href="namespaceIMP_1_1statistics.html#a974ae5760db93ab3cf0afced47455a29">IMP::statistics::get_representatives()</a></td></tr>
319 <tr><td>@ref IMP::statistics::HistogramD</td><td><a href="namespaceIMP_1_1statistics.html#a6f2a5df02a675039a03a695b45947498">IMP::statistics::show_histogram()</a></td></tr>
320 <tr><td>@ref IMP::statistics::Metric</td><td><a href="classIMP_1_1statistics_1_1RecursivePartitionalClusteringMetric.html#a0eb7c7bea72016758a63d42ddcd0552a">IMP::statistics::RecursivePartitionalClusteringMetric::RecursivePartitionalClusteringMetric()</a>, <a href="namespaceIMP_1_1spb.html#a764329bdc6974636ec54abce1c5cf450">IMP::spb::create_gromos_clustering()</a>, <a href="namespaceIMP_1_1statistics.html#a033ac0d9e680dc724a782c219391dc5c">IMP::statistics::create_centrality_clustering()</a>, <a href="namespaceIMP_1_1statistics.html#a7fa3185254b0cf61b8baa2b04e3461c6">IMP::statistics::create_connectivity_clustering()</a>, <a href="namespaceIMP_1_1statistics.html#ae34d7252a499c1f7a6948fa5283f88a6">IMP::statistics::create_diameter_clustering()</a>, <a href="namespaceIMP_1_1statistics.html#a739c887af40a30b27d360f052f3d001b">IMP::statistics::create_gromos_clustering()</a></td></tr>
321 <tr><td>@ref IMP::statistics::PartitionalClustering</td><td><a href="classIMP_1_1statistics_1_1RecursivePartitionalClusteringEmbedding.html#ad2e702ad3bd288cff7f34307c124456c">IMP::statistics::RecursivePartitionalClusteringEmbedding::RecursivePartitionalClusteringEmbedding()</a>, <a href="classIMP_1_1statistics_1_1RecursivePartitionalClusteringEmbedding.html#ad985a95838650906b20fab33bf23b3ea">IMP::statistics::RecursivePartitionalClusteringEmbedding::create_full_clustering()</a>, <a href="classIMP_1_1statistics_1_1RecursivePartitionalClusteringMetric.html#a0eb7c7bea72016758a63d42ddcd0552a">IMP::statistics::RecursivePartitionalClusteringMetric::RecursivePartitionalClusteringMetric()</a>, <a href="classIMP_1_1statistics_1_1RecursivePartitionalClusteringMetric.html#a298cc8279d3029e200a24ce9fb247942">IMP::statistics::RecursivePartitionalClusteringMetric::create_full_clustering()</a>, <a href="namespaceIMP_1_1statistics.html#ac31b5cbb1a3c6722e837341ce0ee872d">IMP::statistics::get_centroids()</a>, <a href="namespaceIMP_1_1statistics.html#a974ae5760db93ab3cf0afced47455a29">IMP::statistics::get_representatives()</a>, <a href="namespaceIMP_1_1statistics.html#a5935bfa801d76e543494e701665dd173">IMP::statistics::validate_partitional_clustering()</a></td></tr>
322 </table>
virtual int get_value_index(Model *m, const ParticleIndexPair &p) const
Compute the predicate and the derivative if needed.
void read_pdb(Model *m, const std::string file, std::vector< std::string > &pdb_file_names, std::vector< IMP::Particles > &particles_vec, bool residue_level=false, bool heavy_atoms_only=true, int multi_model_pdb=2, bool explicit_water=false)
Read PDB (or mmCIF) files.
unsigned int get_number_of_incidences(const ParticlesTemp &psa, const ParticlesTemp &psb, double point_distance)
Definition: counting.h:23
double evaluate_site_contributions(Model *m, const ParticleIndexPair &pip, DerivativeAccumulator *da, boost::tuple< unsigned int, std::vector< unsigned int >, std::vector< unsigned int >, bool >(*contacts_accumulator)) const
FitParameters fit_profile(Profile *partial_profile, double min_c1=0.95, double max_c1=1.05, double min_c2=-2.0, double max_c2=4.0, bool use_offset=false, const std::string fit_file_name="") const
fit experimental profile through optimization of c1 and c2 parameters
virtual IMP::ModelObjectsTemp do_get_inputs(IMP::Model *m, const IMP::ParticleIndexes &pis) const
Overload this method to specify the inputs.
virtual ModelObjectsTemp do_get_outputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the outputs.
const SpherePatch3D & get_sphere_patch_3d_geometry(const SpherePatch3D &g)
Definition: SpherePatch3D.h:48
void do_advance_chunk(double dtfs, double ikt, const ParticleIndexes &ps, unsigned int begin, unsigned int end)
virtual double evaluate_if_good_index(Model *m, const ParticleIndexTriplet &vt, DerivativeAccumulator *da, double max) const
Compute the score and the derivative if needed, only if "good".
void link_particles(RMF::FileConstHandle fh, const ParticlesTemp &hs)
Transform(const algebra::Transformation3D &t, bool ignore_non_xyz=false)
Initialize.
double evaluate_indexes_scores(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
TripletsRestraint(TripletScore *ss, TripletContainerAdaptor pc, std::string name="TripletsRestraint %1%")
Create the restraint with a shared container.
static Symmetric setup_particle(Model *m, ParticleIndex pi, Float symmetric)
Definition: /Symmetric.h:44
virtual ModelObjectsTemp do_get_outputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the outputs.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
TransformationAndReflectionSymmetry(const algebra::Transformation3D &t, const algebra::Reflection3D &r)
Create with both reflection and translation.
SingletonContainerSet(Model *m, std::string name="SingletonContainerSet %1%")
Construct an empty set.
double evaluate_if_good_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
virtual double evaluate_index(IMP::Model *m, const IMP::ParticleIndexPair &p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
virtual double evaluate_index(Model *m, const ParticleIndexPair &p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
static Switching setup_particle(Model *m, ParticleIndex pi)
Definition: Switching.h:34
virtual ModelObjectsTemp do_get_inputs(Model *, const ParticleIndexes &) const
Overload this method to specify the inputs.
double evaluate_indexes_delta(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
A base class for modifiers of ParticlesTemp.
PartitionalClusteringWithCenter * create_lloyds_kmeans(Embedding *embedding, unsigned int k, unsigned int iterations)
double evaluate_if_good_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
void add(const ParticleIndexPair &vt)
Add a single const ParticleIndexPair& to the container.
A class to store a configuration of a model.
Definition: Configuration.h:20
double evaluate_indexes_scores(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
void add_to_derivatives(const algebra::Vector3D &v, DerivativeAccumulator &d)
Add the vector v to the derivative vector of the x,y,z coordinates.
Definition: XYZ.h:82
ConnectingPairContainer(SingletonContainer *sc, double error)
void set_atom_type(AtomType t)
Set the name and corresponding element and mass.
virtual void do_add_score_and_derivatives(ScoreAccumulator sa, const ScoreStatesTemp &ss)=0
void add_bonds(Hierarchy mhd) const
add bonds to the structure defined in the hierarchy
double evaluate_indexes_delta(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
Particles create_dihedrals(Particles bonds) const
Auto-generate Dihedral particles from the passed list of Bond particles.
double evaluate_index(Model *m, const ParticleIndexPair &pip, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
virtual double evaluate_index(Model *m, const ParticleIndexPair &p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
TALOSRestraint(Model *m, Particles p, Floats data, Particle *kappa)
Create restraint from a list of particles and the data.
void set_orientations(const core::RigidBody &rb, const algebra::Rotation3Ds &rots)
Set the possible rotations that a rigid body can have.
Detect cn symmetry in proteins and density maps.
void apply(const TripletModifier *sm) const
Apply a TripletModifier to the contents.
MinimumTripletRestraint(TripletScore *f, TripletContainerAdaptor c, unsigned int n=1, std::string name="MinimumTripletRestraint %1%")
virtual int get_value_index_in_batch(Model *m, const ParticleIndexPair &vt) const
Definition: PairPredicate.h:58
double evaluate_indexes_delta(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
static Nuisance setup_particle(Model *m, ParticleIndex pi)
Definition: Nuisance.h:31
double compute_max_distance(const Particles &particles)
compute max distance
Definition: saxs/utility.h:40
virtual int get_value_index(Model *m, const ParticleIndexPair &p) const
Compute the predicate and the derivative if needed.
void add_to_pore_radius_derivative(double v, DerivativeAccumulator &d)
Definition: SlabWithPore.h:102
Add mass to a particle.
Definition: Mass.h:23
double get_volume_from_residue_type(ResidueType rt)
Return an estimate for the volume of a given residue.
double evaluate_if_good_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
virtual bool get_can_refine(Particle *) const
Return true if this refiner can refine that particle.
A particle with angular velocity.
Hierarchy read_pdb_or_mmcif(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector(), bool select_first_model=true)
Read all the molecules in the first model of the PDB or mmCIF file.
Definition: mmcif.h:40
The ideal topology of a single residue.
Base class for functions of one variable.
void set(Particle *p, Key key, const Value &value)
Assign new properties to the class.
Definition: scoped.h:48
Abstract class for scoring object(s) of type ParticleIndexPair.
Definition: PairScore.h:42
virtual double evaluate_if_good_index(Model *m, const ParticleIndexQuad &vt, DerivativeAccumulator *da, double max) const
Compute the score and the derivative if needed, only if "good".
The base class for simulators.
Definition: Simulator.h:34
GridIndexD< D > get_index(const ExtendedGridIndexD< D > &v) const
Convert a ExtendedIndex into a real Index if possible.
Definition: grid_ranges.h:237
ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
void add_undecorator(ParticleIndex pi, Undecorator *d)
Add the passed Undecorator to the particle.
A shared container for Pairs.
Definition: PairContainer.h:37
void create_masks(const ParticlesTemp &ps)
double get_height(const Surface &s, const XYZR &d)
Get height of sphere above surface.
Definition: Surface.h:129
The base class to handle reading and writing of density maps.
Restraints create_current_decomposition(Model *m, ParticleIndex vt) const
static CHARMMAtom setup_particle(Model *m, ParticleIndex pi, String charmm_type)
Definition: CHARMMAtom.h:37
virtual double evaluate_index(Model *m, ParticleIndex p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
static Charged setup_particle(Model *m, ParticleIndex pi, Float charge)
Definition: Charged.h:46
virtual void add_to_derivatives(const Floats &x1, const Floats &x2, DerivativeAccumulator &accum) const =0
update derivatives of particles
static Resolution setup_particle(Model *m, ParticleIndex pi, Float resolution)
Definition: /Resolution.h:45
virtual int get_value_index(Model *m, const ParticleIndexPair &pi) const
Compute the predicate for types of specific pi.
void set_particles(const Particles &pis)
Set the particles to use.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
SigmoidRestraintSphere(IMP::Model *m, IMP::ParticleIndexAdaptor p1, IMP::ParticleIndexAdaptor p2, double inflection, double slope, double amplitude, double line_slope_=0, std::string name="SigmoidRestraintSphere%1%")
Create the restraint.
virtual Restraints do_create_current_decomposition(Model *m, const ParticleIndexQuad &vt) const
Override this to return your own decomposition.
void add_close_pair_score(PairScore *ps, double distance, const ParticlesTemp &particles, const PairPredicates &filters)
void set_rotation(double phi, double theta, double psi)
Rotation to apply to the model.
double evaluate_index(Model *m, const ParticleIndexPair &pip, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
Hierarchy read_mmcif(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector(), bool select_first_model=true)
Read all the molecules in the first model of the mmCIF file.
PairConstraint(PairModifier *before, PairDerivativeModifier *after, const ParticlePair &vt, std::string name="PairConstraint %1%")
virtual double get_strength(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
The strength is a rough metric of how this filter restricts the subset.
static StructureSource setup_particle(Model *m, ParticleIndex pi, std::string source_id, std::string source_chain_id)
virtual ModelObjectsTemp do_get_inputs(Model *, const ParticleIndexes &) const
Overload this method to specify the inputs.
virtual void do_after_evaluate(DerivativeAccumulator *da)
Do any necessary updates after the model score is calculated.
void save_cache(const ParticlesTemp &particle_ordering, const RestraintsTemp &restraints, RMF::HDF5::Group group, unsigned int max_entries)
A Monte Carlo optimizer.
Definition: MonteCarlo.h:45
double evaluate_if_good_indexes(Model *m, const ParticleIndexTriplets &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
Simple 3D transformation class.
double get_slack_estimate(Model *m, ParticleIndexes ps, double upper_bound, double step, const RestraintsTemp &restraints, bool derivatives, Optimizer *opt, ClosePairContainer *cpc)
Selection(Hierarchy hierarchy=None, Hierarchies hierarchies=[], Strings molecules=[], Ints residue_indexes=[], Strings chain_ids=[], AtomTypes atom_types=[], ResidueTypes residue_types=[], Strings domains=[], double resolution=0, RepresentationType representation_type=IMP.atom.BALLS, std::string molecule=None, int residue_index=None, std::string chain_id=None, AtomType atom_type=None, ResidueType residue_type=None, Ints hierarchy_types=None, Element element=None, Terminus terminus=None, std::string domain=None, core::ParticleType particle_type=None, core::ParticleTypes particle_types=[], int copy_index=-1, Ints copy_indexes=[], int state_index=-1, Ints state_indexes=[])
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
double evaluate_indexes_delta(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
void calculate_profile(const Particles &particles, FormFactorType ff_type=HEAVY_ATOMS, bool reciprocal=false)
computes theoretical profile
Definition: Profile.h:50
void set_vector_geometry(Particle *p, const algebra::Vector3D &v)
Definition: XYZ.h:151
void apply_moved(const TripletModifier *sm, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const
Apply a TripletModifier to the contents.
A decorator to associate a particle with a part of a protein.
Definition: Domain.h:21
Simulator(Model *m, std::string name="Simulator %1%", double wave_factor=1.0)
Float get_secondary_structure_match_score(SecondaryStructureResidue ssr1, SecondaryStructureResidue ssr2)
Compares the secondary structure probabilities of two residues.
VectorD< D > get_random_vector_on(const BoundingBoxD< D > &bb)
Generate a random vector on a box with uniform density.
static Provenance setup_particle(Model *m, ParticleIndex pi)
Definition: provenance.h:74
double evaluate_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
double get_shift_error(const RegistrationResult &rr1, const RegistrationResult &rr2)
Distance between the two in-plane translations.
Images create_evenly_distributed_projections(const ParticlesTemp &ps, unsigned int n, const ProjectingOptions &options)
DynamicListQuadContainer(Container *scope, std::string name="ListQuadContainer %1%")
bool get_contains(const SphereD< D > &o) const
Return true if this sphere contains the other one.
Definition: SphereD.h:43
virtual double get_strength(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
The strength is a rough metric of how this filter restricts the subset.
BodyStatisticsOptimizerState(Particle *p, IMP::npctransport::Statistics *statistics_manager=nullptr, unsigned int periodicity=1)
virtual void do_after_evaluate(DerivativeAccumulator *da)
Do any necessary updates after the model score is calculated.
virtual double evaluate_index(Model *m, const ParticleIndexPair &pip, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
void write_pts(const Vector3Ds &vs, TextOutput out)
Write a set of 3D vectors to a file.
RotamerCalculator(const RotamerLibrary *rl)
constructor
static CenterOfMass setup_particle(Model *m, ParticleIndex pi, ParticleIndexesAdaptor members)
Definition: CenterOfMass.h:81
double evaluate_indexes_scores(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
static Dihedral setup_particle(Model *m, ParticleIndex pi, core::XYZ a, core::XYZ b, core::XYZ c, core::XYZ d)
Chain get_chain(Hierarchy h)
Get the containing chain or Chain() if there is none.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
static CustomXYZR setup_particle(Model *m, ParticleIndex pi, DecoratorTraits tr=get_default_decorator_traits())
Definition: CustomXYZR.h:49
virtual void setup(const ParticleIndexes &ps)
virtual double do_step(const ParticleIndexes &sc, double dt_fs)
CCDLoopClosure(DihedralAngleRevoluteJoints joints, const algebra::Vector3D &F1, const algebra::Vector3D &F2, const algebra::Vector3D &F3, core::XYZ M1, core::XYZ M2, core::XYZ M3)
Constructor.
int get_value(const core::ParticleTypes &types)
Compute the predicate for specified types.
IntsList get_anchor_indices_matching_secondary_structure(const AnchorsData &ad, const atom::SecondaryStructureResidues &ssrs, Float max_rmsd=0.7)
Get lists of anchors that match a sequence of secondary structures.
virtual double evaluate_if_good_indexes(Model *m, const ParticleIndexPairs &o, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
BoxedMover(Particle *p, Float max_tr, algebra::Vector3Ds centers)
virtual double evaluate_indexes_scores(Model *m, const ParticleIndexQuads &o, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
static Transporting setup_particle(Model *m, ParticleIndex pi, bool is_last_entry_from_top=false)
Definition: Transporting.h:63
bool same_origin(const DensityMap *other) const
Checks if two maps have the same origin.
Represent an RGB color.
Definition: Color.h:24
virtual void propagate_velocities(const ParticleIndexes &ps, double step_size)
Second part of velocity Verlet (update velocity)
virtual void setup(const ParticleIndexes &ps)
static void teardown_particle(RigidBody rb)
Make the rigid body no longer rigid.
Float get_threshold_for_approximate_mass(DensityMap *m, Float desired_mass, atom::ProteinDensityReference ref=atom::HARPAZ)
Computes the threshold to consider in an EM map to get a desired mass.
A decorator to associate a particle with a part of a protein/DNA/RNA.
Definition: Fragment.h:20
ProfileFitter(const Profile *exp_profile)
Constructor.
Definition: ProfileFitter.h:35
void set_unknown_score(QuadScore *score)
Vector< AtomTypes > get_chi_dihedral_atom_types(ResidueType rt)
PairsRestraint(PairScore *ss, PairContainerAdaptor pc, std::string name="PairsRestraint %1%")
Create the restraint with a shared container.
MolecularDynamicsWithWte(Model *m, double emin, double emax, double sigma, double gamma, double w0)
static Gaussian setup_particle(Model *m, ParticleIndex pi)
Definition: core/Gaussian.h:48
Atoms get_phi_dihedral_atoms(Residue rd)
Return the atoms comprising the phi dihedral.
void set_particles(const ParticlesTemp &ps, IMP::FloatKey mass_key=IMP::atom::Mass::get_mass_key())
setting particles in case they were not set by the constructor
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
void add_partial_profiles(const Profile *other_profile, double weight=1.0)
add partial profiles
DeltaDistributionFunction(const Particles &particles, double max_distance=0.0, double bin_size=pr_resolution)
Constructor.
DensityMap * interpolate_map(DensityMap *in_map, double new_spacing)
Return a new map with an updated spacing.
Hierarchy create_hierarchy(Model *model) const
Create a new Hierarchy in the given model using this topology.
virtual ModelObjectsTemp do_get_inputs(Model *, const ParticleIndexes &) const
Overload this method to specify the inputs.
Simple implementation of lines in 3D.
Definition: Line3D.h:28
void set_particle_probabilities_on_anchors(Particle *p, multifit::FittingSolutionRecords sols)
Set the probability of a component to be located at each anchor position.
virtual int get_value_index(Model *m, const ParticleIndexQuad &pi) const
Compute the predicate for types of specific pi.
void show_molecular_hierarchy(Hierarchy h)
Print out the molecular hierarchy.
Abstract predicate function.
Definition: QuadPredicate.h:31
TripletsConstraint(TripletModifier *before, TripletModifier *after, TripletContainerAdaptor c, std::string name="TripletsConstraint %1%")
The base class for containers of assignments.
Particles density2particles(DensityMap *dmap, Float threshold, Model *m, int step=1)
Convert a density grid to a set of particles.
void add_floater_stats(IMP::Particle *p)
add statistics about a floater particle
algebra::Vector3Ds density2vectors(DensityMap *dmap, Float threshold)
Convert a density grid to a set of vectors.
void set_incremental_scoring_function(IncrementalScoringFunction *isf)
void set_particle_states(Particle *p, ParticleStates *se)
void remove_representation(ParticleIndexAdaptor rep)
Remove the given representation.
ParticleFactory(SimulationData *sd, double radius, double D_factor, double angular_D_factor, display::Color color, core::ParticleType type, std::string name="Particle factory %1%")
virtual double evaluate_index(Model *m, const ParticleIndexPair &pi, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
Storage and access to force field.
double get_volume(Particle *p, FormFactorType ff_type=HEAVY_ATOMS) const
volume
DistanceTerminiRestraint(IMP::Particle *nterm, IMP::Particle *cterm, IMP::Particle *reqd_dist_term, double sigma0_dist)
Restrains the distance between the termini of a protein.
void set_transformation(const algebra::Transformation3D &rot)
double evaluate_indexes(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
virtual double evaluate_index(Model *m, const ParticleIndexTriplet &pi, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
VectorD< D > get_elementwise_product(const algebra::VectorD< D > &a, const algebra::VectorD< D > &b)
Return the vector that is the elementwise product of the two.
Definition: VectorD.h:457
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pi) const
Overload this method to specify the inputs.
static RigidBodyDiffusion setup_particle(Model *m, ParticleIndex pi)
Definition: Diffusion.h:103
Track creation of a system fragment from running some software.
Definition: provenance.h:562
virtual void apply_indexes(Model *m, const ParticleIndexTriplets &o, unsigned int lower_bound, unsigned int upper_bound) const
const Vector< double > & get_form_factors(Particle *p, FormFactorType ff_type=HEAVY_ATOMS) const
full form factor for reciprocal space profile calculation
void remove_charmm_untyped_atoms(Hierarchy hierarchy)
Remove any atom from the Hierarchy that does not have a CHARMM type.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
virtual void apply_indexes(Model *m, const ParticleIndexes &o, unsigned int lower_bound, unsigned int upper_bound) const
Definition: CoverBond.h:34
Storage of proteomics data.
