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IMP Reference Guide  2.19.0
The Integrative Modeling Platform
factory_index.md
1 Factory Index {#factory_index}
2 =============
3 
4 # Overview #
5 [TOC]
6 Functions that create objects of a given type:
7 
8 See also [Argument Index](@ref argument_index), [Class Examples](@ref class_example_index), [Function Examples](@ref function_example_index)
9 # IMP (kernel) # {#factory_index_kernel}
10 <table><tr>
11 <th>Class</th><th>Factories</th></tr>
12 <tr><td>@ref IMP::AdvancedFlag</td><td><a href="classIMP_1_1AdvancedFlag.html#ac0d94f9da4199a977bf2fd252dd07c96">IMP::AdvancedFlag::operator=()</a></td></tr>
13 <tr><td>@ref IMP::Array</td><td><a href="classIMP_1_1isd_1_1AtomicCrossLinkMSRestraint.html#ad3a2d2fa3c4d2f50b39ec121dac14d33">IMP::isd::AtomicCrossLinkMSRestraint::get_contribution()</a>, <a href="classIMP_1_1isd_1_1AtomicCrossLinkMSRestraint.html#ad294c62610174e2a31c1e1ac03ac9bc3">IMP::isd::AtomicCrossLinkMSRestraint::get_contribution_sigmas()</a>, <a href="classIMP_1_1isd_1_1CrossLinkMSRestraint.html#a8dc02b39b1ebe8e2698abbae8edf6085">IMP::isd::CrossLinkMSRestraint::get_contribution_particle_indexes()</a>, <a href="classIMP_1_1isd_1_1CrossLinkMSRestraint.html#aca287f8352a7fa0931cbdc3ba741247f">IMP::isd::CrossLinkMSRestraint::get_contribution_sigma_indexes()</a>, <a href="namespaceIMP_1_1npctransport.html#a87e4abb800a27fa45024be5679f60084">IMP::npctransport::make_unordered_particle_index_pair()</a>, <a href="namespaceIMP_1_1npctransport.html#a795fe17c17d57c27a5b28f7a9d6d02a3">IMP::npctransport::make_unordered_particle_index_pair()</a></td></tr>
14 <tr><td>@ref IMP::ConfigurationSet</td><td><a href="classIMP_1_1Sampler.html#a9843aae8ed03575f4dd0711c630b8989">IMP::Sampler::create_sample()</a>, <a href="classIMP_1_1Sampler.html#affb28d22d703c4bae56ae21ca0a338b1">IMP::Sampler::do_sample()</a>, <a href="classIMP_1_1core_1_1MCCGSampler.html#a22361abcf3f61ba597bc34c95eee1456">IMP::core::MCCGSampler::do_sample()</a>, <a href="classIMP_1_1core_1_1MCCGSampler.html#a3c2641088f310a8d9ea56e875209454a">IMP::core::MCCGSampler::get_rejected_configurations()</a>, <a href="classIMP_1_1domino_1_1DiscreteSampler.html#a6fb723e7f691731d02b1a1318bfeb8eb">IMP::domino::DiscreteSampler::do_sample()</a>, <a href="classIMP_1_1kinematics_1_1RRT.html#ad73acd098283e23bd42af76cb78b7788">IMP::kinematics::RRT::do_sample()</a></td></tr>
15 <tr><td>@ref IMP::Constraint</td><td><a href="classIMP_1_1atom_1_1CenterOfMass.html#a3d4a0d52dd4a6430c7ca70b76236cbd7">IMP::atom::CenterOfMass::get_constraint()</a>, <a href="classIMP_1_1core_1_1Centroid.html#ae00729aa7256523a7ae601d1b04d59b1">IMP::core::Centroid::get_constraint()</a>, <a href="classIMP_1_1core_1_1Cover.html#acbba65724f3b5cc5ccba6230030bb5a7">IMP::core::Cover::get_constraint()</a></td></tr>
16 <tr><td>@ref IMP::DerivativeAccumulator</td><td><a href="classIMP_1_1DerivativeAccumulator.html#a178f0d7f32a13a18c6c018c60c8b7fa9">IMP::DerivativeAccumulator::operator=()</a>, <a href="classIMP_1_1ScoreAccumulator.html#aa7fc7bf106ff7b6e425a6654d8e045f8">IMP::ScoreAccumulator::get_derivative_accumulator()</a></td></tr>
17 <tr><td>@ref IMP::EventException</td><td><a href="classIMP_1_1EventException.html#a4873604cfcfb61d46a32516adc787c16">IMP::EventException::operator=()</a></td></tr>
18 <tr><td>@ref IMP::Exception</td><td><a href="classIMP_1_1Exception.html#ac6c95788621f6c7a5ced14795a47ff1c">IMP::Exception::operator=()</a></td></tr>
19 <tr><td>@ref IMP::Flag</td><td><a href="classIMP_1_1Flag.html#ade738dcb229586691745bb7208a371ef">IMP::Flag::operator=()</a></td></tr>
20 <tr><td>@ref IMP::IOException</td><td><a href="classIMP_1_1IOException.html#a4d680ce4aaf59c9a653eff24701893ac">IMP::IOException::operator=()</a></td></tr>
21 <tr><td>@ref IMP::IndexException</td><td><a href="classIMP_1_1IndexException.html#a9f58eddac579049208c04326093b7d88">IMP::IndexException::operator=()</a></td></tr>
22 <tr><td>@ref IMP::Key</td><td><a href="classIMP_1_1Key.html#a498f62feed4576505d100d5fec663178">IMP::Key::operator+()</a>, <a href="classIMP_1_1Key.html#a99ee2d411e6951df306fd2500d88f4ec">IMP::Key::operator++()</a>, <a href="classIMP_1_1Key.html#ad6cf0753162983e183e4224a76009769">IMP::Key::operator--()</a>, <a href="classIMP_1_1Key.html#af693f942a3d828618581b1d99eed633b">IMP::Key::add_alias()</a>, <a href="classIMP_1_1misc_1_1CustomXYZR.html#abf684f0db593d848979dc60276e353ee">IMP::misc::CustomXYZR::get_decorator_traits()</a>, <a href="classIMP_1_1misc_1_1CustomXYZR.html#a57fd04d203ea022563739fccb3e008e6">IMP::misc::CustomXYZR::get_default_decorator_traits()</a></td></tr>
23 <tr><td>@ref IMP::Model</td><td><a href="classIMP_1_1ConfigurationSet.html#a155235875a1e68158d49267acaef681b">IMP::ConfigurationSet::get_model()</a>, <a href="classIMP_1_1Decorator.html#a553058bfcf00d1e5de7aff0a99cc3bc5">IMP::Decorator::get_model()</a>, <a href="classIMP_1_1Model.html#ae79bbc844c07d807a8c2942d1629ed1d">IMP::Model::get_by_unique_id()</a>, <a href="classIMP_1_1ModelObject.html#a93ea856693a96d8e4bb44685349395de">IMP::ModelObject::get_model()</a>, <a href="classIMP_1_1ParticleAdaptor.html#a6ccf121171f772b15f1cb295924d2c04">IMP::ParticleAdaptor::get_model()</a>, <a href="classIMP_1_1Sampler.html#a898dc79ade27f53ca100107136122cc3">IMP::Sampler::get_model()</a>, <a href="classIMP_1_1domino_1_1Subset.html#a4d8bbcfc51013721e4d17765edcfef60">IMP::domino::Subset::get_model()</a>, <a href="classIMP_1_1multifit_1_1ProteomicsEMAlignmentAtomic.html#a9d7c6b4b61ff4952e0dcbc6a6ee91279">IMP::multifit::ProteomicsEMAlignmentAtomic::get_model()</a>, <a href="classIMP_1_1npctransport_1_1ParticleFactory.html#a8e321c944e1b03398671c0865e83f6a8">IMP::npctransport::ParticleFactory::get_model()</a>, <a href="classIMP_1_1npctransport_1_1Scoring.html#aa7840b767cfdce2e6f371dcdf5b9b0d4">IMP::npctransport::Scoring::get_model()</a>, <a href="classIMP_1_1npctransport_1_1Scoring.html#aae01932be6be7ea5e905ae7f301868d2">IMP::npctransport::Scoring::get_model()</a>, <a href="classIMP_1_1npctransport_1_1SimulationData.html#abf6532308bb2217d53e031e0dc76a0a6">IMP::npctransport::SimulationData::get_model()</a>, <a href="classIMP_1_1npctransport_1_1SimulationData.html#a093070f639adfcb5ef74b42713067817">IMP::npctransport::SimulationData::get_model()</a>, <a href="classIMP_1_1npctransport_1_1Statistics.html#a077ec2a3a6334249ec7aa5e1572f62ff">IMP::npctransport::Statistics::get_model()</a>, <a href="classIMP_1_1npctransport_1_1Statistics.html#a9499acc5b2a6dcc6efb19bd693955855">IMP::npctransport::Statistics::get_model()</a></td></tr>
24 <tr><td>@ref IMP::ModelException</td><td><a href="classIMP_1_1ModelException.html#a0b3ddd1ebee2fdf6493d17b6064567f9">IMP::ModelException::operator=()</a></td></tr>
25 <tr><td>@ref IMP::Object</td><td><a href="classIMP_1_1Model.html#a4576e3d546cb47cdcfd5984e95372904">IMP::Model::get_data()</a>, <a href="classIMP_1_1RestraintSet.html#a721e37e9e39585c615eb2204f933bf46">IMP::RestraintSet::load_cereal()</a>, <a href="classIMP_1_1atom_1_1DihedralSingletonScore.html#ab59c282680c73f83d9097a733a453ddc">IMP::atom::DihedralSingletonScore::load_cereal()</a>, <a href="classIMP_1_1atom_1_1WritePDBOptimizerState.html#abb3b20ae8f572512f59cb8b524a2658c">IMP::atom::WritePDBOptimizerState::load_cereal()</a>, <a href="classIMP_1_1container_1_1ClosePairContainer.html#ac3943d9918928653dc0ad7ae6e91c8a1">IMP::container::ClosePairContainer::load_cereal()</a>, <a href="classIMP_1_1container_1_1ListPairContainer.html#ad0c33274fcabef147d6eecd68db727ee">IMP::container::ListPairContainer::load_cereal()</a>, <a href="classIMP_1_1container_1_1ListQuadContainer.html#ad0dac3da00e20106563a060135ebd4a4">IMP::container::ListQuadContainer::load_cereal()</a>, <a href="classIMP_1_1container_1_1ListSingletonContainer.html#ad58f05d1c4ea798185170b55925be1d3">IMP::container::ListSingletonContainer::load_cereal()</a>, <a href="classIMP_1_1container_1_1ListTripletContainer.html#ac9bf24552574b158e99b7b74b0645323">IMP::container::ListTripletContainer::load_cereal()</a>, <a href="classIMP_1_1container_1_1PairsConstraint.html#aa375c926c310cf8b6a9fb0f1a653cc74">IMP::container::PairsConstraint::load_cereal()</a>, <a href="classIMP_1_1container_1_1PairsRestraint.html#a7b7e056dd6acb93644fd40f63cdc730f">IMP::container::PairsRestraint::load_cereal()</a>, <a href="classIMP_1_1container_1_1PredicatePairsRestraint.html#a34004609f840a74ab6aabcbbf1afa38f">IMP::container::PredicatePairsRestraint::load_cereal()</a>, <a href="classIMP_1_1container_1_1PredicateQuadsRestraint.html#a8ff33d8c203bd4f88cdbf42eaca72d3c">IMP::container::PredicateQuadsRestraint::load_cereal()</a>, <a href="classIMP_1_1container_1_1PredicateSingletonsRestraint.html#ae7a1496dce1417905a7d0e10c88283d5">IMP::container::PredicateSingletonsRestraint::load_cereal()</a>, <a href="classIMP_1_1container_1_1PredicateTripletsRestraint.html#a2c8f59b9959a232b7371730f0b3d474b">IMP::container::PredicateTripletsRestraint::load_cereal()</a>, <a href="classIMP_1_1container_1_1QuadsConstraint.html#a5a0cf6925e93f66080363aa09110d79c">IMP::container::QuadsConstraint::load_cereal()</a>, <a href="classIMP_1_1container_1_1QuadsRestraint.html#ac015fdc029180c4f302c4ac63f9efb1f">IMP::container::QuadsRestraint::load_cereal()</a>, <a href="classIMP_1_1container_1_1SingletonsConstraint.html#a7de6fca4a0df3069096fdb42c0931428">IMP::container::SingletonsConstraint::load_cereal()</a>, <a href="classIMP_1_1container_1_1SingletonsRestraint.html#a1e095c51c5f460405596c544b5bcfb90">IMP::container::SingletonsRestraint::load_cereal()</a>, <a href="classIMP_1_1container_1_1TripletsConstraint.html#ad265bc846187eeb816bc935a30fe860c">IMP::container::TripletsConstraint::load_cereal()</a>, <a href="classIMP_1_1container_1_1TripletsRestraint.html#a1c5cf2818da373f8705ac8a6af1ec786">IMP::container::TripletsRestraint::load_cereal()</a>, <a href="classIMP_1_1core_1_1AllSamePairPredicate.html#a49e67af27cd9f1f0031ebf858da6d377">IMP::core::AllSamePairPredicate::load_cereal()</a>, <a href="classIMP_1_1core_1_1AllSameQuadPredicate.html#a46184287cfef2196980312e05aa9fbda">IMP::core::AllSameQuadPredicate::load_cereal()</a>, <a href="classIMP_1_1core_1_1AllSameSingletonPredicate.html#a6eb1347ed678a784e6284006191100b7">IMP::core::AllSameSingletonPredicate::load_cereal()</a>, <a href="classIMP_1_1core_1_1AllSameTripletPredicate.html#a26b4820b8bd1175885d2c6c660769dbf">IMP::core::AllSameTripletPredicate::load_cereal()</a>, <a href="classIMP_1_1core_1_1AngleRestraint.html#a3f367e14811307542ffa0db0e944e51c">IMP::core::AngleRestraint::load_cereal()</a>, <a href="classIMP_1_1core_1_1AngleTripletScore.html#a25173e5a7e04cb23201ec5e618c8780c">IMP::core::AngleTripletScore::load_cereal()</a>, <a href="classIMP_1_1core_1_1BallMover.html#ae0f575dcb82f6eeb1e3068735796b0a3">IMP::core::BallMover::load_cereal()</a>, <a href="classIMP_1_1core_1_1ChecksScoreState.html#ae41b82ad7e64ab9f9d1b25112e47440e">IMP::core::ChecksScoreState::load_cereal()</a>, <a href="classIMP_1_1core_1_1ConstantPairPredicate.html#a5ba1976c1bb53db3d31237c17455ffed">IMP::core::ConstantPairPredicate::load_cereal()</a>, <a href="classIMP_1_1core_1_1ConstantQuadPredicate.html#a9a6fe6c1458c5350d944cdb29fe4fdac">IMP::core::ConstantQuadPredicate::load_cereal()</a>, <a href="classIMP_1_1core_1_1ConstantRestraint.html#aa93aff0c5e224fa31afb58f4812d4dff">IMP::core::ConstantRestraint::load_cereal()</a>, <a href="classIMP_1_1core_1_1ConstantSingletonPredicate.html#a244ad2437bde3e17109e483f5d3845cc">IMP::core::ConstantSingletonPredicate::load_cereal()</a>, <a href="classIMP_1_1core_1_1ConstantTripletPredicate.html#a310d783ae12af5fa8fde1cd953fa474b">IMP::core::ConstantTripletPredicate::load_cereal()</a>, <a href="classIMP_1_1core_1_1Cosine.html#aad825a99b61169a85dbf58ca1f80239c">IMP::core::Cosine::load_cereal()</a>, <a href="classIMP_1_1core_1_1DistanceRestraint.html#a9fe0a59089a72ee4c1c0f36a19f195bb">IMP::core::DistanceRestraint::load_cereal()</a>, <a href="classIMP_1_1core_1_1GenericDistanceToSingletonScore.html#a2a37a7ebbeda9a09a7c5757d08433b39">IMP::core::GenericDistanceToSingletonScore::load_cereal()</a>, <a href="classIMP_1_1core_1_1GridClosePairsFinder.html#ac8016a690a8e78be0e042f580ad598ce">IMP::core::GridClosePairsFinder::load_cereal()</a>, <a href="classIMP_1_1core_1_1Harmonic.html#ab6a3e15cd713d98beebb3bbb55c31bc5">IMP::core::Harmonic::load_cereal()</a>, <a href="classIMP_1_1core_1_1HarmonicLowerBound.html#a560d49675fe2f5242d4951b237b13ea4">IMP::core::HarmonicLowerBound::load_cereal()</a>, <a href="classIMP_1_1core_1_1HarmonicUpperBound.html#a5b4af95da621b1eb3a052747977827d1">IMP::core::HarmonicUpperBound::load_cereal()</a>, <a href="classIMP_1_1core_1_1Linear.html#a666de413fea6cc2e35049839a3efd4c8">IMP::core::Linear::load_cereal()</a>, <a href="classIMP_1_1core_1_1PairConstraint.html#a4a718706dce4e45cfdbfda12445f4aea">IMP::core::PairConstraint::load_cereal()</a>, <a href="classIMP_1_1core_1_1PairRestraint.html#a0e47c23800d1c3bffd5e71cc9d7f813a">IMP::core::PairRestraint::load_cereal()</a>, <a href="classIMP_1_1core_1_1QuadConstraint.html#a81b762d6c3001210da6c911aa30e3692">IMP::core::QuadConstraint::load_cereal()</a>, <a href="classIMP_1_1core_1_1QuadRestraint.html#aa27348a29ac3a6a4d3a516592e838293">IMP::core::QuadRestraint::load_cereal()</a>, <a href="classIMP_1_1core_1_1RestraintsScoringFunction.html#a8319ecd35e11ff532c7c40bdf305fee7">IMP::core::RestraintsScoringFunction::load_cereal()</a>, <a href="classIMP_1_1core_1_1RigidBodyMover.html#a01838fbdefc707f364f975013164c346">IMP::core::RigidBodyMover::load_cereal()</a>, <a href="classIMP_1_1core_1_1RigidClosePairsFinder.html#a059fcbdeaa63b21357f85e5a8ef0f35d">IMP::core::RigidClosePairsFinder::load_cereal()</a>, <a href="classIMP_1_1core_1_1SerialMover.html#a7436d097947dd7e320eb237756926f05">IMP::core::SerialMover::load_cereal()</a>, <a href="classIMP_1_1core_1_1SingletonConstraint.html#a970949f6b3d4643d7c1c3b89b9efdc42">IMP::core::SingletonConstraint::load_cereal()</a>, <a href="classIMP_1_1core_1_1SingletonRestraint.html#a5e2a8fbac37ef5c1b80e09897944a0b9">IMP::core::SingletonRestraint::load_cereal()</a>, <a href="classIMP_1_1core_1_1SubsetMover.html#a127c3cd5aa48063bdcaddc730f23d43b">IMP::core::SubsetMover::load_cereal()</a>, <a href="classIMP_1_1core_1_1Transform.html#abbdb08c9732661ef9245b8573aa1987a">IMP::core::Transform::load_cereal()</a>, <a href="classIMP_1_1core_1_1TripletConstraint.html#a5ad0341741e14cb8512b75acc45a6904">IMP::core::TripletConstraint::load_cereal()</a>, <a href="classIMP_1_1core_1_1TripletRestraint.html#a805aa18b30b204319f16026bb9035a38">IMP::core::TripletRestraint::load_cereal()</a>, <a href="classIMP_1_1core_1_1UnorderedTypePairPredicate.html#ae6059df96abb5b3650eba30ac55c19af">IMP::core::UnorderedTypePairPredicate::load_cereal()</a>, <a href="classIMP_1_1core_1_1UnorderedTypeQuadPredicate.html#a5f7f314f1bf2cd5940043c09bc08566e">IMP::core::UnorderedTypeQuadPredicate::load_cereal()</a>, <a href="classIMP_1_1core_1_1UnorderedTypeSingletonPredicate.html#a40cbfc7fb6972b7badcbcfbfba8a9c82">IMP::core::UnorderedTypeSingletonPredicate::load_cereal()</a>, <a href="classIMP_1_1core_1_1UnorderedTypeTripletPredicate.html#a7c2af589ca28712bfacc89ac47819c2f">IMP::core::UnorderedTypeTripletPredicate::load_cereal()</a>, <a href="classIMP_1_1example_1_1ExampleConstraint.html#a3af6bacb3666a598c5d38a635eb44efc">IMP::example::ExampleConstraint::load_cereal()</a>, <a href="classIMP_1_1example_1_1ExamplePairScore.html#a9bc407074152459dedf36f5805ecdf79">IMP::example::ExamplePairScore::load_cereal()</a>, <a href="classIMP_1_1example_1_1ExampleRestraint.html#aba147bdb0b33059f7480dc503d05f2fb">IMP::example::ExampleRestraint::load_cereal()</a>, <a href="classIMP_1_1example_1_1ExampleSingletonModifier.html#ac5f2ba488f29e110579a203e39bf4f1c">IMP::example::ExampleSingletonModifier::load_cereal()</a>, <a href="classIMP_1_1example_1_1ExampleUnaryFunction.html#a0c334ab44d00ab537f4918fd324cd8de">IMP::example::ExampleUnaryFunction::load_cereal()</a>, <a href="classIMP_1_1isd_1_1AmbiguousNOERestraint.html#aa948df1fec928e2d1c62a567c55c5404">IMP::isd::AmbiguousNOERestraint::load_cereal()</a>, <a href="classIMP_1_1isd_1_1AmbiguousRestraint.html#aa3aaf96e92a450b152fe8a2e5fb5508e">IMP::isd::AmbiguousRestraint::load_cereal()</a>, <a href="classIMP_1_1isd_1_1AtomicCrossLinkMSRestraint.html#aaa1409f658d2da013ea10900787f14a0">IMP::isd::AtomicCrossLinkMSRestraint::load_cereal()</a>, <a href="classIMP_1_1isd_1_1CrossLinkMSRestraint.html#a0fab381d61eecc7b2c4133a21eace61e">IMP::isd::CrossLinkMSRestraint::load_cereal()</a>, <a href="classIMP_1_1isd_1_1CysteineCrossLinkRestraint.html#a6e6fc7ab3d54da8d1fbdf43a655d8d7b">IMP::isd::CysteineCrossLinkRestraint::load_cereal()</a>, <a href="classIMP_1_1isd_1_1FretRestraint.html#a93a6b4d2d9a218a3f8b8901faebf6fd6">IMP::isd::FretRestraint::load_cereal()</a>, <a href="classIMP_1_1isd_1_1GaussianEMRestraint.html#a3c047d27f050aadfe28691df2f400196">IMP::isd::GaussianEMRestraint::load_cereal()</a>, <a href="classIMP_1_1isd_1_1JeffreysRestraint.html#a1db5ad9b581f326c07a25081285a6255">IMP::isd::JeffreysRestraint::load_cereal()</a>, <a href="classIMP_1_1isd_1_1LogWrapper.html#a9c6a2bfefc2c610e2312452a62190172">IMP::isd::LogWrapper::load_cereal()</a>, <a href="classIMP_1_1isd_1_1UniformPrior.html#af075cde40ad7b6ef40263a3f23898eaf">IMP::isd::UniformPrior::load_cereal()</a>, <a href="classIMP_1_1npc_1_1AssemblySymmetryByDihedralRestraint.html#a04ac74078a37b432ddcbfd246b133da2">IMP::npc::AssemblySymmetryByDihedralRestraint::load_cereal()</a>, <a href="classIMP_1_1npc_1_1AssemblySymmetryByDistanceRestraint.html#acf4f83a75b418c729587ab10b5f75825">IMP::npc::AssemblySymmetryByDistanceRestraint::load_cereal()</a>, <a href="classIMP_1_1npc_1_1MembraneExclusionRestraint.html#a7cdffb7ba92004d0835eda444c176b47">IMP::npc::MembraneExclusionRestraint::load_cereal()</a>, <a href="classIMP_1_1npc_1_1MembraneSurfaceLocationConditionalRestraint.html#ac0dc2eefdd6856c7f088b4a7fbeb9dfe">IMP::npc::MembraneSurfaceLocationConditionalRestraint::load_cereal()</a>, <a