FGChain * create_fg_chain(IMP::npctransport::SimulationData *sd, atom::Hierarchy parent, const ::npctransport_proto::Assignment_FGAssignment &fg_data, display::Color c)
BoundingBoxD< 3 > get_bounding_box(const Plane3D &g)
Definition: Plane3D.h:78
void remove_Nup42(SimulationData *sd)
remove nup42 and its anchors (also from obstacles)
ParticlesTemp create_particles(RMF::FileConstHandle fh, Model *m)
SingletonRestraint(Model *m, SingletonScore *ss, ParticleIndex vt, std::string name="SingletonRestraint %1%")
Create the restraint.
algebra::BoundingBoxD< 3 > get_bounding_box(const DensityMap *m, Float threshold)
Get the bounding box for a map.
void mark_rotatable_angle(const std::vector< atom::Atom > &dihedral_angle)
atom::Hierarchies create_hierarchies(RMF::FileConstHandle fh, Model *m)
double evaluate_indexes_delta(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
em2d::Images get_projections(const ParticlesTemp &ps, const algebra::SphericalVector3Ds &vs, int rows, int cols, const ProjectingOptions &options, Strings names=Strings())
Generates projections from particles.
virtual void apply_indexes(Model *m, const ParticleIndexes &o, unsigned int lower_bound, unsigned int upper_bound) const
A base class for algorithms to find spatial proximities.
virtual Restraints do_create_current_decomposition(Model *m, const ParticleIndexPair &vt) const
Override this to return your own decomposition.
BallMover(Particle *p, Particles ps, Float max_tr, algebra::Vector3Ds ctrs, algebra::Transformation3Ds trs)
Restraint * create_restraint(Score *s, const typename Score::Argument &t, std::string name=std::string())
Definition: generic.h:36
Set the coordinates of a particle to be a transformed version of a reference.
Definition: core/symmetry.h:76
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
DependencyGraph get_dependency_graph(Model *m)
virtual void do_after_evaluate(DerivativeAccumulator *da)
Do any necessary updates after the model score is calculated.
Definition: Constraint.h:56
GaussianEMRestraint(Model *mdl, ParticleIndexes model_ps, ParticleIndexes density_ps, ParticleIndex global_sigma, Float model_cutoff_dist, Float density_cutoff_dist, Float slope, bool update_model=true, bool backbone_slope=false, bool local=false, std::string name="GaussianEMRestraint%1%")
Setup the GaussianEMRestraint.
Hierarchy create_clone(Hierarchy d)
Clone the Hierarchy.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pi) const
Overload this method to specify the inputs.
Definition: predicates.h:91
virtual int get_value_index(Model *m, const ParticleIndexPair &p) const
Compute the predicate and the derivative if needed.
FittingSolutionRecords get_close_to_point(const FittingSolutionRecords &fit_sols, atom::Hierarchy mh, IMP::Particle *ap, Float dist)
prune solutions by distance to an anchor point
Particles add_bonds(Hierarchy hierarchy) const
Add bonds to the given Hierarchy using this topology, and return them.
virtual double evaluate_index(Model *m, const ParticleIndexPair &pip, DerivativeAccumulator *da) const
Evaluate score for particle pair pip in model m.
DensityMap * bayesem3d_get_density_from_particle(DensityMap *em, const IMP::ParticlesTemp &ps, double resolution, const double window_size=1.0)
void show_with_representations(Hierarchy h, std::ostream &out=std::cout)
Traverse through the tree and show atom info, including representations.
Hierarchy create_simplified_from_volume(Hierarchy h, double resolution)
A connection (bond, angle, dihedral) between some number of endpoints.
double evaluate_indexes_delta(Model *m, const ParticleIndexTriplets &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
virtual Restraints get_chain_restraints(Scoring const *scoring_manager)
double evaluate_indexes_scores(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
virtual double get_strength(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
The strength is a rough metric of how this filter restricts the subset.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
double evaluate_indexes_delta(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
virtual double get_strength(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
The strength is a rough metric of how this filter restricts the subset.
double evaluate_indexes_delta(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
Definition: predicates.h:130
double evaluate_indexes_delta(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
MultipleBinormalRestraint(Model *m, const ParticleIndexQuad &q1, const ParticleIndexQuad &q2)
Create the multiple binormal restraint.
double evaluate_indexes_scores(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
Definition: KinkPairScore.h:35
vonMisesKappaConjugateRestraint(Model *m, Particle *kappa, double c=10.0, double R0=0.0)
Create the restraint.
double evaluate_if_good_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
double get_distance(CustomXYZR a, CustomXYZR b)
Compute the distance between a pair of particles.
Definition: CustomXYZR.h:85
void add_solution(const algebra::Transformation3D &t, Float score)
Add a solution to the fitting solution set.
RadiusOfGyrationRestraint(Particles ps, int num_residues, Float scale=1.)
Constructor.
void compose_adjoint(const Rotation3D &A, const Rotation3D &B, Vector4D DC, Rotation3DAdjoint *DA, Rotation3DAdjoint *DB)
Get adjoint of inputs to compose from adjoint of output.
void add_non_rigid_member(ParticleIndexAdaptor p)
virtual double evaluate_if_good_indexes(Model *m, const ParticleIndexQuads &o, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
double evaluate_indexes_scores(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
double evaluate_indexes_delta(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
PCAAligner(IMP::em::DensityMap *map, float density_threshold)
Constructor.
Definition: PCAAligner.h:35
void add_particles(RMF::FileHandle fh, const ParticlesTemp &hs)
virtual double evaluate_index(Model *m, const ParticleIndexPair &p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
void apply_generic(const QuadModifier *m) const
Just use apply() in the base class.
void add_to_direction_derivatives(const algebra::Vector3D &v, DerivativeAccumulator &d)
Add v to the derivatives of the x,y,z coordinates of the direction.
void apply_moved(const PairModifier *sm, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const
Apply a PairModifier to the contents.
double calculate_I0(const Particles &particles, FormFactorType ff_type=HEAVY_ATOMS)
calculate Intensity at zero (= squared number of electrons)
virtual bool get_can_refine(Particle *) const
Return true if this refiner can refine that particle.
void propagate_coordinates(const ParticleIndexes &ps, double step_size)
First part of velocity Verlet (update coordinates and half-step velocity)
virtual double evaluate_index(Model *m, ParticleIndex p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
double get_volume(const Selection &s)
Get the total volume of a hierarchy, in cubic angstroms.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
virtual double evaluate_indexes(Model *m, const ParticleIndexPairs &pips, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
algebra::BoundingBoxD< 3 > get_bounding_box(const Hierarchy &h)
Get a bounding box for the Hierarchy.
void set_unknown_score(PairScore *score)
Represent an ellipsoid in 3D.
Definition: Ellipsoid3D.h:22
const BoundingBoxD< D > operator+(const BoundingBoxD< D > &o) const
Returning a bounding box containing both.
Definition: BoundingBoxD.h:125
Ints get_numbers_of_particles_outside_of_the_density(DensityMap *dmap, const Particles &ps, const IMP::algebra::Transformation3Ds &transformations, float thr=0.0)
Get numbers of particles (mult transforms) that are outside the density.
A decorator for a particle with x,y,z coordinates and a radius.
Definition: CustomXYZR.h:24
IntsList get_connected_components(em::DensityMap *dmap, float threshold, float edge_threshold)
Return connected components based on density values.
virtual double evaluate_index(Model *m, ParticleIndexPair const &pip, DerivativeAccumulator *da) const
void add_child(Hierarchy o)
Add a child and check that the types are appropriate.
void apply_generic(const PairModifier *m) const
Just use apply() in the base class.
static Provenanced setup_particle(Model *m, ParticleIndex pi, Provenance p)
Definition: provenance.h:657
static Atom setup_particle(Model *m, ParticleIndex pi, Atom other)
Definition: atom/Atom.h:242
double evaluate_indexes_delta(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
double get_coarse_cc_coefficient(const DensityMap *grid1, const DensityMap *grid2, double grid2_voxel_data_threshold, bool allow_padding=false, FloatPair norm_factors=FloatPair(0., 0.))
Calculates the cross correlation coefficient between two maps.
void add_charges(Hierarchy hierarchy) const
Add CHARMM charges to the given Hierarchy using this topology.
double evaluate_if_good_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
Restraint * create_restraint(Score *s, Container *c, std::string name=std::string())
TransformationSymmetry(algebra::Transformation3D t, Particle *px, Particle *py, Particle *pz)
Create with both reflection and translation.
Simple RRT node implementation.
Definition: RRT.h:35
virtual int get_value_index(Model *, const ParticleIndexTriplet &) const
Compute the predicate and the derivative if needed.
ParticleIndex get_root_rigid_body(RigidMember m)
Return the index of the outer-most rigid body containing the member.
Vector< char > write_particles_to_buffer(const ParticlesTemp &particles, const FloatKeys &keys)
return a binary buffer with the data
virtual SubsetFilter * get_subset_filter(const Subset &s, const Subsets &prior_subsets) const =0
algebra::ReferenceFrame3D get_initial_reference_frame(Model *m, const ParticleIndexes &pis)
Class to deal with the header of Electron Microscopy images in IMP.
Definition: ImageHeader.h:28
virtual double evaluate_indexes(Model *m, const ParticleIndexTriplets &o, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
virtual ModelObjectsTemp do_get_inputs(Model *, const ParticleIndexes &) const
Overload this method to specify the inputs.
virtual ParticleIndexes get_refined_indexes(Model *m, ParticleIndex) const
Returns the fixed set of particles, as indexes.
Definition: FixedRefiner.h:52
static Fragment setup_particle(Model *m, ParticleIndex pi)
Definition: Fragment.h:63
Rotation3D()
Create an invalid rotation.
Definition: Rotation3D.h:110
BoundingBoxD< 3 > get_bounding_box(const Geometry &)
Compute the bounding box of any geometric object.
virtual double get_strength(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
The strength is a rough metric of how this filter restricts the subset.
Particles add_dihedrals(Hierarchy hierarchy) const
Add dihedrals to the given Hierarchy using this topology, and return them.
Class for getting the distance from the map envelope.
void add_hierarchy_with_sites(RMF::FileHandle fh, atom::Hierarchy hs)
virtual void setup_for_get_value_index_in_batch(Model *) const
Definition: QuadPredicate.h:53
RigidBodyTunneler(Model *m, ParticleIndexes pis, ParticleIndex ref, double k, double move_probability=1.)
DynamicListTripletContainer(Container *scope, std::string name="ListTripletContainer %1%")
Represent a rotation in 2D space.
Definition: Rotation2D.h:36
virtual void propagate_coordinates(const ParticleIndexes &ps, double step_size)
First part of velocity Verlet (update coordinates and half-step velocity)
double evaluate_indexes_delta(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
virtual double do_evaluate(const ParticleIndexes &moved, bool force_full_score) const
Get the current energy.
Definition: MonteCarlo.h:195
void apply(const QuadModifier *sm) const
Apply a QuadModifier to the contents.
Assignments get_state_clusters(const Subset &subset, const Assignments &states, ParticleStatesTable *pst, double resolution)
Return subset of the passed states which are representative.
Calculates and stores Gaussian kernel parameters.
static Weight setup_particle(Model *m, ParticleIndex pi)
Set up an empty Weight.
Definition: Weight.h:48
void setup(ParticlesTemp &ps, const ProjectingParameters &params, Model *scoring_model, ScoreFunction *score_function, MasksManagerPtr masks=MasksManagerPtr())
RestraintsTemp get_restraints(const Subset &s, const ParticleStatesTable *pst, const DependencyGraph &dg, RestraintSet *rs)
double evaluate_indexes_scores(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
Rotation2D compose(const Rotation2D &a, const Rotation2D &b)
Compose two rotations a and b.
Definition: Rotation2D.h:108
algebra::Vector3D get_coordinates() const
Definition: rigid_bodies.h:196
ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
virtual double evaluate_if_good_index(Model *m, ParticleIndex vt, DerivativeAccumulator *da, double max) const
Compute the score and the derivative if needed, only if "good".
virtual int get_value_index_in_batch(Model *m, const ParticleIndexQuad &pi) const
static Symmetric setup_particle(Model *m, ParticleIndex pi, Float symmetric)
Definition: Symmetric.h:44
BrownianDynamicsTAMDWithSlabSupport(Model *m, std::string name="BrownianDynamicsTAMDWithSlabSupport%1%", double wave_factor=1.0)
Create the optimizer.
UniformBoundedRestraint(Particle *p, FloatKey fk, Particle *a, Particle *b)
Create the restraint.
static XYZR setup_particle(Model *m, ParticleIndex pi)
Definition: XYZR.h:48
The base class for geometry.
void get_correlation2d(const cv::Mat &A, const cv::Mat &B, cv::Mat &corr)
Correlation matrix between two 2D matrices using FFT.
static Direction setup_particle(Model *m, ParticleIndex pi, algebra::Vector3D v)
Definition: direction.h:29
IMP::core::RigidBody create_compatible_rigid_body(Hierarchy h, Hierarchy reference)
Rigidify a molecule or collection of molecules.
virtual double evaluate_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Hierarchy()
Null constructor.
virtual void apply_index(Model *m, ParticleIndex pi) const
Copies weighted derivatives to fine particles.
std::vector< double > bayesem3d_get_value(Particle *p, const algebra::Vector3D &pt, double mass_ii, const IMP::em::KernelParameters &kps)
Compute the score and derivatives for a particle at a given voxel.
A decorator for a particle which has bonds.
void after_evaluate(DerivativeAccumulator *accpt)
Do post evaluation work if needed.
int score_alignment(atom::Hierarchies mhs, float max_allowed_diff)
Return the number of matching eigen vectors by their eigen values.
virtual void do_after_evaluate(DerivativeAccumulator *da)
Do any necessary updates after the model score is calculated.
Hierarchy create_simplified_along_backbone(Hierarchy input, int num_res, bool keep_detailed=false)
virtual void apply_indexes(Model *m, const ParticleIndexes &o, unsigned int lower_bound, unsigned int upper_bound) const
double get_phi(const atom::Residue r) const
get phi angle associated with residue r
virtual void get_indexes_in_place(ParticleIndexes &output) const
Class to provide all the parameters to the segmentation function.
virtual const ParticlesTemp get_refined(Particle *) const
Refine the passed particle into a set of particles.
double fit(const RadialDistributionFunction &model_pr, const std::string &file_name="") const
fit the distributions by scaling according to maximum
int operator()(Model *m, ParticleIndex vt) const
Enable them to be use as functors.
ChainStatisticsOptimizerState(const ParticlesTemp &ps, unsigned int periodicity=1)
void resample(const Profile *model_profile, Profile *resampled_profile) const
resampling of the modeled profile is required to fit the q
XYZRs create_xyzr_particles(Model *m, unsigned int num, Float radius, Float box_side=10)
Create a set of particles with random coordinates.
EM2DRestraint(Particles ps, Particle *sigma, std::string ifile, Float px_size, Float res)
EM2D cross correlation is used to score models in a Bayesian way.
virtual ModelObjectsTemp do_get_outputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the outputs.
DensityMap * binarize(DensityMap *orig_map, float threshold, bool reverse=false)
Return a map with 0 for all voxels below the threshold and 1 for those above.
Vector< VectorD< D > > get_uniform_surface_cover(const SphereD< D > &s, unsigned int n)
Generate a set of vectors which covers a sphere uniformly.
virtual double evaluate_index(Model *m, ParticleIndex p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
virtual void apply_indexes(Model *m, const ParticleIndexes &o, unsigned int lower_bound, unsigned int upper_bound) const
double evaluate_indexes_scores(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
ImproperSingletonScore(UnaryFunction *f)
Use f to penalize deviations in angle.
A class to store an fixed array of same-typed values.
Definition: Array.h:33
void add_to_direction_derivative(int i, Float v, DerivativeAccumulator &d)
Add v to the derivative of the ith coordinate of the direction.
Definition: direction.h:46
BondGraph(Hierarchy bd)
The graph is on the leaves of the atom::Hierarchy.
CADihedralRestraint(Model *m, ParticleIndexAdaptor p1, ParticleIndexAdaptor p2, ParticleIndexAdaptor p3, ParticleIndexAdaptor p4, ParticleIndexAdaptor p5, Floats phi0, Floats phi1, Floats score)
Create the dihedral restraint.
DistanceRestraint(Model *m, UnaryFunction *score_func, ParticleIndexAdaptor a, ParticleIndexAdaptor b, std::string name="DistanceRestraint %1%")
Create the distance restraint.
ReferenceFrame3D get_local_reference_frame(const ReferenceFrame3D &v) const
virtual IMP::ModelObjectsTemp do_get_inputs(IMP::Model *m, const IMP::ParticleIndexes &pis) const
Overload this method to specify the inputs.
AtomicCrossLinkMSRestraint(IMP::Model *m, double length, ParticleIndex psi, Float slope=0.0, bool part_of_log_score=false, std::string name="AtomicCrossLinkMSRestraint%1%")
Constructor.
virtual void set_scoring_function(ScoringFunctionAdaptor sf)
Set the scoring function to use.
virtual ModelObjectsTemp do_get_outputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the outputs.
Restraint * create_bounding_volume_restraint(SingletonContainerAdaptor beads) const
virtual void set_particle_type(Particle *) const
Set the particle's type.
AmbiguousNOERestraint(Model *m, PairContainer *pc, ParticleIndexAdaptor sigma, ParticleIndexAdaptor gamma, double Iexp)
Create the restraint.
double get_sum(const DensityMap *m1)
Return the sum of all voxels.
double evaluate_indexes_delta(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
virtual double evaluate_index(Model *m, const ParticleIndexPair &pip, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
virtual int get_value_index(Model *, const ParticleIndexQuad &) const
Compute the predicate and the derivative if needed.
DerivativesToRefined(Refiner *r, FloatKeys ks=XYZ::get_xyz_keys())
Copy ks to the particles returned by r.
double evaluate_indexes_delta(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
Vector< VectorD< D > > get_vertices(const BoundingBoxD< D > &bb)
Return a list of the 2^D bounding points for the bounding box.
Definition: BoundingBoxD.h:274
Rotation3D operator/(const Rotation3D &r) const
Compute the rotation which when composed with r gives this.
Definition: Rotation3D.h:244
IMP::ParticleIndexPair make_unordered_particle_index_pair(IMP::ParticleIndex pi0, IMP::ParticleIndex pi1)
Definition: typedefs.h:45
double get_mass(ResidueType c)
Get the mass from the residue type.
virtual void apply_indexes(Model *m, const ParticleIndexQuads &o, unsigned int lower_bound, unsigned int upper_bound) const
Definition: QuadModifier.h:46
A single atom in a CHARMM topology.
GaussianEMRestraint(Model *mdl, ParticleIndexes model_ps, ParticleIndexes density_ps, ParticleIndex global_sigma, Float model_cutoff_dist, Float density_cutoff_dist, Float slope, bool update_model=true, bool backbone_slope=false, std::string name="GaussianEMRestraint%1%")
Setup the GaussianEMRestraint.
const Vector< double > & get_vacuum_form_factors(Particle *p, FormFactorType ff_type=HEAVY_ATOMS) const
for reciprocal space profile calculation
void set_assignments(const Subset &s, AssignmentContainer *lsc)
FFTFittingOutput * do_local_fitting(em::DensityMap *dmap, double density_threshold, atom::Hierarchy mol2fit, double angle_sampling_interval_rad, double max_angle_sampling_rad, double max_translation, int num_fits_to_report, bool cluster_fits, int num_angle_per_voxel, double max_clustering_translation, double max_clustering_rotation, const std::string &angles_filename="")
Locally fit a molecule inside its density.
void set(ParticleIndexes cp)
Set the contents of the container to the given ParticleIndexes.
Represent a real cell in a grid (one within the bounding box)
Definition: grid_indexes.h:162
virtual double do_step(const ParticleIndexes &sc, double dt)
Perform a single time step.
virtual bool get_is_ok(const IMP::domino::Assignment &assignment) const
double evaluate_if_good_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
double evaluate_if_good_indexes(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
double evaluate_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
virtual int get_value_index(Model *m, ParticleIndex pi) const
Compute the predicate and the derivative if needed.
Definition: predicates.h:26
SampledDensityMap * particles2binarized_density(const ParticlesTemp &ps, Float resolution, Float apix, int sig_cutoff=3, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key())
Definition: converters.h:76
WeightedProfileFitter(const Profile *exp_profile)
Constructor.
void set_particle(Particle *p, const ParticlesTemp &ps)
Set the mapping for a particular particle.
virtual double evaluate_indexes_delta(Model *m, const ParticleIndexTriplets &o, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
static LennardJones setup_particle(Model *m, ParticleIndex pi)
Definition: LennardJones.h:36
Store a persistent ordering for a subset based on the list.
Definition: Order.h:29
virtual int get_value_index(Model *m, ParticleIndex pi) const
Compute the predicate and the derivative if needed.
double get_angle(Direction a, Direction b)
Get angle between directions.
void add_to_map(DensityMap *dm, const Particles &pis)
Rasterize the particles into an existing density map.
ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
void apply_variance_filter(Image *input, Image *filtered, int kernelsize)
Definition: Image.h:266
void apply(const PairModifier *sm) const
Apply a PairModifier to the contents.
virtual double evaluate_index(Model *m, const ParticleIndexPair &p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
CompositeRestraint(Model *m, ParticleIndexesAdaptor handle_particle_indexes, double coffd, double l, bool tabprob, double plateau, std::string name="CompositeRestraint%1%")
Create the restraint.
Storage of anchors (points and edges)
virtual void apply_indexes(Model *m, const ParticleIndexes &o, unsigned int lower_bound, unsigned int upper_bound) const
void write_segments_as_mrc(em::DensityMap *dmap, const DataPointsAssignment &dpa, Float resolution, Float apix, Float threshold, const std::string &filename)
Write segments in MRC format.
virtual void do_after_evaluate(DerivativeAccumulator *)
Do any necessary updates after the model score is calculated.
void add_to_internal_rotational_derivatives(const algebra::Vector4D &local_qderiv, const algebra::Rotation3D &rot_local_to_parent, const algebra::Rotation3D &rot_parent_to_global, DerivativeAccumulator &da)
double evaluate_index(Model *m, const ParticleIndexPair &pip, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
A class storing a whole rotamer library read from a file.
void set(ParticleIndexes cp)
Set the contents of the container to the given ParticleIndexes.
double evaluate_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
MinimumQuadRestraint(QuadScore *f, QuadContainerAdaptor c, unsigned int n=1, std::string name="MinimumQuadRestraint %1%")
ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
Take Decorator, Particle or ParticleIndex.
double evaluate_if_good_indexes(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
void add_to_normal_derivatives(const algebra::Vector3D &v, DerivativeAccumulator &d)
Add v to the derivatives of the x,y,z coordinates of the normal.
virtual void setup(const ParticleIndexes &ps)
virtual double evaluate_indexes(Model *m, const ParticleIndexes &o, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
void apply_diffusion_filter(Image *input, Image *filtered, double beta, double pixelsize, int time_steps)
Definition: Image.h:279
virtual void apply_index(Model *m, ParticleIndex p) const
void add_radii(Hierarchy d, const ForceFieldParameters *ffp=get_all_atom_CHARMM_parameters(), FloatKey radius_key=FloatKey("radius"))
GaussianAnchorEMRestraint(ParticlesTemp model_ps, Floats model_sigs, Floats model_weights, ParticlesTemp density_ps, Floats density_sigs, Floats density_weights, Particle *global_sigma, Float cutoff_dist, bool rigid, bool tabexp, std::string name="GaussianAnchorEMRestraint%1%")
Constructor.
const algebra::Sphere3D get_sphere_d_geometry(CustomXYZR d)
Definition: CustomXYZR.h:90
virtual const ParticlesTemp get_refined(Particle *p) const
Returns the fixed set of particles.
A decorator for a particle that represents a direction in 3D.
Definition: direction.h:23
virtual double evaluate_index(Model *m, const ParticleIndexPair &p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
void write(const char *filename, const float *data, const DensityHeader &header)
Writes a density file in EM format with the header information.
double get_dihedral(XYZ a, XYZ b, XYZ c, XYZ d)
Compute the dihedral angle (in radians) between the four particles.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
static StructureProvenance setup_particle(Model *m, ParticleIndex pi, std::string filename, std::string chain_id, int residue_offset)
Definition: provenance.h:157
double evaluate_indexes_delta(Model *m, const ParticleIndexQuads &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
virtual void do_after_evaluate(DerivativeAccumulator *)
Do any necessary updates after the model score is calculated.
Definition: Surface.h:217
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
bool is_penetrating(const IMP::algebra::Vector3Ds &points, float penetration_thr) const
IMP::Restraint * create_z_bias_restraint(SingletonContainerAdaptor ps, double k) const
em::DensityMap * remove_background(em::DensityMap *dmap, float threshold, float edge_threshold)
Returns a map containing all density without the background.
A geometric relationship between four atoms.
Represent a unit simplex embedded in D-dimensional real space.
Definition: UnitSimplexD.h:69
virtual bool get_can_refine(Particle *) const
Return true if this refiner can refine that particle.
TripletContainerSet(Model *m, std::string name="TripletContainerSet %1%")
Construct an empty set.
void set_pair_score(PairScore *ps, Int atype, Int btype)
Set the PairScore to delegate to for a given pair of particle types.
DensityMap * mask_and_norm(em::DensityMap *dmap, em::DensityMap *mask)
Return a masked density, and normalize the output map within the mask region.
void set_symmetric_difference(const Selection &s)
Select elements that are in this Selection or the passed one but not both.
void copy_FGs_coordinates(SimulationData const *src_sd, SimulationData *trg_sd)
copy coordinates of src_sd to trg_sd for FG repeats only
A typed index.
Definition: Index.h:25
An index in an infinite grid on space.
Definition: grid_indexes.h:30
double evaluate_index(Model *m, const ParticleIndexPair &pip, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
void set_transformation(algebra::Transformation3D t)
Set a new transformation to use.
Definition: core/symmetry.h:99
Virtual class for reader/writers of images.
void set(TextOutput to)
Assign new properties to the class.
Definition: file.h:148
double get_maximum_length(const BoundingBoxD< D > &a)
Return the maximum axis aligned extent.
Definition: BoundingBoxD.h:262
void set_previous(Provenance p)
Set the previous provenance.
Definition: provenance.h:64
double evaluate_indexes_scores(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
virtual void setup_for_get_value_index_in_batch(Model *m) const
double get_volume(const Cone3D &g)
Definition: Cone3D.h:64
DummyRestraint(IMP::Particle *p, IMP::Particle *q)
A container which contains all consecutive particle pairs from an input list.
IntPairs get_edges(const BoundingBoxD< 3 > &)
Return the edges of the box as indices into the vertices list.
Definition: BoundingBoxD.h:307
virtual int get_value_index(Model *, const ParticleIndexQuad &vt) const
Compute the predicate and the derivative if needed.
A voxel grid in d-dimensional space.
Definition: GridD.h:79
Restraint(Model *m, std::string name)
stores the anchors sampling space for each protein
CloseBipartitePairContainer(SingletonContainerAdaptor a, SingletonContainerAdaptor b, double distance, double slack=1, std::string name="CloseBipartitePairContainer%1%")
Get the individual particles from the passed SingletonContainer.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
Provenance create_clone(Provenance p)
Clone provenance (including previous provenance)
void apply(CHARMMResidueTopology *res) const
Apply the patch to the residue, modifying its topology accordingly.
void add_term(const BinormalTerm &term)
Add a single BinormalTerm to the restraint.
void do_project_particles(const ParticlesTemp &ps, cv::Mat &m2, const algebra::Rotation3D &R, const algebra::Vector3D &translation, const ProjectingOptions &options, MasksManagerPtr masks)
Projects a set of particles. This is the core function that others call.
Vector< double > get_solvent_accessibility(const core::XYZRs &points, double probe_radius=1.8, double density=5.0)
estimate surface accessibility of each atom.
double evaluate_indexes(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
double evaluate_indexes(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
double evaluate_indexes_delta(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
double evaluate_if_good_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
ProteinsAnchorsSamplingSpace get_part_of_sampling_space(const ProteinsAnchorsSamplingSpace &prots_ss, const Strings &prot_names)
Get the sampling space of few of the proteins.
Vector3D operator*(const Vector3D &v) const
Rotate a vector around the origin.
Definition: Rotation3D.h:209
BoundingBoxD< D > get_union(BoundingBoxD< D > a, const BoundingBoxD< D > &b)
Return the union bounding box.
Definition: BoundingBoxD.h:254
virtual void do_add_score_and_derivatives_moved(ScoreAccumulator sa, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis, const ScoreStatesTemp &ss)
Score when only some particles have moved.
bool same_voxel_size(const DensityMap *other) const
Checks if two maps have the same voxel size.
void write_to_ints(const String &filename, em::ImageHeader &header, const cv::Mat &data) const
Writes an EM image in JPG format.
FittingSolutions compute_fitting_scores(const ParticlesTemp &ps, DensityMap *em_map, const algebra::Transformation3Ds &transformations, bool fast_version=false, bool local_score=false, const FloatKey &wei_key=atom::Mass::get_mass_key())
Compute fitting scores for a given set of rigid transformations.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
Base class for MultiStateModel scoring classes.
Display a Surface particle as a cylindrical disk.
Definition: Surface.h:169
Track creation of a system fragment from sampling.
Definition: provenance.h:173
ParticlesTemp create_rigid_bodies(Model *m, unsigned int n, bool no_members=false)
static Cover setup_particle(Model *m, ParticleIndex pi, ParticleIndexesAdaptor members)
Definition: CoverRefined.h:72
Float get_radius(Atom atom) const
get radius
void get_autocorrelation2d(const cv::Mat &m, cv::Mat &corr)
Computes the autocorrelation matrix.
double get_reciprocal_product(const Line3D &l) const
Get reciprocal (or virtual) product, the moment of either line about the other.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
A simple list of fitting solutions.
Definition: rigid_fitting.h:33
Atoms get_omega_dihedral_atoms(Residue rd)
Return the atoms comprising the omega dihedral.
ParticleIndexQuads get_chi_dihedral_particle_indexes(Residue rd)
BrownianDynamicsTAMD(Model *m, std::string name="BrownianDynamicsTAMD%1%", double wave_factor=1.0)
Create the optimizer.
DensityMap * get_threshold_map(const DensityMap *orig_map, float threshold)
Return a map with 0 for all voxels below the threshold.
LogWrapper(Model *m, double weight, const std::string &name="LogWrapper %1%")
Create an empty set that is registered with the model.
double do_evaluate_index_harmonic(Model *m, const ParticleIndexPair &pp, DerivativeAccumulator *da, const algebra::Vector3D &delta, double delta_length, double x0, double k)
EnvelopeFitRestraint(Particles particles, DensityMap *em_map, double density_threshold, double penetration_threshold)
Constructor.
void add(const DensityMap *other)
Sums two grids; the result is kept in the map.
virtual void add_to_particle_derivative(unsigned particle_no, double value, DerivativeAccumulator &accum) const =0
update derivatives of particles
void add_representation(ParticleIndexAdaptor rep, RepresentationType type=BALLS, double resolution=-1)
Add the representation for the given resolution.
virtual IntPairs get_close_pairs(const algebra::BoundingBox3Ds &) const
double evaluate_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
void write_pdb(const Selection &mhd, TextOutput out, unsigned int model=1)
DensityMap * get_segment_by_masking(DensityMap *map_to_segment, DensityMap *mask, float mas_threshold)
Get a segment of the map covered by another map.
void add(const ParticleIndexTriplet &vt)
Add a single const ParticleIndexTriplet& to the container.
double get_squared_distance(const VectorD< D > &v1, const VectorD< D > &v2)
Compute the squared distance between two vectors.
Definition: VectorD.h:201
void do_main_loop(SimulationData *sd, const RestraintsTemp &init_restraints)
Transformation3D get_transformation_from_first_triangle_to_second(Triangle3D first_tri, Triangle3D second_tri)
Return a transformation between two triangles.
double evaluate_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
double evaluate_index(Model *m, const ParticleIndexPair &pip, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
Assignment get_nearest_assignment(const Subset &s, const algebra::VectorKD &embedding, ParticleStatesTable *pst)
Return the nearest assignment from an embedding.
double evaluate_indexes_scores(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
double evaluate_indexes_scores(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
void do_extend_borders(cv::Mat &orig, cv::Mat &dst, unsigned int pix)
double evaluate_if_good_indexes(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
double get_dummy_form_factor(Particle *p, FormFactorType ff_type=HEAVY_ATOMS) const
f(0) for solvent
virtual void setup_for_get_value_index_in_batch(Model *) const
double evaluate_indexes_delta(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
void calculate_profile_constant_form_factor(const Particles &particles, double form_factor=1.0)
calculate profile for any type of Particles that have coordinates
void setup_as_approximation(Particle *h, const ParticlesTemp &other)
virtual double do_step(const ParticleIndexes &sc, double dt)
Perform a single time step.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
static State setup_particle(Model *m, ParticleIndex pi, unsigned int index)
Definition: State.h:39
void validate_partitional_clustering(PartitionalClustering *pc, unsigned int n)
Check that the clustering is a valid clustering of n elements.
Parameters given as options to the get_projections() functions.
Definition: project.h:59
void destroy(Hierarchy d)
Delete the Hierarchy.
Base class for writing geometry to a file.
Definition: Writer.h:28
FretRestraint(Particles pd, Particles pa, Particle *kda, Particle *Ida, Particle *R0, Particle *sigma0, Particle *Pbl, double fexp, double m_d=1.0, double m_a=1.0)
Create the restraint.
bool get_are_close_and_filtered(Particle *a, Particle *b) const
internal::PredicateEquals< Pred, false > make_predicate_not_equal(const Pred *p, Model *m, int value)
Definition: functor.h:28
ParticlesTemp get_particles(Model *m, const ParticleIndexes &ps)
Get the particles from a list of indexes.
PbcBoxedRigidBodyMover(core::RigidBody d, Particles ps, Float max_translation, Float max_rotation, algebra::Vector3Ds centers, algebra::Transformation3Ds transformations, Particle *px, Particle *py, Particle *pz)
virtual IMP::ModelObjectsTemp do_get_inputs(IMP::Model *m, const IMP::ParticleIndexes &pis) const
Overload this method to specify the inputs.
void set_chain_type(ChainType t)
Set the chain type, using IMP::atom::ChainType.
Definition: Chain.h:137
ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
double get_surface_area(const Ellipsoid3D &g)
Definition: Ellipsoid3D.h:46
void add_member(ParticleIndexAdaptor p)
void add_upstream_joint(Joint *j)
Adds a joint at the front of the list (closest to the parent rigid body)
PCAFitRestraint(ParticlesTemp ps, DensityMap *em_map, float threshold, float max_pca_size_diff, float max_angle_diff, float max_centroid_diff, FloatKey weight_key=atom::Mass::get_mass_key())
Constructor.
Represent a cylinder in 3D.
Definition: Cylinder3D.h:26
virtual void do_after_evaluate(DerivativeAccumulator *da)
Do any necessary updates after the model score is calculated.
FGChain(IMP::Particle *root, double backbone_k=0.0, double rest_length_factor=1.0, std::string name="chain %1%")
Definition: FGChain.h:83
void set_union(const Selection &s)
Select elements that are in either this Selection or the passed one.
ConfigurationSetXYZEmbedding(ConfigurationSet *cs, SingletonContainerAdaptor pi, bool align=false)
double evaluate_indexes_scores(Model *m, const ParticleIndexTriplets &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
double do_evaluate(const ParticleIndexes &, bool) const
Get the current energy.
int operator()(Model *m, const ParticleIndexPair &vt) const
Enable them to be use as functors.
Definition: PairPredicate.h:65
double evaluate_indexes_scores(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
Scoring(SimulationData *owner_sd, const ::npctransport_proto::Assignment &data)
BoundingBoxD< 3 > get_bounding_box(const Cylinder3D &g)
Definition: Cylinder3D.h:78
double get_distance_if_smaller_than(const Subset &s, const Assignment &a, const Assignment &b, ParticleStatesTable *pst, const statistics::Metrics &metrics, double max)
void add_to_torque(const algebra::Vector3D &torque_local, DerivativeAccumulator &da)
double get_surface_area(const Torus3D &g)
Definition: Torus3D.h:61
void apply_mean_outside_mask(Image *img, double radius)
void add_to_normal_derivative(int i, Float v, DerivativeAccumulator &d)
Add v to the derivative of the ith coordinate of the normal.
Definition: Surface.h:68
double evaluate_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
MinimumSingletonRestraint(SingletonScore *f, SingletonContainerAdaptor c, unsigned int n=1, std::string name="MinimumSingletonRestraint %1%")
virtual double evaluate_index(Model *m, ParticleIndex p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
DensityFillingRestraint(Particles ps, DensityMap *em_map, Float threshold)
Constructor.
void apply_default_patches(const CHARMMParameters *ff)
Apply patches to the first and last residue in the segment.
SampledDensityMap * particles2density(const ParticlesTemp &ps, Float resolution, Float apix, int sig_cutoff=3, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key())
Resample a set of particles into a density grid.
multifit::SettingsData * get_partial_assembly_setting_data(multifit::SettingsData *prots_sd, const Strings &prot_names)
Get the assembly data for a few of the proteins.
double evaluate_indexes_delta(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
double evaluate_indexes_delta(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
ExtendedGridIndexD< D > get_extended_index(const VectorD< D > &o) const
Return the index that would contain the voxel if the grid extended there.
virtual int get_value_index(Model *m, const ParticleIndexPair &pi) const
Compute the predicate and the derivative if needed.
Definition: predicates.h:67
ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
Vector3D get_reflected(const Plane3D &pln, const Vector3D &p)
Return the point reflected about the plane.
Definition: Plane3D.h:68
Track the pairs of particles passed.
Definition: LogPairScore.h:21
double evaluate_indexes_scores(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
void add_to_derivatives(const Floats &x, DerivativeAccumulator &accum) const
update derivatives of particles
Base class for all samplers.
Definition: Sampler.h:31
double get_area(const SpherePatch3D &g)
Definition: SpherePatch3D.h:48
Add scale parameter to particle.
Definition: Scale.h:24
static SlabWithPore setup_particle(Model *m, ParticleIndex pi, double thickness, double pore_radius)
Definition: SlabWithPore.h:70
virtual double evaluate_index(Model *m, const ParticleIndexPair &p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
void destroy_bond(Bond b)
Destroy the bond connecting two particles.
BallMover(Model *m, ParticleIndex pi, const FloatKeys &vars, double radius)
Move specified variables of particle pi within a ball of specified radius.
double evaluate_if_good_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
double evaluate_indexes_scores(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
MarginalNOERestraint(Model *m)
Create the restraint.
Represent a subset of the particles being optimized.
Definition: Subset.h:33
double compute_score(const ProfilesTemp &profiles, Vector< double > &weights, bool use_offset=false, bool NNLS=true) const
compute a weighted score that minimizes chi
virtual void apply_indexes(Model *m, const ParticleIndexes &o, unsigned int lower_bound, unsigned int upper_bound) const
void get_random_numbers_uniform(Vector< RealType > &v, unsigned int n)
Fill the float array with random uniformly distributed values.
Definition: random_utils.h:86
The type of an atom.
double get_coarse_cc_score(DensityMap *data, SampledDensityMap *model_map, double scalefactor, bool recalc_rms=true, bool resample=true, FloatPair norm_factors=FloatPair(0., 0.))
Calculates the value of the EM fitting term.
algebra::Vector3D get_centroid(const XYZs &ps)
Get the centroid.
static Surface setup_particle(Model *m, ParticleIndex pi)
Definition: Surface.h:45
HierarchyTree get_hierarchy_tree(Hierarchy h)
Get a graph for the passed Hierarchy.
double evaluate_indexes_scores(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
void add_restrained_anchor_bead(IMP::Particle *p)
virtual void setup_for_get_value_index_in_batch(Model *m) const
void add_particle(RMF::FileHandle fh, Particle *hs)
void set_torus_3d_geometry(Torus3D &g, const Torus3D &v)
Definition: Torus3D.h:61
double evaluate_index(Model *m, const ParticleIndexPair &pip, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
A score on the distance between the surfaces of two spheres.
AngleRestraint(Model *m, UnaryFunction *score_func, ParticleIndexAdaptor p1, ParticleIndexAdaptor p2, ParticleIndexAdaptor p3)
Create the angle restraint.
Atoms get_charmm_untyped_atoms(Hierarchy hierarchy)
Get all atoms in the Hierarchy that do not have CHARMM types.
Statistics and order parameters about the simulations.
virtual void do_after_evaluate(DerivativeAccumulator *)
Do any necessary updates after the model score is calculated.
Definition: Surface.h:266
void read_from_floats(const String &filename, em::ImageHeader &header, cv::Mat &data) const
virtual bool get_is_ok(const Assignment &state) const =0
void set_score(int predicate_value, SingletonScore *score)
Return all close unordered pairs of particles taken from the SingletonContainer.
IncrementalScoringFunction(Model *m, const ParticleIndexes &to_move, const RestraintsTemp &rs, double weight=1.0, double max=NO_MAX, std::string name="IncrementalScoringFunction%1%")
Constructor.
static Residue setup_particle(Model *m, ParticleIndex pi, ResidueType t, int index, int insertion_code)
Definition: Residue.h:160
static Representation setup_particle(Model *m, ParticleIndex pi)
virtual const ParticlesTemp get_refined(Particle *) const
Refine the passed particle into a set of particles.
const Plane3D & get_plane_3d_geometry(const Plane3D &g)
Definition: Plane3D.h:78
void set(Object *o, LogLevel l)
Assign new properties to the class.
Definition: SetLogState.h:43
OptimizerStates add_optimizer_states(Optimizer *o=nullptr)
add all statistics-related optimizer states to o
virtual IMP::ModelObjectsTemp do_get_outputs(IMP::Model *m, const IMP::ParticleIndexes &pis) const
Overload this method to specify the outputs.
LognormalRestraint(Particle *x, Particle *mu, Particle *sigma)
Gaussian restraint.
Restraints do_create_current_decomposition(Model *m, ParticleIndex vt) const
Override this to return your own decomposition.
std::pair< double, algebra::Vector3Ds > bayesem3d_get_score_and_derivative(DensityMap *em, const IMP::ParticlesTemp &ps, double resolution, double sigma, const double window_size=1.0)
The function returns the negative log of the Normal distributed difference between a normalized EM de...
Hierarchy create_fragment(const Hierarchies &ps)
Create a fragment containing the specified nodes.
double evaluate_indexes_delta(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
char get_one_letter_code(ResidueType c)
Get the 1-letter amino acid code from the residue type.
void add_restraints(const RestraintsAdaptor &rs)
A single binormal term in a MultipleBinormalRestraint.
PartitionalClustering * create_gromos_clustering(Metric *d, double cutoff)
virtual int get_value_index(Model *m, const ParticleIndexQuad &pi) const
Compute the predicate and the derivative if needed.
void add_hierarchies(RMF::FileHandle fh, const atom::Hierarchies &hs)
ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
virtual double evaluate_indexes(Model *m, const ParticleIndexQuads &o, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
GenericHierarchies get_leaves(Hierarchy mhd)
Get all the leaves of the bit of hierarchy.
virtual double evaluate_indexes_delta(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
void apply_generic(const SingletonModifier *m) const
Just use apply() in the base class.
double score(const IMP::algebra::Vector3Ds &points) const
static Domain setup_particle(Model *m, ParticleIndex pi, Domain other)
Definition: Domain.h:61
virtual void apply_indexes(Model *m, const ParticleIndexes &o, unsigned int lower_bound, unsigned int upper_bound) const
Definition: CoverRefined.h:60
virtual void do_after_evaluate(DerivativeAccumulator *accpt)=0
Do any necessary updates after the model score is calculated.
double operator()(unsigned int id1, unsigned int id2, const ClusterSet &cluster_set, const FloatsList &distances)
Distance between the clusters.
double evaluate_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
double evaluate_if_good_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
virtual double evaluate_index(IMP::Model *m, const IMP::ParticleIndexPair &p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
DynamicListTripletContainer * add_predicate(TripletPredicate *predicate, int value)
void load_pb_conformation(const ::npctransport_proto::Conformation &conformation, IMP::SingletonContainerAdaptor beads, boost::unordered_map< core::ParticleType, algebra::Sphere3Ds > &sites)
virtual ModelObjectsTemp do_get_outputs(Model *m, const ParticleIndexes &pis) const =0
Overload this method to specify the outputs.
Track creation of a system fragment by combination.
Definition: provenance.h:280
Color get_interpolated_rgb(const Color &a, const Color &b, double f)
Return a color interpolated between a and b in RGB space.
Definition: Color.h:143
StatisticalPairScore(IntKey k, double threshold, TextInput data_file)
ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
double get_rotation_error(const RegistrationResult &rr1, const RegistrationResult &rr2)
Atom get_atom(Residue rd, AtomType at)
Return a particle atom from the residue.
double evaluate_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
virtual int get_value_index_in_batch(Model *m, ParticleIndex vt) const
Represent a triangle in 3D.
Definition: Triangle3D.h:23
void copy_hierarchy_reference_frame_recursive(Particle *src_p, Particle *trg_p)
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
static XYZ setup_particle(Model *m, ParticleIndex pi)
Definition: XYZ.h:51
double evaluate_indexes(Model *m, const ParticleIndexQuads &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
A particle with linear (XYZ) velocity.
void add(ParticleIndex vt)
Add a single ParticleIndex to the container.