href="classIMP_1_1npc_1_1MembraneSurfaceLocationRestraint.html#a524748f815c9b6650f917d8a07bd3a92">IMP::npc::MembraneSurfaceLocationRestraint::load_cereal()</a>, <a href="classIMP_1_1npc_1_1MinimumSphereDistancePairScore.html#aee47967f75f1774228b3da62135987ba">IMP::npc::MinimumSphereDistancePairScore::load_cereal()</a>, <a href="classIMP_1_1npc_1_1PerinuclearVolumeLocationRestraint.html#aca22c1217731a97ab8a14347bd10fe6b">IMP::npc::PerinuclearVolumeLocationRestraint::load_cereal()</a>, <a href="classIMP_1_1npc_1_1PoreSideVolumeLocationRestraint.html#a44c891d3475cea507b7dcaee8422592b">IMP::npc::PoreSideVolumeLocationRestraint::load_cereal()</a>, <a href="classIMP_1_1npc_1_1ProteinChainRestraint.html#a89d4c04e378c2bae3327fa85acd51c87">IMP::npc::ProteinChainRestraint::load_cereal()</a>, <a href="classIMP_1_1npc_1_1ProteinContactRestraint.html#a2876703f0eb14048fb35e30f718771eb">IMP::npc::ProteinContactRestraint::load_cereal()</a>, <a href="classIMP_1_1npc_1_1ProteinProximityRestraint.html#a2f1893751dad0ac6771b5707189f0ce9">IMP::npc::ProteinProximityRestraint::load_cereal()</a>, <a href="classIMP_1_1npc_1_1XYRadialPositionLowerRestraint.html#abfab8a1c59ce40fd8b9affdf8bfc0223">IMP::npc::XYRadialPositionLowerRestraint::load_cereal()</a>, <a href="classIMP_1_1npc_1_1XYRadialPositionRestraint.html#a31a1366baa3ec7348f487098c3a0b36a">IMP::npc::XYRadialPositionRestraint::load_cereal()</a>, <a href="classIMP_1_1npc_1_1XYRadialPositionUpperRestraint.html#a65f330312a76bb8f8147eed80a5a72ca">IMP::npc::XYRadialPositionUpperRestraint::load_cereal()</a>, <a href="classIMP_1_1npc_1_1YAxialPositionLowerRestraint.html#a8428a1cba7ac8e0b17217cf2ffc9cd1b">IMP::npc::YAxialPositionLowerRestraint::load_cereal()</a>, <a href="classIMP_1_1npc_1_1YAxialPositionRestraint.html#a8d92c11845b19de5abfbad37126ddc08">IMP::npc::YAxialPositionRestraint::load_cereal()</a>, <a href="classIMP_1_1npc_1_1YAxialPositionUpperRestraint.html#a4d935a2cab2bbf742c73a48f05cc279e">IMP::npc::YAxialPositionUpperRestraint::load_cereal()</a>, <a href="classIMP_1_1npc_1_1ZAxialPositionLowerRestraint.html#a9b3df035f2960fae3934b3970ae13586">IMP::npc::ZAxialPositionLowerRestraint::load_cereal()</a>, <a href="classIMP_1_1npc_1_1ZAxialPositionRestraint.html#aaaf23d6f154030f47707320cfcf07896">IMP::npc::ZAxialPositionRestraint::load_cereal()</a>, <a href="classIMP_1_1npc_1_1ZAxialPositionUpperRestraint.html#a994e9ea94a1dd92edbee7303726b4671">IMP::npc::ZAxialPositionUpperRestraint::load_cereal()</a>, <a href="classIMP_1_1npctransport_1_1Scoring.html#ad8e7271031722c22a033e31afd7a4094">IMP::npctransport::Scoring::create_backbone_restraint()</a>, <a href="classIMP_1_1pmi_1_1CrossLinkRestraintSet.html#a3a2491f3d552f12e699e1f70c840fd1d">IMP::pmi::CrossLinkRestraintSet::load_cereal()</a>, <a href="classIMP_1_1pmi_1_1TransformMover.html#a10e6e9aa97cb1e2b1b9a509ee063df83">IMP::pmi::TransformMover::load_cereal()</a>, <a href="classIMP_1_1saxs_1_1Profile.html#aaf12c11a1e7cc42aef0ba3e0efc4ff8e">IMP::saxs::Profile::load_cereal()</a>, <a href="classIMP_1_1saxs_1_1Restraint.html#a8d1129c021660759afb6f6933d68561e">IMP::saxs::Restraint::load_cereal()</a></td></tr>
26 <tr><td>@ref IMP::Optimizer</td><td><a href="classIMP_1_1OptimizerState.html#ac601ca928b88a1828dfbc3288f7300a6">IMP::OptimizerState::get_optimizer()</a>, <a href="classIMP_1_1core_1_1MonteCarloWithLocalOptimization.html#ae53418c0e3fc6d230233d6ac3eac0917">IMP::core::MonteCarloWithLocalOptimization::get_local_optimizer()</a></td></tr>
27 <tr><td>@ref IMP::OptimizerState</td><td><a href="classIMP_1_1Optimizer.html#a6a64aef807c00416188924b7e4af2f7d">IMP::Optimizer::get_optimizer_state()</a>, <a href="classIMP_1_1core_1_1MCCGSampler.html#aad24ef9b8f969b2603c4602712bce831">IMP::core::MCCGSampler::get_optimizer_state()</a></td></tr>
28 <tr><td>@ref IMP::PairContainer</td><td><a href="classIMP_1_1container_1_1PairContainerSet.html#ae343941d5a5f5e1b547bead72eee531c">IMP::container::PairContainerSet::get_pair_container()</a>, <a href="classIMP_1_1display_1_1PairsGeometry.html#ac743a4c3064830a62e521e029c55a78e">IMP::display::PairsGeometry::get_container()</a>, <a href="classIMP_1_1misc_1_1DecayPairContainerOptimizerState.html#ac20026831c9aff9573601adbd41dba6f">IMP::misc::DecayPairContainerOptimizerState::get_output_container()</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#aa8442a8627971126904de6b8622f8435">IMP::npctransport::Scoring::get_close_beads_container()</a></td></tr>
29 <tr><td>@ref IMP::PairPredicate</td><td><a href="classIMP_1_1container_1_1CloseBipartitePairContainer.html#a61e9b66e1775997dbde246a6be83a059">IMP::container::CloseBipartitePairContainer::get_pair_filter()</a>, <a href="classIMP_1_1container_1_1ClosePairContainer.html#a1425b187f76d11ec599f14310c3dae41">IMP::container::ClosePairContainer::get_pair_filter()</a>, <a href="classIMP_1_1core_1_1ClosePairsFinder.html#a6e954feff41233daa12a4aa6d3783008">IMP::core::ClosePairsFinder::get_pair_filter()</a>, <a href="classIMP_1_1core_1_1ExcludedVolumeRestraint.html#a10843c7ebf6a7886e2764dbb2fa4279b">IMP::core::ExcludedVolumeRestraint::get_pair_filter()</a></td></tr>
30 <tr><td>@ref IMP::PairScore</td><td><a href="classIMP_1_1container_1_1PredicatePairsRestraint.html#abf50c8d4e48bd3caf1c34bef7ff0c177">IMP::container::PredicatePairsRestraint::get_score_for_predicate()</a>, <a href="classIMP_1_1core_1_1ConnectivityRestraint.html#ab32c76d5aceb791d65f5da9564d294c3">IMP::core::ConnectivityRestraint::get_pair_score()</a>, <a href="classIMP_1_1core_1_1MSConnectivityRestraint.html#adbb8bd7d4b45c8f7ce115788afd16b13">IMP::core::MSConnectivityRestraint::get_pair_score()</a>, <a href="classIMP_1_1core_1_1TypedPairScore.html#a573f8d688cb31552696738a2f197bb06">IMP::core::TypedPairScore::get_pair_score()</a>, <a href="classIMP_1_1npctransport_1_1Scoring.html#aa5cbef8b44cd00022f00d413fd979bb6">IMP::npctransport::Scoring::get_predicate_pair_score()</a>, <a href="classIMP_1_1npctransport_1_1Scoring.html#a657cb19846800e2cb7a52853ccb88bc6">IMP::npctransport::Scoring::get_predicate_pair_score()</a></td></tr>
31 <tr><td>@ref IMP::Particle</td><td><a href="classIMP_1_1Decorator.html#ad1accb02f8c3be95582c0a6021c61fcb">IMP::Decorator::get_particle()</a>, <a href="classIMP_1_1Decorator.html#ad2907c239b46cf65dab071a14b27b115">IMP::Decorator::operator->()</a>, <a href="classIMP_1_1Model.html#a5557ecdab824617aab45889f5258a1df">IMP::Model::get_particle()</a>, <a href="classIMP_1_1Refiner.html#aee8d61be106d561f9be0e7ace3bbef34">IMP::Refiner::get_refined()</a>, <a href="classIMP_1_1atom_1_1Angle.html#a5f3bb0b13aa7dd63d2ec82691394a725">IMP::atom::Angle::get_particle()</a>, <a href="classIMP_1_1atom_1_1Angle.html#a2764b1dbd93398f3df9330a01bf83057">IMP::atom::Angle::get_particle()</a>, <a href="classIMP_1_1atom_1_1Dihedral.html#a4a1e3bd4480803221e3e4de4966afdc5">IMP::atom::Dihedral::get_particle()</a>, <a href="classIMP_1_1atom_1_1Dihedral.html#a67118254e85dc8d4e78447fac259516e">IMP::atom::Dihedral::get_particle()</a>, <a href="classIMP_1_1atom_1_1SecondaryStructureResidue.html#ae1f85afa673bbb46990162ef4bb9614a">IMP::atom::SecondaryStructureResidue::get_particle()</a>, <a href="classIMP_1_1atom_1_1Simulator.html#a5f8dc26a3c63e2b521d705bb2747aefa">IMP::atom::Simulator::get_particle()</a>, <a href="classIMP_1_1core_1_1DirectionAngle.html#a12550055e316228476033a05aa042037">IMP::core::DirectionAngle::get_particle()</a>, <a href="classIMP_1_1core_1_1DirectionAngle.html#a5d08f0b235c346a78b4556a0be0cd7b2">IMP::core::DirectionAngle::get_particle()</a>, <a href="classIMP_1_1core_1_1Reference.html#a47b4077482ebea6db7717e5a301794b9">IMP::core::Reference::get_reference_particle()</a>, <a href="classIMP_1_1display_1_1SingletonGeometry.html#ada39b5b10776bd8ec103f0c20b046435">IMP::display::SingletonGeometry::get_particle()</a>, <a href="classIMP_1_1em_1_1DensityFillingRestraint.html#ad7f1dd04891d72c5d27a5439a3cb7297">IMP::em::DensityFillingRestraint::get_particle()</a>, <a href="classIMP_1_1em_1_1EnvelopePenetrationRestraint.html#a4f6f4bc25647efaa28938fa88b39499d">IMP::em::EnvelopePenetrationRestraint::get_particle()</a>, <a href="classIMP_1_1em_1_1FitRestraint.html#a3a18b0d9d5c087a618fad597196cfdc8">IMP::em::FitRestraint::get_particle()</a>, <a href="classIMP_1_1em_1_1PCAFitRestraint.html#a9ce836e6cc025607663c7c48418cc8f2">IMP::em::PCAFitRestraint::get_particle()</a>, <a href="classIMP_1_1kinematics_1_1KinematicForest.html#ac5f968f9f21a40d3b97b587752d90242">IMP::kinematics::KinematicForest::get_parent()</a>, <a href="classIMP_1_1multifit_1_1RadiusOfGyrationRestraint.html#afb2e30a4fedd196e99c3302cae8a5961">IMP::multifit::RadiusOfGyrationRestraint::get_particle()</a>, <a href="classIMP_1_1multifit_1_1WeightedExcludedVolumeRestraint.html#acda9c29315d608a8510ddbce9b7b55af">IMP::multifit::WeightedExcludedVolumeRestraint::get_particle()</a>, <a href="classIMP_1_1npctransport_1_1BodyStatisticsOptimizerState.html#a872aba8024efc9cea8332dddd7b42aee">IMP::npctransport::BodyStatisticsOptimizerState::get_particle()</a>, <a href="classIMP_1_1npctransport_1_1FGChain.html#abda53276ceea983c5c307d0604bceba2">IMP::npctransport::FGChain::get_bead()</a>, <a href="classIMP_1_1npctransport_1_1ParticleFactory.html#a918d7c02c32576f81616813a145fcb41">IMP::npctransport::ParticleFactory::create()</a>, <a href="classIMP_1_1npctransport_1_1ParticleTransportStatisticsOptimizerState.html#a974986244418fba151d5faaa3d45b4e5">IMP::npctransport::ParticleTransportStatisticsOptimizerState::get_particle()</a>, <a href="classIMP_1_1npctransport_1_1RelaxingSpring.html#ae9bc619a157e41acd2cdd17c5eebc63e">IMP::npctransport::RelaxingSpring::get_bonded_particle_0()</a>, <a href="classIMP_1_1npctransport_1_1RelaxingSpring.html#a5792a22459f17669e5ead13e779b2439">IMP::npctransport::RelaxingSpring::get_bonded_particle_1()</a>, <a href="classIMP_1_1npctransport_1_1SimulationData.html#a6b6b9d4f83a9ae230edca68779a9747a">IMP::npctransport::SimulationData::get_slab_particle()</a>, <a href="classIMP_1_1rmf_1_1HierarchyLoadLink.html#a8cd7af6a50fa7fc2677a5ac2420b01aa">IMP::rmf::HierarchyLoadLink::do_create()</a>, <a href="namespaceIMP_1_1spb.html#ae1bbb466a333fd88c5c6307d628165b9">IMP::spb::add_ISD_particles()</a></td></tr>
32 <tr><td>@ref IMP::QuadContainer</td><td><a href="classIMP_1_1container_1_1QuadContainerSet.html#acba780ec6cd198930851e9bf829d8802">IMP::container::QuadContainerSet::get_quad_container()</a></td></tr>
33 <tr><td>@ref IMP::QuadScore</td><td><a href="classIMP_1_1container_1_1PredicateQuadsRestraint.html#a1f4e366d4876bb506c5b70190b618641">IMP::container::PredicateQuadsRestraint::get_score_for_predicate()</a></td></tr>
34 <tr><td>@ref IMP::Restraint</td><td><a href="classIMP_1_1Model.html#a65e544e1ddfbb7eb08f009d2375afc45">IMP::Model::get_dependent_restraints()</a>, <a href="classIMP_1_1Restraint.html#a884c8cc8b6fb790f8b0f057958f4d4ee">IMP::Restraint::create_current_decomposition()</a>, <a href="classIMP_1_1Restraint.html#ae21bbd0c803b1ea05fc04d0aa6a6c200">IMP::Restraint::create_decomposition()</a>, <a href="classIMP_1_1RestraintSet.html#aef5d095584b22674ea4f6cfef714ef37">IMP::RestraintSet::get_restraint()</a>, <a href="classIMP_1_1RestraintsAdaptor.html#a4480138e5bbff398b8f3bc2aeb516b22">IMP::RestraintsAdaptor::get()</a>, <a href="classIMP_1_1core_1_1MinimumRestraint.html#a208f37e990ceb4d47b80df8a74b7e512">IMP::core::MinimumRestraint::get_restraint()</a>, <a href="classIMP_1_1display_1_1RestraintGeometry.html#adadb9d6eda2e6ed7ebdfafa0c538756e">IMP::display::RestraintGeometry::get_restraint()</a>, <a href="classIMP_1_1npctransport_1_1Scoring.html#ad8e7271031722c22a033e31afd7a4094">IMP::npctransport::Scoring::create_backbone_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#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#a1f680b9c0df4420c40174fd40819e169">IMP::npctransport::Scoring::get_bounding_volume_restraint()</a>, <a href="classIMP_1_1npctransport_1_1Scoring.html#adbf1ec70afa9a6cb717ccfe65e110329">IMP::npctransport::Scoring::get_pore_radius_restraint()</a>, <a href="classIMP_1_1npctransport_1_1Scoring.html#aa04e72cc5132af0ace408ff0687a8810">IMP::npctransport::Scoring::get_slab_restraint()</a>, <a href="namespaceIMP_1_1atom.html#adb6ec371e048f639a51292a67268f432">IMP::atom::create_connectivity_restraint()</a>, <a href="namespaceIMP_1_1atom.html#a76ad13aa02ece8e2a110250b4be878b7">IMP::atom::create_connectivity_restraint()</a>, <a href="namespaceIMP_1_1atom.html#abc59e05e0e702438730b01f225858438">IMP::atom::create_distance_restraint()</a>, <a href="namespaceIMP_1_1atom.html#a64f18ad8ce0534736253b21f84c7c308">IMP::atom::create_excluded_volume_restraint()</a>, <a href="namespaceIMP_1_1atom.html#af115fdd772a04d5e4f775825a56b61d9">IMP::atom::create_excluded_volume_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_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_1multifit.html#a8273d850c0ab1cd53983c9f169af3cd6">IMP::multifit::create_weighted_excluded_volume_restraint()</a></td></tr>
35 <tr><td>@ref IMP::RestraintInfo</td><td><a href="classIMP_1_1Restraint.html#a38bbb37b0e8dc92785b1834233f577c6">IMP::Restraint::get_dynamic_info()</a>, <a href="classIMP_1_1Restraint.html#af07a7d34ad419288411fd39b97cfd2b2">IMP::Restraint::get_static_info()</a>, <a href="classIMP_1_1bayesianem_1_1GaussianEMRestraint.html#afbafe5bdaa3205edbb03c3fdefc206b2">IMP::bayesianem::GaussianEMRestraint::get_dynamic_info()</a>, <a href="classIMP_1_1bayesianem_1_1GaussianEMRestraint.html#aeed5ab1e782178dcc5060f9750ae5b42">IMP::bayesianem::GaussianEMRestraint::get_static_info()</a>, <a href="classIMP_1_1em2d_1_1PCAFitRestraint.html#a9315225ccd08ff6c6c0f745c5830d4f4">IMP::em2d::PCAFitRestraint::get_dynamic_info()</a>, <a href="classIMP_1_1em2d_1_1PCAFitRestraint.html#a9b55cd43afbdbcad80347fff29b10152">IMP::em2d::PCAFitRestraint::get_static_info()</a>, <a href="classIMP_1_1isd_1_1CrossLinkMSRestraint.html#a986efc57d63786ba4a08fcfba62b170d">IMP::isd::CrossLinkMSRestraint::get_static_info()</a>, <a href="classIMP_1_1isd_1_1GaussianEMRestraint.html#a40cea4833ace7ed6b5f300223abd3763">IMP::isd::GaussianEMRestraint::get_dynamic_info()</a>, <a href="classIMP_1_1isd_1_1GaussianEMRestraint.html#aa5ff5374157d6d1ac507e5464dbd2d0e">IMP::isd::GaussianEMRestraint::get_static_info()</a>, <a href="classIMP_1_1isd_1_1UniformPrior.html#abcef5f2db468cc20575a281bc283e4e7">IMP::isd::UniformPrior::get_dynamic_info()</a>, <a href="classIMP_1_1isd_1_1UniformPrior.html#ae78dbc6906bed4f6a979d2b1644fd443">IMP::isd::UniformPrior::get_static_info()</a>, <a href="classIMP_1_1npc_1_1MembraneExclusionRestraint.html#a7bfa44d403fce004d6dbf82f23616615">IMP::npc::MembraneExclusionRestraint::get_static_info()</a>, <a href="classIMP_1_1npc_1_1MembraneSurfaceLocationConditionalRestraint.html#a0632927bd1b15d62cd7983b71963b7bf">IMP::npc::MembraneSurfaceLocationConditionalRestraint::get_static_info()</a>, <a href="classIMP_1_1npc_1_1MembraneSurfaceLocationRestraint.html#a26f9e734838d33fe547db7837ee57ac7">IMP::npc::MembraneSurfaceLocationRestraint::get_static_info()</a>, <a href="classIMP_1_1npc_1_1XYRadialPositionLowerRestraint.html#a2f5872ddac29d262012aaf8f6af3b290">IMP::npc::XYRadialPositionLowerRestraint::get_static_info()</a>, <a href="classIMP_1_1npc_1_1XYRadialPositionRestraint.html#a4d5f3df75cd28b72a7b7f580bb164591">IMP::npc::XYRadialPositionRestraint::get_static_info()</a>, <a href="classIMP_1_1npc_1_1XYRadialPositionUpperRestraint.html#a1ab15112aefdbb85d93f775e54ff352f">IMP::npc::XYRadialPositionUpperRestraint::get_static_info()</a>, <a href="classIMP_1_1npc_1_1YAxialPositionLowerRestraint.html#ac2a6e4650922b0861568310f1e46dc26">IMP::npc::YAxialPositionLowerRestraint::get_static_info()</a>, <a href="classIMP_1_1npc_1_1YAxialPositionRestraint.html#ae702b81295cdefc863013463d828ae68">IMP::npc::YAxialPositionRestraint::get_static_info()</a>, <a href="classIMP_1_1npc_1_1YAxialPositionUpperRestraint.html#aad5c43f25d5fac0c6d728d0cda656ff5">IMP::npc::YAxialPositionUpperRestraint::get_static_info()</a>, <a href="classIMP_1_1npc_1_1ZAxialPositionLowerRestraint.html#a53a25851888e057bea962f3c45190ccb">IMP::npc::ZAxialPositionLowerRestraint::get_static_info()</a>, <a href="classIMP_1_1npc_1_1ZAxialPositionRestraint.html#a0600956339c89679fa968459eb8c100a">IMP::npc::ZAxialPositionRestraint::get_static_info()</a>, <a href="classIMP_1_1npc_1_1ZAxialPositionUpperRestraint.html#ab7d921665a2a639f909beb0b97785b28">IMP::npc::ZAxialPositionUpperRestraint::get_static_info()</a>, <a href="classIMP_1_1pmi_1_1CrossLinkRestraintSet.html#a4f0fac1095fb14a6446a2c150c4939e2">IMP::pmi::CrossLinkRestraintSet::get_static_info()</a>, <a href="classIMP_1_1saxs_1_1Restraint.html#abd1d9d53d1488583dcfe6db27518601d">IMP::saxs::Restraint::get_static_info()</a></td></tr>
36 <tr><td>@ref IMP::RestraintSet</td><td><a href="classIMP_1_1display_1_1RestraintSetGeometry.html#a9780a9653138663ce2b468cc13405e4d">IMP::display::RestraintSetGeometry::get_restraint_set()</a>, <a href="classIMP_1_1multifit_1_1ProteomicsEMAlignmentAtomic.html#a065c8a22465b882c0c07518c097b721e">IMP::multifit::ProteomicsEMAlignmentAtomic::get_restraint_set()</a>, <a href="namespaceIMP_1_1pmi.html#a136fbe0c4b8cf1f652b8786ae448bc24">IMP::pmi::create_elastic_network()</a>, <a href="namespaceIMP_1_1pmi1.html#a2995df7ccbc9bebba29bf2f879e92fc7">IMP::pmi1::create_elastic_network()</a>, <a href="namespaceIMP_1_1spb.html#a7c113921b584fd1fce234cdb478f354b">IMP::spb::spb_assemble_restraints()</a></td></tr>
37 <tr><td>@ref IMP::ScoreAccumulator</td><td><a href="classIMP_1_1ScoreAccumulator.html#a746acbdaf292c3f705cd5cbe9ad84770">IMP::ScoreAccumulator::operator=()</a>, <a href="classIMP_1_1ScoringFunction.html#a841e932d67b3ee8e33cf968068036658">IMP::ScoringFunction::get_score_accumulator()</a>, <a href="classIMP_1_1ScoringFunction.html#a06398684dc918020b96cbe064413bf02">IMP::ScoringFunction::get_score_accumulator_if_below()</a>, <a href="classIMP_1_1ScoringFunction.html#ad1b2d5d08138c74a31baa27992eed403">IMP::ScoringFunction::get_score_accumulator_if_good()</a></td></tr>