QuadRestraint(Model *m, QuadScore *ss, const ParticleIndexQuad &vt, std::string name="QuadRestraint %1%")
Create the restraint.
Definition: QuadRestraint.h:41
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
double get_score(Image *image, Image *projection) const
Given an image and a projection, returns the appropriate score.
Definition: scores2D.h:60
virtual void setup_for_get_value_index_in_batch(Model *) const
Definition: PairPredicate.h:53
double evaluate_if_good_indexes(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
double evaluate_indexes_scores(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
Restraint * create_excluded_volume(Model *m, const ParticleIndexes &ps, double k, std::string name)
double evaluate_if_good_indexes(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
virtual double evaluate_if_good_indexes(Model *m, const ParticleIndexes &o, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
Eigen::MatrixXd get_jacobian_of_composed_wrt_first(const Rotation3D &q, const Rotation3D &p, bool wrt_unnorm=false)
Get gradient of quaternion product with respect to first quaternion.
A more IMP-like version of the std::vector.
Definition: Vector.h:40
double evaluate_indexes_scores(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
double evaluate_if_good_indexes(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
virtual Restraints do_create_current_decomposition(Model *m, ParticleIndex vt) const
Override this to return your own decomposition.
virtual double evaluate_index(Model *m, ParticleIndex p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
ParticlePairsTemp get_possible_interactions(const ParticlesTemp &ps, double max_distance, ParticleStatesTable *pst)
void add_in_plane_transformation(algebra::Transformation2D t)
GenericHierarchies get_all_descendants(Hierarchy mhd)
Get all the particles in the subtree.
virtual int get_value_index(Model *m, const ParticleIndexTriplet &vt) const =0
Compute the predicate and the derivative if needed.
Atom get_atom(const CHARMMResidueTopology *current_residue, const CHARMMResidueTopology *previous_residue, const CHARMMResidueTopology *next_residue, const std::map< const CHARMMResidueTopology *, Hierarchy > &resmap) const
Map the endpoint to an Atom particle.
CompositeJoint(IMP::core::RigidBody parent, IMP::core::RigidBody child, Joints joints=Joints())
Constructor.
The end of a bond, angle, dihedral, improper, or internal coordinate.
void add_contribution(const ParticleIndexPair &ppi, const ParticleIndexPair &sigmas)
Add a contribution to this xlink.
void pull_back_members_adjoints(DerivativeAccumulator &da)
Pull back global adjoints from members.
double evaluate_indexes_scores(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
display::Geometries create_blame_geometries(const RestraintsTemp &rs, const ParticlesTemp &ps, double max=NO_MAX, std::string name=std::string())
double evaluate_indexes_delta(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
double evaluate_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
double evaluate_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
GaussianProcessInterpolation(FloatsList x, Floats sample_mean, Floats sample_std, unsigned n_obs, UnivariateFunction *mean_function, BivariateFunction *covariance_function, Particle *sigma, double sparse_cutoff=1e-7)
virtual ParticleIndexPairs get_close_pairs(Model *m, const ParticleIndexes &pc) const =0
return all close pairs among pc in model m
ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
virtual int get_value_index(Model *m, const ParticleIndexPair &pi) const
Compute the predicate and the derivative if needed.
Floats get_histogram(Image *img, int bins)
Definition: Image.h:255
core::MonteCarloMover * create_serial_mover(Model *m, const ParticleIndexes &pis)
static Uncertainty setup_particle(Model *m, ParticleIndex pi, Float uncertainty)
Definition: Uncertainty.h:45
em::FittingSolutions pca_based_rigid_fitting(core::RigidBody rb, Refiner *rb_refiner, em::DensityMap *em_map, Float threshold, FloatKey wei_key=atom::Mass::get_mass_key(), algebra::PrincipalComponentAnalysis dens_pca_input=algebra::PrincipalComponentAnalysis())
Compute fitting scores for a given set of rigid transformations.
double get_angle(const Line3D &a, const Line3D &b)
Get angle in radians between two lines around their closest points.
void calculate_profile_partial(const Particles &particles, const Vector< double > &surface=Vector< double >(), FormFactorType ff_type=HEAVY_ATOMS)
compute profile for fitting with hydration layer and excluded volume
InteractionGraph get_interaction_graph(ScoringFunctionAdaptor rs, const ParticleStatesTable *pst)
Transformation3D()
Default construct (makes an invalid transformation)
virtual void setup_for_get_value_index_in_batch(Model *m) const
virtual void apply_index(Model *m, const ParticleIndexPair &v) const =0
static SlabWithCylindricalPore setup_particle(Model *m, ParticleIndex pi, double thickness, double radius)
void do_subtract_images(Image *first, Image *second, Image *result)
The topology of a single residue in a model.
const BoundingBoxD< D > & operator+=(const BoundingBoxD< D > &o)
Extend the current bounding box to include the other.
Definition: BoundingBoxD.h:98
A reference frame in 3D.
ClosePairContainer(SingletonContainerAdaptor c, double distance_cutoff, double slack=1, std::string name="ClosePairContainer%1%")
Get the individual particles from the passed SingletonContainer.
CHARMM force field parameters.
BrownianDynamics(Model *m, std::string name="BrownianDynamics%1%", double wave_factor=1.0, unsigned int random_pool_size=10000)
Create the optimizer.
double evaluate_indexes_scores(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
static Centroid setup_particle(Model *m, ParticleIndex pi, ParticleIndexesAdaptor members)
virtual int get_value_index(Model *, ParticleIndex) const
Compute the predicate and the derivative if needed.
double evaluate_indexes(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
double evaluate_index(Model *m, const ParticleIndexPair &pip, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
void do_combined_fill_holes_and_threshold(cv::Mat &m, cv::Mat &result, double n_stddevs, double threshold=0.0)
Combines the fill holes and thresholding operations together with normalize.
virtual double do_step(const ParticleIndexes &sc, double dt)=0
Perform a single time step.
Object used to hold a set of restraints.
Definition: RestraintSet.h:37
A base class for modifiers of ParticlePairsTemp.
Definition: PairModifier.h:32
algebra::Transformation3Ds get_symm_axis_alignments_from_model_to_density(atom::Hierarchies mhs, bool sample_translation, bool fine_rotation_sampling=true) const
void mark_rotatable_angles(const std::vector< atom::Atoms > &dihedral_angles)
void do_after_evaluate(DerivativeAccumulator *da)
Do any necessary updates after the model score is calculated.
void add_to_particle_derivative(unsigned particle_no, double value, DerivativeAccumulator &accum) const
update derivatives of particles
ISDRestraint(Model *m, std::string name)
Create the restraint.
void show_rigid_body_hierarchy(RigidBody rb, TextOutput out=TextOutput(std::cout))
virtual double evaluate_index(Model *m, const ParticleIndexPair &p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
algebra::GridD< 3, algebra::DenseGridStorageD< 3, float >, float > get_grid(DensityMap *in_map)
Return a dense grid containing the voxels of the passed density map.
virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) const
Base class for sampling certain combinations of degrees of freedom.
Definition: DOFsSampler.h:17
void set_residue_type(ResidueType type)
Select only residues with the passed type.
double evaluate_indexes_scores(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
void save_pb_conformation(IMP::SingletonContainerAdaptor beads, const boost::unordered_map< core::ParticleType, algebra::Sphere3Ds > &sites,::npctransport_proto::Conformation *conformation)
double evaluate_indexes(Model *m, const ParticleIndexTriplets &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
Take Decorator, Particle or ParticleIndex.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
TripletRestraint(Model *m, TripletScore *ss, const ParticleIndexTriplet &vt, std::string name="TripletRestraint %1%")
Create the restraint.
static Molecule setup_particle(Model *m, ParticleIndex pi)
Definition: Molecule.h:37
Restraint * create_excluded_volume_restraint(const Hierarchies &hs, double resolution=-1)
Bond create_custom_bond(Bonded a, Bonded b, Float length, Float stiffness=-1)
Connect the two wrapped particles by a custom bond.
ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
void reset_root(IMP::Particle *new_root)
rebuild tree (same topology but change directionality)
Soap(double threshold=std::numeric_limits< double >::max())
Set up using the default SOAP-PP potential file.
Definition: Soap.h:47
SphereGeometry * create_geometry(const algebra::Sphere3D &t, std::string name="algebra::Sphere3D"+"%1""%")
Class for storing model, its restraints, constraints, and particles.
Definition: Model.h:73
void write_pdb_of_c_alphas(const Selection &mhd, TextOutput out, unsigned int model=1)
Write a hierarchy to a PDB as C_alpha atoms.
ClosePairsPairScore(PairScore *f, Refiner *r, Float max_distance)
Constructor.
double evaluate_indexes_delta(Model *m, const ParticleIndexTriplets &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
Segment3D get_shortest_segment(const Segment3D &s, const Vector3D &p)
virtual double evaluate_indexes_delta(Model *m, const ParticleIndexPairs &o, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
void bayesem3d_get_normalized_intensities(DensityMap *em, const IMP::ParticlesTemp &ps, double resolution)
algebra::Vector2Ds do_project_vectors(const algebra::Vector3Ds &ps, const algebra::Rotation3D &R, const algebra::Vector3D &translation)
Project the points contained in Vector3Ds to gen vectors in 2D.
double evaluate_indexes_scores(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
virtual double evaluate_index(Model *m, ParticleIndex vt, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
Vector3Ds read_pts(TextInput input)
Read a set of 3D vectors from a file.
double evaluate_if_good_indexes(Model *m, const ParticleIndexPairs &pips, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
virtual void setup(const ParticleIndexes &)
Definition: Simulator.h:178
static SlabWithToroidalPore setup_particle(Model *m, ParticleIndex pi, double thickness, double major_radius)
void set_unknown_score(SingletonScore *score)
virtual double evaluate_indexes(Model *m, const ParticleIndexPairs &pips, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
FloatPair bayesem3d_get_em_density_squared(DensityMap *em, long number_of_voxels)
Compute the sum of the density and the sum of the squares of the density.
virtual double evaluate_indexes_scores(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
void apply_generic_moved(const SingletonModifier *m, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const
Just use apply_moved() in the base class.
double evaluate_index(algebra::Sphere3D const &s0, algebra::Sphere3D const &s1, algebra::Sphere3D &ds0, algebra::Sphere3D &ds1, DerivativeAccumulator *da) const
Hierarchies read_multimodel_mmcif(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector())
Read all models from the mmCIF file.
virtual ModelObjectsTemp do_get_outputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the outputs.
virtual double evaluate_index(Model *m, const ParticleIndexPair &p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
double evaluate_indexes_delta(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
double evaluate_indexes_scores(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
Definition: predicates.h:130
Transformation2D()
Default constructor. An invalid transformation is built.
virtual int get_value_index(Model *, ParticleIndex) const
Compute the predicate and the derivative if needed.
virtual double evaluate_index(Model *m, const ParticleIndexPair &vt, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
RigidBodyUmbrella(Model *m, ParticleIndex pi, ParticleIndex ref, Floats x0, double alpha, double k, std::string name="RigidBodyUmbrella %1%")
Create the restraint by specifying directly.
void ImageHeader_to_DensityHeader(const ImageHeader &h, DensityHeader &header)
void set_reference_frame_safe(IMP::core::RigidBody rb, IMP::algebra::ReferenceFrame3D r)
unsigned int get_number_of_masks(const core::RigidBody &rb) const
Return the number of precomputed masks associated with the rigid body.
Class for handling density maps.
Definition: DensityMap.h:93
double evaluate_indexes_scores(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
double evaluate_index(Model *m, const ParticleIndexPair &pip, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
double evaluate_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
double get_vacuum_form_factor(Particle *p, FormFactorType ff_type=HEAVY_ATOMS) const
f(0) in vacuum
CompositeRestraint(Model *m, PairScore *ps)
Create with the given PairScore.
Store a subset of a subset or assignment.
Definition: Slice.h:27
ChildrenRefiner(HierarchyTraits tr)
Create a refiner for a particular type of hierarchy.
IMP::algebra::BoundingBoxD< 3 > calculate_particles_bounding_box(const Particles &ps)
Calculate the parameters of the particles bounding box.
BoundingBoxD< D > get_intersection(const BoundingBoxD< D > &a, const BoundingBoxD< D > &b)
Return the intersecting bounding box.
Definition: BoundingBoxD.h:223
double evaluate_if_good_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
Definition: KinkPairScore.h:35
virtual double evaluate_index(Model *m, ParticleIndex p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
EnvelopePenetrationRestraint(Particles ps, DensityMap *em_map, Float threshold)
Constructor.
MergeTree get_merge_tree(ScoringFunctionAdaptor input, const ParticleStatesTable *pst)
double evaluate_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
Transformation2D get_rotation_about_point(const Vector2D &point, const Rotation2D &rotation)
Generate a Transformation2D object from a rotation around a point.
Base class for a simple primitive-like type.
Definition: Value.h:23
Represent an eigen analysis of some data.
A Gaussian distribution in 3D.
Definition: Gaussian3D.h:24
virtual void do_after_evaluate(DerivativeAccumulator *da)
Do any necessary updates after the model score is calculated.
virtual double evaluate_index(IMP::Model *m, const IMP::ParticleIndexPair &p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
void add_restraint(RMF::FileHandle fh, Restraint *hs)
virtual double evaluate_index(Model *m, const ParticleIndexPair &pip, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
void read(String filename, const ImageReaderWriter *reader)
Definition: Image.h:125
ModelObjectsTemp get_inputs(Model *m, const ParticleIndexes &pis) const
Get the ModelObjects read when the given list of particles is used.
void setup(ScoreFunction *score_function, const Em2DRestraintParameters &params)
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
const VectorD< C::DIMENSION > & get_vector_geometry(const C &g)
Definition: VectorD.h:444
Class for sampling a density map from particles.
DynamicListPairContainer * add_predicate(PairPredicate *predicate, int value)
double evaluate_if_good_indexes(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
PairRestraint(Model *m, PairScore *ss, const ParticleIndexPair &vt, std::string name="PairRestraint %1%")
Create the restraint.
Definition: PairRestraint.h:41
float cn_symm_score(atom::Hierarchies mhs, const algebra::Vector3D &center, const algebra::Vector3D &direction, int symm_deg)
scores an input vector as a symmetry axis
The class represents a molecule as shells of distance from the surface.
double evaluate_if_good_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
ReferenceFrame3D get_global_reference_frame(const ReferenceFrame3D &v) const
virtual double evaluate_index(Model *m, const ParticleIndexPair &p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
double evaluate_if_good_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
Abstract class for scoring object(s) of type ParticleIndexQuad.
Definition: QuadScore.h:42
Bonds get_internal_bonds(Hierarchy mhd)
Get the bonds internal to this tree.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
Base class for objects in a Model that depend on other objects.
Definition: ModelObject.h:26
Particles add_impropers(Hierarchy hierarchy) const
Add impropers to the given Hierarchy using this topology, and return them.
static Hierarchy setup_particle(Model *m, ParticleIndex pi, ParticleIndexesAdaptor children=ParticleIndexesAdaptor())
Create a Hierarchy of level t by adding the needed attributes.
double get_volume(const BoundingBoxD< D > &bb)
See BoundingBoxD.
Definition: BoundingBoxD.h:163
FitRestraintBayesEM3D(ParticlesTemp ps, DensityMap *em_map, FloatKey weight_key=atom::Mass::get_mass_key(), bool use_rigid_bodies=true, double sigma=.1, double window_size=1.0)
Constructor.
Rotation3D get_random_rotation_3d()
Pick a rotation at random from all possible rotations.
double convolute(const DensityMap *m1, const DensityMap *m2)
Return a convolution between density maps m1 and m2.
UniformPrior(IMP::Model *m, Particle *p, Float k, Float upperb, Float lowerb, std::string name="UniformPrior%1%")
Create the restraint.
double get_displacement_magnitude(SlabWithCylindricalPore const &slab, const algebra::Vector3D &v) const
returns the displacement magnitude of point v relative to the pore walls of slab
BondPairContainer(SingletonContainer *sc)
The container containing the bonds.
void apply_generic_moved(const QuadModifier *m, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const
Just use apply_moved() in the base class.
DensityMap * get_resampled(DensityMap *input, double scaling)
Get a resampled version of the map.
void add_rigid_bodies_in_chain(IMP::core::RigidBodies rbs)
bool get_contains(const VectorD< D > &p, double atol=std::numeric_limits< double >::epsilon()) const
Get whether the point is on the unit simplex.
Definition: UnitSimplexD.h:46
BoundingBoxD< 3 > get_bounding_box(const Segment3D &g)
Definition: Segment3D.h:46
void link_hierarchies_with_sites(RMF::FileConstHandle fh, const atom::Hierarchies &hs)
FloatPair get_component_placement_score(const core::XYZs &ref1, const core::XYZs &ref2, const core::XYZs &mdl1, const core::XYZs &mdl2)
Measure the difference between two placements of the same set of points.
Vector2D operator*(const Vector2D &v) const
Perform the transformation on a 2D vector.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
void get_transformed_into(const DensityMap *source, const algebra::Transformation3D &tr, DensityMap *into, bool calc_rms=true)
Rotate a density map into another map.
virtual void apply_index(Model *m, ParticleIndex a) const
void do_fill_holes(const cv::Mat &m, cv::Mat &result, double h)
Fills the holes in the matrix m of height h.
Scoring associated with a SimulationData object.
Definition: Scoring.h:47
void add_hierarchy(RMF::FileHandle fh, atom::Hierarchy hs)
void set_particles(const Particles &pis)
Set the particles to use.
virtual bool get_can_refine(Particle *) const
Return true if this refiner can refine that particle.
Definition: Refiner.h:52
Simple Brownian dynamics simulator.
virtual int get_value_index(Model *, const ParticleIndexPair &) const
Compute the predicate and the derivative if needed.
Abstract predicate function.
std::string get_molecule_name_and_copy(atom::Hierarchy h)
Walk up a PMI2 hierarchy/representations and get the "molname.copynum".
Definition: pmi/utilities.h:85
virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) const
PartitionalClustering * create_diameter_clustering(Metric *d, double maximum_diameter)
ParticlesTemp get_non_optimizable_particles(ParticlesTemp const &particles)
ScoreStatesTemp get_required_score_states(const ModelObjectsTemp &mos, ScoreStatesTemp exclude=ScoreStatesTemp())
Compute the set of score states required by the passed ModelObjects.
ConsecutivePairFilter(ConsecutivePairContainer *cpc)
Hierarchy get_root(Hierarchy h)
Return the root of the hierarchy.
virtual double evaluate_indexes_scores(Model *m, const ParticleIndexTriplets &o, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
static FilterProvenance setup_particle(Model *m, ParticleIndex pi, std::string method, double threshold, int frames)
Definition: provenance.h:416
virtual double evaluate_index(Model *m, const ParticleIndexPair &p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
Restraint * create_slab_restraint(SingletonContainerAdaptor beads) const
void transform(Hierarchy h, const algebra::Transformation3D &tr)
Transform a hierarchy. This is aware of rigid bodies.
AnchorToCylidnricalPorePairScore(Float rot_angle, Float pore_radial_d, Float z, Float k)
double evaluate_indexes(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
double evaluate_index(Model *m, const ParticleIndexPair &pip, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
double evaluate_if_good_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
double get_volume(const Torus3D &g)
Definition: Torus3D.h:61
void add_surface_index(core::Hierarchy mhd, Float apix, FloatKey shell_key=FloatKey("surf_ind"), FloatKey radius_key=core::XYZR::get_radius_key(), FloatKey weight_key=atom::Mass::get_mass_key())
Add shell index to leaves.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
double evaluate_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
void set_score(int predicate_value, PairScore *score)
A decorator for a representation.
core::XYZR create_cover(const Selection &s, std::string name=std::string())
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
bool get_interiors_intersect(const BoundingBoxD< D > &a, const BoundingBoxD< D > &b)
Return true if they intersect.
Definition: BoundingBoxD.h:209
Fitting of multiple profiles to the experimental one.
const Cone3D & get_cone_3d_geometry(const Cone3D &g)
Definition: Cone3D.h:64
void copy_particle_reference_frame_if_applicable(Particle *src_p, Particle *trg_p)
VectorD< D > get_increasing_from_embedded(const UnitSimplexD< D > &s, const VectorD< D > &p)
Convert point on simplex from embedded to increasing coordinates.
Definition: UnitSimplexD.h:137
RigidBodyMover(core::RigidBody d, Particles ps, Float max_tr, Float max_ang, algebra::Vector3Ds ctrs, algebra::Transformation3Ds trs)
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
The standard decorator for manipulating molecular structures.
virtual double evaluate_index(Model *m, const ParticleIndexTriplet &vt, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
void set_reference_frame(const IMP::algebra::ReferenceFrame3D &tr)
Set the current reference frame.
A Cartesian vector in D-dimensions.
Definition: VectorD.h:52
void set_restraints(RestraintsAdaptor rs)
Set the Restraints to use in the RestraintScoreSubsetFilterTable.
Ints get_index(const ParticlesTemp &particles, const Subset &subset, const Subsets &excluded)
virtual void apply_index(Model *m, ParticleIndex p) const
RestraintSet * create_elastic_network(const Particles &ps, Float dist_cutoff, Float strength)
Create an elastic network restraint set.
Definition: pmi/utilities.h:26
double evaluate_indexes_delta(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
double evaluate_indexes(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
double evaluate_if_good_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
Common base class for heavy weight IMP objects.
Definition: Object.h:106
DensityMap * multiply(const DensityMap *m1, const DensityMap *m2)
Return a density map for which voxel i contains the result of m1[i]*m2[i].
ExampleComplexRestraint(UnaryFunction *f, SingletonContainer *sc, Float diameter, std::string name="ExampleComplexRestraint%1%")
Use f to restrain particles in sc to be within diameter of one another.
BoundingBoxD()
Create an empty bounding box.
Definition: BoundingBoxD.h:37
algebra::Sphere3D get_bounding_sphere(const Hierarchy &h)
virtual int get_value_index(Model *, ParticleIndex vt) const
Compute the predicate and the derivative if needed.
ParticleIndexes get_particle_indexes(ParticlesTemp const &particles)
Hierarchy create_protein(Model *m, std::string name, double target_radius, int number_of_residues, int first_residue_index=0, double volume=-1)
Create a coarse grained molecule.
Store a list of ParticleIndexes.
MinimumPairRestraint(PairScore *f, PairContainerAdaptor c, unsigned int n=1, std::string name="MinimumPairRestraint %1%")
double evaluate_indexes_scores(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
VectorD< D > get_embedded_from_increasing(const UnitSimplexD< D > &s, const VectorD< D > &p)
Convert point on simplex from increasing to embedded coordinates.