38 <tr><td>@ref IMP::ScoreState</td><td><a href="classIMP_1_1Model.html#a4cc23d80a0df9baa1163f8d3f961b1d0">IMP::Model::get_score_state()</a></td></tr>
39 <tr><td>@ref IMP::ScoringFunction</td><td><a href="classIMP_1_1Optimizer.html#a6be2b10dcfb0be4616a54ac32ece8a67">IMP::Optimizer::get_scoring_function()</a>, <a href="classIMP_1_1Restraint.html#a2bf725ecf399f8fe8ab65980e0386f00">IMP::Restraint::create_scoring_function()</a>, <a href="classIMP_1_1Restraint.html#a4b9095c8c23e1d3b631cb7af90353a02">IMP::Restraint::create_internal_scoring_function()</a>, <a href="classIMP_1_1Sampler.html#a15adf816246a121950892cbc957f0681">IMP::Sampler::get_scoring_function()</a>, <a href="classIMP_1_1ScoringFunctionAdaptor.html#aad09f1973c5383ea3d1d0430910beeb6">IMP::ScoringFunctionAdaptor::get()</a>, <a href="classIMP_1_1ScoringFunctionAdaptor.html#a7b5d074185fc11c9e19a4c1b2445f795">IMP::ScoringFunctionAdaptor::get()</a>, <a href="classIMP_1_1ScoringFunctionAdaptor.html#acc7e332f6cadb42dbab6a698270876e3">IMP::ScoringFunctionAdaptor::get()</a>, <a href="classIMP_1_1ScoringFunctionAdaptor.html#a8703032ecda559760ce1c4a8c2a8c1e3">IMP::ScoringFunctionAdaptor::get()</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_1Scoring.html#ae64c9d924a678c15cfdb9b940fb1ad82">IMP::npctransport::Scoring::get_scoring_function()</a></td></tr>
40 <tr><td>@ref IMP::Showable</td><td><a href="classIMP_1_1Showable.html#afff2b30ce6828ef7c7622a0939120cc6">IMP::Showable::operator=()</a></td></tr>
41 <tr><td>@ref IMP::SingletonContainer</td><td><a href="classIMP_1_1container_1_1SingletonContainerSet.html#a808361141dbec1c0ea1231dfa1ef36c9">IMP::container::SingletonContainerSet::get_singleton_container()</a>, <a href="classIMP_1_1display_1_1SingletonsGeometry.html#a641a621f321c7e664f368b49a9371063">IMP::display::SingletonsGeometry::get_container()</a></td></tr>
42 <tr><td>@ref IMP::SingletonScore</td><td><a href="classIMP_1_1container_1_1PredicateSingletonsRestraint.html#a30bc2d7d996e33863d2ff8abef6b52e6">IMP::container::PredicateSingletonsRestraint::get_score_for_predicate()</a></td></tr>
43 <tr><td>@ref IMP::TextOutput</td><td><a href="namespaceIMP.html#ab80a40f6e42e620a158a956ec33acb68">IMP::create_temporary_file()</a>, <a href="namespaceIMP.html#a8187645ef8e14666eefada67c6cd317f">IMP::get_log_target()</a></td></tr>
44 <tr><td>@ref IMP::TripletContainer</td><td><a href="classIMP_1_1container_1_1TripletContainerSet.html#aec704f8ab29206b4bccff59800ed1a7b">IMP::container::TripletContainerSet::get_triplet_container()</a></td></tr>
45 <tr><td>@ref IMP::TripletScore</td><td><a href="classIMP_1_1container_1_1PredicateTripletsRestraint.html#af745b55e98b3cecb3c4c811955f9cab1">IMP::container::PredicateTripletsRestraint::get_score_for_predicate()</a></td></tr>
46 <tr><td>@ref IMP::TypeException</td><td><a href="classIMP_1_1TypeException.html#a1b1dcb534b31db39e9beed0d9ffe28ba">IMP::TypeException::operator=()</a></td></tr>
47 <tr><td>@ref IMP::UnaryFunction</td><td><a href="classIMP_1_1atom_1_1BondSingletonScore.html#a89a5490a606195d94967444c74017632">IMP::atom::BondSingletonScore::get_unary_function()</a>, <a href="classIMP_1_1core_1_1WeightedSum.html#a37c6825d7d6a7a1a78710d05cf0421ef">IMP::core::WeightedSum::get_function()</a>, <a href="classIMP_1_1core_1_1WeightedSumOfExponential.html#ad00abf7d65d6ce742da73b478ec0dd49">IMP::core::WeightedSumOfExponential::get_function()</a></td></tr>
48 <tr><td>@ref IMP::UsageException</td><td><a href="classIMP_1_1UsageException.html#a091a4f13f3da703e5b18fbccee1cb193">IMP::UsageException::operator=()</a></td></tr>
49 <tr><td>@ref IMP::Value</td><td><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></td></tr>
50 <tr><td>@ref IMP::ValueException</td><td><a href="classIMP_1_1ValueException.html#af6613e03220c474744a1f27ebaf73c27">IMP::ValueException::operator=()</a></td></tr>
51 <tr><td>@ref IMP::Vector</td><td><a href="classIMP_1_1ConstVector.html#aea5e00cd3a596d70b5e5691c23f1d487">IMP::ConstVector::ConstVector()</a>, <a href="classIMP_1_1Container.html#a3c1564f6fe55ed0bbb9e0d7ca2d41abe">IMP::Container::get_all_possible_indexes()</a>, <a href="classIMP_1_1Key.html#a0f163e7862cfb282d4a29fe2cbee3b89">IMP::Key::get_all_strings()</a>, <a href="classIMP_1_1LRUCache.html#a376fc0f05d785e74b937fe6991aee7a1">IMP::LRUCache::get_keys()</a>, <a href="classIMP_1_1Model.html#a276023d2d04d40fa02cf8658749182b7">IMP::Model::get_dependent_particles()</a>, <a href="classIMP_1_1Model.html#af7c7e0c0efb8c8bd3cd425ef1528eb54">IMP::Model::get_particle_indexes()</a>, <a href="classIMP_1_1ModelObject.html#ad36883c4a980f5d8f0fe1dd512f2d46e">IMP::ModelObject::get_interactions()</a>, <a href="classIMP_1_1ModelObject.html#a119f13183a7a4f2e79c3bbd719329486">IMP::ModelObject::do_get_interactions()</a>, <a href="classIMP_1_1Refiner.html#a5472c3ed2b59a73d39ca58fba0aad9d9">IMP::Refiner::get_refined()</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_1RestraintInfo.html#a80e65ed136d91ca7fd2d95b315793696">IMP::RestraintInfo::get_particle_indexes_value()</a>, <a href="classIMP_1_1SingletonContainer.html#ac939d4895b35849464f750c855a41195">IMP::SingletonContainer::get_contents()</a>, <a href="classIMP_1_1SingletonContainer.html#a0f805ae830a2b77dc47d2528822a0308">IMP::SingletonContainer::get_indexes()</a>, <a href="classIMP_1_1SingletonContainer.html#aeebe47b7201a29319f0a522c33f6d738">IMP::SingletonContainer::get_range_indexes()</a>, <a href="classIMP_1_1algebra_1_1BoundedGridRangeD.html#a7a7bb6e98f48c2153626ad288340363f">IMP::algebra::BoundedGridRangeD::get_all_indexes()</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_1DenseGridStorageD.html#a6ddabec5b4d956d7de1dd36eac335462">IMP::algebra::DenseGridStorageD::get_all_voxels()</a>, <a href="classIMP_1_1algebra_1_1PrincipalComponentAnalysisD.html#a0ba09fe87df97ebef41f58c73ffaa710">IMP::algebra::PrincipalComponentAnalysisD::get_principal_components()</a>, <a href="classIMP_1_1algebra_1_1SparseGridStorageD.html#a9943a6836e190dd7f3f1bff9c550ed8b">IMP::algebra::SparseGridStorageD::get_indexes()</a>, <a href="classIMP_1_1algebra_1_1UnboundedGridRangeD.html#ae36705377d9f2caf5c06984d1ce8bfaa">IMP::algebra::UnboundedGridRangeD::get_extended_indexes()</a>, <a href="classIMP_1_1atom_1_1BondEndpointsRefiner.html#a6b9ea8e922099c435e8cc872ceab7557">IMP::atom::BondEndpointsRefiner::get_refined()</a>, <a href="classIMP_1_1atom_1_1BondPairContainer.html#ada22e8d1ead0a1a6c7097389c8de0107">IMP::atom::BondPairContainer::get_all_possible_indexes()</a>, <a href="classIMP_1_1atom_1_1Bonded.html#aa7db7f5257bb014fe5111661aff3c814">IMP::atom::Bonded::get_bond_indexes()</a>, <a href="classIMP_1_1atom_1_1CHARMMConnection.html#adf29f3ca8131dfa961d939a35ce4af60">IMP::atom::CHARMMConnection::get_atoms()</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_1CHARMMTopology.html#a403b30e23e492dc1da0514bd8f5dd149">IMP::atom::CHARMMTopology::add_bonds()</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_1Hierarchy.html#ad21bb9279754451fbe57bdebd170faf3">IMP::atom::Hierarchy::get_children()</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#a88d34e2044a5fbfbb25069331da1b527">IMP::atom::Hierarchy::get_leaves()</a>, <a href="classIMP_1_1atom_1_1Hierarchy.html#aa8687c81bbcdd0a54c247d9b6b4a2821">IMP::atom::Hierarchy::get_leaves()</a>, <a href="classIMP_1_1atom_1_1Representation.html#ab31fd97c8a0dda88abe16f0744c17d6a">IMP::atom::Representation::get_representations()</a>, <a href="classIMP_1_1atom_1_1Selection.html#afe161e06395cbac13aa681457cad1a24">IMP::atom::Selection::get_hierarchies()</a>, <a href="classIMP_1_1atom_1_1Selection.html#aaacb47f72e389270dd6217399580480b">IMP::atom::Selection::get_selected_particle_indexes()</a>, <a href="classIMP_1_1atom_1_1Selection.html#abab4978f28c318d2e05e61c8441de4e5">IMP::atom::Selection::get_selected_particles()</a>, <a href="classIMP_1_1atom_1_1Simulator.html#a83441a44bae6268bc408569c43c61dd4">IMP::atom::Simulator::get_particles()</a>, <a href="classIMP_1_1atom_1_1Simulator.html#a924853b2f3567b3acebea871cbeadd7c">IMP::atom::Simulator::get_simulation_particle_indexes()</a>, <a href="classIMP_1_1atom_1_1Simulator.html#a62a921c063c2f41bed110af9985a1b21">IMP::atom::Simulator::get_simulation_particles()</a>, <a href="classIMP_1_1bayesianem_1_1GaussianEMRestraint.html#abdcfd8452afc2a86614ed205d0b85909">IMP::bayesianem::GaussianEMRestraint::get_indexes()</a>, <a href="classIMP_1_1container_1_1AllBipartitePairContainer.html#a9f7a29ec5c98621808b0f3b95d7e97ac">IMP::container::AllBipartitePairContainer::get_all_possible_indexes()</a>, <a href="classIMP_1_1container_1_1AllPairContainer.html#a42763a1231569ab26c101ce649e294e9">IMP::container::AllPairContainer::get_all_possible_indexes()</a>, <a href="classIMP_1_1container_1_1CloseBipartitePairContainer.html#aae326a7f4a274edc03713b317e99eaf1">IMP::container::CloseBipartitePairContainer::get_all_possible_indexes()</a>, <a href="classIMP_1_1container_1_1ClosePairContainer.html#aacaec307a253333b49f28964e0d75cb8">IMP::container::ClosePairContainer::get_all_possible_indexes()</a>, <a href="classIMP_1_1container_1_1ConnectingPairContainer.html#a67dd9abbb047ffcc34ffe1b9c63deb38">IMP::container::ConnectingPairContainer::get_all_possible_indexes()</a>, <a href="classIMP_1_1container_1_1ConsecutivePairContainer.html#a8486fabfae14f299e4cbe771d380b9d8">IMP::container::ConsecutivePairContainer::get_all_possible_indexes()</a>, <a href="classIMP_1_1container_1_1ExclusiveConsecutivePairContainer.html#aeb5f32335c59c7eb4a30ef7001b4bcf5">IMP::container::ExclusiveConsecutivePairContainer::get_all_possible_indexes()</a>, <a href="classIMP_1_1container_1_1PairContainerSet.html#a8bf14bca242623c31ba1db63b07370e8">IMP::container::PairContainerSet::get_all_possible_indexes()</a>, <a href="classIMP_1_1container_1_1PredicateSingletonsRestraint.html#afe7b9e126e74db54f3f9023a00b52009">IMP::container::PredicateSingletonsRestraint::get_indexes()</a>, <a href="classIMP_1_1container_1_1QuadContainerSet.html#aef9b2be20d398e7c00ec72a867df0bac">IMP::container::QuadContainerSet::get_all_possible_indexes()</a>, <a href="classIMP_1_1container_1_1SingletonContainerSet.html#a1804b70cde37afde55d61500969d6c74">IMP::container::SingletonContainerSet::get_all_possible_indexes()</a>, <a href="classIMP_1_1container_1_1TripletContainerSet.html#a82aee24cf4bd1d4b404247a985b01895">IMP::container::TripletContainerSet::get_all_possible_indexes()</a>, <a href="classIMP_1_1core_1_1ChildrenRefiner.html#abccfb2e3525a3f3c71087af49a6aeb4d">IMP::core::ChildrenRefiner::get_refined()</a>, <a href="classIMP_1_1core_1_1FixedRefiner.html#a032bf5815adb4b876220eab17db0bb6a">IMP::core::FixedRefiner::get_refined()</a>, <a href="classIMP_1_1core_1_1FixedRefiner.html#a7a3282cd0b2ecdcc6c3cbdcf02953986">IMP::core::FixedRefiner::get_refined_indexes()</a>, <a href="classIMP_1_1core_1_1FixedRefiner.html#a6f5f1258501bedda8ce309bdf7d91359">IMP::core::FixedRefiner::get_refined_indexes_by_ref()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#a3371ae91f1a36c9aff85fa5d185d632c">IMP::core::Hierarchy::get_children_indexes()</a>, <a href="classIMP_1_1core_1_1IncrementalScoringFunction.html#ab936c5698c02c09dc99e12040038291b">IMP::core::IncrementalScoringFunction::get_movable_indexes()</a>, <a href="classIMP_1_1core_1_1LeavesRefiner.html#a7cbc3d2ac175308b5525a211506743f9">IMP::core::LeavesRefiner::get_refined()</a>, <a href="classIMP_1_1core_1_1MonteCarlo.html#a81a1ed94226894a4d44315e85b860c76">IMP::core::MonteCarlo::get_movable_particles()</a>, <a href="classIMP_1_1core_1_1NeighborsTable.html#a1c9e3ba91c37fe4efb7df9c090679343">IMP::core::NeighborsTable::get_neighbors()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#ae409738df900de261fbf6a8b4f7b55e4">IMP::core::RigidBody::get_body_member_particle_indexes()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#ac4ca78b1b154b54eeebe62e22b2425a6">IMP::core::RigidBody::get_member_indexes()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#a04cbb350db3ffa071668c236772e66be">IMP::core::RigidBody::get_member_particle_indexes()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#a01768cb77a2b5321ce1d5c49eb18e77a">IMP::core::RigidBody::get_rigid_members()</a>, <a href="classIMP_1_1core_1_1TableRefiner.html#a2ccef93c340c87078fc8d96397afa219">IMP::core::TableRefiner::get_refined()</a>, <a href="classIMP_1_1domino_1_1DisjointSetsSubsetFilterTable.html#a87b82a0650db798f234bf20cdeee6d0a">IMP::domino::DisjointSetsSubsetFilterTable::get_set()</a>, <a href="classIMP_1_1domino_1_1ParticleStatesTable.html#a594192bb135e6694bf712941b3f48ccd">IMP::domino::ParticleStatesTable::get_particles()</a>, <a href="classIMP_1_1domino_1_1Subset.html#abc363518286114870ac4546205ac71af">IMP::domino::Subset::get_sorted()</a>, <a href="classIMP_1_1em_1_1DensityFillingRestraint.html#ad6eef2a0762f8c15bad951708fecb671">IMP::em::DensityFillingRestraint::get_particles()</a>, <a href="classIMP_1_1em_1_1EnvelopePenetrationRestraint.html#ab8f4ca1991d0e58327fe87a488dfa4aa">IMP::em::EnvelopePenetrationRestraint::get_particles()</a>, <a href="classIMP_1_1em_1_1FitRestraint.html#a730ada38bb3201563d23c2adc91f0c4e">IMP::em::FitRestraint::get_particles()</a>, <a href="classIMP_1_1em_1_1PCAFitRestraint.html#ae5b63ae4b18e0ab5fbb1c9c9bd941d7d">IMP::em::PCAFitRestraint::get_particles()</a>, <a href="classIMP_1_1em_1_1SampledDensityMap.html#a39c374164a620c8d9b192f9544b6ff91">IMP::em::SampledDensityMap::get_sampled_particles()</a>, <a href="classIMP_1_1em_1_1SampledDensityMap.html#ae745f6d6ea9515917c359ef7505bfc4e">IMP::em::SampledDensityMap::get_xyzr_particles()</a>, <a href="classIMP_1_1isd_1_1GaussianAnchorEMRestraint.html#a7eb182a4cca0d5e4ed61aaf004b8304f">IMP::isd::GaussianAnchorEMRestraint::get_density_particles()</a>, <a href="classIMP_1_1kinematics_1_1KinematicForest.html#a7c78844070f513f8d8118604e8399924">IMP::kinematics::KinematicForest::get_children()</a>, <a href="classIMP_1_1kinematics_1_1ProteinKinematics.html#a1be4d31ffe157cbd577c1deee42d5657">IMP::kinematics::ProteinKinematics::get_rigid_bodies()</a>, <a href="classIMP_1_1kinematics_1_1ProteinKinematics.html#a6c1567bf70bfaa7ed75330f75915d91b">IMP::kinematics::ProteinKinematics::quick_hack_converter()</a>, <a href="classIMP_1_1multi__state_1_1MultiStateModel.html#a228a8de4795302cfd9d07fb4f5d1de5a">IMP::multi_state::MultiStateModel::get_states()</a>, <a href="classIMP_1_1multifit_1_1AnchorsData.html#a816d3e8dd82c3dae5aa2294751016ea7">IMP::multifit::AnchorsData::get_secondary_structure_particles()</a>, <a href="classIMP_1_1multifit_1_1Ensemble.html#a4156aa95772ba0636c50f0528ff278ac">IMP::multifit::Ensemble::get_molecules()</a>, <a href="classIMP_1_1multifit_1_1Ensemble.html#a90987f6d8f5bcdaa856b3effcc6b224b">IMP::multifit::Ensemble::get_rigid_bodies()</a>, <a href="classIMP_1_1multifit_1_1GeometricHash.html#ad836b61873521a48bf1a0211f2d139f2">IMP::multifit::GeometricHash::neighbors_data()</a>, <a href="classIMP_1_1multifit_1_1ProteomicsEMAlignmentAtomic.html#a8a3bce24cdbd4c2ff9fca7e726560fd0">IMP::multifit::ProteomicsEMAlignmentAtomic::get_molecules()</a>, <a href="classIMP_1_1multifit_1_1ProteomicsEMAlignmentAtomic.html#a8db692880725a7de95df804f50deaeed">IMP::multifit::ProteomicsEMAlignmentAtomic::get_rigid_bodies()</a>, <a href="classIMP_1_1multifit_1_1RadiusOfGyrationRestraint.html#aab75ced79c6728b64ab4ee8cfdeb3439">IMP::multifit::RadiusOfGyrationRestraint::get_particles()</a>, <a href="classIMP_1_1multifit_1_1RigidLeavesRefiner.html#a42116e2b0e24cdf0bde9c9aebe031e82">IMP::multifit::RigidLeavesRefiner::get_refined()</a>, <a href="classIMP_1_1multifit_1_1WeightedExcludedVolumeRestraint.html#aef5d9066289f76259952823c0add7ff8">IMP::multifit::WeightedExcludedVolumeRestraint::get_particles()</a>, <a href="classIMP_1_1npctransport_1_1FGChain.html#af525394f2d40de0e2582fd7b74451d24">IMP::npctransport::FGChain::get_beads()</a>, <a href="classIMP_1_1npctransport_1_1SimulationData.html#ac74ed5ad4a9b3e5df4efaf8c2ef64221">IMP::npctransport::SimulationData::get_beads()</a>, <a href="classIMP_1_1npctransport_1_1SimulationData.html#a9fd32e5f37d18e0a7f7fa0928f12776f">IMP::npctransport::SimulationData::get_beads_byref()</a>, <a href="classIMP_1_1npctransport_1_1SimulationData.html#a7fd6303499deed5e9c6e2c0cea99d0f7">IMP::npctransport::SimulationData::get_fg_chain_roots()</a>, <a href="classIMP_1_1npctransport_1_1SimulationData.html#aff2a4f1e5c3fe124d47f7747d8cc5177">IMP::npctransport::SimulationData::get_fg_chains()</a>, <a href="classIMP_1_1npctransport_1_1SimulationData.html#a59e5c508e8d5f8b3a3867476bf649c25">IMP::npctransport::SimulationData::get_non_optimizable_beads()</a>, <a href="classIMP_1_1npctransport_1_1SimulationData.html#a986e19289e25a3317b55ca5e7bb45784">IMP::npctransport::SimulationData::get_obstacle_particles()</a>, <a href="classIMP_1_1npctransport_1_1SimulationData.html#accc16c1b9bd4f5223e6ab1c4b243011f">IMP::npctransport::SimulationData::get_optimizable_beads()</a>, <a href="classIMP_1_1rmf_1_1SimpleLoadLink.html#a8c568d0291111015e06845c3c6466f39">IMP::rmf::SimpleLoadLink::create()</a>, <a href="classIMP_1_1rmf_1_1SimpleLoadLink.html#acb250839c30652b3b67bb63c8beb3429">IMP::rmf::SimpleLoadLink::create()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#a41e3c1b2e22f41645e9dff51f31a5b19">IMP::saxs::FormFactorTable::get_dummy_form_factors()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#ab90fa63100485221a07d9549b5ac32fb">IMP::saxs::FormFactorTable::get_form_factors()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#ad841c2816abc2dcf15547ed76ef2ffda">IMP::saxs::FormFactorTable::get_vacuum_form_factors()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#a5c4c424ba167aa6b10159f3163853813">IMP::saxs::FormFactorTable::get_water_dummy_form_factors()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#adfb626e687665ddf2b7a58dbe5cfc23f">IMP::saxs::FormFactorTable::get_water_form_factors()</a>, <a href="classIMP_1_1saxs_1_1FormFactorTable.html#ace61d6c9bf5b3211bb7865e214be8bad">IMP::saxs::FormFactorTable::get_water_vacuum_form_factors()</a>, <a