Definition: UnitSimplexD.h:151
Base class for all CHARMM residue-based topology.
virtual void do_after_evaluate(DerivativeAccumulator *da)
Do any necessary updates after the model score is calculated.
void add_to_particle_derivative(unsigned particle_no, double value, DerivativeAccumulator &accum) const
update derivatives of particles
void set_particles(const Particles &pis)
Set the particles to use.
A lookup based particle refiner.
Definition: TableRefiner.h:21
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
A decorator for wrapping a particle representing a molecular bond.
FixedXYZ get_fixed_xyz_from_rotation(const Rotation3D &r)
The inverse of rotation_from_fixed_xyz()
double evaluate_indexes_delta(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
void add_data(ModelKey mk, Object *o)
Store a piece of data in the model referenced by the key.
double evaluate_indexes_delta(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
Atoms get_psi_dihedral_atoms(Residue rd)
Return the atoms comprising the psi dihedral.
A decorator for a particle representing an atom.
Definition: atom/Atom.h:234
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
Abstract class for scoring object(s) of type ParticleIndex.
std::map< double, int > bayesem3d_get_distinct_and_counts(DensityMap *em)
Get histogram of density in EM map.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
virtual int get_value_index(Model *m, const ParticleIndexPair &p) const
Compute the predicate and the derivative if needed.
void add_to_particle_derivative(unsigned particle_no, double value, DerivativeAccumulator &accum) const
update derivatives of particles
AngleSingletonScore(UnaryFunction *f)
Use f to penalize deviations in angle.
double get_psi(const atom::Residue r) const
get psi angle associated with residue r
ParticleTransportStatisticsOptimizerState(Particle *p, Float bottom_z, Float top_z, WeakPointer< IMP::npctransport::Statistics > statistics_manager=nullptr, WeakPointer< IMP::atom::Simulator > owner=nullptr)
ScoreStates maintain invariants in the Model.
Definition: ScoreState.h:54
bool get_has_index(const ExtendedGridIndexD< D > &i) const
Return true if the voxel has been added.
void set_particles(SingletonContainer *particles_container)
RevoluteJoint(IMP::core::RigidBody parent, IMP::core::RigidBody child)
Construct on the line connecting a and b, with an initial angle 'angle'.
double evaluate_indexes_scores(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
virtual int get_value_index(Model *, const ParticleIndexPair &vt) const
Compute the predicate and the derivative if needed.
static float convolution(const DensityMap *em_map, DensityMap *model_map, float voxel_data_threshold, bool recalc_ccnormfac=true)
ParticlesTemp get_order(const Subset &s, const SubsetFilterTables &sft)
void copy_map(const DensityMap *other)
Copy map into this map.
int compare(const VectorD< D > &a, const VectorD< D > &b)
lexicographic comparison of two vectors
Definition: VectorD.h:179
void set_atom_type(AtomType types)
Select atoms with only the passed type.
const IMP::algebra::Vector3D & get_coordinates(unsigned index, const IMP::atom::AtomType &at) const
get coordinates of the specified atom
bool get_has_index(const ExtendedGridIndexD< D > &v) const
Return true if the ExtendedIndex is also a normal index value.
Definition: grid_ranges.h:242
void set_moved_particles(const ParticleIndexes &p)
Set which particles have moved since the last evaluate.
static Mass setup_particle(Model *m, ParticleIndex pi, Float mass)
Definition: Mass.h:48
SurfaceSymmetryConstraint(Model *m, const ParticleIndexPair &ss, const ParticleIndexPair &rbs)
Create restraint from particle pairs.
ExtendedGridIndexD< D > get_extended_index(const VectorD< D > &o) const
Return the index that would contain the voxel if the grid extended there.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
void set_reference_frame(const algebra::ReferenceFrame3D &rf)
Set coordinates and normal from a reference frame.
Definition: Surface.h:106
Bond create_bond(Bonded a, Bonded b, Int t)
Connect the two wrapped particles by a bond.
FFTFittingOutput * do_global_fitting(em::DensityMap *dmap, double density_threshold, atom::Hierarchy mol2fit, double angle_sampling_interval_rad, int num_fits_to_report, double max_clustering_translation, double max_clustering_angle, bool cluster_fits=true, int num_angle_per_voxel=1, const std::string &angles_filename="")
Fit a molecule inside its density.
void add(const ParticleIndexPair &vt)
Add a single const ParticleIndexPair& to the container.
virtual void setup_for_get_value_index_in_batch(Model *) const
Ints get_partial_index(const ParticlesTemp &particles, const Subset &subset, const Subsets &excluded)
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pi) const
Overload this method to specify the inputs.
double get_radius(Particle *p, FormFactorType ff_type=HEAVY_ATOMS) const
radius
WeightedExcludedVolumeRestraint(core::RigidBodies rbs, Refiner *refiner, FloatKey weight_key=IMP::atom::Mass::get_mass_key())
Constructor.
void set_transformation_child_to_parent(IMP::algebra::Transformation3D transformation)
virtual void apply_indexes(Model *m, const ParticleIndexes &o, unsigned int lower_bound, unsigned int upper_bound) const
void do_advance_chunk(double dtfs, double ikt, const ParticleIndexes &ps, unsigned int begin, unsigned int end)
Track creation of a system fragment by filtering.
Definition: provenance.h:340
FixedRefiner(const ParticlesTemp &ps)
Store the set of particles.
void read(const char *filename, float **data, DensityHeader &header)
Reads a density file in EM format and stores the information.
void add(ParticleIndex vt)
Add a single ParticleIndex to the container.
virtual int get_value_index_in_batch(Model *m, const ParticleIndexTriplet &vt) const
ExampleRestraint(Model *m, ParticleIndex p, double k)
Create the restraint.
void load_leaf_assignments(const Subset &subset, AssignmentsTable *at, AssignmentContainer *ac)
Fill in assignments for a leaf.
virtual void do_after_evaluate(DerivativeAccumulator *da)
Do any necessary updates after the model score is calculated.
PartitionalClustering * create_connectivity_clustering(Metric *metric, double dist)
virtual ModelObjectsTemp do_get_outputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the outputs.
double evaluate_if_good_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
void read(const char *fn_in, float **data, DensityHeader &head)
Reads an MRC file and translates the header to the general DensityHeader.
PairsOptimizerState(PairContainerAdaptor c, PairModifier *gf, std::string name="PairsOptimizerState %1%")
Sphere3Ds read_spheres(TextInput input)
Read a set of 3D spheres from a file.
double evaluate_indexes(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
double evaluate_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
DensityHeader create_density_header(const algebra::BoundingBoxD< 3 > &bb, float spacing)
Create a header from a bounding box in 3D.
AngleTripletScore(UnaryFunction *f)
Score the angle (in radians) using f.
void set_cone_3d_geometry(Cone3D &g, const Cone3D &v)
Definition: Cone3D.h:64
void show_histogram(HistogramD h, std::string xscale="linear", std::string yscale="linear", Functions curves=Functions())
A base class for classes which perturb particles.
Hierarchy get_residue(Hierarchy mhd, unsigned int index)
Get the residue with the specified index.
void load_merged_assignments(const Subset &first_subset, AssignmentContainer *first, const Subset &second_subset, AssignmentContainer *second, const SubsetFilterTablesTemp &filters, AssignmentContainer *ret)
Fill in assignments for an internal node.
double evaluate_indexes(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
A class to store the clusters generated during hierarchical clustering.
Base class for all optimizers.
Definition: Optimizer.h:46
DynamicListSingletonContainer(Container *scope, std::string name="ListSingletonContainer %1%")
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
BoundingBoxD< 3 > get_bounding_box(const Cone3D &g)
Definition: Cone3D.h:64
double evaluate_indexes_delta(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
static Bonded setup_particle(Model *m, ParticleIndex pi)
CHARMMParameters(TextInput topology_file_name, TextInput par_file_name=TextInput(), bool translate_names_to_pdb=false)
Construction with CHARMM topology (and optionally parameters) file.
virtual double evaluate_index(Model *m, ParticleIndex p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
void get_anchors_for_density(em::DensityMap *dmap, int number_of_means, float density_threshold, std::string pdb_filename, std::string cmm_filename, std::string seg_filename, std::string txt_filename)
Generate anchors in several formats for a given density map.
Provide a consistent interface for things that take Restraints as arguments.
Definition: Restraint.h:338
static Hierarchy setup_particle(Model *m, ParticleIndex pi, DecoratorTraits tr=get_default_decorator_traits())
PairContainerSet(Model *m, std::string name="PairContainerSet %1%")
Construct an empty set.
Images read_images(const Strings &names, const ImageReaderWriter *rw)
Vector3D get_projected(const Line3D &l, const Vector3D &p)
Project a point onto the line.
static Typed setup_particle(Model *m, ParticleIndex pi, ParticleType t)
Definition: Typed.h:44
virtual std::vector< DOFValues > plan(DOFValues q_from, DOFValues q_rand, ScoringFunction *sf)
virtual void do_advance_chunk(double dtfs, double ikt, const ParticleIndexes &ps, unsigned int begin, unsigned int end)
algebra::Vector3D get_global_from_local_v3(Particle *p, const algebra::Vector3D &local)
Definition: util.h:111
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
void compute_chisquare_derivative(const Profile *model_profile, const Particles &particles1, const Particles &particles2, Vector< algebra::Vector3D > &derivatives, const Vector< double > &effect_size) const
compute derivatives for particles1 with respect to particles2
ConnectivityRestraint(PairScore *ps, SingletonContainerAdaptor sc)
Use the given PairScore.
LognormalAmbiguousRestraint(Particle *p1, Particle *p2, Particle *ki, Particle *sigmaG)
Create the restraint.
Float evaluate_for_contributions(Ints c, DerivativeAccumulator *accum) const
Evaluate the restraint just for a subset of contribution indexes.
double evaluate_if_good_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
algebra::VectorKD get_embedding(const Subset &s, const Assignment &a, ParticleStatesTable *pst)
Return an embedding for an assignment.
virtual int get_value_index(Model *, const ParticleIndexTriplet &) const
Compute the predicate and the derivative if needed.
void set_coordinates_safe(IMP::core::RigidBody rb, IMP::algebra::Vector3D c)
The type for a residue.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
virtual void apply_indexes_moved(Model *m, const ParticleIndexQuads &o, unsigned int lower_bound, unsigned int upper_bound, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const
Definition: QuadModifier.h:58
SurfaceGeometry * create_geometry(const Surface s, std::string name=std::string("SurfaceGeometry%1%"))
Create a geometry from a Surface.
Definition: Surface.h:191
double evaluate_indexes_scores(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
Represent a cone in 3D.
Definition: Cone3D.h:31
const Cylinder3D & get_cylinder_3d_geometry(const Cylinder3D &g)
Definition: Cylinder3D.h:78
Define the type for a type of hierarchy.
algebra::BoundingBoxD< 3 > get_bounding_box(const XYZRs &ps)
Get the bounding box.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
A class that holds DOF values for DOFs.
Definition: DOFValues.h:20
FilterGeometry(const algebra::Plane3D &p)
Pay attention to the orientation of the plane.
int operator()(Model *m, const ParticleIndexTriplet &vt) const
Enable them to be use as functors.
MolecularDynamics(Model *m=nullptr)
virtual int get_value_index_in_batch(Model *m, const ParticleIndexQuad &vt) const
Definition: QuadPredicate.h:58
double evaluate_if_good_indexes(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
Hierarchy get_previous_residue(Residue rd)
Return the residue from the same chain with one lower index.
void write_to_floats(const String &filename, em::ImageHeader &header, const cv::Mat &data) const
Writes an EM image in Spider format.
void set(Particle *p, Key key, const Value &value)
Assign new properties to the class.
Definition: scoped.h:75
virtual bool get_can_refine(Particle *) const
Return true if this refiner can refine that particle.
static ExampleDecorator setup_particle(Model *m, ParticleIndex pi, std::string name)
double evaluate_if_good_indexes(Model *m, const ParticleIndexTriplets &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
Class for adding up scores during ScoringFunction evaluation.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
Float compute_fitting_score(const ParticlesTemp &ps, DensityMap *em_map, FloatKey wei_key=atom::Mass::get_mass_key())
Compute fitting scores for a given set of rigid transformations.
SecondaryStructureResidue setup_coarse_secondary_structure_residue(const Particles &ssr_ps, Model *mdl, bool winner_takes_all_per_res=false)
Coarsen some SecondaryStructureResidues.
void add_to_derivatives(const Floats &x1, const Floats &x2, DerivativeAccumulator &accum) const
update derivatives of particles
GaussianRestraint(Particle *x, Particle *mu, Particle *sigma)
Gaussian restraint.
virtual void propagate_coordinates(const ParticleIndexes &ps, double step_size)
First part of velocity Verlet (update coordinates and half-step velocity)
A sphere patch is defined as all points above the plane and on the sphere.
Definition: SpherePatch3D.h:18
virtual double evaluate_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
void add(const ParticleIndexTriplet &vt)
Add a single const ParticleIndexTriplet& to the container.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const =0
Overload this method to specify the inputs.
ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
void set_proper_ranges_for_keys(Model *m, const algebra::Vector3D &min_translation_values, const algebra::Vector3D &max_translation_values)
VectorD< D > get_random_vector_in(const BoundingBoxD< D > &bb)
Generate a random vector in a box with uniform density.
void optimize_balls(Model *m, const ParticleIndexes &pis, const RestraintsTemp &rs=RestraintsTemp(), const PairPredicates &excluded=PairPredicates(), const OptimizerStates &opt_states=OptimizerStates(), LogLevel ll=DEFAULT)
virtual unsigned int get_number_of_refined(Particle *a) const
Definition: Refiner.h:105
const Transformation2D & operator*=(const Transformation2D &o)
See help for operator*.
virtual void do_after_evaluate(DerivativeAccumulator *da)
Do any necessary updates after the model score is calculated.
double get_coarse_cc_local_coefficient(const DensityMap *em_map, DensityMap *model_map, double voxel_data_threshold)
Local cross correlation function.
DynamicListQuadContainer * add_predicate(QuadPredicate *predicate, int value)
Restraints create_current_decomposition(Model *m, const ParticleIndexTriplet &vt) const
virtual ModelObjectsTemp do_get_inputs(Model *, const ParticleIndexes &) const
Overload this method to specify the inputs.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
double bayesem3d_get_cross_correlation_coefficient(const DensityMap *em1, const DensityMap *em2)
Compute a normalized cross-correlation coefficient.
virtual int get_value_index(Model *m, const ParticleIndexQuad &pi) const
Compute the predicate and the derivative if needed.
PartitionalClusteringWithCenter * create_bin_based_clustering(Embedding *embed, double side)
Simple 2D transformation class.
void add(const Profile *other_profile, double weight=1.0)
add another profile - useful for rigid bodies
OptimizerState(Model *m, std::string name)
Constructor.
virtual ParticleIndexes get_refined_indexes(Model *m, ParticleIndex pi) const
Return the indexes of the particles returned by get_refined()
void DensityHeader_to_ImageHeader(const DensityHeader &header, ImageHeader &h)
GridIndexD< D > get_index(const ExtendedGridIndexD< D > &i) const
requires get_has_index(i) is true.
Base class for all scoring functions related to em2d.
Definition: scores2D.h:55
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
void apply_moved(const SingletonModifier *sm, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const
Apply a SingletonModifier to the contents.
Floats bayesem3d_get_cumulative_sum(DensityMap *em)
Compute the cumulative sum of the histogram computed from EM map.
Hierarchy read_mol2(TextInput mol2_file, Model *model, Mol2Selector *mol2sel=nullptr)
Create a hierarchy from a Mol2 file.
double evaluate_if_good_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
virtual int get_value_index_in_batch(Model *m, ParticleIndex pi) const
AttributeDistancePairScore(UnaryFunction *f, FloatKey k)
Apply function f to attribute k.
virtual double get_strength(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
The strength is a rough metric of how this filter restricts the subset.
GaussianProcessInterpolationRestraint(Model *m, GaussianProcessInterpolation *gpi)
static TAMDCentroid setup_particle(Model *m, ParticleIndex pi, ParticleIndexesAdaptor members)
Definition: TAMDCentroid.h:63
void set_size(int rows, int cols)
AlignSymmetric(em::DensityMap *dmap, float threshold, int cn_symm_deg)
Constructor.
Track creation of a system fragment from a PDB file.
Definition: provenance.h:86
virtual bool get_can_refine(Particle *) const
Return true if this refiner can refine that particle.
Definition: FixedRefiner.h:33
void apply_generic_moved(const PairModifier *m, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const
Just use apply_moved() in the base class.
double get_surface_area(const Cone3D &g)
Definition: Cone3D.h:64
Hierarchy create_clone_one(Hierarchy d)
Clone the node in the Hierarchy.
Restraint(const Particles &particles, const Profile *exp_profile, FormFactorType ff_type=HEAVY_ATOMS)
Constructor.
static RelaxingSpring setup_particle(Model *m, ParticleIndex pi, ParticleIndex bonded_pi0, ParticleIndex bonded_pi1, double equilibrium_rest_length_factor, double rest_length_diffusion_coefficient)
FittingSolutions local_rigid_fitting_around_point(Particle *p, Refiner *refiner, const FloatKey &weight_key, DensityMap *dmap, const algebra::Vector3D &anchor_centroid, OptimizerStates display_log, Int number_of_optimization_runs=5, Int number_of_mc_steps=10, Int number_of_cg_steps=100, Float max_translation=2., Float max_rotation=.3, bool fast=false)
Local rigid fitting of a rigid body around a center point.
double evaluate_indexes_delta(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
Definition: KinkPairScore.h:35
void optimize_assembly(Model *m, const ParticleIndexes &components, const RestraintsTemp &interactions, const RestraintsTemp &other_restraints, const algebra::BoundingBox3D &bb, PairScore *ev, double cutoff, const PairPredicates &excluded=PairPredicates())
SurfaceShellDensityMap()
Creates a new density map.
Restraints create_decomposition(const RestraintsTemp &rs)
Return the decomposition of a list of restraints.
std::pair< Vector3D, double > get_axis_and_angle(const Rotation3D &rot)
Decompose a Rotation3D object into a rotation around an axis.
void project(const ParticlesTemp &ps, int x_margin, int y_margin, int z_margin, algebra::Vector3D shift=algebra::Vector3D(0., 0., 0.), FloatKey mass_key=atom::Mass::get_mass_key())
Project particles on the grid by their mass value.
Holds header data for optimization.
Definition: SettingsData.h:135
double evaluate_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
virtual double evaluate_index(Model *m, const ParticleIndexQuad &vt, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
bool same_dimensions(const DensityMap *other) const
Checks if two maps have the same dimensions.
void add_to_internal_derivatives(const algebra::Vector3D &deriv_parent, DerivativeAccumulator &da)
Add to derivatives of local coordinates.
Definition: rigid_bodies.h:766
ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
CoverRefined(Refiner *ref, Float slack=0)
Create with the given refiner and radius key.
double evaluate_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
A class to store a set of configurations of a model.
std::vector< double > bayesem3d_get_value_no_deriv(Particle *p, const algebra::Vector3D &pt, double mass_ii, const IMP::em::KernelParameters &kps)
Compute the score without its derivative.
void setup_hierarchy(Hierarchy hierarchy) const
Make the Hierarchy conform with this topology.
virtual int get_value_index(Model *m, const ParticleIndexQuad &vt) const =0
Compute the predicate and the derivative if needed.
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
double evaluate_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
double get_volume(const Ellipsoid3D &g)
Definition: Ellipsoid3D.h:46
A decorator for a particle with x,y,z coordinates.
Definition: XYZ.h:30
static Angle setup_particle(Model *m, ParticleIndex pi, core::XYZ a, core::XYZ b, core::XYZ c)
void set_particles(const Particles &pis)
Set the particles to use.
void set_log_target(TextOutput l)
Set the target for the log.
Base class for functions of two variables.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
void set_in_image(em::ImageHeader &header) const
Sets the registration results to the header of an image.
double get_density(const DensityMap *m, const algebra::Vector3D &v)
Get density value at point v, interpolating linearly from the sample values.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
void setup(ScoreFunction *score_function, const Em2DRestraintParameters &params)
Initializes the parameters to generate and match projections.
long get_number_of_particles_outside_of_the_density(DensityMap *dmap, const Particles &ps, const IMP::algebra::Transformation3D &t=IMP::algebra::get_identity_transformation_3d(), float thr=0.0)
Get the number of particles that are outside of the density.
void crop(Image *img, const IntPair &center, int size)
double evaluate_indexes(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
A shared container for Quads.
Definition: QuadContainer.h:37
void read_from_image(const em::ImageHeader &header)
Reads the registration parameters from an image.
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
virtual IMP::ModelObjectsTemp do_get_outputs(IMP::Model *m, const IMP::ParticleIndexes &pis) const
Overload this method to specify the outputs.
Transformation3Ds get_alignments_from_first_to_second(const PrincipalComponentAnalysisD< 3 > &pca1, const PrincipalComponentAnalysisD< 3 > &pca2)
Get all alignments of the first principal component system to the second one.
static Scale setup_particle(Model *m, ParticleIndex pi)
Definition: Scale.h:30
ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
ExtendedGridIndexD< D > get_extended_index(const GridIndexD< D > &index) const
Convert an index back to an extended index.
Definition: GridD.h:247
void apply_moved(const QuadModifier *sm, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const
Apply a QuadModifier to the contents.
virtual ModelObjectsTemp do_get_outputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the outputs.
DiameterRestraint(UnaryFunction *f, SingletonContainer *sc, Float diameter)
Use f to restrain sc to be within diameter of one another.
void transform(const IMP::atom::Hierarchy &protein, const IMP::PairScore *score, double thr, double K, int num_iter) const
set coordinates of side chains of the given protein
double evaluate_if_good_indexes(Model *m, const ParticleIndexQuads &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
static KinematicNode setup_particle(Model *m, ParticleIndex pi, KinematicForest *owner)
Definition: KinematicNode.h:36
virtual double get_strength(const Subset &s, const Subsets &prior_subsets) const =0
The strength is a rough metric of how this filter restricts the subset.
void inflate_floater(SimulationData *sd, const std::string floater_name, const float new_radius)
inflate floater of specified type to new_radius
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
void read(const char *filename, float **data, DensityHeader &header)
Reads a map in Spider format and transfers the data and header.
DensityMap * create_density_map(const DensityMap *other)
Create a copy of another map.