href="classIMP_1_1saxs_1_1ProfileClustering.html#a4ea42910bc4f3b151a5d690fb436c5f5">IMP::saxs::ProfileClustering::get_clusters()</a>, <a href="classIMP_1_1saxs_1_1SolventAccessibleSurface.html#a219d7fc61ef2b987317334a260246b19">IMP::saxs::SolventAccessibleSurface::get_solvent_accessibility()</a>, <a href="classIMP_1_1saxs_1_1WeightedFitParameters.html#aa72f43d7dcbba4b099355869ca622341">IMP::saxs::WeightedFitParameters::get_weights()</a>, <a href="classIMP_1_1spb_1_1CellMover.html#a705875dfcd4c101bc54274bcaa94a8c8">IMP::spb::CellMover::get_particles()</a>, <a href="classIMP_1_1spb_1_1PbcBoxedRigidBodyMover.html#a9f71be4c0d64eef754e6ba2bf2c0b478">IMP::spb::PbcBoxedRigidBodyMover::get_particles()</a>, <a href="classIMP_1_1symmetry_1_1RigidBodyMover.html#a46b76b01c2cd25d8b05ad691ca14bbbc">IMP::symmetry::RigidBodyMover::get_particles()</a>, <a href="namespaceIMP.html#af488ed0d8a9b736cc3be4fce11d19829">IMP::get_input_particles()</a>, <a href="namespaceIMP.html#afe628c07ef885af644a24a23643ae5b2">IMP::get_output_particles()</a>, <a href="namespaceIMP.html#ac49fedd9ea52d5339c003cc00c1b906e">IMP::write_particles_to_buffer()</a>, <a href="namespaceIMP.html#ae762869ee2f6a3888dcd62a1f4213566">IMP::get_dependent_particles()</a>, <a href="namespaceIMP.html#aabc6b814ba85ea74a1b3f9f0ce8c06cf">IMP::get_indexes()</a>, <a href="namespaceIMP.html#a282964e47bdd3107ef2e3ef72df66001">IMP::get_particles()</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#a8f2e62640647e36570c22b0328283a9c">IMP::atom::get_charmm_untyped_atoms()</a>, <a href="namespaceIMP_1_1atom.html#ad62901c76275a45e34aed68c76548508">IMP::atom::get_chi_dihedral_atom_types()</a>, <a href="namespaceIMP_1_1atom.html#a30ce58af4f3485274c3c59c7170d6698">IMP::atom::get_chi_dihedral_atoms()</a>, <a href="namespaceIMP_1_1atom.html#af5b0cc808be9672d3996baeb2f9210fd">IMP::atom::get_leaves()</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#a1c15e940e47a1a8f5872029fcb93c601">IMP::atom::get_psi_dihedral_atoms()</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#a886a95c9c35244e6120f8484f501bdb9">IMP::atom::setup_coarse_secondary_structure_residues()</a>, <a href="namespaceIMP_1_1core.html#aa9f324c68944164bd609b55bb3ca3b44">IMP::core::create_rigid_bodies()</a>, <a href="namespaceIMP_1_1core.html#ad63b32c4f50e42d6ca6d72fa75b5cc02">IMP::core::create_xyzr_particles()</a>, <a href="namespaceIMP_1_1domino.html#a0f43ef4b4efed8a9481e65694ce3fadb">IMP::domino::get_order()</a>, <a href="namespaceIMP_1_1em.html#ad7c905f64de2740109026908aaa1e952">IMP::em::density2particles()</a>, <a href="namespaceIMP_1_1npctransport.html#af4eac42b841cb74c967c2f4284ddb1d0">IMP::npctransport::create_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_1rmf.html#a34bff2a310116bc205e199ae6442be5d">IMP::rmf::create_hierarchies()</a>, <a href="namespaceIMP_1_1rmf.html#af3c5165b1f2cb083d98c36bd202ef275">IMP::rmf::create_particles()</a>, <a href="namespaceIMP_1_1spb.html#af9854762e7ddee17e6b588f2a8502c20">IMP::spb::create_coiled_coil()</a>, <a href="namespaceIMP_1_1spb.html#ae9d935784a933409cd306c7c046cfff6">IMP::spb::create_representation()</a></td></tr>
52 <tr><td>@ref IMP::VersionInfo</td><td><a href="classIMP_1_1Configuration.html#a642f7dca965a2836d0e81c2eac26f0d3">IMP::Configuration::get_version_info()</a>, <a href="classIMP_1_1ConfigurationSet.html#aacea1a78983a83d1a4b50ce97b0823a3">IMP::ConfigurationSet::get_version_info()</a>, <a href="classIMP_1_1Model.html#a47e96f8e30231b2858ae9af6d28f494c">IMP::Model::get_version_info()</a>, <a href="classIMP_1_1Object.html#a0bed6774bc4e0652d9de26295d9439cf">IMP::Object::get_version_info()</a>, <a href="classIMP_1_1Particle.html#af042b70035d9c879ca622e182d4cada5">IMP::Particle::get_version_info()</a>, <a href="classIMP_1_1RestraintInfo.html#a9a6b74ea5dfbdad897a15c8ba0c2bcdd">IMP::RestraintInfo::get_version_info()</a>, <a href="classIMP_1_1RestraintSet.html#a10446d56e7dd2dc6c5ad626c16048d14">IMP::RestraintSet::get_version_info()</a>, <a href="classIMP_1_1SaveToConfigurationSetOptimizerState.html#ac5d97e31680960e80669a30078c694aa">IMP::SaveToConfigurationSetOptimizerState::get_version_info()</a>, <a href="classIMP_1_1algebra_1_1DynamicNearestNeighbor3D.html#a6cd80c9eb6264ce8639666c3006f5ae7">IMP::algebra::DynamicNearestNeighbor3D::get_version_info()</a>, <a href="classIMP_1_1algebra_1_1EuclideanVectorKDMetric.html#a4a8941aca8e98679d014411eef1d84a3">IMP::algebra::EuclideanVectorKDMetric::get_version_info()</a>, <a href="classIMP_1_1algebra_1_1MaxVectorKDMetric.html#a1c0e14cbdeded47506e4cf4c9f903277">IMP::algebra::MaxVectorKDMetric::get_version_info()</a>, <a href="classIMP_1_1algebra_1_1NearestNeighborD.html#accf99b31a4479e4c274eebd4a9a5e1ab">IMP::algebra::NearestNeighborD::get_version_info()</a>, <a href="classIMP_1_1atom_1_1ATOMPDBSelector.html#a9030c17872ae35157c221906f6ebd80c">IMP::atom::ATOMPDBSelector::get_version_info()</a>, <a href="classIMP_1_1atom_1_1AllPDBSelector.html#a8bc71eab92de2570e774cdfd772db30b">IMP::atom::AllPDBSelector::get_version_info()</a>, <a href="classIMP_1_1atom_1_1AndPDBSelector.html#aedf27e500c2c398d5946431bdb96723b">IMP::atom::AndPDBSelector::get_version_info()</a>, <a href="classIMP_1_1atom_1_1AngleSingletonScore.html#acb64ab9ca16a761b691e7044c9185400">IMP::atom::AngleSingletonScore::get_version_info()</a>, <a href="classIMP_1_1atom_1_1AtomTypePDBSelector.html#a55ade5f60487d81812788b3d4dcf772a">IMP::atom::AtomTypePDBSelector::get_version_info()</a>, <a href="classIMP_1_1atom_1_1BackbonePDBSelector.html#a9e68a3717e0ce5cac1965a6cd08275b7">IMP::atom::BackbonePDBSelector::get_version_info()</a>, <a href="classIMP_1_1atom_1_1BerendsenThermostatOptimizerState.html#a4711270d062cf949787d7db1c052f21e">IMP::atom::BerendsenThermostatOptimizerState::get_version_info()</a>, <a href="classIMP_1_1atom_1_1BondEndpointsRefiner.html#a2558c81dc27aa82469bc59f41fdddb23">IMP::atom::BondEndpointsRefiner::get_version_info()</a>, <a href="classIMP_1_1atom_1_1BondGeometry.html#aa8247ddfae28098c0fd2d9701cd07df6">IMP::atom::BondGeometry::get_version_info()</a>, <a href="classIMP_1_1atom_1_1BondPairContainer.html#a972f9797588f1113586d77e36df90d2a">IMP::atom::BondPairContainer::get_version_info()</a>, <a href="classIMP_1_1atom_1_1BondSingletonScore.html#a34d06d7c28474a417543ee01c1ecedb0">IMP::atom::BondSingletonScore::get_version_info()</a>, <a href="classIMP_1_1atom_1_1BondedPairFilter.html#abef2a7853eccff57a0188ab0ae502df7">IMP::atom::BondedPairFilter::get_version_info()</a>, <a href="classIMP_1_1atom_1_1BondsGeometry.html#aafd91c8215178c7b7991370cfec198bf">IMP::atom::BondsGeometry::get_version_info()</a>, <a href="classIMP_1_1atom_1_1BrownianDynamics.html#a59748d75325cfcc0cd96a7bde16f2501">IMP::atom::BrownianDynamics::get_version_info()</a>, <a href="classIMP_1_1atom_1_1CAAngleRestraint.html#a7ef9c66f36f61174214d3f41a945b114">IMP::atom::CAAngleRestraint::get_version_info()</a>, <a href="classIMP_1_1atom_1_1CADihedralRestraint.html#a29554dab5ffb793509b188a1f0b8d390">IMP::atom::CADihedralRestraint::get_version_info()</a>, <a href="classIMP_1_1atom_1_1CAlphaPDBSelector.html#a141a7787a2fe1da090a0ad6ee24b9a1a">IMP::atom::CAlphaPDBSelector::get_version_info()</a>, <a href="classIMP_1_1atom_1_1CBetaPDBSelector.html#a58cb0796262e88f695bf27dd7c90b112">IMP::atom::CBetaPDBSelector::get_version_info()</a>, <a href="classIMP_1_1atom_1_1CHARMMIdealResidueTopology.html#a1641996294b127530e6cd03f459dde0a">IMP::atom::CHARMMIdealResidueTopology::get_version_info()</a>, <a href="classIMP_1_1atom_1_1CHARMMParameters.html#a16b862167ea91ff9599638d989462087">IMP::atom::CHARMMParameters::get_version_info()</a>, <a href="classIMP_1_1atom_1_1CHARMMPatch.html#a714a9bbecb6a43e58d26bed5e4152fc3">IMP::atom::CHARMMPatch::get_version_info()</a>, <a href="classIMP_1_1atom_1_1CHARMMResidueTopology.html#a668d1a4db113166fd8d2a16105f0a073">IMP::atom::CHARMMResidueTopology::get_version_info()</a>, <a href="classIMP_1_1atom_1_1CHARMMResidueTopologyBase.html#aa24eab2dac7f6775be376088fc1a0ab8">IMP::atom::CHARMMResidueTopologyBase::get_version_info()</a>, <a href="classIMP_1_1atom_1_1CHARMMSegmentTopology.html#addf51458afe95fcba0a5dcad6ed7fdd7">IMP::atom::CHARMMSegmentTopology::get_version_info()</a>, <a href="classIMP_1_1atom_1_1CHARMMStereochemistryRestraint.html#ad9669e39e743dc27a0ad7b8b8f349a0a">IMP::atom::CHARMMStereochemistryRestraint::get_version_info()</a>, <a href="classIMP_1_1atom_1_1CHARMMTopology.html#a57fb211fbd26b5c82b58827515071f69">IMP::atom::CHARMMTopology::get_version_info()</a>, <a href="classIMP_1_1atom_1_1CPDBSelector.html#a3872a37dd93def75335ff3c6add58e2e">IMP::atom::CPDBSelector::get_version_info()</a>, <a href="classIMP_1_1atom_1_1ChainPDBSelector.html#abc52914f1e44438c3868b434fa750d4b">IMP::atom::ChainPDBSelector::get_version_info()</a>, <a href="classIMP_1_1atom_1_1CoulombPairScore.html#a05dd6e490181c3b784925651bd81dc70">IMP::atom::CoulombPairScore::get_version_info()</a>, <a href="classIMP_1_1atom_1_1CoverBond.html#a4925de49cab27cbfb4f42c9eb2e6eb5c">IMP::atom::CoverBond::get_version_info()</a>, <a href="classIMP_1_1atom_1_1DihedralSingletonScore.html#a27ebdc261f0c7a206875e6a929111cd4">IMP::atom::DihedralSingletonScore::get_version_info()</a>, <a href="classIMP_1_1atom_1_1EzRestraint.html#a1cfb4a581eb882607a210f63ee4f4f19">IMP::atom::EzRestraint::get_version_info()</a>, <a href="classIMP_1_1atom_1_1ForceSwitch.html#a2ce2594f0553727e1dde640999f462cf">IMP::atom::ForceSwitch::get_version_info()</a>, <a href="classIMP_1_1atom_1_1HelixRestraint.html#abd639e3953e5cdd7564678d7ba9e7205">IMP::atom::HelixRestraint::get_version_info()</a>, <a href="classIMP_1_1atom_1_1HierarchiesGeometry.html#ae0f99e132e30e4570da194581e9af16a">IMP::atom::HierarchiesGeometry::get_version_info()</a>, <a href="classIMP_1_1atom_1_1HierarchyGeometry.html#a141991f6445a80433ba8bc8047d8319f">IMP::atom::HierarchyGeometry::get_version_info()</a>, <a href="classIMP_1_1atom_1_1HydrogenPDBSelector.html#a10745b17b15e2b4269a82fb0d7192034">IMP::atom::HydrogenPDBSelector::get_version_info()</a>, <a href="classIMP_1_1atom_1_1ImproperSingletonScore.html#a57481a650b6a1b92aec993f58d35d385">IMP::atom::ImproperSingletonScore::get_version_info()</a>, <a href="classIMP_1_1atom_1_1LangevinThermostatOptimizerState.html#a68a1ab9ffe98c29919969d8c7278d43a">IMP::atom::LangevinThermostatOptimizerState::get_version_info()</a>, <a href="classIMP_1_1atom_1_1LennardJonesPairScore.html#ab6ed1d60c65025eb0cb4eb8404887d6d">IMP::atom::LennardJonesPairScore::get_version_info()</a>, <a href="classIMP_1_1atom_1_1MolecularDynamics.html#a43bf305498c71fc9f23231aabfae723f">IMP::atom::MolecularDynamics::get_version_info()</a>, <a href="classIMP_1_1atom_1_1NPDBSelector.html#a82912364ae2d344239586989d20355e2">IMP::atom::NPDBSelector::get_version_info()</a>, <a href="classIMP_1_1atom_1_1NonAlternativePDBSelector.html#afc5d92e1a5bacd2f16edd11f95b7258a">IMP::atom::NonAlternativePDBSelector::get_version_info()</a>, <a href="classIMP_1_1atom_1_1NonHydrogenPDBSelector.html#a2c68badf35586e4363a2ab8a5823a4a8">IMP::atom::NonHydrogenPDBSelector::get_version_info()</a>, <a href="classIMP_1_1atom_1_1NonWaterNonHydrogenPDBSelector.html#a99b626391cde6e1e4ccfd685ab2878b9">IMP::atom::NonWaterNonHydrogenPDBSelector::get_version_info()</a>, <a href="classIMP_1_1atom_1_1NonWaterPDBSelector.html#a4bce63a26b48fbb9cfdf26bd8a4a5342">IMP::atom::NonWaterPDBSelector::get_version_info()</a>, <a href="classIMP_1_1atom_1_1NotPDBSelector.html#a6677c2db194718035bc8d4a1625a57d0">IMP::atom::NotPDBSelector::get_version_info()</a>, <a href="classIMP_1_1atom_1_1OrPDBSelector.html#a3862f7d8cf8f31853b7d6525f70e161d">IMP::atom::OrPDBSelector::get_version_info()</a>, <a href="classIMP_1_1atom_1_1PPDBSelector.html#a4b2725b3bad9a4688a1264dbab333d9d">IMP::atom::PPDBSelector::get_version_info()</a>, <a href="classIMP_1_1atom_1_1RemoveRigidMotionOptimizerState.html#ab44d646a5416b3ed0f239c574e76ed8e">IMP::atom::RemoveRigidMotionOptimizerState::get_version_info()</a>, <a href="classIMP_1_1atom_1_1RemoveTranslationOptimizerState.html#a89445cb6edfe932bb855dfd90a78f01a">IMP::atom::RemoveTranslationOptimizerState::get_version_info()</a>, <a href="classIMP_1_1atom_1_1ResidueTypePDBSelector.html#a691599e8942f56405d5e29971d20e0ed">IMP::atom::ResidueTypePDBSelector::get_version_info()</a>, <a href="classIMP_1_1atom_1_1SameResiduePairFilter.html#a6e9a27135568a9d6ea92ee431075b5b6">IMP::atom::SameResiduePairFilter::get_version_info()</a>, <a href="classIMP_1_1atom_1_1SelectionGeometry.html#a0f9fb05eb9f263666b0262ddddf47dd2">IMP::atom::SelectionGeometry::get_version_info()</a>, <a href="classIMP_1_1atom_1_1SoapPairFilter.html#a706725399dacf424ef6de245846acfa1">IMP::atom::SoapPairFilter::get_version_info()</a>, <a href="classIMP_1_1atom_1_1StereochemistryPairFilter.html#a5b65309e5f6b88589ecaada4632295c2">IMP::atom::StereochemistryPairFilter::get_version_info()</a>, <a href="classIMP_1_1atom_1_1VelocityScalingOptimizerState.html#aab31f8971091d973c66fedcbab32a00e">IMP::atom::VelocityScalingOptimizerState::get_version_info()</a>, <a href="classIMP_1_1atom_1_1WaterPDBSelector.html#abe0b0fdf0a6505a6abb8df512c547104">IMP::atom::WaterPDBSelector::get_version_info()</a>, <a href="classIMP_1_1atom_1_1WritePDBOptimizerState.html#a11196ae6bfb7ea838791155f0c88222f">IMP::atom::WritePDBOptimizerState::get_version_info()</a>, <a href="classIMP_1_1atom_1_1XorPDBSelector.html#ad29f0eee7834d5c5d9bf152c82cf52c1">IMP::atom::XorPDBSelector::get_version_info()</a>, <a href="classIMP_1_1bayesianem_1_1GaussianEMRestraint.html#a1be3304855ff269a9646bc8b79476724">IMP::bayesianem::GaussianEMRestraint::get_version_info()</a>, <a href="classIMP_1_1container_1_1AllBipartitePairContainer.html#a6919824d107703d71158c4e590b40979">IMP::container::AllBipartitePairContainer::get_version_info()</a>, <a href="classIMP_1_1container_1_1AllPairContainer.html#a3a875947efd33e1a692c587685c55f95">IMP::container::AllPairContainer::get_version_info()</a>, <a href="classIMP_1_1container_1_1CloseBipartitePairContainer.html#a716be53e4501823d55fb420353b54c68">IMP::container::CloseBipartitePairContainer::get_version_info()</a>, <a href="classIMP_1_1container_1_1ClosePairContainer.html#a2428f7f09f3231fef7ee1c26fde88934">IMP::container::ClosePairContainer::get_version_info()</a>, <a href="classIMP_1_1container_1_1ConnectingPairContainer.html#a1721e1c17b5596ae45310354ddcda0b6">IMP::container::ConnectingPairContainer::get_version_info()</a>, <a href="classIMP_1_1container_1_1ConsecutivePairContainer.html#aa8d192b014f93d5f44c0c3bc5971db20">IMP::container::ConsecutivePairContainer::get_version_info()</a>, <a href="classIMP_1_1container_1_1ConsecutivePairFilter.html#ace071852674fb3183446885b02646928">IMP::container::ConsecutivePairFilter::get_version_info()</a>, <a href="classIMP_1_1container_1_1DistributePairsScoreState.html#a478e0711dc9a0082c9656586b4c73f87">IMP::container::DistributePairsScoreState::get_version_info()</a>, <a href="classIMP_1_1container_1_1DistributeQuadsScoreState.html#a62a1ac3837ee57165e3ef1cd345cc4e0">IMP::container::DistributeQuadsScoreState::get_version_info()</a>, <a href="classIMP_1_1container_1_1DistributeSingletonsScoreState.html#a5ec5d3a7147d1fed9d9c88b56b2f0e98">IMP::container::DistributeSingletonsScoreState::get_version_info()</a>, <a href="classIMP_1_1container_1_1DistributeTripletsScoreState.html#a468847b73fca37ca5ab9acebc137eaa0">IMP::container::DistributeTripletsScoreState::get_version_info()</a>, <a href="classIMP_1_1container_1_1DynamicListPairContainer.html#a503ebbc5e13cdb47012b7cf5c642107f">IMP::container::DynamicListPairContainer::get_version_info()</a>, <a href="classIMP_1_1container_1_1DynamicListQuadContainer.html#a06c501bec30c08383e12f99200117370">IMP::container::DynamicListQuadContainer::get_version_info()</a>, <a href="classIMP_1_1container_1_1DynamicListSingletonContainer.html#a069afeef43ce1f9063379275361ddb6c">IMP::container::DynamicListSingletonContainer::get_version_info()</a>, <a href="classIMP_1_1container_1_1DynamicListTripletContainer.html#a3390516c18da2a63364dc7c3b5d35707">IMP::container::DynamicListTripletContainer::get_version_info()</a>, <a href="classIMP_1_1container_1_1EventPairsOptimizerState.html#a310f27c31635073a7481fa5df129657a">IMP::container::EventPairsOptimizerState::get_version_info()</a>, <a href="classIMP_1_1container_1_1EventQuadsOptimizerState.html#a8d70721101abb838e8684b03255caaff">IMP::container::EventQuadsOptimizerState::get_version_info()</a>, <a href="classIMP_1_1container_1_1EventSingletonsOptimizerState.html#a3198fa0278cb61bdc2d6f0c4f120ab59">IMP::container::EventSingletonsOptimizerState::get_version_info()</a>, <a href="classIMP_1_1container_1_1EventTripletsOptimizerState.html#ae00b0a02c4781514f4eae50707cd1fae">IMP::container::EventTripletsOptimizerState::get_version_info()</a>, <a href="classIMP_1_1container_1_1ExclusiveConsecutivePairContainer.html#a2ce7ed54e82bd4969b45e5d88c23ed5f">IMP::container::ExclusiveConsecutivePairContainer::get_version_info()</a>, <a href="classIMP_1_1container_1_1ExclusiveConsecutivePairFilter.html#a96c54908fae456885dd090090a10ecdf">IMP::container::ExclusiveConsecutivePairFilter::get_version_info()</a>, <a href="classIMP_1_1container_1_1InContainerPairFilter.html#a512612247ec285bf5832b8464327bc39">IMP::container::InContainerPairFilter::get_version_info()</a>, <a href="classIMP_1_1container_1_1InContainerQuadFilter.html#a21ee7ee5bc957f8b2cf36aaf546972b7">IMP::container::InContainerQuadFilter::get_version_info()</a>, <a href="classIMP_1_1container_1_1InContainerSingletonFilter.html#ab434cf92695ad1084daef1052a3351c3">IMP::container::InContainerSingletonFilter::get_version_info()</a>, <a href="classIMP_1_1container_1_1InContainerTripletFilter.html#a4415d38a5a2708bfcf2967ae4f2ee8bc">IMP::container::InContainerTripletFilter::get_version_info()</a>, <a href="classIMP_1_1container_1_1ListPairContainer.html#ae2e4132e8c4fabaad2e26e4c15849589">IMP::container::ListPairContainer::get_version_info()</a>, <a href="classIMP_1_1container_1_1ListQuadContainer.html#ad69af7d05d0dc1a57073f613ae79cf4e">IMP::container::ListQuadContainer::get_version_info()</a>, <a href="classIMP_1_1container_1_1ListSingletonContainer.html#aea5ca5f30fcd1ff4dd6d55a2175edcf7">IMP::container::ListSingletonContainer::get_version_info()</a>, <a href="classIMP_1_1container_1_1ListTripletContainer.html#a88a32cf5fd31d988b79cc9a44d98a5f5">IMP::container::ListTripletContainer::get_version_info()</a>, <a href="classIMP_1_1container_1_1MinimumPairRestraint.html#a21745843143a2df77b883f0929929d11">IMP::container::MinimumPairRestraint::get_version_info()</a>, <a href="classIMP_1_1container_1_1MinimumPairScore.html#ab8be7bef9aedba065d2a21a8e51b3d12">IMP::container::MinimumPairScore::get_version_info()</a>, <a href="classIMP_1_1container_1_1MinimumQuadRestraint.html#a64584d72ae4787ce0a11c0ce2856717a">IMP::container::MinimumQuadRestraint::get_version_info()</a>, <a href="classIMP_1_1container_1_1MinimumQuadScore.html#a8762a50b51c4e7e56961f11a10e83cd6">IMP::container::MinimumQuadScore::get_version_info()</a>, <a href="classIMP_1_1container_1_1MinimumSingletonRestraint.html#ace4cc4a1182771083f1e94313f7d5ba3">IMP::container::MinimumSingletonRestraint::get_version_info()</a>, <a href="classIMP_1_1container_1_1MinimumSingletonScore.html#a3cc214f9c00a7884ab206be03dffad29">IMP::container::MinimumSingletonScore::get_version_info()</a>, <a href="classIMP_1_1container_1_1MinimumTripletRestraint.html#af4bfd9dc8d55daf618f1b4dccfa87192">IMP::container::MinimumTripletRestraint::get_version_info()</a>, <a href="classIMP_1_1container_1_1MinimumTripletScore.html#aabd51d38ee165586e34badd93c5a8ec2">IMP::container::MinimumTripletScore::get_version_info()</a>, <a href="classIMP_1_1container_1_1PairContainerSet.html#a3bd84a3b4291df676bf662a7627272c3">IMP::container::PairContainerSet::get_version_info()</a>, <a href="classIMP_1_1container_1_1PairContainerStatistics.html#a99c22c55be6110504a9b7adc8156313d">IMP::container::PairContainerStatistics::get_version_info()</a>, <a href="classIMP_1_1container_1_1PairsConstraint.html#a624808749bb574a76c5263b73c40a8d5">IMP::container::PairsConstraint::get_version_info()</a>, <a href="classIMP_1_1container_1_1PairsOptimizerState.html#a0db91ac40ac18b54dbce4840c22c6c7a">IMP::container::PairsOptimizerState::get_version_info()</a>, <a href="classIMP_1_1container_1_1PairsRestraint.html#ad15a32d447ab05d2ae425e70f24a2465">IMP::container::PairsRestraint::get_version_info()</a>, <a href="classIMP_1_1container_1_1PredicatePairsRestraint.html#afa3e90241fd497148cf818f9f8aa1b45">IMP::container::PredicatePairsRestraint::get_version_info()</a>, <a href="classIMP_1_1container_1_1PredicateQuadsRestraint.html#a5c3d487f59d696fae0ecfef4f86d25d5">IMP::container::PredicateQuadsRestraint::get_version_info()</a>, <a href="classIMP_1_1container_1_1PredicateSingletonsRestraint.html#a3335f24bebd3cf17ef17b998e655a9a1">IMP::container::PredicateSingletonsRestraint::get_version_info()</a>, <a href="classIMP_1_1container_1_1PredicateTripletsRestraint.html#a1e4835ab03a07617bd1ccde05a57cd39">IMP::container::PredicateTripletsRestraint::get_version_info()</a>, <a href="classIMP_1_1container_1_1QuadContainerSet.html#a881937021c94e22eae98dad41a6f520a">IMP::container::QuadContainerSet::get_version_info()</a>, <a href="classIMP_1_1container_1_1QuadContainerStatistics.html#a21115e6c22bf9f9505150660aac3612c">IMP::container::QuadContainerStatistics::get_version_info()</a>, <a href="classIMP_1_1container_1_1QuadsConstraint.html#abb6cb2bca3a2883afd7eec747fb0adb2">IMP::container::QuadsConstraint::get_version_info()</a>, <a href="classIMP_1_1container_1_1QuadsOptimizerState.html#ada81bd2555a9c176beaf942061fc65cb">IMP::container::QuadsOptimizerState::get_version_info()</a>, <a href="classIMP_1_1container_1_1QuadsRestraint.html#a58bfa88657d718a5e6295c216e7cdd90">IMP::container::QuadsRestraint::get_version_info()</a>, <a href="classIMP_1_1container_1_1SingletonContainerSet.html#a49fdc075e9ec79fb15fd0d38daae37e7">IMP::container::SingletonContainerSet::get_version_info()</a>, <a href="classIMP_1_1container_1_1SingletonContainerStatistics.html#adcca63ef3c7f057347b9f0d2dc27e67a">IMP::container::SingletonContainerStatistics::get_version_info()</a>, <a href="classIMP_1_1container_1_1SingletonsConstraint.html#ab03e1c7a3bfd875425427da524361362">IMP::container::SingletonsConstraint::get_version_info()</a>, <a href="classIMP_1_1container_1_1SingletonsOptimizerState.html#a374d3fa889be72bfddf6663aaa977c49">IMP::container::SingletonsOptimizerState::get_version_info()</a>, <a href="classIMP_1_1container_1_1SingletonsRestraint.html#a1d6662394a1a90967290c9c36c5ad42e">IMP::container::SingletonsRestraint::get_version_info()</a>, <a href="classIMP_1_1container_1_1TripletContainerSet.html#a1b70a80d5eab7d3b0a60e39622d5756b">IMP::container::TripletContainerSet::get_version_info()</a>, <a href="classIMP_1_1container_1_1TripletContainerStatistics.html#a0067ca67d339544db824ba159f6fcac7">IMP::container::TripletContainerStatistics::get_version_info()</a>, <a href="classIMP_1_1container_1_1TripletsConstraint.html#a4d1eb74f72e59f5adb0597fe0ab7a0d0">IMP::container::TripletsConstraint::get_version_info()</a>, <a href="classIMP_1_1container_1_1TripletsOptimizerState.html#a62cb8868569f8f46b416161f7509c76b">IMP::container::TripletsOptimizerState::get_version_info()</a>, <a href="classIMP_1_1container_1_1TripletsRestraint.html#aaf8f24029c5e4b20d0b86a4b407cde07">IMP::container::TripletsRestraint::get_version_info()</a>, <a href="classIMP_1_1core_1_1AllSamePairPredicate.html#a2045c89755ea96f273413f3af9cf1609">IMP::core::AllSamePairPredicate::get_version_info()</a>, <a href="classIMP_1_1core_1_1AllSameQuadPredicate.html#af2108573f721058bf755299009284e8d">IMP::core::AllSameQuadPredicate::get_version_info()</a>, <a href="classIMP_1_1core_1_1AllSameSingletonPredicate.html#a985dbc66ebef32db5b166b692c4f750c">IMP::core::AllSameSingletonPredicate::get_version_info()</a>, <a href="classIMP_1_1core_1_1AllSameTripletPredicate.html#a082276e7039cca8e25e738aabe555969">IMP::core::AllSameTripletPredicate::get_version_info()</a>, <a href="classIMP_1_1core_1_1AngleRestraint.html#a0ea0ce359e847791ecb151e9b599e6df">IMP::core::AngleRestraint::get_version_info()</a>, <a href="classIMP_1_1core_1_1AngleTripletScore.html#a60c5de78eec04b54c1a32b9db2ec8b27">IMP::core::AngleTripletScore::get_version_info()</a>, <a href="classIMP_1_1core_1_1AttributeSingletonPredicate.html#a3f8bfe6c31fa7c39a058b9f574ea4f17">IMP::core::AttributeSingletonPredicate::get_version_info()</a>, <a href="classIMP_1_1core_1_1BallMover.html#a826e1e2850dda7ddb668fe7403f61371">IMP::core::BallMover::get_version_info()</a>, <a href="classIMP_1_1core_1_1BoxSweepClosePairsFinder.html#aaee4e470b8b6fea0b7612faf9b5a69b9">IMP::core::BoxSweepClosePairsFinder::get_version_info()</a>, <a href="classIMP_1_1core_1_1CentroidOfRefined.html#a1ea3434021e782b8fdd7f9b62a7c086c">IMP::core::CentroidOfRefined::get_version_info()</a>, <a href="classIMP_1_1core_1_1ChecksScoreState.html#ad03ecf077a44d72fac8e32f2ca1941d5">IMP::core::ChecksScoreState::get_version_info()</a>, <a href="classIMP_1_1core_1_1ChildrenRefiner.html#ace419b81338ce37c8d2ebd3c46f69ccc">IMP::core::ChildrenRefiner::get_version_info()</a>, <a href="classIMP_1_1core_1_1ClosePairsPairScore.html#a7fd079b974cfb23f6c1518cf34409a2d">IMP::core::ClosePairsPairScore::get_version_info()</a>, <a href="classIMP_1_1core_1_1ClosedCubicSpline.html#a405f78e6e5bd904eff982596b823b87f">IMP::core::ClosedCubicSpline::get_version_info()</a>, <a href="classIMP_1_1core_1_1CoinFlipPairPredicate.html#a0d781f49e2cff9886949cd6083ef4e76">IMP::core::CoinFlipPairPredicate::get_version_info()</a>, <a href="classIMP_1_1core_1_1CoinFlipQuadPredicate.html#af3f2dd8155fb7f9b2fe5637f667062df">IMP::core::CoinFlipQuadPredicate::get_version_info()</a>, <a href="classIMP_1_1core_1_1CoinFlipSingletonPredicate.html#addee88d742fc838a44249fc77f2e1726">IMP::core::CoinFlipSingletonPredicate::get_version_info()</a>, <a href="classIMP_1_1core_1_1CoinFlipTripletPredicate.html#a11c82a62110494a113a8d805d065801c">IMP::core::CoinFlipTripletPredicate::get_version_info()</a>, <a href="classIMP_1_1core_1_1ConjugateGradients.html#a0dfb8d0269b3d64d69c51314bc592e2c">IMP::core::ConjugateGradients::get_version_info()</a>, <a href="classIMP_1_1core_1_1ConnectivityRestraint.html#a04f6c872430cc6a105b29971814b8a89">IMP::core::ConnectivityRestraint::get_version_info()</a>, <a href="classIMP_1_1core_1_1ConstantPairPredicate.html#af6bd094d78eaa98332f549b9fad3aba8">IMP::core::ConstantPairPredicate::get_version_info()</a>, <a href="classIMP_1_1core_1_1ConstantQuadPredicate.html#ac6e82a3b3af08b6e43072f42289ce725">IMP::core::ConstantQuadPredicate::get_version_info()</a>, <a href="classIMP_1_1core_1_1ConstantRestraint.html#ae541fa3946f584a30d99b040c80987d3">IMP::core::ConstantRestraint::get_version_info()</a>, <a href="classIMP_1_1core_1_1ConstantSingletonPredicate.html#a360a262b46bac600bc988d2742c34834">IMP::core::ConstantSingletonPredicate::get_version_info()</a>, <a href="classIMP_1_1core_1_1ConstantTripletPredicate.html#a5e3dc53bc881aec0de98cc6904d0458d">IMP::core::ConstantTripletPredicate::get_version_info()</a>, <a href="classIMP_1_1core_1_1Cosine.html#a26a102c4ec7a56cecf78ce1a8fe04001">IMP::core::Cosine::get_version_info()</a>, <a href="classIMP_1_1core_1_1CoverRefined.html#a31dae7b2c84905622ac509b12d6fb6b7">IMP::core::CoverRefined::get_version_info()</a>, <a href="classIMP_1_1core_1_1DerivativesFromRefined.html#a944c5fdde1cb212d1a0bc15ef7999dc1">IMP::core::DerivativesFromRefined::get_version_info()</a>, <a href="classIMP_1_1core_1_1DerivativesToRefined.html#ab9416814b36e8897ad88ee48eb9ba669">IMP::core::DerivativesToRefined::get_version_info()</a>, <a href="classIMP_1_1core_1_1DiameterRestraint.html#a87137d4ed9009b6d51392a8c9773caea">IMP::core::DiameterRestraint::get_version_info()</a>, <a href="classIMP_1_1core_1_1DihedralRestraint.html#ab89d061135684e4f91880790ee12163c">IMP::core::DihedralRestraint::get_version_info()</a>, <a href="classIMP_1_1core_1_1DirectionMover.html#a67f8d1e4a71162c69849e3a5d1ebac53">IMP::core::DirectionMover::get_version_info()</a>, <a href="classIMP_1_1core_1_1DistancePairScore.html#aa04e6eb6643d0b4abbe37cf1db1a6106">IMP::core::DistancePairScore::get_version_info()</a>, <a href="classIMP_1_1core_1_1EdgePairGeometry.html#aca90f6a05e23796898337c71a09af079">IMP::core::EdgePairGeometry::get_version_info()</a>, <a href="classIMP_1_1core_1_1EdgePairsGeometry.html#ac8add77f0c667e2a872a326186545243">IMP::core::EdgePairsGeometry::get_version_info()</a>, <a href="classIMP_1_1core_1_1ExcludedVolumeRestraint.html#afc65a22721ede4863036b1f8bb2f1f88">IMP::core::ExcludedVolumeRestraint::get_version_info()</a>, <a href="classIMP_1_1core_1_1FixedRefiner.html#a047634a9b796356e021900f421c24060">IMP::core::FixedRefiner::get_version_info()</a>, <a href="classIMP_1_1core_1_1GenericAttributeSingletonScore.html#a4add52896ed146541e3861de31f26ecc">IMP::core::GenericAttributeSingletonScore::get_version_info()</a>, <a href="classIMP_1_1core_1_1GenericBoundingBox3DSingletonScore.html#a1af1ad06f964d8153d29bea5be4493c3">IMP::core::GenericBoundingBox3DSingletonScore::get_version_info()</a>, <a href="classIMP_1_1core_1_1GenericBoundingSphere3DSingletonScore.html#a2eafae038fa09ce1d25b3dc5dfa3a25e">IMP::core::GenericBoundingSphere3DSingletonScore::get_version_info()</a>, <a href="classIMP_1_1core_1_1GenericDistanceToSingletonScore.html#a8f801980562376c37fac09dce6a1125a">IMP::core::GenericDistanceToSingletonScore::get_version_info()</a>, <a href="classIMP_1_1core_1_1GridClosePairsFinder.html#af082c2359c726e2381b1f19a5923dc18">IMP::core::GridClosePairsFinder::get_version_info()</a>, <a href="classIMP_1_1core_1_1Harmonic.html#aa649fd86144ce3aafeab32f6dffbb453">IMP::core::Harmonic::get_version_info()</a>, <a href="classIMP_1_1core_1_1HarmonicDistancePairScore.html#a68beedb901567c5021e4dfec26f66c97">IMP::core::HarmonicDistancePairScore::get_version_info()</a>, <a href="classIMP_1_1core_1_1HarmonicLowerBound.html#aba357b2404e5350b41227629011dcf2f">IMP::core::HarmonicLowerBound::get_version_info()</a>, <a href="classIMP_1_1core_1_1HarmonicSphereDistancePairScore.html#a64c7da07d35fb4d70e83f31ccb95a00d">IMP::core::HarmonicSphereDistancePairScore::get_version_info()</a>, <a href="classIMP_1_1core_1_1HarmonicSurfaceDepthPairScore.html#a5c8afebd948c11fb198b987f37444d2f">IMP::core::HarmonicSurfaceDepthPairScore::get_version_info()</a>, <a href="classIMP_1_1core_1_1HarmonicSurfaceDistancePairScore.html#a9ef5eb6dcd15de9fb6787949fd70fabb">IMP::core::HarmonicSurfaceDistancePairScore::get_version_info()</a>, <a href="classIMP_1_1core_1_1HarmonicSurfaceHeightPairScore.html#a6edc47301a017785fb59ec7739346833">IMP::core::HarmonicSurfaceHeightPairScore::get_version_info()</a>, <a href="classIMP_1_1core_1_1HarmonicUpperBound.html#ad393e8d01cffc3ebfae6f831b908f9be">IMP::core::HarmonicUpperBound::get_version_info()</a>, <a href="classIMP_1_1core_1_1HarmonicUpperBoundSphereDiameterPairScore.html#a2966c83adf43116eaa53c6295176a6c5">IMP::core::HarmonicUpperBoundSphereDiameterPairScore::get_version_info()</a>, <a href="classIMP_1_1core_1_1HarmonicUpperBoundSphereDistancePairScore.html#aef92f1baf06d57350f132ad48ca4284f">IMP::core::HarmonicUpperBoundSphereDistancePairScore::get_version_info()</a>, <a href="classIMP_1_1core_1_1HarmonicWell.html#abe23fc54376fe31700b9f35a8243bb86">IMP::core::HarmonicWell::get_version_info()</a>, <a href="classIMP_1_1core_1_1InBoundingBox3DSingletonPredicate.html#a3fced30f670011ab2b3addda888829d5">IMP::core::InBoundingBox3DSingletonPredicate::get_version_info()</a>, <a href="classIMP_1_1core_1_1IncrementalScoringFunction.html#a2833a3ac2d04cf1e28afc14b15d45e49">IMP::core::IncrementalScoringFunction::get_version_info()</a>, <a href="classIMP_1_1core_1_1IsCollisionPairPredicate.html#a0d6133d87ab96f5ca2e715b85a3eadaa">IMP::core::IsCollisionPairPredicate::get_version_info()</a>, <a href="classIMP_1_1core_1_1KClosePairsPairScore.html#a9b548fd16f0d5bf6b20f4f2ff77fdc98">IMP::core::KClosePairsPairScore::get_version_info()</a>, <a href="classIMP_1_1core_1_1LateralSurfaceConstraint.html#afca9bc35048c05d1812984a5f4ba201d">IMP::core::LateralSurfaceConstraint::get_version_info()</a>, <a href="classIMP_1_1core_1_1LeavesRefiner.html#a1c8abc973f8c5357078a77bf5a9518a9">IMP::core::LeavesRefiner::get_version_info()</a>, <a href="classIMP_1_1core_1_1Linear.html#a7cac48120c4e69622ddae0ed43fe0880">IMP::core::Linear::get_version_info()</a>, <a href="classIMP_1_1core_1_1LogNormalMover.html#a450beaf15b9e8012ff3dfa88e8accaa7">IMP::core::LogNormalMover::get_version_info()</a>, <a href="classIMP_1_1core_1_1MCCGSampler.html#ac3396625a0d1c9678dc4d8800b80f301">IMP::core::MCCGSampler::get_version_info()</a>, <a href="classIMP_1_1core_1_1MSConnectivityRestraint.html#a6d1ea94a30275176399ba894cb0c4cc2">IMP::core::MSConnectivityRestraint::get_version_info()</a>, <a href="classIMP_1_1core_1_1MinimumRestraint.html#a2c325d655bf25b1be46be2c9f9c4b55c">IMP::core::MinimumRestraint::get_version_info()</a>, <a href="classIMP_1_1core_1_1MonteCarlo.html#ac508d54a76462d3c723e09fe873e3e12">IMP::core::MonteCarlo::get_version_info()</a>, <a href="classIMP_1_1core_1_1MonteCarloWithBasinHopping.html#a7412ce72eb40736d72d0c74bdb4243d9">IMP::core::MonteCarloWithBasinHopping::get_version_info()</a>, <a href="classIMP_1_1core_1_1MonteCarloWithLocalOptimization.html#aa1f6b62c17ae9943179c549ceb83f900">IMP::core::MonteCarloWithLocalOptimization::get_version_info()</a>, <a href="classIMP_1_1core_1_1MoveStatisticsScoreState.html#a44b32ba695142bd8d47880b1d2fa0dfd">IMP::core::MoveStatisticsScoreState::get_version_info()</a>, <a href="classIMP_1_1core_1_1MultipleBinormalRestraint.html#ae70053b941e286eba4342a6012305c08">IMP::core::MultipleBinormalRestraint::get_version_info()</a>, <a href="classIMP_1_1core_1_1NearestNeighborsClosePairsFinder.html#a4f3b4d320dfcb0277fb7cddc09fc2e3d">IMP::core::NearestNeighborsClosePairsFinder::get_version_info()</a>, <a href="classIMP_1_1core_1_1NeighborsTable.html#ab49acfb8eecb1e9844d0e52cfa4cb575">IMP::core::NeighborsTable::get_version_info()</a>, <a href="classIMP_1_1core_1_1NormalMover.html#a4778d8a4171946f3c737971183feed26">IMP::core::NormalMover::get_version_info()</a>, <a href="classIMP_1_1core_1_1NormalizedSphereDistancePairScore.html#a762cf5853d8969a6ba230c86985d46f1">IMP::core::NormalizedSphereDistancePairScore::get_version_info()</a>, <a href="classIMP_1_1core_1_1OrderedTypePairPredicate.html#a922f3b8f4244bd18157fe4df50abebf8">IMP::core::OrderedTypePairPredicate::get_version_info()</a>, <a href="classIMP_1_1core_1_1OrderedTypeQuadPredicate.html#af24d388f986df36b48d0e49c9db77b58">IMP::core::OrderedTypeQuadPredicate::get_version_info()</a>, <a href="classIMP_1_1core_1_1OrderedTypeSingletonPredicate.html#a334d8736b03caf2db23f1c354a9a3abb">IMP::core::OrderedTypeSingletonPredicate::get_version_info()</a>, <a href="classIMP_1_1core_1_1OrderedTypeTripletPredicate.html#a012956e9d2d70f741dcb9367970d48ba">IMP::core::OrderedTypeTripletPredicate::get_version_info()</a>, <a href="classIMP_1_1core_1_1PairConstraint.html#a6192d0300e74162d5187d91686c4cb48">IMP::core::PairConstraint::get_version_info()</a>, <a href="classIMP_1_1core_1_1PairRestraint.html#afef8bc56c661c096345aa1518d1e055f">IMP::core::PairRestraint::get_version_info()</a>, <a href="classIMP_1_1core_1_1PredicateSingletonScore.html#a937e540a5f2ff9c5f05d540f13a4893d">IMP::core::PredicateSingletonScore::get_version_info()</a>, <a href="classIMP_1_1core_1_1QuadConstraint.html#a785df8031afa0f6d0db8bfcfc73990ce">IMP::core::QuadConstraint::get_version_info()</a>, <a href="classIMP_1_1core_1_1QuadRestraint.html#af9cc15fcf9e57324d3846e207d282f6e">IMP::core::QuadRestraint::get_version_info()</a>, <a href="classIMP_1_1core_1_1QuadraticClosePairsFinder.html#acd9da2a086300d9ee37262b5cbd2a600">IMP::core::QuadraticClosePairsFinder::get_version_info()</a>, <a