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
void add_loop_statistical_score_data(atom::Hierarchy h)
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
O * object_cast(Object *o)
Up (or down) cast an IMP Object-derived class.
Definition: object_cast.h:23
A base class for Keys.
Definition: Key.h:44
Restraint * create_internal_connectivity_restraint(const Selection &s, double k, std::string name="Connectivity%1%")
Create a restraint connecting the selection.
double evaluate_if_good_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
virtual IMP::ModelObjectsTemp do_get_inputs(IMP::Model *m, const IMP::ParticleIndexes &pis) const
Overload this method to specify the inputs.
Restraints create_current_decomposition(Model *m, const ParticleIndexQuad &vt) const
void write_to_ints(const String &filename, em::ImageHeader &header, const cv::Mat &data) const
Writes an EM image in TIFF format.
virtual void do_after_evaluate(DerivativeAccumulator *da)
Do any necessary updates after the model score is calculated.
BondAngleRevoluteJoint(IMP::core::RigidBody parent, IMP::core::RigidBody child, IMP::core::XYZ a, IMP::core::XYZ b, IMP::core::XYZ c)
IMP::Restraint * create_weighted_excluded_volume_restraint(core::RigidBody rb1, core::RigidBody rb2, FloatKey shell_key=FloatKey("surf_ind"))
Create a weighted excluded volume restraint between two rigid bodies.
BoundingBoxD< 3 > get_bounding_box(const Ellipsoid3D &g)
Definition: Ellipsoid3D.h:46
LeavesRefiner(HierarchyTraits tr)
Create a refiner for a particular type of hierarchy.
const algebra::Vector3D & get_vector_geometry(XYZ d)
Definition: XYZ.h:135
Holds data about the assembly density needed for optimization.
Definition: SettingsData.h:76
virtual double get_strength(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
The strength is a rough metric of how this filter restricts the subset.
virtual IMP::ModelObjectsTemp do_get_inputs(IMP::Model *m, const IMP::ParticleIndexes &pis) const
Overload this method to specify the inputs.
A shared container for Singletons.
void pull_back_body_member_adjoints(ParticleIndex pi, DerivativeAccumulator &da)
Pull back global adjoints from member that is also a rigid body.
double get_cross_correlation_coefficient(Image *im1, Image *im2)
Cross correlation between two images.
A decorator for a particle that has a Lennard-Jones potential well.
Definition: LennardJones.h:26
virtual double evaluate_index(Model *m, ParticleIndex pi, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
Rotation3D get_interpolated(const Rotation3D &a, const Rotation3D &b, double f)
Interpolate between two rotations.
Definition: Rotation3D.h:609
static Voxel setup_particle(Model *m, ParticleIndex pi, algebra::Vector3D position, Float radius, Float density)
Definition: Voxel.h:39
The type for a chain.
void write_mol2(Hierarchy rhd, TextOutput file_name)
Write a ligand hierarchy as a mol2 file.
virtual void apply_indexes_moved(Model *m, const ParticleIndexes &o, unsigned int lower_bound, unsigned int upper_bound, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const
double evaluate_if_good_indexes(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
virtual ModelObjectsTemp do_get_inputs(Model *, const ParticleIndexes &) const
Overload this method to specify the inputs.
MapDistanceTransform(IMP::em::DensityMap *map, float density_threshold, float max_distance)
static SoftwareProvenance setup_particle(Model *m, ParticleIndex pi, std::string name, std::string version, std::string location)
Definition: provenance.h:627
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pi) const
Overload this method to specify the inputs.
Definition: predicates.h:30
void setup_secondary_structure(Model *mdl)
Sets up default secondary structure particles for every anchor (run first)
Rotation3D get_rotation_from_vector4d(const VectorD< 4 > &v)
Compute a rotation from an unnormalized quaternion.
Definition: Rotation3D.h:488
virtual ParticleIndexes const & get_refined_indexes_by_ref(Model *m, ParticleIndex pi) const
Return the indexes of the particles returned by get_refined()
Definition: Refiner.h:82
virtual double evaluate_index(IMP::Model *m, const IMP::ParticleIndex p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
RotamerAngleTuples get_rotamers(IMP::atom::ResidueType residue, float phi, float psi, float probability_thr) const
query the rotamer library for the rotamer data
double get_surface_area(const Cylinder3D &g)
Definition: Cylinder3D.h:78
Hierarchy read_pdb(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector(), bool select_first_model=true)
Read all the molecules in the first model of the PDB file.
virtual void apply_index(Model *m, const ParticleIndexQuad &v) const =0
TextWriter(TextOutput fn)
Create a writer opening the file with the passed sink.
Store data to be clustered for embedding based algorithms.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
double get_area(const Plane3D &g)
Definition: Plane3D.h:78
const Storage::Value get_trilinearly_interpolated(const GridD< 3, Storage, typename Storage::Value, Embedding > &g, const Vector3D &v, const typename Storage::Value &outside=0)
Use trilinear interpolation to compute a smoothed value at v.
Definition: grid_utility.h:36
Transformation3D operator/(const Transformation3D &b) const
Compute the transformation which, when composed with b, gives *this.
bool get_atom_exists(const IMP::atom::AtomType &at) const
check if a given atom is present in the data structure
void set_bounding_box(const BoundingBoxD< D > &bb3)
Change the bounding box but not the grid or contents.
Definition: GridD.h:270
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
int get_state_index(Hierarchy h)
Walk up the hierarchy to find the current state.
virtual ModelObjectsTemp do_get_inputs(Model *, const ParticleIndexes &) const
Overload this method to specify the inputs.
Definition: LogPairScore.h:30
static Colored setup_particle(Model *m, ParticleIndex pi, Color color)
Definition: Colored.h:62
virtual double get_strength(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
The strength is a rough metric of how this filter restricts the subset.
JeffreysRestraint(Model *m, Particle *p)
Create the restraint.
virtual Restraints do_create_current_decomposition(Model *m, const ParticleIndexTriplet &vt) const
Override this to return your own decomposition.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
DensityMap * get_binarized_interior(DensityMap *dmap)
Return a binarized map with 1 for voxels that are internal in the input map.
void set_gaussian(const algebra::Gaussian3D &g)
Get the covariance attributes from a Gaussian3D object.
virtual const ParticlesTemp get_refined(Particle *a) const =0
Refine the passed particle into a set of particles.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
virtual double evaluate_index(Model *m, const ParticleIndexQuad &vt, DerivativeAccumulator *da) const =0
Compute the score and the derivative if needed.
virtual void do_after_evaluate(DerivativeAccumulator *da)
Do any necessary updates after the model score is calculated.
Represent a torus in 3D.
Definition: Torus3D.h:26
PrincipalComponentAnalysisD< D > get_principal_components(const Vector< VectorD< D > > &ps)
Perform principal components analysis on a set of vectors.
GammaPrior(IMP::Model *m, Particle *p, Float k, Float theta, std::string name="GammaPrior%1%")
Create the restraint.
Restraints do_create_current_decomposition(Model *m, const ParticleIndexQuad &vt) const
Override this to return your own decomposition.
double evaluate_if_good_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
void initialize_positions(SimulationData *sd, const RestraintsTemp &extra_restraints=RestraintsTemp(), bool debug=false, double short_init_factor=1.0, bool is_disable_randomize=false, bool are_fgs_pre_initialized=false)
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
MSConnectivityRestraint(Model *m, PairScore *ps, double eps=0.1)
Use the given PairScore.
A CHARMM patch residue.
double evaluate_site_contributions_with_internal_tables(algebra::Sphere3D const *spheres_table, double const **quaternions_tables, algebra::Sphere3D *sphere_derivatives_table, double **torques_tables, const ParticleIndexPair &pip, DerivativeAccumulator *da, boost::tuple< unsigned int, std::vector< unsigned int >, std::vector< unsigned int >, bool >(*contacts_accumulator)=nullptr) const
Holds data about a component needed for optimization.
Definition: SettingsData.h:22
static ClusterProvenance setup_particle(Model *m, ParticleIndex pi, int members)
Definition: provenance.h:499
virtual int get_value_index(Model *m, const ParticleIndexPair &pip) const
Compute the predicate and the derivative if needed.
virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) const
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
void save_images(Images images, const Strings &names, const ImageReaderWriter *rw)
double evaluate_indexes(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
MarginalHBondRestraint(Model *m)
Create the restraint.
double operator()(unsigned int id1, unsigned int id2, const ClusterSet &cluster_set, const FloatsList &distances)
Distance between the clusters.
void add_internal_transformations(core::RigidBody d, algebra::Transformation3Ds transforms)
GenericHierarchies get_internal(Hierarchy mhd)
Get all the non-leaves of the bit of hierarchy.
double evaluate_if_good_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pi) const
Overload this method to specify the inputs.
QuadsConstraint(QuadModifier *before, QuadModifier *after, QuadContainerAdaptor c, std::string name="QuadsConstraint %1%")
void add_z_bias_restraint(SingletonContainerAdaptor ps, double k)
double evaluate_if_good_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
algebra::Vector3Ds get_points_close_to_molecule(const atom::Hierarchy &mh, const algebra::Vector3Ds points, Float max_dist)
void write(const String &filename, const ImageReaderWriter *writer)
Definition: Image.h:139
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
float get_cn_rmsd(atom::Hierarchies mh1, atom::Hierarchies mh2)
Find correspondence between the two rings and calculate rmsd.
virtual double evaluate_indexes_scores(Model *m, const ParticleIndexes &o, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
static Resolution setup_particle(Model *m, ParticleIndex pi, Float resolution)
Definition: Resolution.h:45
Reflect about a plane in 3D.
Definition: Reflection3D.h:18
A decorator for a particle that represents a surface, its coordinates, and orientation.
Definition: Surface.h:35
virtual double evaluate_index(Model *m, const ParticleIndexPair &p, DerivativeAccumulator *da) const
virtual int get_value_index(Model *m, const ParticleIndexTriplet &pi) const
Compute the predicate and the derivative if needed.
static DirectionAngle setup_particle(Model *m, ParticleIndex pi, ParticleIndexPair ds)
Definition: direction.h:95
Float approximate_molecular_mass(DensityMap *m, Float threshold)
Estimate the molecular mass from a map.
virtual void apply_index(Model *m, ParticleIndex a) const
double evaluate_indexes_delta(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
algebra::Vector3D get_vector_to(const XYZ &b) const
Get the vector from this particle to another.
Definition: XYZ.h:102
void update_particle_type_xyz_distribution_map(Particle *p)
virtual int get_value_index(Model *m, ParticleIndex pi) const
Compute the predicate for types of specific pi.
virtual double evaluate_index(Model *m, const ParticleIndexPair &pi, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
void set_internal_transformation(const algebra::Transformation3D &v)
Definition: rigid_bodies.h:640
void get_random_numbers_normal(Vector< RealType > &v, unsigned int n, RealType mean=0.0, RealType stddev=1.0)
Fill the double array with random normally distributed values.
Definition: random_utils.h:48
bool get_is_canonical(atom::Hierarchy h)
Walk up a PMI2 hierarchy/representations and check if the root is named System.
Definition: pmi/utilities.h:91
void get_segmentation(em::DensityMap *dmap, double apix, double density_threshold, int num_means, const std::string pdb_filename, const std::string cmm_filename, const std::string seg_filename, const std::string txt_filename)
Segment a density map using the anchor graph.
unsigned get_number_of_cases(const IMP::atom::AtomType &at) const
get number of coordinate sets for a given atom
void do_normalize(Image *im, bool force=false)
double evaluate_indexes_scores(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
SecondaryStructureResidues setup_coarse_secondary_structure_residues(const Particles &ssr_ps, Model *mdl, int coarse_factor, int start_res_num, bool winner_takes_all_per_res=false)
double evaluate_indexes(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
Definition: predicates.h:130
void add_coordinates(Hierarchy hierarchy) const
Add atom Cartesian coordinates to the given Hierarchy using this topology.
void set_score(int predicate_value, QuadScore *score)
Store all parameters for a simulation.
static Uncertainty setup_particle(Model *m, ParticleIndex pi, Float uncertainty)
Definition: /Uncertainty.h:45
void add_protein_ligand_score_data(Hierarchy h)
void downsample(Profile *downsampled_profile, unsigned int point_number) const
downsample the profile to a given number of points
std::map< double, double > bayesem3d_get_cumulative_sum_with_reference(DensityMap *em)
Compute the cumulative sum of the histogram given a reference.
double evaluate_indexes_scores(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
double evaluate_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
double get_percentage_of_voxels_covered_by_particles(DensityMap *dmap, const Particles &ps, float smoothing_radius=3., const IMP::algebra::Transformation3D &t=IMP::algebra::get_identity_transformation_3d(), float thr=0.0)
Get the number of density voxels that are not covered by particles.
void add_to_derivatives(const Floats &x, DerivativeAccumulator &accum) const
update derivatives of particles
An axis-aligned bounding box.
Definition: BoundingBoxD.h:27
Transformation2D operator/(const Transformation2D &b) const
Compute the transformation d which, when composed with b, gives this one.
WeightedDerivativesToRefined(Refiner *r, FloatKey w=FloatKey(), FloatKeys keys=XYZ::get_xyz_keys())
double evaluate_if_good_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
PathLocalPlanner(Model *model, DOFsSampler *dofs_sampler, DirectionalDOF *directional_dof, int save_step_interval=1)
Construct a path planner (default planning is linear)
Interface to specialized Particle types (e.g. atoms)
Definition: Decorator.h:118
void add(const ParticleIndexQuad &vt)
Add a single const ParticleIndexQuad& to the container.
static void set_reduced_coordinates(Model *m, ParticleIndex target, ParticleIndex ref, Floats coords)
sets rigid body coordinates in the reference frame of ref
Parameters needed for the core projection routine.
Definition: project.h:30
static Copy setup_particle(Model *m, ParticleIndex pi, Int number)
Definition: Copy.h:42
3D rotation class.
Definition: Rotation3D.h:51
std::string get_molecule_name(Hierarchy h)
Ints get_nearest_neighbors(unsigned int i, unsigned int k) const
Search using the ith point in the input set.
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
double get_score(Restraint *r, const Assignment &a) const
Get the score of a set or restraint.
RigidBodyMover(Model *m, ParticleIndex pi, Float max_translation, Float max_rotation)
Constructor. The given rigid body is rotated and translated.
void set_transformation_child_to_parent_no_checks(IMP::algebra::Transformation3D transformation)
Definition: Joint.h:95
virtual const ParticlesTemp get_refined(Particle *) const
Refine the passed particle into a set of particles.
void write_connolly_surface(atom::Atoms atoms, TextOutput fn, float density, float probe_radius)
Write the Connolly surface for a set of atoms to a file.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pi) const
Overload this method to specify the inputs.
Definition: predicates.h:52
RestraintSet(Model *m, double weight, const std::string &name="RestraintSet %1%")
Create an empty set that is registered with the model.
std::ostream & show(Hierarchy h, std::ostream &out=std::cout)
Print the hierarchy using a given decorator to display each node.
void add_atom_types(Hierarchy hierarchy) const
Add CHARMM atom types to the given Hierarchy using this topology.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
double evaluate_if_good_indexes(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
Return 1 if two XYZRs collide.
Definition: predicates.h:63
virtual void apply_index(Model *m, ParticleIndex p) const
virtual ModelObjectsTemp do_get_outputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the outputs.
double evaluate_indexes_scores(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
void add_type(ParticleIndexes ps)
Add all Particles of a single type.
SingletonsRestraint(SingletonScore *ss, SingletonContainerAdaptor pc, std::string name="SingletonsRestraint %1%")
Create the restraint with a shared container.
Vector< Atoms > get_chi_dihedral_atoms(Residue rd)
const Segment3D & get_segment_3d_geometry(const Segment3D &g)
Definition: Segment3D.h:46
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
virtual bool operator()(Hierarchy p)=0
Return true if the traversal should visit this node's children.
void set_sphere_d_geometry(CustomXYZR d, const algebra::Sphere3D &v)
Definition: CustomXYZR.h:95
Hierarchies read_multimodel_pdb_or_mmcif(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector())
Read all models from the PDB or mmCIF file.
Definition: mmcif.h:60
virtual int get_value_index(Model *m, const ParticleIndexPair &p) const
Compute the predicate and the derivative if needed.
void propagate_velocities(const ParticleIndexes &ps, double step_size)
Second part of velocity Verlet (update velocity)
Restraints do_create_current_decomposition(Model *m, const ParticleIndexPair &vt) const
Override this to return your own decomposition.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
unsigned int get_enclosing_image_size(const ParticlesTemp &ps, double pixel_size, unsigned int slack)
Get an automatic size for an image that contains the particles.
void add_to_angle_derivative(Float v, DerivativeAccumulator &d)
Add to the derivative of the angle.
void distribution_2_profile(const RadialDistributionFunction &r_dist)
convert to reciprocal space I(q) = Sum(P(r)*sin(qr)/qr)
internal::PredicateEquals< Pred, true > make_predicate_equal(const Pred *p, Model *m, int value)
Return a functor that returns true when the predicate has a certain value.
Definition: functor.h:19
Eigen::MatrixXd get_jacobian_of_composed_wrt_second(const Rotation3D &q, const Rotation3D &p, bool wrt_unnorm=false)
Get Jacobian of quaternion product with respect to second quaternion.
double compute_offset(const Profile *model_profile) const
computes offset for fitting for fitting the modeled profile
Definition: ProfileFitter.h:88
Simple implementation of segments in 3D.
Definition: Segment3D.h:24
BondSingletonScore(UnaryFunction *f)
Use f to penalize deviations in length.
void set_owner_kf(KinematicForest *kf)
Definition: Joint.h:85
void do_resample_polar(Image *im1, Image *im2, const PolarResamplingParameters &polar_params)
PbcBoxedMover(Particle *p, Particles ps, Float max_tr, algebra::Vector3Ds centers, algebra::Transformation3Ds transformations, Particle *px, Particle *py, Particle *pz)
RestraintSet * create_elastic_network(const Particles &ps, Float dist_cutoff, Float strength)
Create an elastic network restraint set.
double evaluate_indexes_scores(Model *m, const ParticleIndexTriplets &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
void add_downstream_joint(Joint *j)
Adds a joint at the end of the list (closest to the child rigid body)
virtual IMP::ModelObjectsTemp do_get_inputs(IMP::Model *m, const IMP::ParticleIndexes &pis) const
Overload this method to specify the inputs.
virtual double evaluate_indexes(Model *m, const ParticleIndexPairs &pips, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
const Ellipsoid3D & get_ellipsoid_3d_geometry(const Ellipsoid3D &g)
Definition: Ellipsoid3D.h:46
SingletonsOptimizerState(SingletonContainerAdaptor c, SingletonModifier *gf, std::string name="SingletonsOptimizerState %1%")
virtual int get_value_index(Model *m, const ParticleIndexTriplet &pi) const
Compute the predicate for types of specific pi.
void add_to_radius_derivative(double v, DerivativeAccumulator &d)
add v to the derivative of the radius attribute
Definition: XYZR.h:79
A decorator for a residue with probability of secondary structure.
SingletonConstraint(SingletonModifier *before, SingletonDerivativeModifier *after, Particle *vt, std::string name="SingletonConstraint %1%")
double evaluate_indexes_scores(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
ParticlesTemp get_optimizable_particles(ParticlesTemp const &particles)
double get_pairwise_rmsd_score(const core::XYZs &ref1, const core::XYZs &ref2, const core::XYZs &mdl1, const core::XYZs &mdl2)
Measure the RMSD between two placements of the same set of points.
double evaluate_index(Model *m, const ParticleIndexPair &p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
RestraintsTemp get_restraints(const Subset &s, const Subsets &exclusions) const
Statistical(IntKey k, double threshold, TextInput data_file)
Definition: Statistical.h:64
void set_particles(const Particles &pis)
Set the particles to use.
Parameters of a weighted fit, from WeightedProfileFitter.
void pick_max(const DensityMap *other)
Pick the max value between two corresponding voxels between two maps.
algebra::Sphere3D get_enclosing_sphere(const XYZs &v)
Get a sphere enclosing the set of XYZRs.
multifit::FittingSolutionRecords fft_based_rigid_fitting(atom::Hierarchy mol2fit, em::DensityMap *dmap, double density_threshold, double angle_sampling_interval_rad)
FFT fit of a molecule in the density.
FittingSolutions local_rigid_fitting(Particle *p, Refiner *refiner, const FloatKey &weight_key, DensityMap *dmap, OptimizerStates display_log, Int number_of_optimization_runs=5, Int number_of_mc_steps=10, Int number_of_cg_steps=100, Float max_translation=2., Float max_rotation=.3, bool fast=true)
Local rigid fitting of a rigid body.
void load_merged_assignments_random_order(const Subset &first_subset, AssignmentContainer *first, const Subset &second_subset, AssignmentContainer *second, const SubsetFilterTablesTemp &filters, unsigned int maximum_tries, AssignmentContainer *ret)
Sample from the merged assignments.
algebra::Vector3D get_displacement_direction(SlabWithCylindricalPore const &slab, const algebra::Vector3D &v) const
returns the direction vector for the displacement of point v relative to the pore walls of slab ...
A decorator for a residue.
Definition: Residue.h:137
double evaluate_indexes(Model *m, const ParticleIndexTriplets &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
virtual void apply_indexes(Model *m, const ParticleIndexes &o, unsigned int lower_bound, unsigned int upper_bound) const
virtual double evaluate_index(Model *m, ParticleIndex p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
IMP::ScoringFunction * get_custom_scoring_function(const RestraintsTemp &extra_restraints, SingletonContainerAdaptor non_optimizable_beads, SingletonContainerAdaptor optimizable_beads, bool is_attr_interactions_on=true) const
void add_fg_chain_stats(FGChain *fg_chain)
add statistics about an FG chain
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
SurfaceGeometry * get_constrained_surface_geometry(const Surface s, std::string name="SurfaceGeometry%1%")
Get surface geometry constrained to the surface.
Definition: Surface.h:236
Abstract predicate function.