href="classIMP_1_1core_1_1RefinedPairsPairScore.html#ac17297cd323aafba4b203106f2c05e25">IMP::core::RefinedPairsPairScore::get_version_info()</a>, <a href="classIMP_1_1core_1_1RigidBodyAnglePairScore.html#a44ceb3c6e04d35e73c0db95235bb2964">IMP::core::RigidBodyAnglePairScore::get_version_info()</a>, <a href="classIMP_1_1core_1_1RigidBodyDerivativeGeometry.html#a8c7c6999ec2ff8d4bea0796c84d9828a">IMP::core::RigidBodyDerivativeGeometry::get_version_info()</a>, <a href="classIMP_1_1core_1_1RigidBodyDerivativesGeometry.html#a8548bbdceccaa870c3b5c9a8abf33d31">IMP::core::RigidBodyDerivativesGeometry::get_version_info()</a>, <a href="classIMP_1_1core_1_1RigidBodyFrameGeometry.html#a7f1b099e00eaef27475000e119acf5aa">IMP::core::RigidBodyFrameGeometry::get_version_info()</a>, <a href="classIMP_1_1core_1_1RigidBodyFramesGeometry.html#af602c54b8f1fb6f4bb2e6b365936900b">IMP::core::RigidBodyFramesGeometry::get_version_info()</a>, <a href="classIMP_1_1core_1_1RigidBodyHierarchyGeometry.html#a70dbbe0d391ff16da919bf56e3497ff4">IMP::core::RigidBodyHierarchyGeometry::get_version_info()</a>, <a href="classIMP_1_1core_1_1RigidBodyMover.html#ad56111744317e19e52e7b4c6b555f513">IMP::core::RigidBodyMover::get_version_info()</a>, <a href="classIMP_1_1core_1_1RigidBodyTunneler.html#a5764ac5d59b3d36094112623258a3165">IMP::core::RigidBodyTunneler::get_version_info()</a>, <a href="classIMP_1_1core_1_1RigidBodyUmbrella.html#a11c8d8b515321524b074dbb6768e7171">IMP::core::RigidBodyUmbrella::get_version_info()</a>, <a href="classIMP_1_1core_1_1RigidClosePairsFinder.html#af7c263cacf63630775054bf620456d58">IMP::core::RigidClosePairsFinder::get_version_info()</a>, <a href="classIMP_1_1core_1_1SerialMover.html#aca7b1a6b6d49fa12df24890f1cbb6fd6">IMP::core::SerialMover::get_version_info()</a>, <a href="classIMP_1_1core_1_1SingletonConstraint.html#ab115551d27b3d326d98ce63f891e9468">IMP::core::SingletonConstraint::get_version_info()</a>, <a href="classIMP_1_1core_1_1SingletonRestraint.html#a27d752b4b67de2c72d3f8469a040cc3f">IMP::core::SingletonRestraint::get_version_info()</a>, <a href="classIMP_1_1core_1_1SoftSpherePairScore.html#a11e82edbb8c56764e73767905d04f7ad">IMP::core::SoftSpherePairScore::get_version_info()</a>, <a href="classIMP_1_1core_1_1SoftSubSurfacePairScore.html#a822fc07ea4d8c52e8e15570c5f53af38">IMP::core::SoftSubSurfacePairScore::get_version_info()</a>, <a href="classIMP_1_1core_1_1SoftSuperSurfacePairScore.html#aaae29f0862260f2c70f69aa1333d4aff">IMP::core::SoftSuperSurfacePairScore::get_version_info()</a>, <a href="classIMP_1_1core_1_1SphereDistancePairScore.html#a5448b4334f35992c0a2c25a2f209749b">IMP::core::SphereDistancePairScore::get_version_info()</a>, <a href="classIMP_1_1core_1_1SphereDistanceToSingletonScore.html#a609b2f1ae75371e1273bbc0202e0f4ef">IMP::core::SphereDistanceToSingletonScore::get_version_info()</a>, <a href="classIMP_1_1core_1_1SteepestDescent.html#a6c7d6d51a6e517499e781952ec1cef78">IMP::core::SteepestDescent::get_version_info()</a>, <a href="classIMP_1_1core_1_1SubsetMover.html#af4cdffc0967af09b2abf4cadabe08c97">IMP::core::SubsetMover::get_version_info()</a>, <a href="classIMP_1_1core_1_1SurfaceDepthPairScore.html#ad3ec5697dac543d3f43c8454afa996ee">IMP::core::SurfaceDepthPairScore::get_version_info()</a>, <a href="classIMP_1_1core_1_1SurfaceDistancePairScore.html#a0565c8a9d4576100fcfd082bd18d0281">IMP::core::SurfaceDistancePairScore::get_version_info()</a>, <a href="classIMP_1_1core_1_1SurfaceGeometry.html#a77e8341fc9ed66b1a70d5a72bd3af930">IMP::core::SurfaceGeometry::get_version_info()</a>, <a href="classIMP_1_1core_1_1SurfaceGeometryConstraint.html#af8efa4270601e35c3a2d80e0d562e360">IMP::core::SurfaceGeometryConstraint::get_version_info()</a>, <a href="classIMP_1_1core_1_1SurfaceHeightPairScore.html#a2e5417046142a5e25ac670d8e768ca4f">IMP::core::SurfaceHeightPairScore::get_version_info()</a>, <a href="classIMP_1_1core_1_1SurfaceMover.html#a90808498e543af315be2575b095d1a55">IMP::core::SurfaceMover::get_version_info()</a>, <a href="classIMP_1_1core_1_1SurfaceSymmetryConstraint.html#a1cb82d5d22f7cd7bb551bd9c9b0eb435">IMP::core::SurfaceSymmetryConstraint::get_version_info()</a>, <a href="classIMP_1_1core_1_1SurfaceTetheredChain.html#aaded762c06d29f39d9b431a50dd587cb">IMP::core::SurfaceTetheredChain::get_version_info()</a>, <a href="classIMP_1_1core_1_1TableRefiner.html#a7434d8f91c298a0a800c158fd102afcb">IMP::core::TableRefiner::get_version_info()</a>, <a href="classIMP_1_1core_1_1Transform.html#acf5e7941f8a06e93c0ed99d3bba52e56">IMP::core::Transform::get_version_info()</a>, <a href="classIMP_1_1core_1_1TransformationAndReflectionSymmetry.html#a1c28ee89e7438613b16bae476261d12b">IMP::core::TransformationAndReflectionSymmetry::get_version_info()</a>, <a href="classIMP_1_1core_1_1TransformationSymmetry.html#aa96761970b195bb89037ae198180e61d">IMP::core::TransformationSymmetry::get_version_info()</a>, <a href="classIMP_1_1core_1_1TransformationSymmetryMover.html#adb43d3b58a0d29de849d0895afb7227d">IMP::core::TransformationSymmetryMover::get_version_info()</a>, <a href="classIMP_1_1core_1_1TransformedDistancePairScore.html#aff4c0c7e0769020f978a097afc5da2cb">IMP::core::TransformedDistancePairScore::get_version_info()</a>, <a href="classIMP_1_1core_1_1TripletConstraint.html#a060ab80d9e52d5b2d959a0c09a86d0f2">IMP::core::TripletConstraint::get_version_info()</a>, <a href="classIMP_1_1core_1_1TripletRestraint.html#ad2f64ca1321aa5e597e64089fb2e23c1">IMP::core::TripletRestraint::get_version_info()</a>, <a href="classIMP_1_1core_1_1TruncatedHarmonic.html#a39bc8e92149bf161f532e91e35be49d4">IMP::core::TruncatedHarmonic::get_version_info()</a>, <a href="classIMP_1_1core_1_1TypedPairScore.html#a8d75924232bf6d6c8fdad83fb9acba18">IMP::core::TypedPairScore::get_version_info()</a>, <a href="classIMP_1_1core_1_1UnorderedTypePairPredicate.html#a12d9da2dd084d45317f4e8f1ce128fc1">IMP::core::UnorderedTypePairPredicate::get_version_info()</a>, <a href="classIMP_1_1core_1_1UnorderedTypeQuadPredicate.html#af7c0bf0e09343177a52e5202e206bef2">IMP::core::UnorderedTypeQuadPredicate::get_version_info()</a>, <a href="classIMP_1_1core_1_1UnorderedTypeSingletonPredicate.html#a3819b931338457b30f97a7f88af1ec76">IMP::core::UnorderedTypeSingletonPredicate::get_version_info()</a>, <a href="classIMP_1_1core_1_1UnorderedTypeTripletPredicate.html#a908ab43001c12ab48e0e97df246d9fad">IMP::core::UnorderedTypeTripletPredicate::get_version_info()</a>, <a href="classIMP_1_1core_1_1VolumeRestraint.html#aaf4b4dbfccda4d19f2da7ae4629fad0c">IMP::core::VolumeRestraint::get_version_info()</a>, <a href="classIMP_1_1core_1_1WeightedDerivativesToRefined.html#a23ac53e59d63bb5d11f09696b2dcb03d">IMP::core::WeightedDerivativesToRefined::get_version_info()</a>, <a href="classIMP_1_1core_1_1WeightedSphereDistancePairScore.html#af7bec48a3c44ffaadb174bf7afecd7d7">IMP::core::WeightedSphereDistancePairScore::get_version_info()</a>, <a href="classIMP_1_1core_1_1WeightedSum.html#ae97231726e71370335892f4fe48ffc83">IMP::core::WeightedSum::get_version_info()</a>, <a href="classIMP_1_1core_1_1WeightedSumOfExponential.html#ab8f5824a3fc236042ffc12c0ebfde346">IMP::core::WeightedSumOfExponential::get_version_info()</a>, <a href="classIMP_1_1core_1_1WriteRestraintScoresOptimizerState.html#af4f09dc3d0a2508fb69eb373906830c8">IMP::core::WriteRestraintScoresOptimizerState::get_version_info()</a>, <a href="classIMP_1_1core_1_1XYZDerivativeGeometry.html#a01cc72eadd6ad637f0a012e17c2654e6">IMP::core::XYZDerivativeGeometry::get_version_info()</a>, <a href="classIMP_1_1core_1_1XYZDerivativesGeometry.html#a9b3df6901016aa27bb81e37a83ed9d66">IMP::core::XYZDerivativesGeometry::get_version_info()</a>, <a href="classIMP_1_1core_1_1XYZRGeometry.html#ae63154553a16fc4ca7ade8fc502475cb">IMP::core::XYZRGeometry::get_version_info()</a>, <a href="classIMP_1_1core_1_1XYZRsGeometry.html#ac416a1db8be8fa6d8a9489c2fe91b6fd">IMP::core::XYZRsGeometry::get_version_info()</a>, <a href="classIMP_1_1display_1_1BoundingBoxGeometry.html#aea29210f485ea140c006eb3a82e718a0">IMP::display::BoundingBoxGeometry::get_version_info()</a>, <a href="classIMP_1_1display_1_1CylinderGeometry.html#af38a1ebf06b08686acfbaf630b9bba41">IMP::display::CylinderGeometry::get_version_info()</a>, <a href="classIMP_1_1display_1_1EllipsoidGeometry.html#a5d783e287415a263c07f921d2623a271">IMP::display::EllipsoidGeometry::get_version_info()</a>, <a href="classIMP_1_1display_1_1FilterGeometry.html#abf88d821f89b7ec4d6dab6417c9e9488">IMP::display::FilterGeometry::get_version_info()</a>, <a href="classIMP_1_1display_1_1GeometrySet.html#a16436b6e60c1dd71866171cb7de7a178">IMP::display::GeometrySet::get_version_info()</a>, <a href="classIMP_1_1display_1_1LabelGeometry.html#a86607c74e4e87e1a8a176404c08dacfb">IMP::display::LabelGeometry::get_version_info()</a>, <a href="classIMP_1_1display_1_1PlaneGeometry.html#a6b329da548c0d95e884735391be01693">IMP::display::PlaneGeometry::get_version_info()</a>, <a href="classIMP_1_1display_1_1PointGeometry.html#a42464075e7d2c6f91689ad90dfe7dce1">IMP::display::PointGeometry::get_version_info()</a>, <a href="classIMP_1_1display_1_1PolygonGeometry.html#a74b2a6b9d315decd2bce40f015fe58c9">IMP::display::PolygonGeometry::get_version_info()</a>, <a href="classIMP_1_1display_1_1PymolWriter.html#aee0912e007c16e3cd692979deaf41d42">IMP::display::PymolWriter::get_version_info()</a>, <a href="classIMP_1_1display_1_1ReferenceFrameGeometry.html#afaea72e3f57a2ba033e4b98ab29d9bcd">IMP::display::ReferenceFrameGeometry::get_version_info()</a>, <a href="classIMP_1_1display_1_1RestraintGeometry.html#a8a2f943f7870b4b52dc41300e2faba6b">IMP::display::RestraintGeometry::get_version_info()</a>, <a href="classIMP_1_1display_1_1RestraintSetGeometry.html#a8af53063398d296e9709801d2d385cdd">IMP::display::RestraintSetGeometry::get_version_info()</a>, <a href="classIMP_1_1display_1_1SegmentGeometry.html#aa3363fc6c13db3bc70973f5329f021d2">IMP::display::SegmentGeometry::get_version_info()</a>, <a href="classIMP_1_1display_1_1SphereGeometry.html#a2d6e3bf351cc9fd9fe0b5c2f402616a9">IMP::display::SphereGeometry::get_version_info()</a>, <a href="classIMP_1_1display_1_1SurfaceMeshGeometry.html#a0edad036b29e4074ec29e3cfe5c51450">IMP::display::SurfaceMeshGeometry::get_version_info()</a>, <a href="classIMP_1_1display_1_1TriangleGeometry.html#a4436bc755393ea934c5d02121c940da9">IMP::display::TriangleGeometry::get_version_info()</a>, <a href="classIMP_1_1display_1_1WriteOptimizerState.html#a6127ea0530dfc571c516002fc2b8a2c6">IMP::display::WriteOptimizerState::get_version_info()</a>, <a href="classIMP_1_1domino_1_1BranchAndBoundAssignmentsTable.html#ac00a002ba6634d67393615acc8df1555">IMP::domino::BranchAndBoundAssignmentsTable::get_version_info()</a>, <a href="classIMP_1_1domino_1_1BranchAndBoundSampler.html#a0b1c142e1299f182f4448d5872ff954c">IMP::domino::BranchAndBoundSampler::get_version_info()</a>, <a href="classIMP_1_1domino_1_1CappedAssignmentContainer.html#a65e5f0000d6d39176de37c48b74f7cba">IMP::domino::CappedAssignmentContainer::get_version_info()</a>, <a href="classIMP_1_1domino_1_1CompoundStates.html#a27f4d825beff38d25658b1255963ba65">IMP::domino::CompoundStates::get_version_info()</a>, <a href="classIMP_1_1domino_1_1DependencyScoreState.html#acbb8a7b784a27b19b9bcd02c5e25a743">IMP::domino::DependencyScoreState::get_version_info()</a>, <a href="classIMP_1_1domino_1_1DominoSampler.html#a0280a26aea5ad30f6b6a283332130909">IMP::domino::DominoSampler::get_version_info()</a>, <a href="classIMP_1_1domino_1_1EqualitySubsetFilterTable.html#a2e5c7c5af60dfe0fd7187b049dda8f35">IMP::domino::EqualitySubsetFilterTable::get_version_info()</a>, <a href="classIMP_1_1domino_1_1EquivalenceAndExclusionSubsetFilterTable.html#a453ef3ccac3fd973597a72126aff9944">IMP::domino::EquivalenceAndExclusionSubsetFilterTable::get_version_info()</a>, <a href="classIMP_1_1domino_1_1EquivalenceSubsetFilterTable.html#a645c5fadf84bca8511339919cf4f6c8f">IMP::domino::EquivalenceSubsetFilterTable::get_version_info()</a>, <a href="classIMP_1_1domino_1_1ExclusionSubsetFilterTable.html#a4677d4ed2c1517e1a95d342606854042">IMP::domino::ExclusionSubsetFilterTable::get_version_info()</a>, <a href="classIMP_1_1domino_1_1HeapAssignmentContainer.html#a611aa58e2517dc73fe0bab52911fe4b5">IMP::domino::HeapAssignmentContainer::get_version_info()</a>, <a href="classIMP_1_1domino_1_1IndexStates.html#a56e653212698961c6f90049d9334e33e">IMP::domino::IndexStates::get_version_info()</a>, <a href="classIMP_1_1domino_1_1ListAssignmentContainer.html#a92e5c39deb5ebdd9d90cf55df7309e68">IMP::domino::ListAssignmentContainer::get_version_info()</a>, <a href="classIMP_1_1domino_1_1ListAssignmentsTable.html#ad26ed109596cd5c716efdd5f16afa7be">IMP::domino::ListAssignmentsTable::get_version_info()</a>, <a href="classIMP_1_1domino_1_1ListSubsetFilterTable.html#aead7c604bac1a9270155b5f10fd78b42">IMP::domino::ListSubsetFilterTable::get_version_info()</a>, <a href="classIMP_1_1domino_1_1MinimumRestraintScoreSubsetFilterTable.html#ae82b67e82322f9ca1bfcba1527943fb6">IMP::domino::MinimumRestraintScoreSubsetFilterTable::get_version_info()</a>, <a href="classIMP_1_1domino_1_1NestedRigidBodyStates.html#ab1e3a003adc2c919b48eece0209024ce">IMP::domino::NestedRigidBodyStates::get_version_info()</a>, <a href="classIMP_1_1domino_1_1PackedAssignmentContainer.html#af18d053b1724fc86a1445095d789fe88">IMP::domino::PackedAssignmentContainer::get_version_info()</a>, <a href="classIMP_1_1domino_1_1PairListSubsetFilterTable.html#aa2a6f3f069959b6b5b62b0e29fc21855">IMP::domino::PairListSubsetFilterTable::get_version_info()</a>, <a href="classIMP_1_1domino_1_1ParticleStatesTable.html#af8734dfdc6574db7edd6e23b3e4d9210">IMP::domino::ParticleStatesTable::get_version_info()</a>, <a href="classIMP_1_1domino_1_1PermutationStates.html#abb7aa61a82398a8ec609be5f38585813">IMP::domino::PermutationStates::get_version_info()</a>, <a href="classIMP_1_1domino_1_1ProbabilisticSubsetFilterTable.html#a8088455aa8776c75ec4d8e608171e294">IMP::domino::ProbabilisticSubsetFilterTable::get_version_info()</a>, <a href="classIMP_1_1domino_1_1RangeViewAssignmentContainer.html#a5f75653051db5c9674832b3c88a602dc">IMP::domino::RangeViewAssignmentContainer::get_version_info()</a>, <a href="classIMP_1_1domino_1_1ReadAssignmentContainer.html#a9f950f81f4aaabe66a38d7497f4b594c">IMP::domino::ReadAssignmentContainer::get_version_info()</a>, <a href="classIMP_1_1domino_1_1ReadHDF5AssignmentContainer.html#ad1bfe7f63326f5e5872bd014c951ce8e">IMP::domino::ReadHDF5AssignmentContainer::get_version_info()</a>, <a href="classIMP_1_1domino_1_1RecursiveAssignmentsTable.html#a7277eca2056cd5f4f001025b53791f8f">IMP::domino::RecursiveAssignmentsTable::get_version_info()</a>, <a href="classIMP_1_1domino_1_1RecursiveStates.html#ac29a3bf098dc7244bddd3bb19e6f998f">IMP::domino::RecursiveStates::get_version_info()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#a886eba211145ea7b38913a48b918b4a8">IMP::domino::RestraintCache::get_version_info()</a>, <a href="classIMP_1_1domino_1_1RestraintScoreSubsetFilterTable.html#ad50b6c1d68356cafa1c51752102f039a">IMP::domino::RestraintScoreSubsetFilterTable::get_version_info()</a>, <a href="classIMP_1_1domino_1_1RigidBodyStates.html#a297fcd641df60667b4bc55342dc53778">IMP::domino::RigidBodyStates::get_version_info()</a>, <a href="classIMP_1_1domino_1_1SampleAssignmentContainer.html#a7f7b6a7735bed5548f3bc928214c9ec5">IMP::domino::SampleAssignmentContainer::get_version_info()</a>, <a href="classIMP_1_1domino_1_1SimpleAssignmentsTable.html#a98c54efb667b399ab14be8d685689e5e">IMP::domino::SimpleAssignmentsTable::get_version_info()</a>, <a href="classIMP_1_1domino_1_1WriteAssignmentContainer.html#aa97ab46179815bf8f34fe60537d35e38">IMP::domino::WriteAssignmentContainer::get_version_info()</a>, <a href="classIMP_1_1domino_1_1WriteHDF5AssignmentContainer.html#abc900f3eb2dae7fa7d53ba9a417307f7">IMP::domino::WriteHDF5AssignmentContainer::get_version_info()</a>, <a href="classIMP_1_1domino_1_1XYZStates.html#aa413cb4e08a670af7cf1bce59f95e84b">IMP::domino::XYZStates::get_version_info()</a>, <a href="classIMP_1_1em2d_1_1CollisionCrossSection.html#a76c4e020f522fae45a51719605baa3ad">IMP::em2d::CollisionCrossSection::get_version_info()</a>, <a href="classIMP_1_1em2d_1_1DistanceFilter.html#a3da423b3b7e3cc865fc838aa435e570d">IMP::em2d::DistanceFilter::get_version_info()</a>, <a href="classIMP_1_1em2d_1_1DistanceFilterTable.html#a693cad94d9eb94bb0f779f2aecb722e9">IMP::em2d::DistanceFilterTable::get_version_info()</a>, <a href="classIMP_1_1em2d_1_1DummyRestraint.html#a3f1bb1fcd809c828a45573f822a42d1a">IMP::em2d::DummyRestraint::get_version_info()</a>, <a href="classIMP_1_1em2d_1_1Em2DRestraint.html#aa9e70b3f477b256d136db1de97d61801">IMP::em2d::Em2DRestraint::get_version_info()</a>, <a href="classIMP_1_1em2d_1_1GridStates.html#a9fc4a0823ab128ed3af51450d12af5d9">IMP::em2d::GridStates::get_version_info()</a>, <a href="classIMP_1_1em2d_1_1Image.html#a51ff9ad6178713656310c9e8c4a03122">IMP::em2d::Image::get_version_info()</a>, <a href="classIMP_1_1em2d_1_1ImageReaderWriter.html#a05c699b3c44b2ef9f8eed2801e6bc196">IMP::em2d::ImageReaderWriter::get_version_info()</a>, <a href="classIMP_1_1em2d_1_1JPGImageReaderWriter.html#ad0e50f0647d4fd391b8f9c997fa4ef7b">IMP::em2d::JPGImageReaderWriter::get_version_info()</a>, <a href="classIMP_1_1em2d_1_1PCAFitRestraint.html#ac89e17192b8611be035782cca5ee140a">IMP::em2d::PCAFitRestraint::get_version_info()</a>, <a href="classIMP_1_1em2d_1_1ParticlesDummyRestraint.html#a0e53c9de542cfaf30abc4ee93c2c4b07">IMP::em2d::ParticlesDummyRestraint::get_version_info()</a>, <a href="classIMP_1_1em2d_1_1ProjectionFinder.html#a3c99d56acb924c5c38c7044633600320">IMP::em2d::ProjectionFinder::get_version_info()</a>, <a href="classIMP_1_1em2d_1_1ProjectionParametersScoreState.html#aeed261658f026112a0a069bf1564cb76">IMP::em2d::ProjectionParametersScoreState::get_version_info()</a>, <a href="classIMP_1_1em2d_1_1ProjectionStates.html#a5c9495dec8839069fac3d923b17ec315">IMP::em2d::ProjectionStates::get_version_info()</a>, <a