Definition: PairPredicate.h:31
Joint * add_edge(IMP::core::RigidBody parent, IMP::core::RigidBody child)
RotamerRange get_rotamers_fast(IMP::atom::ResidueType residue, float phi, float psi, float probability_thr) const
query the rotamer library for the rotamer data
double evaluate_indexes(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
virtual void propagate_velocities(const ParticleIndexes &ps, double step_size)
Second part of velocity Verlet (update velocity)
Transformation3D get_transformation_3d(const Transformation2D &t2d)
Build a 3D transformation from a 2D one.
static bool get_is_setup(Model *m, ParticleIndex p)
Check if the particle has the needed attributes for a cast to succeed.
void do_segmentation(const cv::Mat &m, cv::Mat &result, const SegmentationParameters &params)
Segmentation of images.
void set_root(Particle *p)
Definition: FGChain.h:107
void add_radii(Hierarchy mhd, double scale=1.0, FloatKey radius_key=FloatKey("radius")) const
Add or replace radii in the structure defined in the hierarchy.
virtual double evaluate_index(Model *m, const ParticleIndexPair &p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
virtual void apply_index(Model *m, ParticleIndex v) const =0
Vector3D operator*(const Vector3D &v) const
Apply transformation (rotate and then translate)
ConfigurationSetRMSDMetric(ConfigurationSet *cs, SingletonContainer *sc, bool align=false)
void get_transformed(const cv::Mat &input, cv::Mat &transformed, const algebra::Transformation2D &T)
virtual double evaluate_index(Model *m, ParticleIndex p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
CompositeRestraint(Model *m, ParticleIndexesAdaptor handle_particle_indexes, double coffd, double l, bool tabprob, double plateau, std::string name="CompositeRestraint%1%")
Create the restraint.
Parameters used by Em2DRestraint and ProjectionFinder.
double evaluate_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
Value get_linearly_interpolated(const GridD< D, Storage, Value, Embedding > &g, const VectorD< D > &pt)
Get the value from the grid with linear interpolation.
Definition: grid_utility.h:23
virtual void setup_for_get_value_index_in_batch(Model *m) const
Represents a scoring function on the model.
Base class for joints between rigid bodies in a kinematic tree.
Definition: Joint.h:30
A class for fast alignment of a cyclic model to its density.
double get_rmsd(const core::XYZs &s0, const core::XYZs &s1)
Hierarchies read_multimodel_pdb(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector())
double evaluate_index(Model *m, const ParticleIndexPair &pip, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
void show_restraint_hierarchy(ScoringFunctionAdaptor rs, std::ostream &out=std::cout)
Print the hierarchy of restraints.
Store a configuration of a subset.
Definition: Assignment.h:32
double get_relative_projection_on_segment(const Segment3D &s, const algebra::Vector3D &p)
Return the 'relative' projection of a point p onto the line that contains s.
virtual void do_after_evaluate(DerivativeAccumulator *da)
Do any necessary updates after the model score is calculated.
void set_subject_image(em2d::Image *subject)
void set_cylinder_3d_geometry(Cylinder3D &g, const Cylinder3D &v)
Definition: Cylinder3D.h:78
void set_simulator(atom::Simulator *sim)
Use the simulator to tag frames with current time.
DependencyGraph get_pruned_dependency_graph(Model *m)
static CombineProvenance setup_particle(Model *m, ParticleIndex pi, int runs, int frames)
Definition: provenance.h:325
virtual void add_to_particle_derivative(unsigned particle_no, double value, DerivativeAccumulator &accum) const =0
update derivatives of particles
virtual double evaluate_indexes(Model *m, const ParticleIndexPairs &o, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
IMP::PairContainer * create_close_beads_container(SingletonContainerAdaptor non_optimiziable_beads, SingletonContainerAdaptor optimizable_beads) const
void set_vector_geometry(XYZ d, const algebra::Vector3D &v)
Definition: XYZ.h:131
virtual double get_strength(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
The strength is a rough metric of how this filter restricts the subset.
Restraints do_create_current_decomposition(Model *m, const ParticleIndexTriplet &vt) const
Override this to return your own decomposition.
atom::Hierarchies create_hierarchies_with_sites(RMF::FileConstHandle fh, Model *m)
virtual int get_value_index(IMP::Model *m, const IMP::ParticleIndexPair &p) const
Compute the predicate and the derivative if needed.
WeightRestraint(Particle *w, Float wmin, Float wmax, Float kappa)
Create the restraint.
virtual void apply_index(Model *m, const ParticleIndexTriplet &v) const =0
virtual int get_value_index(Model *, const ParticleIndexPair &pip) const
Compute the predicate and the derivative if needed.
AmbiguousRestraint(Model *m, int d, Restraint *r0, Restraint *r1)
Create the restraint.
virtual double evaluate_index(Model *m, const ParticleIndexTriplet &vt, DerivativeAccumulator *da) const =0
Compute the score and the derivative if needed.
Associate an integer "state" index with a hierarchy node.
Definition: State.h:27
ParticlesDummyRestraint(SingletonContainer *sc)
static SecondaryStructureResidue setup_particle(Model *m, ParticleIndex pi, Float prob_helix, Float prob_strand, Float prob_coil)
void read_from_ints(const String &filename, em::ImageHeader &header, cv::Mat &data) const
Reads an image file in TIFF format.
FitRestraint(ParticlesTemp ps, DensityMap *em_map, FloatPair norm_factors=FloatPair(0., 0.), FloatKey weight_key=atom::Mass::get_mass_key(), float scale=1, bool use_rigid_bodies=true, KernelType kt=GAUSSIAN)
Constructor.
virtual bool get_can_refine(Particle *) const
Return true if this refiner can refine that particle.
Joint(IMP::core::RigidBody parent, IMP::core::RigidBody child)
Constructor.
virtual void apply_index(Model *m, ParticleIndex pi) const
const algebra::Vector3D & get_vector_geometry(Particle *p)
Definition: XYZ.h:147
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
Eigen::Matrix3d get_covariance(const Gaussian3D &g)
double evaluate_if_good_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
double evaluate_if_good_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
const Line3D & get_line_3d_geometry(const Line3D &g)
Definition: Line3D.h:70
double evaluate_indexes_scores(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
void add_particle_indexes(std::string key, ParticleIndexes value)
Add ParticleIndexes referenced by the given key.
const Transformation2D & operator/=(const Transformation2D &o)
See help for operator/.
double evaluate_indexes_delta(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
virtual double evaluate_index(Model *m, const ParticleIndexPair &p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
static Diffusion setup_particle(Model *m, ParticleIndex pi, Float D)
Definition: Diffusion.h:58
virtual int get_value_index(Model *, const ParticleIndexTriplet &vt) const
Compute the predicate and the derivative if needed.
void add(const RadialDistributionFunction &model_pr)
add another distribution
SurfaceShellDensityMap * particles2surface(const ParticlesTemp &ps, Float apix, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key())
Resample a set of particles into a density grid.
void apply_generic(const TripletModifier *m) const
Just use apply() in the base class.
static ProjectionParameters setup_particle(Model *m, ParticleIndex pi)
static SampleProvenance setup_particle(Model *m, ParticleIndex pi, std::string method, int frames, int iterations, int replicas)
Definition: provenance.h:266
CrossLinkMSRestraint(IMP::Model *m, double length, bool get_log_prob=false, std::string name="CrossLinkMSRestraint%1%")
Create the restraint.
double operator()(unsigned int id1, unsigned int id2, const ClusterSet &cluster_set, const FloatsList &distances) const
double evaluate_moved(bool derivatives, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis)
Score when some particles have moved.
static TAMDParticle setup_particle(Model *m, ParticleIndex pi, ParticleIndex pi_ref, Float tsf, Float fsf)
Definition: TAMDParticle.h:80
void add_score_and_derivatives(ScoreAccumulator sa) const
Perform the actual restraint scoring.
double evaluate_indexes_scores(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
void pull_back_member_adjoints(ParticleIndex pi, DerivativeAccumulator &da)
Pull back global adjoints from member that is a point.
IMP::algebra::Transformation3D get_transformation_aligning_first_to_second(const IMP::atom::Selection &s1, const IMP::atom::Selection &s2)
Get the transformation to align two selections.
Residue get_residue(Atom d, bool nothrow=false)
Return the Residue containing this atom.
Restraints create_restraints(RMF::FileConstHandle fh, Model *m)
Shared optimizer state that is invoked upon commitment of new coordinates.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
DerivativeAccumulator(double weight=1.0)
the weight is one by default
vonMisesKappaJeffreysRestraint(Model *m, Particle *kappa)
Create the restraint.
void apply(const SingletonModifier *sm) const
Apply a SingletonModifier to the contents.
Hierarchy get_root(Hierarchy h)
Return the root of the hierarchy.
Abstract predicate function.
ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
double evaluate_indexes_scores(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
void add_hierarchies_with_sites(RMF::FileHandle fh, const atom::Hierarchies &hs)
Abstract class to implement hierarchical methods.
Definition: Refiner.h:34
virtual int get_value_index(Model *m, const ParticleIndexPair &pi) const
Compute the predicate and the derivative if needed.
Track creation of a system fragment from clustering.
Definition: provenance.h:426
KClosePairsPairScore(PairScore *f, Refiner *r, int k=1)
only score the k closest pairs.
PairsConstraint(PairModifier *before, PairModifier *after, PairContainerAdaptor c, std::string name="PairsConstraint %1%")
Profile * compute_profile(Particles particles, double min_q=0.0, double max_q=0.5, double delta_q=0.001, FormFactorTable *ft=get_default_form_factor_table(), FormFactorType ff_type=HEAVY_ATOMS, bool hydration_layer=true, bool fit=true, bool reciprocal=false, bool ab_initio=false, bool vacuum=false, std::string beam_profile_file="")
profile calculation for particles and a given set of options
Particles create_angles(Particles bonds) const
Auto-generate Angle particles from the passed list of Bond particles.
Restraints create_current_decomposition(Model *m, const ParticleIndexPair &vt) const
double R_factor_score(const RadialDistributionFunction &model_pr, const std::string &file_name="") const
analogy crystallographic R-factor score
static Reference setup_particle(Model *m, ParticleIndex pi, ParticleIndexAdaptor reference)
Definition: core/symmetry.h:32
double evaluate_if_good_indexes(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
BoundingBoxD< 3 > get_bounding_box(const Torus3D &g)
Definition: Torus3D.h:61
void multiply(const algebra::Transformation3D &t)
Definition: rigid_fitting.h:83
virtual double evaluate_indexes_delta(Model *m, const ParticleIndexes &o, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
virtual double evaluate_index(Model *m, ParticleIndex pi, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
double get_depth(const Surface &s, const XYZR &d)
Get depth of sphere below surface.
Definition: Surface.h:143
Store an array of values of the same type.
Definition: ConstVector.h:27
void set_enclosing_radius(XYZR b, const XYZs &v)
Set the radius of the first to enclose the list.
virtual double get_strength(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
The strength is a rough metric of how this filter restricts the subset.
double evaluate_indexes_scores(Model *m, const ParticleIndexQuads &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
void link_hierarchies(RMF::FileConstHandle fh, const atom::Hierarchies &hs)
Class to handle individual particles of a Model object.
Definition: Particle.h:41
Ints get_unique_index(const algebra::Rotation3D &rot)
Map a rotation to a list of 4 "unique" integers.
virtual ModelObjectsTemp do_get_inputs(Model *, const ParticleIndexes &) const
Overload this method to specify the inputs.
virtual const ParticlesTemp get_refined(Particle *) const
Refine the passed particle into a set of particles.
void remove_particle(Particle *p)
Remove a mapping from the table.
void profile_2_distribution(RadialDistributionFunction &rd, double max_distance) const
convert to real space P(r) function P(r) = 1/2PI^2 Sum(I(q)*qr*sin(qr))
double evaluate_indexes_scores(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
virtual double evaluate_indexes_delta(Model *m, const ParticleIndexQuads &o, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
double evaluate_if_good_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
void add_to_rotational_derivatives(const algebra::Vector4D &other_qderiv, const algebra::Rotation3D &rot_other_to_local, const algebra::Rotation3D &rot_local_to_global, DerivativeAccumulator &da)
double get_surface_area(const Selection &s)
Get the total surface area of a hierarchy, in square angstroms.
void set_ellipsoid_3d_geometry(Ellipsoid3D &g, const Ellipsoid3D &v)
Definition: Ellipsoid3D.h:46
A base class for modifiers of ParticleTripletsTemp.
void set_plane_3d_geometry(Plane3D &g, const Plane3D &v)
Definition: Plane3D.h:78
em::FittingSolutions fit_cn_assembly(atom::Hierarchies mhs, int dn_symm_deg, em::DensityMap *dmap, float threshold, const AlignSymmetric &aligner, bool sample_translation=false, bool fine_rotational_sampling=true)
Fit a symmetric model to its density.
void add_dope_score_data(atom::Hierarchy h)
BipartitePairsStatisticsOptimizerState(IMP::npctransport::Statistics *statistics_manager, InteractionType interaction_type, const ParticlesTemp &particlesI, const ParticlesTemp &particlesII, double contact_range=1.0, double slack=1.0)
DistanceFilter(const domino::Subset &subset_to_act_on, const domino::Subset &subset_to_restrain, domino::ParticleStatesTable *ps_table, double max_distance)
void set_model_particles(const ParticlesTemp &ps)
NOERestraint(Model *m, Particle *p0, Particle *p1, Particle *sigma, Particle *gamma, double Iexp)
Create the restraint.
Bond get_bond(Bonded a, Bonded b)
Get the bond between two particles.
virtual ModelObjectsTemp do_get_inputs(Model *, const ParticleIndexes &) const
Overload this method to specify the inputs.
void write_spheres(const Sphere3Ds &vs, TextOutput out)
Write a set of 3D spheres to a file.
virtual void apply_index(Model *m, ParticleIndex p) const
Base class for smoothing nonbonded interactions as a function of distance.
double evaluate_if_good_indexes(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
SubsetGraph get_restraint_graph(ScoringFunctionAdaptor rs, const ParticleStatesTable *pst)
void add_noise(cv::Mat &v, double op1, double op2, const String &mode="uniform", double df=3)
Add noise to the values of a matrix.
VectorD< D > operator*(double s, VectorD< D > o)
Definition: VectorD.h:193
void do_remove_small_objects(cvIntMat &m, double percentage, int background=0, int foreground=1)
Removes small objects from a matrix of integers.
static void teardown_particle(CenterOfMass com)
Make the particle no longer a center of mass.
virtual void apply(const DOFValues &values)
double evaluate_indexes_delta(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
virtual void apply_indexes_moved(Model *m, const ParticleIndexTriplets &o, unsigned int lower_bound, unsigned int upper_bound, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const
Restraint * create_distance_restraint(const Selection &n0, const Selection &n1, double x0, double k, std::string name="Distance%1%")
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
double evaluate_if_good_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
Class to manage registration results.
double evaluate_indexes_delta(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
void transform(RigidBody a, const algebra::Transformation3D &tr)
Transform a rigid body.
Definition: rigid_bodies.h:864
void apply_generic_moved(const TripletModifier *m, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const
Just use apply_moved() in the base class.
double evaluate_index(algebra::Sphere3D const &s0, algebra::Sphere3D const &s1, algebra::Sphere3D &ds0, algebra::Sphere3D &ds1, DerivativeAccumulator *da) const
SingletonsConstraint(SingletonModifier *before, SingletonModifier *after, SingletonContainerAdaptor c, std::string name="SingletonsConstraint %1%")
virtual void apply(const DOFValues &values)
Auxiliary class for FRET_R restraint.
Definition: FretData.h:22
Representation get_representation(Hierarchy h, bool nothrow=false)
Return the Representation object containing this hierarchy.
virtual void apply(const DOFValues &values)=0
double evaluate_indexes_scores(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
QuadsOptimizerState(QuadContainerAdaptor c, QuadModifier *gf, std::string name="QuadsOptimizerState %1%")
void resample(const Profile *exp_profile, Profile *resampled_profile) const
return a profile that is sampled on the q values of the exp_profile
FloatPair get_placement_score(const core::XYZs &source, const core::XYZs &target)
Measure the difference between two placements of the same set of points.
virtual double evaluate_index(Model *m, ParticleIndex vt, DerivativeAccumulator *da) const =0
Compute the score and the derivative if needed.
double get_radius_of_gyration(const ParticlesTemp &ps, bool weighted=true)
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
std::pair< double, algebra::Vector3Ds > evaluate(DensityMap *em_map, SampledDensityMap *model_map, const algebra::Vector3Ds &deriv, float scalefac, bool lderiv, unsigned long eval_interval)
Evaluate the cross-correlation value only every X calls to the function.
GlobalStatisticsOptimizerState(IMP::npctransport::Statistics *statistics_manager=nullptr, unsigned int periodicity=1)
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
double evaluate_index(Model *m, const ParticleIndexPair &p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
Ints get_in_ball(unsigned int i, double distance) const
Find all points within the provided distance.
void assign_blame(const RestraintsTemp &rs, const ParticlesTemp &ps, FloatKey attribute)
void set(const char *fname, const Object *object=nullptr)
Assign new properties to the class.
The topology of a single CHARMM segment in a model.
SampledDensityMap(KernelType kt=GAUSSIAN)
Creates a new density map for sampled map.
void set_reference_frame_from_members(const ParticleIndexes &members)
PairPredicate * create_in_container_filter(Container *c, std::string name=std::string())
double evaluate_index(Model *m, const ParticleIndexPair &p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
RadiusOfGyrationRestraint(const Particles &particles, const Profile *exp_profile, const double end_q_rg=1.3)
Constructor.
void read_files(Model *m, const std::vector< std::string > &files, std::vector< std::string > &pdb_file_names, std::vector< std::string > &dat_files, std::vector< IMP::Particles > &particles_vec, Profiles &exp_profiles, bool residue_level=false, bool heavy_atoms_only=true, int multi_model_pdb=2, bool explicit_water=false, float max_q=0.0, int units=1)
Parse PDB and profile files.
double evaluate_indexes_delta(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
algebra::Segment3D get_segment_connecting_first_to_second(const Line3D &a, const Line3D &b)
Get shortest possible segment from the first line to the second.
LowestRefinedPairScore(Refiner *r, PairScore *f)
double evaluate_index(Model *m, const ParticleIndexPair &p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
static Key< ID > add_alias(Key< ID > old_key, std::string new_name)
Make new_name an alias for old_key.
Definition: Key.h:184
void write_multimodel_pdb(const Hierarchies &mhd, TextOutput out)
Vector< VectorD< D > > get_grid_interior_cover_by_spacing(const BoundingBoxD< D > &bb, double s)
virtual void apply_index(IMP::Model *m, IMP::ParticleIndex p) const
void set_sphere_patch_3d_geometry(SpherePatch3D &g, const SpherePatch3D &v)
Definition: SpherePatch3D.h:48
void set_secondary_structure_probabilities(const Particles &ssres_ps, const Ints &indices=Ints())
Assign secondary structure particles. Provide indices if out of order.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
StateAdaptor(Model *m, OptimizerState *before, OptimizerState *after)
set the before and after states
FittingSolutions local_rigid_fitting_around_points(Particle *p, Refiner *refiner, const FloatKey &wei_key, DensityMap *dmap, const algebra::Vector3Ds &anchor_centroids, OptimizerStates display_log, Int number_of_optimization_runs=5, Int number_of_mc_steps=10, Int number_of_cg_steps=100, Float max_translation=2., Float max_rotation=.3)
Local rigid fitting of a rigid body around a set of center points.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
virtual ModelObjectsTemp do_get_inputs(Model *, const ParticleIndexes &) const
Overload this method to specify the inputs.
virtual double get_strength(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
The strength is a rough metric of how this filter restricts the subset.
void add_geometry(RMF::FileHandle file, display::Geometry *r)
Add a single geometry to the file.
FittingSolutions local_rigid_fitting_grid_search(const ParticlesTemp &ps, const FloatKey &wei_key, DensityMap *dmap, Int max_voxels_translation=2, Int translation_step=1, Float max_angle_in_radians=0.174, Int number_of_rotations=100)
Local grid search rigid fitting.
bool get_contains(const VectorD< D > &o) const
True if the point o is contained within this bounding box.
Definition: BoundingBoxD.h:145
Store info for a chain of a protein.
Definition: Chain.h:61
TransformationSymmetry(const algebra::Transformation3D &t)
Create with both rotation and translation.
const Vector< double > & get_dummy_form_factors(Particle *p, FormFactorType ff_type=HEAVY_ATOMS) const
for reciprocal space profile calculation
void add_to_weight_derivative(int i, Float dwi, const DerivativeAccumulator &da)
Add to derivative wrt ith weight.
void add_well_depths(Hierarchy mhd) const
Add LennardJones well depths to the structure.
double evaluate_index(Model *m, const ParticleIndexPair &pip, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
void set_ff_table(FormFactorTable *ff_table)
required for reciprocal space calculation
Definition: Profile.h:197
void reset_box_size(SimulationData *sd, double box_size)
change box size sd to specified box size and update output file
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pi) const
Overload this method to specify the inputs.
void read_from_ints(const String &filename, em::ImageHeader &header, cv::Mat &data) const
Reads an image file in JPG format.
PrismaticJoint(IMP::core::RigidBody parent, IMP::core::RigidBody child, IMP::core::XYZ a, IMP::core::XYZ b)
QuadsRestraint(QuadScore *ss, QuadContainerAdaptor pc, std::string name="QuadsRestraint %1%")
Create the restraint with a shared container.
virtual double evaluate_indexes(Model *m, const ParticleIndexPairs &pips, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
double evaluate_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
double evaluate_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
double evaluate_indexes(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
double get_form_factor(Particle *p, FormFactorType ff_type=HEAVY_ATOMS) const
get f(0), ie q=0 for real space profile calculation
virtual void apply_indexes(Model *m, const ParticleIndexes &o, unsigned int lower_bound, unsigned int upper_bound) const
double evaluate_indexes_delta(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
Keep track of multiple states.
int get_copy_index(Hierarchy h)
Walk up the hierarchy to find the current copy index.
double evaluate_indexes_delta(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
Restraint * create_chain_restraint(Model *m, const ParticleIndexes &ps, double length_factor, double k, std::string name)
double get_rmsd_transforming_first(const IMP::algebra::Transformation3D &tr, const core::XYZs &s0, const core::XYZs &s1)
A decorator for helping deal with a generalized hierarchy.
CHARMMResidueTopology(ResidueType type)
Create an empty topology, containing no atoms or bonds.
virtual int get_value_index(Model *m, const ParticleIndexTriplet &pi) const
Compute the predicate and the derivative if needed.
virtual void apply_indexes(Model *m, const ParticleIndexes &o, unsigned int lower_bound, unsigned int upper_bound) const
virtual int get_value_index_in_batch(Model *m, const ParticleIndexTriplet &pi) const
double get_maximum_time_step_estimate(BrownianDynamics *bd)
void set_model_particles(const ParticlesTemp &ps)
Set the particles where the em2D restraint is applied.
void write(const char *filename, const float *data, const DensityHeader &header)
Writes a map in Spider format from data and header.
int operator()(Model *m, const ParticleIndexQuad &vt) const
Enable them to be use as functors.
Definition: QuadPredicate.h:65
double evaluate_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
double evaluate_index(Model *m, const ParticleIndexPair &pip, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
virtual double evaluate_if_good_index(Model *m, const ParticleIndexPair &vt, DerivativeAccumulator *da, double max) const
Compute the score and the derivative if needed, only if "good".
ReferenceFrame3D()
Create the default reference frame.
A base class for modifiers of ParticleQuadsTemp.
Definition: QuadModifier.h:32
const Torus3D & get_torus_3d_geometry(const Torus3D &g)
Definition: Torus3D.h:61
Score the model efficiently when a small number of particles are changed.
virtual ModelObjectsTemp do_get_inputs(Model *, const ParticleIndexes &) const
Overload this method to specify the inputs.
virtual double evaluate_if_good_index(Model *m, const ParticleIndexPair &vt, DerivativeAccumulator *da, double max) const
Compute the score and the derivative if needed, only if "good".
void add(const algebra::VectorD< D > &x, double weight=1)
Definition: HistogramD.h:35
virtual double evaluate_if_good_indexes(Model *m, const ParticleIndexTriplets &o, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
Track how parts of the system were created.
Definition: provenance.h:31
virtual int get_value_index_in_batch(Model *m, const ParticleIndexPair &pi) const
virtual void apply_indexes_moved(Model *m, const ParticleIndexPairs &o, unsigned int lower_bound, unsigned int upper_bound, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const
Definition: PairModifier.h:58
double evaluate_indexes_delta(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
DensityMap * get_transformed(const DensityMap *input, const algebra::Transformation3D &tr, double threshold)
Return a new density map containing a rotated version of the old one.
void set_particle_states(Particle *p, ParticleStates *e)
virtual double evaluate_index(Model *m, const ParticleIndexPair &pip, DerivativeAccumulator *da) const
evaluate score for particle pair pip in model m
virtual ModelObjectsTemp do_get_outputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the outputs.
double compute_score(const Profile *model_profile, bool use_offset=false, const std::string fit_file_name="") const
compute fit score
void apply_transform_safely(IMP::algebra::Transformation3D tr)
apply a rigid body transformation to the entire forest safely
double get_resolution(Model *m, ParticleIndex pi)
Estimate the resolution of the hierarchy as used by Representation.
A decorator for a rigid body.
Definition: rigid_bodies.h:82
double get_rmsd_transforming_first(const Transformation3D &tr, const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2)
Calculate the root mean square deviation between two sets of 3D points.
virtual void apply_index(Model *m, ParticleIndex p) const
void add_to_weights_derivatives(const algebra::VectorKD &dw, const DerivativeAccumulator &da)
Add to derivatives wrt all weights.
ConstantRestraint(Model *m, Float v)
Add v to the total score.
The topology of a complete CHARMM model.
virtual ModelObjectsTemp do_get_outputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the outputs.
virtual int get_value_index(Model *m, const ParticleIndexPair &vt) const =0
Compute the predicate and the derivative if needed.
A Cartesian vector in D-dimensions.
Definition: VectorBaseD.h:50
BoundingBoxD< 3 > get_bounding_box(const Line3D &g)
Definition: Line3D.h:70
virtual int get_value_index(Model *, const ParticleIndexQuad &) const
Compute the predicate and the derivative if needed.
Dynamically build a histogram embedded in D-dimensional space.
Definition: HistogramD.h:27
double evaluate_indexes_delta(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
virtual void apply_index(Model *m, ParticleIndex a) const
algebra::Transformation3D get_transformation_aligning_first_to_second(const Selection &s1, const Selection &s2)
Get the transformation to align two selections.
A shared container for Triplets.
bool get_is_heterogen(Hierarchy h)
Return true if the piece of hierarchy should be classified as a heterogen.
QuadContainerSet(Model *m, std::string name="QuadContainerSet %1%")
Construct an empty set.
double get_maximum_range(Model *m, const Array< D, ParticleIndex > &p) const
Return an upper bound on the distance at which the score can be non-zero.
Definition: AddScores.h:49
DynamicListSingletonContainer * add_predicate(SingletonPredicate *predicate, int value)
void add(const ParticleIndexQuad &vt)
Add a single const ParticleIndexQuad& to the container.
ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
Represent a plane in 3D.
Definition: Plane3D.h:20
DihedralRestraint(Model *m, UnaryFunction *score_func, ParticleIndexAdaptor p1, ParticleIndexAdaptor p2, ParticleIndexAdaptor p3, ParticleIndexAdaptor p4)
Create the dihedral restraint.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
RigidBodyNewMover(core::RigidBody d, Float max_x_translation, Float max_y_translation, Float max_z_translation, Float max_rot)
void add_to_derivative(int i, Float v, DerivativeAccumulator &d)
Definition: XYZ.h:78
void add_chain_restraints(FGChain *chain)
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
Hierarchies get_by_type(Hierarchy mhd, GetByType t)
Gather all the molecular particles of a certain level in the hierarchy.
double evaluate_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
DerivativesFromRefined(Refiner *r, FloatKeys ks=XYZ::get_xyz_keys())
Copy ks from the particles returned by r.
static bool get_is_setup(Model *m, ParticleIndex pi)
return true if the particle has a name
double evaluate_indexes_scores(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
void load_vertex_assignments(unsigned int node_index, AssignmentContainer *ac, unsigned int max_states=std::numeric_limits< int >::max()) const
Fill in assignments for a leaf.
Restraints get_chain_restraints_on(SingletonContainerAdaptor beads) const
void load_last_score(Restraint *r, const Subset &s, const Assignment &a)
Make it so Restraint::get_last_score() returns the score.
ResidueRotamer get_rotamer(const IMP::atom::Residue &rd, double thr) const
get the coordinates of the residue atoms
double evaluate_indexes_delta(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
virtual int get_next_state(int pos, const Assignment &state) const
Return a next possible acceptable state for the particle in pos.
void write(const char *fn_out, const float *data, const DensityHeader &head)
Writes an MRC file from the data and the general DensityHeader.
Hierarchy create_simplified_assembly_from_volume(Hierarchy h, double resolution)
void load_particle_states(const Subset &s, const Assignment &ss, const ParticleStatesTable *pst)
Load the appropriate state for each particle in a Subset.
FGChain * get_fg_chain(atom::Hierarchy root)
void set_bounding_box(const algebra::BoundingBoxD< 3 > &bb)
Set the bounding box for randomizing the Cartesian coordinates.
std::string get_chain_id(Hierarchy h)
Walk up the hierarchy to determine the chain id.
Define and manipulate a kinematic structure over a model.
Float get_molecular_mass_at_threshold(DensityMap *m, Float threshold, atom::ProteinDensityReference ref=atom::HARPAZ)
Compute an approximate molecular mass.
Vector< VectorD< D > > get_uniform_upper_hemisphere_cover(const SphereD< D > &s, unsigned int n)
Generate a set of 3D points that uniformly cover a hemisphere.
container::PredicatePairsRestraint * create_predicates_pair_restraint(PairContainer *bead_pairs, bool is_attr_interactions_on=true) const
Assignments get_sample_assignments(const Subset &s) const
virtual void apply_indexes(Model *m, const ParticleIndexes &o, unsigned int lower_bound, unsigned int upper_bound) const
Abstract class for scoring object(s) of type ParticleIndexTriplet.
Definition: TripletScore.h:42
IMP::core::RigidBody create_rigid_body(const Hierarchies &h, std::string name=std::string("created rigid body"))
Rigidify a molecule or collection of molecules.
void add_provenance(Model *m, ParticleIndex pi, Provenance p)
Add provenance to part of the model.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pi) const
Overload this method to specify the inputs.
Particle(Model *m, std::string name)
Construct a particle and add it to the Model.
boost::tuple< unsigned int, std::vector< unsigned int >, std::vector< unsigned int >, bool > get_site_interactions_statistics(ParticleIndex pi1, ParticleIndex pi2) const
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
Hierarchies get_leaves(Hierarchy h)
void set_local_optimizer(Optimizer *opt)
Set a local optimizer to use instead of ConjugateGradients.
static Chain setup_particle(Model *m, ParticleIndex pi, std::string id)
Definition: Chain.h:81
Hierarchies get_leaves(const Selection &h)
PCAFitRestraint(Particles particles, const std::vector< std::string > &image_files, double pixel_size, double resolution=10.0, unsigned int projection_number=100, bool reuse_direction=false, unsigned int n_components=1)
Constructor.
virtual void do_after_evaluate(DerivativeAccumulator *da)
Do any necessary updates after the model score is calculated.
virtual double evaluate_if_good_index(Model *m, const ParticleIndexPair &vt, DerivativeAccumulator *da, double max) const
Compute the score and the derivative if needed, only if "good".
double evaluate_indexes(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
void set_residue_type(ResidueType t)
Update the stored ResidueType and the atom::Hierarchy::Name.
boost::tuple< Restraint *, Object * > create_backbone_restraint(double rest_length_factor, double backbone_k, ParticlesTemp beads, std::string name) const
Create a backbone bond restraint over beads according to class flags.
virtual void do_after_evaluate(DerivativeAccumulator *da)
Do any necessary updates after the model score is calculated.
Select which atoms to read from a PDB file.
Definition: pdb.h:40
void do_add_score_and_derivatives(IMP::ScoreAccumulator sa, const ScoreStatesTemp &ss)
double evaluate_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pi) const
Overload this method to specify the inputs.
PartitionalClustering * create_centrality_clustering(Metric *d, double far, int k)
virtual int get_value_index(Model *m, ParticleIndex pi) const
Compute the predicate and the derivative if needed.
double evaluate_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
Definition: KinkPairScore.h:35
A decorator for a molecule.
Definition: Molecule.h:24
CentroidOfRefined(Refiner *r, FloatKey weight=FloatKey(), FloatKeys ks=XYZ::get_xyz_keys())
Set the keys ks to be the average of the refined particles.
static ScriptProvenance setup_particle(Model *m, ParticleIndex pi, std::string filename)
Definition: provenance.h:548
double evaluate_index(Model *m, const ParticleIndexPair &pip, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
Select hierarchy particles identified by the biological name.
Definition: Selection.h:66
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
virtual IMP::ModelObjectsTemp do_get_inputs(IMP::Model *m, const IMP::ParticleIndexes &pis) const
Overload this method to specify the inputs.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
double get_distance(const Surface &s, const XYZR &d)
Get distance from sphere to surface.
Definition: Surface.h:153
void set_reference_frame_lazy(const IMP::algebra::ReferenceFrame3D &tr)
Change the reference, delay updating the members until evaluate.
Definition: rigid_bodies.h:242
double evaluate_index(Model *m, const ParticleIndexPair &pip, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
double evaluate_if_good_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
double evaluate_indexes_delta(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
CysteineCrossLinkRestraint(Model *m, ParticleIndexAdaptor beta, ParticleIndexAdaptor sigma, ParticleIndexAdaptor epsilon, ParticleIndexAdaptor weight, CrossLinkData *data, double fexp)
Create the restraint.
double do_evaluate_index(algebra::Sphere3D &d_xyzr0, algebra::Sphere3D &d_xyzr1, DerivativeAccumulator *da, const algebra::Vector3D &delta, double delta_length, double x0, double k)
DihedralAngleRevoluteJoint(IMP::core::RigidBody parent, IMP::core::RigidBody child, IMP::core::XYZ a, IMP::core::XYZ b, IMP::core::XYZ c, IMP::core::XYZ d)
ParticleIndexes get_indexes(const ParticlesTemp &ps)
Get the indexes from a list of particles.
DensityMap * get_segment(DensityMap *map_to_segment, int nx_start, int nx_end, int ny_start, int ny_end, int nz_start, int nz_end)
Get a segment of the map according to xyz indexes.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
virtual ModelObjectsTemp do_get_inputs(Model *, const ParticleIndexes &) const
Overload this method to specify the inputs.
Vector3Ds get_grid_surface_cover(const Cylinder3D &cyl, int number_of_cycles, int number_of_points_on_cycle)
Generate a grid of 3d points on a cylinder surface.
virtual double evaluate_indexes_scores(Model *m, const ParticleIndexPairs &o, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
double evaluate_indexes_scores(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
ModelObjectsTemp get_outputs(Model *m, const ParticleIndexes &pis) const
Get the ModelObjects changed when the given list of particles is used.
double radius_of_gyration(const Particles &particles)
compute radius_of_gyration
Definition: saxs/utility.h:74
Constraint * create_constraint(Before *b, After *a, Container *c, std::string name=std::string())
double compute_scale_factor(const Profile *model_profile, double offset=0.0) const
computes the scaling factor needed for fitting the modeled profile
Definition: ProfileFitter.h:76
Atoms get_atoms(const CHARMMResidueTopology *current_residue, const CHARMMResidueTopology *previous_residue, const CHARMMResidueTopology *next_residue, const std::map< const CHARMMResidueTopology *, Hierarchy > &resmap) const
Map the bond to a list of Atom particles.
algebra::VectorKDs get_centroids(Embedding *d, PartitionalClustering *pc)
virtual ParticleIndexes const & get_refined_indexes_by_ref(Model *m, ParticleIndex pi) const
Return the indexes of the particles returned by get_refined()
Definition: FixedRefiner.h:61
static RigidBody setup_particle(Model *m, ParticleIndex pi, ParticleIndexesAdaptor ps)
Definition: rigid_bodies.h:174
Abstract class for containers of particles.
void add_missing_atoms(Hierarchy hierarchy) const
Add any missing atoms to the given Hierarchy using this topology.
void set_unknown_score(TripletScore *score)
virtual int get_value_index(Model *m, ParticleIndex vt) const =0
Compute the predicate and the derivative if needed.
QuadConstraint(QuadModifier *before, QuadDerivativeModifier *after, const ParticleQuad &vt, std::string name="QuadConstraint %1%")
Slice get_slice(Restraint *r, const Subset &s) const
Return the slice for that restraint given the subset.
GridD()
An empty, undefined grid.
Definition: GridD.h:201
double evaluate_index(Model *m, const ParticleIndexPair &p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
virtual ModelObjectsTemp do_get_inputs(Model *, const ParticleIndexes &) const
Overload this method to specify the inputs.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
double evaluate_indexes_scores(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
TripletConstraint(TripletModifier *before, TripletDerivativeModifier *after, const ParticleTriplet &vt, std::string name="TripletConstraint %1%")
void add_to_derivatives(const algebra::Vector3D &local_derivative, const algebra::Vector3D &local_location, DerivativeAccumulator &da)
void set_score(int predicate_value, TripletScore *score)
void set_intersection(const Selection &s)
Select elements that are in both this Selection and the passed one.
void calculate_derivative_distribution(Particle *particle)
calculates distribution for an atom defined by particle
Represent a sphere in D-dimensions.
Definition: SphereD.h:25
void update_particle_type_zr_distribution_map(Particle *p)
static Floats get_reduced_coordinates(Model *m, ParticleIndex target, ParticleIndex ref)
returns center of mass and quaternion of rotation wrt ref
void create(const em::KernelParameters &kparams, double mass=1.0)
Generates the mask.
A base class for choosing which Mol2 atoms to read.
Definition: mol2.h:26
double evaluate_indexes_delta(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
void add_particle(Particle *p, const ParticlesTemp &ps)
Add a mapping to the table.
void read_particles_from_buffer(const Vector< char > &buffer, const ParticlesTemp &particles, const FloatKeys &keys)
load found attributes into the particles
double evaluate_indexes(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
Compute the score and the derivative if needed over a set.
virtual double evaluate_index(Model *m, ParticleIndex p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
GridIndexD< D > add_voxel(const ExtendedGridIndexD< D > &i, const VT &gi)
Add a voxel to the storage, this voxel will now have a GridIndex3D.
double evaluate_indexes_scores(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
double evaluate_indexes_delta(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
Hierarchy get_next_residue(Residue rd)
Return the residue from the same chain with one higher index.
Abstract single variable functor class for score functions.
Definition: UnaryFunction.h:25
double evaluate_indexes_scores(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const
Compute the score and the derivative if needed over a set.
virtual const ParticlesTemp get_refined(Particle *) const
Refine the passed particle into a set of particles.
CHARMMTopology * create_topology(Hierarchy hierarchy) const
Create topology that corresponds to the primary sequence of the Hierarchy.
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const
RRT(Model *m, DOFsSampler *sampler, LocalPlanner *planner, const DOFs &cspace_dofs, unsigned int iteration_number=1000, unsigned int tree_size=100, unsigned int number_of_sampled_dofs=0)
Constructor.
Track creation of a system fragment from running a script.
Definition: provenance.h:511
virtual bool operator()(Hierarchy p)
Return true if the traversal should visit this node's children.
AllPairContainer(SingletonContainerAdaptor c, std::string name="AllPairContainer%1%")
Get the individual particles from the passed SingletonContainer.
DynamicListPairContainer(Container *scope, std::string name="ListPairContainer %1%")
void set_enclosing_sphere(XYZR b, const XYZs &v, double slack=0)
Set the coordinates and radius of the first to enclose the list.
virtual void apply_index(Model *m, ParticleIndex p) const
double get_distance(const Line3D &s, const Vector3D &p)
Get closest distance between a line and a point.
DensityMap * get_cropped(float threshold)
Create and return a new cropped map.
ResidueType get_residue_type(char c)
Get the residue type from the 1-letter amino acid code.
double evaluate_indexes_delta(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
virtual void apply_index(IMP::Model *m, IMP::ParticleIndex p) const
RigidBodiesImageFitRestraint(ScoreFunction *scf, const core::RigidBodies &rbs, Image *img)
Initialize the class.
virtual double evaluate_index(Model *m, const ParticleIndexPair &vt, DerivativeAccumulator *da) const =0
Compute the score and the derivative if needed.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
double get_volume(const Cylinder3D &g)
Definition: Cylinder3D.h:78
virtual void apply_indexes(Model *m, const ParticleIndexes &o, unsigned int lower_bound, unsigned int upper_bound) const
Definition: core/symmetry.h:67
virtual void apply_indexes(Model *m, const ParticleIndexPairs &o, unsigned int lower_bound, unsigned int upper_bound) const
Definition: PairModifier.h:46
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
void add_bonds(Hierarchy d, const ForceFieldParameters *ffp=get_all_atom_CHARMM_parameters())
Class for adding derivatives from restraints to the model.
ProteinKinematics(atom::Hierarchy mhd, bool flexible_backbone=true, bool flexible_side_chains=false)
Constructor with all phi/psi rotatable.
double evaluate_indexes_delta(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
Compute the change in score and the derivative if needed over a set.
A particle that is the center of mass of other particles.
Definition: CenterOfMass.h:33
ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
virtual void add_to_derivatives(const Floats &x, DerivativeAccumulator &accum) const =0
update derivatives of particles
ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
2D Electron Microscopy images in IMP
Definition: Image.h:27
CAAngleRestraint(Model *m, ParticleIndexAdaptor p1, ParticleIndexAdaptor p2, ParticleIndexAdaptor p3, Floats phi0, Floats score)
Create the angle restraint.
double evaluate_if_good_indexes(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
virtual double evaluate_index(Model *m, ParticleIndex p, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
A text label for a ball in space.
virtual int get_value_index(IMP::Model *m, const IMP::ParticleIndexPair &p) const
Compute the predicate and the derivative if needed.
void write_fit_file(ProfilesTemp partial_profiles, const WeightedFitParameters &fp, const std::string fit_file_name, bool use_offset=false) const
write a fit file
double evaluate_if_good_indexes(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
Definition: predicates.h:130
Statistics(SimulationData *sd, unsigned int statistics_interval_frames, std::string output_file_name)
BoundingBoxD< 3 > get_bounding_box(const SpherePatch3D &g)
Definition: SpherePatch3D.h:48
A base class for clustering results where each item is in one cluster.
void get_projection(em2d::Image *img, const ParticlesTemp &ps, const RegistrationResult &reg, const ProjectingOptions &options, MasksManagerPtr masks=MasksManagerPtr(), String name="")
Generates a projection from particles.
virtual int get_value_index(Model *, const ParticleIndexPair &) const
Compute the predicate and the derivative if needed.
Float get_threshold_for_approximate_volume(DensityMap *m, Float desired_volume)
Computes the threshold consider in an EM map to get a desired volume.
TripletsOptimizerState(TripletContainerAdaptor c, TripletModifier *gf, std::string name="TripletsOptimizerState %1%")
Ints get_representatives(Embedding *d, PartitionalClustering *pc)
Float get_epsilon(Atom atom) const
get epsilon for non bonded vdW
Float get_volume_at_threshold(DensityMap *m, Float threshold)
Compute an approximate volume.
WeightMover(Particle *w, Float radius)
VectorD(const Range &r)
Will accept a list of floats from Python.
Definition: VectorD.h:55
A restraint is a term in an IMP ScoringFunction.
Definition: Restraint.h:54
void set_difference(const Selection &s)
Select elements that are in this Selection but not the passed one.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.
Slice get_slice(Subset outer, Subset inner, const Subsets &excluded)
Definition: Slice.h:66
void transform_safe(IMP::algebra::Transformation3D tr)
double get_power_distance(const SphereD< D > &a, const SphereD< D > &b)
Return the power distance between the two spheres.
Definition: SphereD.h:123
virtual IMP::ModelObjectsTemp do_get_inputs(IMP::Model *m, const IMP::ParticleIndexes &pis) const
Overload this method to specify the inputs.
virtual void apply_indexes(Model *m, const ParticleIndexes &o, unsigned int lower_bound, unsigned int upper_bound) const
Definition: Transform.h:36
Store data to be clustered for distance metric based algorithms.
Definition: Metric.h:25
RefinedPairsPairScore(Refiner *r, PairScore *f)
virtual ModelObjectsTemp do_get_outputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the outputs.
double evaluate_if_good_indexes(Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
atom::Hierarchy create_coarse_molecule_from_density(em::DensityMap *dmap, float dens_threshold, int num_beads, Model *mdl, float bead_radius)
Coarsen a density map based on voxels clustering.
virtual int get_value_index(Model *m, ParticleIndex pi) const
Compute the predicate and the derivative if needed.
Definition: predicates.h:48
RigidBodyDistancePairScore(PairScore *ps, Refiner *r)
void set(Object *o, CheckLevel l)
Assign new properties to the class.
Definition: SetCheckState.h:43
double evaluate_if_good_indexes(Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
A decorator for a particle with x,y,z coordinates and a radius.
Definition: XYZR.h:27
ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
Overload this method to specify the inputs.