href="classIMP_1_1em2d_1_1RelativePositionMover.html#ab055515237e5f58dab5a711ad3889cd4">IMP::em2d::RelativePositionMover::get_version_info()</a>, <a href="classIMP_1_1em2d_1_1RigidBodiesImageFitRestraint.html#a8635d3ec42f718d3120131fff7f5d1b8">IMP::em2d::RigidBodiesImageFitRestraint::get_version_info()</a>, <a href="classIMP_1_1em2d_1_1ScoreFunction.html#aed5d5636adbe8597873ed8e782c5941d">IMP::em2d::ScoreFunction::get_version_info()</a>, <a href="classIMP_1_1em2d_1_1SpiderImageReaderWriter.html#a6d0b9f574ab7e186682c3ffe1c66c672">IMP::em2d::SpiderImageReaderWriter::get_version_info()</a>, <a href="classIMP_1_1em2d_1_1TIFFImageReaderWriter.html#a2b9c81001b2a001b63e075aaff4a8944">IMP::em2d::TIFFImageReaderWriter::get_version_info()</a>, <a href="classIMP_1_1em_1_1CoarseCCatIntervals.html#addf19cdb6d385805c6ce50e3fedf3afb">IMP::em::CoarseCCatIntervals::get_version_info()</a>, <a href="classIMP_1_1em_1_1DensityFillingRestraint.html#ae63b7fe9ac592cf3867e2cc390798d37">IMP::em::DensityFillingRestraint::get_version_info()</a>, <a href="classIMP_1_1em_1_1DensityMap.html#ab66058c8b7f96141130ead7add7dd371">IMP::em::DensityMap::get_version_info()</a>, <a href="classIMP_1_1em_1_1EMReaderWriter.html#af6dc21993c1e8d32771f3049c968d63f">IMP::em::EMReaderWriter::get_version_info()</a>, <a href="classIMP_1_1em_1_1EnvelopeFitRestraint.html#ae496bc9e4fb714926d16658d58142971">IMP::em::EnvelopeFitRestraint::get_version_info()</a>, <a href="classIMP_1_1em_1_1EnvelopePenetrationRestraint.html#ac833173606c9684cd1161358c434d2af">IMP::em::EnvelopePenetrationRestraint::get_version_info()</a>, <a href="classIMP_1_1em_1_1EnvelopeScore.html#a3cba2fa6a842d5c1ec65e9be540d897b">IMP::em::EnvelopeScore::get_version_info()</a>, <a href="classIMP_1_1em_1_1FitRestraint.html#aa6eb5a26a4679a82ecf65d67802206b3">IMP::em::FitRestraint::get_version_info()</a>, <a href="classIMP_1_1em_1_1FitRestraintBayesEM3D.html#ac499adbb5922a3110c8b6c315c67029c">IMP::em::FitRestraintBayesEM3D::get_version_info()</a>, <a href="classIMP_1_1em_1_1HighDensityEmbedding.html#abbb8f17a41db4fc80c9e8a2b0913a047">IMP::em::HighDensityEmbedding::get_version_info()</a>, <a href="classIMP_1_1em_1_1MRCReaderWriter.html#ada267e699ad9ae6dbbccb7e0bf63a484">IMP::em::MRCReaderWriter::get_version_info()</a>, <a href="classIMP_1_1em_1_1MapReaderWriter.html#a90905acb2c19f8f024b4ed67564d89cc">IMP::em::MapReaderWriter::get_version_info()</a>, <a href="classIMP_1_1em_1_1PCAAligner.html#a58ff89ccfa55080b82ff341b1fc4b55b">IMP::em::PCAAligner::get_version_info()</a>, <a href="classIMP_1_1em_1_1PCAFitRestraint.html#a75c76062a0212a3234ff5616620da081">IMP::em::PCAFitRestraint::get_version_info()</a>, <a href="classIMP_1_1em_1_1SpiderMapReaderWriter.html#a28f93cad2af732a12ee72659d64a0b54">IMP::em::SpiderMapReaderWriter::get_version_info()</a>, <a href="classIMP_1_1em_1_1XplorReaderWriter.html#aa3d8216172fd1ef885d60ab8f451ca03">IMP::em::XplorReaderWriter::get_version_info()</a>, <a href="classIMP_1_1example_1_1ExampleComplexRestraint.html#af24dc82830b36e39a6d385f1f87010f8">IMP::example::ExampleComplexRestraint::get_version_info()</a>, <a href="classIMP_1_1example_1_1ExampleConstraint.html#afe3e37c55728ac56c66808d93a2b5f16">IMP::example::ExampleConstraint::get_version_info()</a>, <a href="classIMP_1_1example_1_1ExampleObject.html#a6ed7736943d4286750eb03a31bb34bdd">IMP::example::ExampleObject::get_version_info()</a>, <a href="classIMP_1_1example_1_1ExamplePairScore.html#a1aefcfbd8d12577e6986dcd40c09f8f3">IMP::example::ExamplePairScore::get_version_info()</a>, <a href="classIMP_1_1example_1_1ExampleRestraint.html#ad508f33af7229ef56a8936fdeec97760">IMP::example::ExampleRestraint::get_version_info()</a>, <a href="classIMP_1_1example_1_1ExampleSingletonModifier.html#a340cd0ff38bfa6ee34eb9fe54dec878f">IMP::example::ExampleSingletonModifier::get_version_info()</a>, <a href="classIMP_1_1example_1_1ExampleSubsetFilterTable.html#a6b0cc7d3de0999d6415620e36d72ebce">IMP::example::ExampleSubsetFilterTable::get_version_info()</a>, <a href="classIMP_1_1example_1_1ExampleUnaryFunction.html#aae72f0974717a8a2062b53b953f29345">IMP::example::ExampleUnaryFunction::get_version_info()</a>, <a href="classIMP_1_1gsl_1_1ConjugateGradients.html#a0bfacd7345e7e5534e750199320f8403">IMP::gsl::ConjugateGradients::get_version_info()</a>, <a href="classIMP_1_1gsl_1_1QuasiNewton.html#a5dd88d80c846870442dd60fb1146f258">IMP::gsl::QuasiNewton::get_version_info()</a>, <a href="classIMP_1_1gsl_1_1Simplex.html#ab236686e12c7b1d29c4f3b790892a6d0">IMP::gsl::Simplex::get_version_info()</a>, <a href="classIMP_1_1isd_1_1AmbiguousNOERestraint.html#abf35b9b836c1b7dcd0af6729ee7903a1">IMP::isd::AmbiguousNOERestraint::get_version_info()</a>, <a href="classIMP_1_1isd_1_1AmbiguousRestraint.html#a6631fe7b8224931b83cdaee3e2dd0106">IMP::isd::AmbiguousRestraint::get_version_info()</a>, <a href="classIMP_1_1isd_1_1AtomicCrossLinkMSRestraint.html#aec2a097e4f76babf865a9a3485cf9faa">IMP::isd::AtomicCrossLinkMSRestraint::get_version_info()</a>, <a href="classIMP_1_1isd_1_1Covariance1DFunction.html#aa0ef9005511da100427e5fe2554e059b">IMP::isd::Covariance1DFunction::get_version_info()</a>, <a href="classIMP_1_1isd_1_1CrossLinkData.html#a8071c058dfca7a3ede54bd84d4fa94d1">IMP::isd::CrossLinkData::get_version_info()</a>, <a href="classIMP_1_1isd_1_1CrossLinkMSRestraint.html#ab5fc84a1dd06aa682c78fb021cb2a97c">IMP::isd::CrossLinkMSRestraint::get_version_info()</a>, <a href="classIMP_1_1isd_1_1CysteineCrossLinkData.html#aaa0167f64d45b16ba8b70cf0e0094df0">IMP::isd::CysteineCrossLinkData::get_version_info()</a>, <a href="classIMP_1_1isd_1_1CysteineCrossLinkRestraint.html#a8df19f4dfb913e411469650d8e57e270">IMP::isd::CysteineCrossLinkRestraint::get_version_info()</a>, <a href="classIMP_1_1isd_1_1Distribution.html#ae84155b1f44f55662368d26109663f93">IMP::isd::Distribution::get_version_info()</a>, <a href="classIMP_1_1isd_1_1FNormal.html#ab8410c9218fce4ad2760123bfcfd3cf5">IMP::isd::FNormal::get_version_info()</a>, <a href="classIMP_1_1isd_1_1FStudentT.html#ac83a1b7297f91c99a6af3640c2fb8555">IMP::isd::FStudentT::get_version_info()</a>, <a href="classIMP_1_1isd_1_1FretData.html#a017a916b9de48eccc67739937efb5ece">IMP::isd::FretData::get_version_info()</a>, <a href="classIMP_1_1isd_1_1FretRestraint.html#a4af90cc84ac0a1f6570c93b06c3ab2e1">IMP::isd::FretRestraint::get_version_info()</a>, <a href="classIMP_1_1isd_1_1GammaPrior.html#a96a9b5aaedfbf00c5e302862a6aa88a7">IMP::isd::GammaPrior::get_version_info()</a>, <a href="classIMP_1_1isd_1_1GaussianAnchorEMRestraint.html#afae1a39fb67954ea44d212bae9bf9fa1">IMP::isd::GaussianAnchorEMRestraint::get_version_info()</a>, <a href="classIMP_1_1isd_1_1GaussianEMRestraint.html#a9820faa683832785ad3e3e37489c351e">IMP::isd::GaussianEMRestraint::get_version_info()</a>, <a href="classIMP_1_1isd_1_1GaussianProcessInterpolation.html#a7579ee03748476c194d3664e42772666">IMP::isd::GaussianProcessInterpolation::get_version_info()</a>, <a href="classIMP_1_1isd_1_1GaussianProcessInterpolationRestraint.html#a57f8ab9fd3795a62f3fa83e71ba5c609">IMP::isd::GaussianProcessInterpolationRestraint::get_version_info()</a>, <a href="classIMP_1_1isd_1_1GaussianRestraint.html#a7856c91b062a7ffd2043e0459b6f87e7">IMP::isd::GaussianRestraint::get_version_info()</a>, <a href="classIMP_1_1isd_1_1GeneralizedGuinierPorodFunction.html#a778379890331be73f65b85d7825b78b1">IMP::isd::GeneralizedGuinierPorodFunction::get_version_info()</a>, <a href="classIMP_1_1isd_1_1HybridMonteCarlo.html#a1a40e2761e4b8e891798a08d1c544de5">IMP::isd::HybridMonteCarlo::get_version_info()</a>, <a href="classIMP_1_1isd_1_1ISDRestraint.html#ada418319542534a9efa592d3714fdf69">IMP::isd::ISDRestraint::get_version_info()</a>, <a href="classIMP_1_1isd_1_1JeffreysRestraint.html#a7698d67995bf5286c5c57fa4562f1498">IMP::isd::JeffreysRestraint::get_version_info()</a>, <a href="classIMP_1_1isd_1_1Linear1DFunction.html#a4c634a3f434fa35a6cb7ea4846689e3c">IMP::isd::Linear1DFunction::get_version_info()</a>, <a href="classIMP_1_1isd_1_1LogWrapper.html#a2c9fd90c2ca0b92fdef8eccba537d29e">IMP::isd::LogWrapper::get_version_info()</a>, <a href="classIMP_1_1isd_1_1LognormalAmbiguousRestraint.html#a4ef51ae9d5511f264e968acf6334dbf6">IMP::isd::LognormalAmbiguousRestraint::get_version_info()</a>, <a href="classIMP_1_1isd_1_1LognormalRestraint.html#a6dfbee049b8cb072984aea43b80ffb96">IMP::isd::LognormalRestraint::get_version_info()</a>, <a href="classIMP_1_1isd_1_1MarginalHBondRestraint.html#a108bd8c4a940cb8d3a90adf17cf1f60b">IMP::isd::MarginalHBondRestraint::get_version_info()</a>, <a href="classIMP_1_1isd_1_1MarginalNOERestraint.html#ae46fc18bbcff68355f91916916aea9c9">IMP::isd::MarginalNOERestraint::get_version_info()</a>, <a href="classIMP_1_1isd_1_1MolecularDynamicsMover.html#a2e12f54855c0825ec54df55f1ed2763b">IMP::isd::MolecularDynamicsMover::get_version_info()</a>, <a href="classIMP_1_1isd_1_1MultivariateFNormalSufficient.html#a588661042d20576ef04971d32c5b1f4f">IMP::isd::MultivariateFNormalSufficient::get_version_info()</a>, <a href="classIMP_1_1isd_1_1NOERestraint.html#a734bb1f0bcd661c74db055985e8b6ef8">IMP::isd::NOERestraint::get_version_info()</a>, <a href="classIMP_1_1isd_1_1NormalSigmaPCRestraint.html#ac2346432e6d4336d15629da25fcc1f09">IMP::isd::NormalSigmaPCRestraint::get_version_info()</a>, <a href="classIMP_1_1isd_1_1OneDimensionalDistribution.html#ac49cc9ac2adfcbe5d81aa949b09510be">IMP::isd::OneDimensionalDistribution::get_version_info()</a>, <a href="classIMP_1_1isd_1_1OneDimensionalSufficientDistribution.html#aeda7c1561ee5d6512bf0d5f05bd9f2a6">IMP::isd::OneDimensionalSufficientDistribution::get_version_info()</a>, <a href="classIMP_1_1isd_1_1PenalizedComplexityPrior.html#a2914910aeb598b48dfa221969793b933">IMP::isd::PenalizedComplexityPrior::get_version_info()</a>, <a href="classIMP_1_1isd_1_1RepulsiveDistancePairScore.html#a5f952e83093b5e2776c2ea185eadb688">IMP::isd::RepulsiveDistancePairScore::get_version_info()</a>, <a href="classIMP_1_1isd_1_1ResidueProteinProximityRestraint.html#ae8c6be4f2330226cc7773ad97acd4adc">IMP::isd::ResidueProteinProximityRestraint::get_version_info()</a>, <a href="classIMP_1_1isd_1_1StudentTRestraint.html#a9e05e9582094951095d8446dae32f3c7">IMP::isd::StudentTRestraint::get_version_info()</a>, <a href="classIMP_1_1isd_1_1TALOSRestraint.html#ae9949b36ba73a255d18344fc28cba7ab">IMP::isd::TALOSRestraint::get_version_info()</a>, <a href="classIMP_1_1isd_1_1UniformPrior.html#a988edba183182c6422701addf7c2bedd">IMP::isd::UniformPrior::get_version_info()</a>, <a href="classIMP_1_1isd_1_1WeightMover.html#a5a48116cb40437548ac24b1d258f4f2a">IMP::isd::WeightMover::get_version_info()</a>, <a href="classIMP_1_1isd_1_1WeightRestraint.html#af604df12728b1edd56a3ad16e76dbd5c">IMP::isd::WeightRestraint::get_version_info()</a>, <a href="classIMP_1_1isd_1_1vonMises.html#a34a9c740f20819cb258919916b1e5c60">IMP::isd::vonMises::get_version_info()</a>, <a href="classIMP_1_1isd_1_1vonMisesKappaConjugateRestraint.html#a8ec075f4b2700e0509016dc207e1426c">IMP::isd::vonMisesKappaConjugateRestraint::get_version_info()</a>, <a href="classIMP_1_1isd_1_1vonMisesKappaJeffreysRestraint.html#ae2c835da17d0d8c745f41acdd4ea78ee">IMP::isd::vonMisesKappaJeffreysRestraint::get_version_info()</a>, <a href="classIMP_1_1isd_1_1vonMisesSufficient.html#adea29aa6c99474e438f30b6cfc26ec8b">IMP::isd::vonMisesSufficient::get_version_info()</a>, <a href="classIMP_1_1kinematics_1_1DOF.html#a87d841d84fe17b7950e9aeb28f307b4f">IMP::kinematics::DOF::get_version_info()</a>, <a href="classIMP_1_1kinematics_1_1DOFsSampler.html#ad7b46f5d8e0a9725c96111cf46f5246a">IMP::kinematics::DOFsSampler::get_version_info()</a>, <a href="classIMP_1_1kinematics_1_1DihedralMover.html#ab5f537a3e03e3741cfa4a7d8cf06b707">IMP::kinematics::DihedralMover::get_version_info()</a>, <a href="classIMP_1_1kinematics_1_1DirectionalDOF.html#aaf0044f1a78b6a5e8c0aa07083a68ec2">IMP::kinematics::DirectionalDOF::get_version_info()</a>, <a href="classIMP_1_1kinematics_1_1Joint.html#a007e1c1cfce7e7730c5fef144a65298c">IMP::kinematics::Joint::get_version_info()</a>, <a href="classIMP_1_1kinematics_1_1KinematicForest.html#a16b6ce03bb0fba3a5a8ca97bf2bc2b4e">IMP::kinematics::KinematicForest::get_version_info()</a>, <a href="classIMP_1_1kinematics_1_1KinematicForestScoreState.html#a4967e3524cc36c26fae49eccfd14da81">IMP::kinematics::KinematicForestScoreState::get_version_info()</a>, <a href="classIMP_1_1kinematics_1_1LocalPlanner.html#a1ecea8ea120b5305bcef865b8440f556">IMP::kinematics::LocalPlanner::get_version_info()</a>, <a href="classIMP_1_1kinematics_1_1ProteinKinematics.html#a098090057d248ad41f4b7abc2be0a3ae">IMP::kinematics::ProteinKinematics::get_version_info()</a>, <a href="classIMP_1_1kinematics_1_1RRT.html#ad2f94ba2c286907386d453a674c23190">IMP::kinematics::RRT::get_version_info()</a>, <a href="classIMP_1_1kinematics_1_1RevoluteJointMover.html#a52772966cd5b32f5bee21aaa705b82d8">IMP::kinematics::RevoluteJointMover::get_version_info()</a>, <a href="classIMP_1_1kmeans_1_1KMeans.html#a4934b3b97ad6314b2530f7d5cf242840">IMP::kmeans::KMeans::get_version_info()</a>, <a href="classIMP_1_1misc_1_1CommonEndpointPairFilter.html#a9ad6e5df3c47aca04268be436158afa4">IMP::misc::CommonEndpointPairFilter::get_version_info()</a>, <a href="classIMP_1_1misc_1_1DecayPairContainerOptimizerState.html#addda42d4586fbec248627eebc6521345">IMP::misc::DecayPairContainerOptimizerState::get_version_info()</a>, <a href="classIMP_1_1misc_1_1FreelyJointedChain.html#a1ab13da635bc5fd70ed6d5532205a290">IMP::misc::FreelyJointedChain::get_version_info()</a>, <a href="classIMP_1_1misc_1_1LogPairScore.html#a03143a56b280e7a7f9ad4bb8c34bca7e">IMP::misc::LogPairScore::get_version_info()</a>, <a href="classIMP_1_1misc_1_1LowestRefinedPairScore.html#a4bfbb573f377d2ed6ada902fecaad69f">IMP::misc::LowestRefinedPairScore::get_version_info()</a>, <a href="classIMP_1_1misc_1_1MetricClosePairsFinder.html#ad033de1219ecf9acc7c61459b3165481">IMP::misc::MetricClosePairsFinder::get_version_info()</a>, <a href="classIMP_1_1misc_1_1SoftCylinderPairScore.html#a678f661a0cdd65a6a88d9c573984ca7e">IMP::misc::SoftCylinderPairScore::get_version_info()</a>, <a href="classIMP_1_1misc_1_1StateAdaptor.html#a7f3f089944b4bff027d89494459cdd07">IMP::misc::StateAdaptor::get_version_info()</a>, <a href="classIMP_1_1misc_1_1WormLikeChain.html#a394176c2d2a8839192a1883e2bd6afd9">IMP::misc::WormLikeChain::get_version_info()</a>, <a href="classIMP_1_1mpi_1_1ReplicaExchange.html#a2cc42707b549ed6d587ebe75390be13f">IMP::mpi::ReplicaExchange::get_version_info()</a>, <a href="classIMP_1_1multifit_1_1AssemblyHeader.html#ab182e67eb0f992e5a81fa41bbc7e8643">IMP::multifit::AssemblyHeader::get_version_info()</a>, <a href="classIMP_1_1multifit_1_1ComplementarityRestraint.html#a3fb871bbb061e460881096b1864139a8">IMP::multifit::ComplementarityRestraint::get_version_info()</a>, <a href="classIMP_1_1multifit_1_1ComponentHeader.html#a81aced1ad9ac945c66d954e0c0be71e7">IMP::multifit::ComponentHeader::get_version_info()</a>, <a href="classIMP_1_1multifit_1_1DensityDataPoints.html#a8e71fc485fa957575c42e6001a91548b">IMP::multifit::DensityDataPoints::get_version_info()</a>, <a href="classIMP_1_1multifit_1_1DummyRestraint.html#aae8c8ee56232b6bd0d7588e441eef333">IMP::multifit::DummyRestraint::get_version_info()</a>, <a href="classIMP_1_1multifit_1_1Ensemble.html#a5a02b2e14f7be4f3b790040d17db2477">IMP::multifit::Ensemble::get_version_info()</a>, <a href="classIMP_1_1multifit_1_1FFTFitting.html#a62c07961bde4c2ae78346345ce27f9ab">IMP::multifit::FFTFitting::get_version_info()</a>, <a href="classIMP_1_1multifit_1_1FFTFittingOutput.html#a3daf74185ac58f0ca7affcb67073cbd7">IMP::multifit::FFTFittingOutput::get_version_info()</a>, <a href="classIMP_1_1multifit_1_1FittingStates.html#aca8c255de582acdef6198c68ea65ac9e">IMP::multifit::FittingStates::get_version_info()</a>, <a href="classIMP_1_1multifit_1_1ProbabilisticAnchorGraph.html#a1f40bf6af06636a9d3a05ad2d5c13803">IMP::multifit::ProbabilisticAnchorGraph::get_version_info()</a>, <a href="classIMP_1_1multifit_1_1ProteomicsData.html#afa1e74f7eca6ee59f2e7d2a345975133">IMP::multifit::ProteomicsData::get_version_info()</a>, <a href="classIMP_1_1multifit_1_1ProteomicsEMAlignmentAtomic.html#a35f786bf818d87dea5605de4889ab8e8">IMP::multifit::ProteomicsEMAlignmentAtomic::get_version_info()</a>, <a href="classIMP_1_1multifit_1_1RadiusOfGyrationRestraint.html#af319510c563d76d6fc852076a950c703">IMP::multifit::RadiusOfGyrationRestraint::get_version_info()</a>, <a href="classIMP_1_1multifit_1_1RigidLeavesRefiner.html#a2be9ae3cd9ed95d1cdf5d08d77b3cfe1">IMP::multifit::RigidLeavesRefiner::get_version_info()</a>, <a href="classIMP_1_1multifit_1_1SettingsData.html#a4034d9d91078a8fe34d2ce572333744f">IMP::multifit::SettingsData::get_version_info()</a>, <a href="classIMP_1_1multifit_1_1WeightedExcludedVolumeRestraint.html#adeb5c5034841fd693ddc848a32919763">IMP::multifit::WeightedExcludedVolumeRestraint::get_version_info()</a>, <a href="classIMP_1_1npc_1_1AssemblySymmetryByDihedralRestraint.html#a140ed9b1b5614f2f91d82fda40c63239">IMP::npc::AssemblySymmetryByDihedralRestraint::get_version_info()</a>, <a href="classIMP_1_1npc_1_1AssemblySymmetryByDistanceRestraint.html#a992739e602abb4d4d6bf5d4c76877961">IMP::npc::AssemblySymmetryByDistanceRestraint::get_version_info()</a>, <a href="classIMP_1_1npc_1_1CompositeRestraint.html#a9756e8a8f8f49a44a1bc9a916f6e26ac">IMP::npc::CompositeRestraint::get_version_info()</a>, <a href="classIMP_1_1npc_1_1MembraneExclusionRestraint.html#a7fd5a1c598cd68e91b07e9a26fe6ec2b">IMP::npc::MembraneExclusionRestraint::get_version_info()</a>, <a href="classIMP_1_1npc_1_1MembraneSurfaceLocationConditionalRestraint.html#a1f9f11f01a2a03e285286aa6165ce577">IMP::npc::MembraneSurfaceLocationConditionalRestraint::get_version_info()</a>, <a href="classIMP_1_1npc_1_1MembraneSurfaceLocationRestraint.html#a80772590591003e269de6fba3450afa4">IMP::npc::MembraneSurfaceLocationRestraint::get_version_info()</a>, <a href="classIMP_1_1npc_1_1MinimumSphereDistancePairScore.html#ac98afbe144d2c7b8d632b6a42b697e08">IMP::npc::MinimumSphereDistancePairScore::get_version_info()</a>, <a href="classIMP_1_1npc_1_1PerinuclearVolumeLocationRestraint.html#aa01a7ead0d7a451e6cf714dbda83b1f4">IMP::npc::PerinuclearVolumeLocationRestraint::get_version_info()</a>, <a href="classIMP_1_1npc_1_1PoreSideVolumeLocationRestraint.html#a4bdf805a8a9b42e49e6d8a0ee0f79679">IMP::npc::PoreSideVolumeLocationRestraint::get_version_info()</a>, <a href="classIMP_1_1npc_1_1ProteinChainRestraint.html#a8a3f58f4e6468970106eceb8fb2e6dd7">IMP::npc::ProteinChainRestraint::get_version_info()</a>, <a href="classIMP_1_1npc_1_1ProteinContactRestraint.html#acd7869cb0f9efdc40f42ca74c1c79d3c">IMP::npc::ProteinContactRestraint::get_version_info()</a>, <a href="classIMP_1_1npc_1_1ProteinProximityRestraint.html#a7aab1a992492014168fcdd2b217755fe">IMP::npc::ProteinProximityRestraint::get_version_info()</a>, <a href="classIMP_1_1npc_1_1XYRadialPositionLowerRestraint.html#ab717b815bf4bb1d572b071e16d0cf8b1">IMP::npc::XYRadialPositionLowerRestraint::get_version_info()</a>, <a href="classIMP_1_1npc_1_1XYRadialPositionRestraint.html#acfb2474c360a4e55e6469c435d702060">IMP::npc::XYRadialPositionRestraint::get_version_info()</a>, <a href="classIMP_1_1npc_1_1XYRadialPositionUpperRestraint.html#a2ed5ccc504f78e581738a898fd49bc87">IMP::npc::XYRadialPositionUpperRestraint::get_version_info()</a>, <a href="classIMP_1_1npc_1_1YAxialPositionLowerRestraint.html#aa64a3eb685b46bd6cfe62200df75a208">IMP::npc::YAxialPositionLowerRestraint::get_version_info()</a>, <a href="classIMP_1_1npc_1_1YAxialPositionRestraint.html#a8581d8209b64e39b29e9c8c85a09b5c9">IMP::npc::YAxialPositionRestraint::get_version_info()</a>, <a href="classIMP_1_1npc_1_1YAxialPositionUpperRestraint.html#acf17a2015c652dd4d6be5208dc6f7c32">IMP::npc::YAxialPositionUpperRestraint::get_version_info()</a>, <a href="classIMP_1_1npc_1_1ZAxialPositionLowerRestraint.html#a8c3dde801d2765e86ed57b34cac74933">IMP::npc::ZAxialPositionLowerRestraint::get_version_info()</a>, <a href="classIMP_1_1npc_1_1ZAxialPositionRestraint.html#ab03fc99300c114a21ce4b370d83c9520">IMP::npc::ZAxialPositionRestraint::get_version_info()</a>, <a href="classIMP_1_1npc_1_1ZAxialPositionUpperRestraint.html#a410786e860f865f6d12a609be5bbe43e">IMP::npc::ZAxialPositionUpperRestraint::get_version_info()</a>, <a href="classIMP_1_1npctransport_1_1AnchorToCylidnricalPorePairScore.html#a584fd03dc03f322ae55821fc2ce50d6d">IMP::npctransport::AnchorToCylidnricalPorePairScore::get_version_info()</a>, <a href="classIMP_1_1npctransport_1_1BipartitePairsStatisticsOptimizerState.html#ad9d2fb83dbeb59aeb4db095ab56c08fe">IMP::npctransport::BipartitePairsStatisticsOptimizerState::get_version_info()</a>, <a href="classIMP_1_1npctransport_1_1BodyStatisticsOptimizerState.html#ab83d13cd39a4f20beb838013c04439c9">IMP::npctransport::BodyStatisticsOptimizerState::get_version_info()</a>, <a href="classIMP_1_1npctransport_1_1ChainStatisticsOptimizerState.html#a95fd57a71aab706605cb50bd4e2e89a0">IMP::npctransport::ChainStatisticsOptimizerState::get_version_info()</a>, <a href="classIMP_1_1npctransport_1_1ExcludeZRangeSingletonScore.html#a5f86995b805ab748118f7ff9b922b73c">IMP::npctransport::ExcludeZRangeSingletonScore::get_version_info()</a>, <a href="classIMP_1_1npctransport_1_1FGChain.html#a90160465aabfad94fd129acec27d2fe0">IMP::npctransport::FGChain::get_version_info()</a>, <a href="classIMP_1_1npctransport_1_1FunctorLinearInteractionPairScore.html#af63bfcb958c1cf433ba45a071364f0ce">IMP::npctransport::FunctorLinearInteractionPairScore::get_version_info()</a>, <a href="classIMP_1_1npctransport_1_1FunctorLinearSoftSpherePairScore.html#a16376fdb70bb4a4fde08c01f47129f59">IMP::npctransport::FunctorLinearSoftSpherePairScore::get_version_info()</a>, <a href="classIMP_1_1npctransport_1_1GlobalStatisticsOptimizerState.html#a32b2995b34c78febd0bf45f1b262bb01">IMP::npctransport::GlobalStatisticsOptimizerState::get_version_info()</a>, <a href="classIMP_1_1npctransport_1_1HarmonicSpringSingletonScore.html#a1500b159715ae70e68703303920c6918">IMP::npctransport::HarmonicSpringSingletonScore::get_version_info()</a>, <a href="classIMP_1_1npctransport_1_1HarmonicWellPairScore.html#a1d59e522feec95a5e741b5fda63ea574">IMP::npctransport::HarmonicWellPairScore::get_version_info()</a>, <a href="classIMP_1_1npctransport_1_1LinearInteractionPairScore.html#a54bc05a0e1afb64aed0aca1309af7cf2">IMP::npctransport::LinearInteractionPairScore::get_version_info()</a>, <a href="classIMP_1_1npctransport_1_1LinearSoftSpherePairScore.html#a876705cd618c3a7de622c72f665b7766">IMP::npctransport::LinearSoftSpherePairScore::get_version_info()</a>, <a href="classIMP_1_1npctransport_1_1LinearWellPairScore.html#ac37957f725d58cb0a2a3ad203977e161">IMP::npctransport::LinearWellPairScore::get_version_info()</a>, <a href="classIMP_1_1npctransport_1_1ParticleFactory.html#ae9db36e861ebaa604238a4db9782c106">IMP::npctransport::ParticleFactory::get_version_info()</a>, <a href="classIMP_1_1npctransport_1_1ParticleTransportStatisticsOptimizerState.html#afd09d4579f0f44a3c2a2c94049bdffa6">IMP::npctransport::ParticleTransportStatisticsOptimizerState::get_version_info()</a>, <a href="classIMP_1_1npctransport_1_1Scoring.html#aa48d05c74867d83c2c24d2ef11806709">IMP::npctransport::Scoring::get_version_info()</a>, <a href="classIMP_1_1npctransport_1_1SimulationData.html#a07019e72d2243e2ac5654a8ec898d596">IMP::npctransport::SimulationData::get_version_info()</a>, <a href="classIMP_1_1npctransport_1_1SitesGeometry.html#a7fb0358bc97c398e4d951670168b6a9f">IMP::npctransport::SitesGeometry::get_version_info()</a>, <a href="classIMP_1_1npctransport_1_1SitesPairScore.html#a4159600a0397fdebb2c4074d42bffcae">IMP::npctransport::SitesPairScore::get_version_info()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithCylindricalPorePairScore.html#a3551f3c2bfe855da791cdf7b409d6d1c">IMP::npctransport::SlabWithCylindricalPorePairScore::get_version_info()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithCylindricalPoreWireGeometry.html#a9c786e29c02ea78e3500158469706446">IMP::npctransport::SlabWithCylindricalPoreWireGeometry::get_version_info()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithToroidalPorePairScore.html#a7935782b3a7398d139b361e3e391702b">IMP::npctransport::SlabWithToroidalPorePairScore::get_version_info()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithToroidalPoreWireGeometry.html#a1709ba59630f148845141c94417101b1">IMP::npctransport::SlabWithToroidalPoreWireGeometry::get_version_info()</a>, <a href="classIMP_1_1npctransport_1_1Statistics.html#a5b01e56c08fbda8d44cacfee4d8f062d">IMP::npctransport::Statistics::get_version_info()</a>, <a href="classIMP_1_1npctransport_1_1TypedSitesGeometry.html#a3d0f5b6b840d84dd950ce91de88a0b91">IMP::npctransport::TypedSitesGeometry::get_version_info()</a>, <a href="classIMP_1_1npctransport_1_1ZBiasSingletonScore.html#a4b3385417ecdddfe6a813442c1a75433">IMP::npctransport::ZBiasSingletonScore::get_version_info()</a>, <a href="classIMP_1_1pmi1_1_1CompositeRestraint.html#abb94ac9a91d60f46462b1acc63f34029">IMP::pmi1::CompositeRestraint::get_version_info()</a>, <a href="classIMP_1_1pmi1_1_1InternalCoordinatesConstraint.html#acc766eee82c603f717a7ad9590aee460">IMP::pmi1::InternalCoordinatesConstraint::get_version_info()</a>, <a href="classIMP_1_1pmi1_1_1MembraneRestraint.html#afcd88b9f4b16906a006a64400bae439b">IMP::pmi1::MembraneRestraint::get_version_info()</a>, <a href="classIMP_1_1pmi1_1_1SigmoidRestraintSphere.html#a19c5049f66a7cfbfd84766ecc90f1c6d">IMP::pmi1::SigmoidRestraintSphere::get_version_info()</a>, <a href="classIMP_1_1pmi1_1_1TransformMover.html#a80bd2d0c27771fa4d6a2716939d1195d">IMP::pmi1::TransformMover::get_version_info()</a>, <a href="classIMP_1_1pmi_1_1CompositeRestraint.html#a07cac0a6aa483ef01e59b6c3a0f49baf">IMP::pmi::CompositeRestraint::get_version_info()</a>, <a href="classIMP_1_1pmi_1_1CrossLinkRestraintSet.html#abc6148c07fd31be8c8b3a91916dc2435">IMP::pmi::CrossLinkRestraintSet::get_version_info()</a>, <a href="classIMP_1_1pmi_1_1MembraneRestraint.html#afe7e0e84d5f69bf869cd96716a66e0cb">IMP::pmi::MembraneRestraint::get_version_info()</a>, <a href="classIMP_1_1pmi_1_1TransformMover.html#a14f2b94f34f318131d457f8d5038820b">IMP::pmi::TransformMover::get_version_info()</a>, <a href="classIMP_1_1rmf_1_1HierarchyLoadLink.html#a51cd666b48b447c287b1f1e64f220a3d">IMP::rmf::HierarchyLoadLink::get_version_info()</a>, <a href="classIMP_1_1rmf_1_1HierarchySaveLink.html#a570a24f2be728bd61e279e913ae50992">IMP::rmf::HierarchySaveLink::get_version_info()</a>, <a href="classIMP_1_1rmf_1_1SaveOptimizerState.html#aa2be9922499fe17fe1211121c3e3ad04">IMP::rmf::SaveOptimizerState::get_version_info()</a>, <a href="classIMP_1_1rotamer_1_1RotamerCalculator.html#a256b6b112265933e6c1f13e56e6542d7">IMP::rotamer::RotamerCalculator::get_version_info()</a>, <a href="classIMP_1_1rotamer_1_1RotamerLibrary.html#a17335d183429f41a88463ed2bd9f2396">IMP::rotamer::RotamerLibrary::get_version_info()</a>, <a href="classIMP_1_1saxs_1_1ChiScore.html#ac69555b23c21d4f5d3879bbd73964d1b">IMP::saxs::ChiScore::get_version_info()</a>, <a href="classIMP_1_1saxs_1_1ChiScoreLog.html#a23fe48947fc3e1a9bb5e78e9e189380e">IMP::saxs::ChiScoreLog::get_version_info()</a>, <a href="classIMP_1_1saxs_1_1Profile.html#a8e0ed7d2bb30b17f97b9b92ca09f3209">IMP::saxs::Profile::get_version_info()</a>, <a href="classIMP_1_1saxs_1_1RadiusOfGyrationRestraint.html#a99e179581b124b79ac3d9fd091122b41">IMP::saxs::RadiusOfGyrationRestraint::get_version_info()</a>, <a href="classIMP_1_1saxs_1_1RatioVolatilityScore.html#aeb54ada9a5f6a0004a6bfbd022479da9">IMP::saxs::RatioVolatilityScore::get_version_info()</a>, <a href="classIMP_1_1saxs_1_1Restraint.html#a3f834872ef44459f87e7ccfa47f77bec">IMP::saxs::Restraint::get_version_info()</a>, <a href="classIMP_1_1saxs_1_1RigidBodiesProfileHandler.html#a3d9ee7d91000ba8d8682cd528e29177d">IMP::saxs::RigidBodiesProfileHandler::get_version_info()</a>, <a href="classIMP_1_1score__functor_1_1DistancePairScore.html#a1a67f29a44377c6d45ee0c9e14fcf2be">IMP::score_functor::DistancePairScore::get_version_info()</a>, <a href="classIMP_1_1score__functor_1_1DistancePairScoreWithCache.html#a2a04b780c2867aa2d842a8650999a730">IMP::score_functor::DistancePairScoreWithCache::get_version_info()</a>, <a href="classIMP_1_1score__functor_1_1ScoreUnaryFunction.html#a06593c61dd70c347f2250188c7b8418d">IMP::score_functor::ScoreUnaryFunction::get_version_info()</a>, <a href="classIMP_1_1score__functor_1_1SurfaceDistancePairScore.html#a376ac706e46c53b2426efe5322bc0f69">IMP::score_functor::SurfaceDistancePairScore::get_version_info()</a>, <a href="classIMP_1_1spb_1_1AttributeDistancePairScore.html#a712d8203b0cc4fd24ae1a1ad11c6d309">IMP::spb::AttributeDistancePairScore::get_version_info()</a>, <a href="classIMP_1_1spb_1_1BoxedMover.html#a13858fcd3581bc3d222839f5845db11b">IMP::spb::BoxedMover::get_version_info()</a>, <a href="classIMP_1_1spb_1_1CellMover.html#a96366c6aaba9d5fae391cd927995e502">IMP::spb::CellMover::get_version_info()</a>, <a href="classIMP_1_1spb_1_1ChiSquareMetric.html#a1c72aae2c5e5a4fbbf7d152554fd776d">IMP::spb::ChiSquareMetric::get_version_info()</a>, <a href="classIMP_1_1spb_1_1ContactMapMetric.html#ab14e00eeed77d0ff2dfc4ca892b34eb3">IMP::spb::ContactMapMetric::get_version_info()</a>, <a href="classIMP_1_1spb_1_1DiameterRgyrRestraint.html#ab09a6d47b6953e127afb413899254634">IMP::spb::DiameterRgyrRestraint::get_version_info()</a>, <a href="classIMP_1_1spb_1_1DistanceRMSDMetric.html#adf1b20f4840efa19033c88c7cb8ad8a5">IMP::spb::DistanceRMSDMetric::get_version_info()</a>, <a href="classIMP_1_1spb_1_1DistanceTerminiRestraint.html#a40c7008cf30ddfdcf034a96e754c9600">IMP::spb::DistanceTerminiRestraint::get_version_info()</a>, <a href="classIMP_1_1spb_1_1EM2DRestraint.html#a618cbcc25da2a0cc0664487224d4ea25">IMP::spb::EM2DRestraint::get_version_info()</a>, <a href="classIMP_1_1spb_1_1Gaussian.html#aafd1d2d706f6136bcb13f184fe03cd04">IMP::spb::Gaussian::get_version_info()</a>, <a href="classIMP_1_1spb_1_1KinkPairScore.html#a5eafd8aeab32a4fcc68a0fdd242d2157">IMP::spb::KinkPairScore::get_version_info()</a>, <a href="classIMP_1_1spb_1_1MonteCarloWithWte.html#a63fbbe0782870f2ba04e99abf0992046">IMP::spb::MonteCarloWithWte::get_version_info()</a>, <a href="classIMP_1_1spb_1_1NuisanceRangeModifier.html#a9ef012045a0073af25842a532a33d8c3">IMP::spb::NuisanceRangeModifier::get_version_info()</a>, <a href="classIMP_1_1spb_1_1PbcBoxedMover.html#a9e70e4714329a55e800ca95258bc8f14">IMP::spb::PbcBoxedMover::get_version_info()</a>, <a href="classIMP_1_1spb_1_1PbcBoxedRigidBodyMover.html#a4b98f808ee6f4f48d8228513f10cabb9">IMP::spb::PbcBoxedRigidBodyMover::get_version_info()</a>, <a href="classIMP_1_1spb_1_1RMSDMetric.html#a69236b51b869fb6652b4268c7f8c215a">IMP::spb::RMSDMetric::get_version_info()</a>, <a href="classIMP_1_1spb_1_1RigidBodyNewMover.html#a2b9f66d24c831710eaa31dc4e585edf7">IMP::spb::RigidBodyNewMover::get_version_info()</a>, <a href="classIMP_1_1spb_1_1SameParticlePairFilter.html#a4ef95ddfb6b4d4b27c74d86498c81e01">IMP::spb::SameParticlePairFilter::get_version_info()</a>, <a href="classIMP_1_1spb_1_1SameRigidBodyPairFilter.html#a06c4b88d18e97ee2df626855a3567ee4">IMP::spb::SameRigidBodyPairFilter::get_version_info()</a>, <a href="classIMP_1_1spb_1_1TiltSingletonScore.html#a29d625ac5350e407a0f75baeb94ff7dd">IMP::spb::TiltSingletonScore::get_version_info()</a>, <a href="classIMP_1_1spb_1_1TransformationSymmetry.html#ace73cf7a2f119cdfe73911e25a702712">IMP::spb::TransformationSymmetry::get_version_info()</a>, <a href="classIMP_1_1spb_1_1TwoStateGoModelRestraint.html#ae85a46b2c7144b0103effac2d53f7662">IMP::spb::TwoStateGoModelRestraint::get_version_info()</a>, <a href="classIMP_1_1spb_1_1UniformBoundedRestraint.html#a87b071effd27529147cbac5de93691ce">IMP::spb::UniformBoundedRestraint::get_version_info()</a>, <a href="classIMP_1_1statistics_1_1ChiSquareMetric.html#a80160eec7589afaa6dbb6a4d6bdacc03">IMP::statistics::ChiSquareMetric::get_version_info()</a>, <a href="classIMP_1_1statistics_1_1ConfigurationSetRMSDMetric.html#a28a30cacd860baa44d16a632e893ee31">IMP::statistics::ConfigurationSetRMSDMetric::get_version_info()</a>, <a href="classIMP_1_1statistics_1_1ConfigurationSetXYZEmbedding.html#ac7e3e2a8b5e8048d7e75312ec611c228">IMP::statistics::ConfigurationSetXYZEmbedding::get_version_info()</a>, <a href="classIMP_1_1statistics_1_1EuclideanMetric.html#a2285eb83641ba468733c1dc3fa65d0ac">IMP::statistics::EuclideanMetric::get_version_info()</a>, <a href="classIMP_1_1statistics_1_1ParticleEmbedding.html#ab6822358cddc553d0e16905722a8b20c">IMP::statistics::ParticleEmbedding::get_version_info()</a>, <a href="classIMP_1_1statistics_1_1PartitionalClusteringWithCenter.html#af0fa1d9e9ed02cc10ecfda8c5ad0ed2b">IMP::statistics::PartitionalClusteringWithCenter::get_version_info()</a>, <a href="classIMP_1_1statistics_1_1RecursivePartitionalClusteringEmbedding.html#acf076ee7169764e17f39bb36164be35c">IMP::statistics::RecursivePartitionalClusteringEmbedding::get_version_info()</a>, <a href="classIMP_1_1statistics_1_1RecursivePartitionalClusteringMetric.html#a6a0c8fa95d119254e0acfcb2cad560e6">IMP::statistics::RecursivePartitionalClusteringMetric::get_version_info()</a>, <a href="classIMP_1_1statistics_1_1VectorDEmbedding.html#a5ed1368248335c0e99a8ab536364b224">IMP::statistics::VectorDEmbedding::get_version_info()</a>, <a href="classIMP_1_1symmetry_1_1BallMover.html#a59745e95c1ce4d2d7e593748edb327ea">IMP::symmetry::BallMover::get_version_info()</a>, <a href="classIMP_1_1symmetry_1_1RigidBodyMover.html#a32e40d9add968b9f0e2365328d15cf58">IMP::symmetry::RigidBodyMover::get_version_info()</a></td></tr>
53 </table>
54 # IMP.algebra # {#factory_index_algebra}
55 <table><tr>
56 <th>Class</th><th>Factories</th></tr>
57 <tr><td>@ref IMP::algebra::BoundingBoxD</td><td><a href="classIMP_1_1algebra_1_1BoundingBoxD.html#aa8092895377c9aca82b78050456b33c9">IMP::algebra::BoundingBoxD::operator+=()</a>, <a href="classIMP_1_1algebra_1_1BoundingBoxD.html#abe7e39f1ee5d58dae32272ee29e51f0b">IMP::algebra::BoundingBoxD::operator+=()</a>, <a href="classIMP_1_1algebra_1_1BoundingBoxD.html#a83c31adcb8aafca645af67822d996eed">IMP::algebra::BoundingBoxD::operator+=()</a>, <a href="classIMP_1_1algebra_1_1Cone3D.html#a42215f5c82c6b41689887aee272d6f29">IMP::algebra::Cone3D::get_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1Cylinder3D.html#a2c0e1a36a0080caf666ff5e8657c44ea">IMP::algebra::Cylinder3D::get_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1DefaultEmbeddingD.html#aa939cc38c61633c05ba8f512671c9922">IMP::algebra::DefaultEmbeddingD::get_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1DefaultEmbeddingD.html#a2ef44b764283d6da46c20bfbf17dbff7">IMP::algebra::DefaultEmbeddingD::get_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1Ellipsoid3D.html#a51e51989d370ac6d1f72605ea2b55659">IMP::algebra::Ellipsoid3D::get_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1GridD.html#a008aec5907f2445fdb9ab7f0ad9857b4">IMP::algebra::GridD::get_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1Line3D.html#a0ddee92213d742382802d0fe52ca8e44">IMP::algebra::Line3D::get_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#afcefc82a3dc1a028efd0ef7a76ae3f62">IMP::algebra::LogEmbeddingD::get_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#a19437cca74047a689ad5622534007858">IMP::algebra::LogEmbeddingD::get_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1Plane3D.html#aedce7034965a145fc52252f640761b26">IMP::algebra::Plane3D::get_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1Segment3D.html#abd21d39499ca4acd3616d7a9355b90fd">IMP::algebra::Segment3D::get_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1SpherePatch3D.html#ae5375e21b4c4a14ecf4278d36cab2387">IMP::algebra::SpherePatch3D::get_bounding_box()</a>, <a href="classIMP_1_1algebra_1_1Torus3D.html#aaaa8ffb3b19028f35539da46be602814">IMP::algebra::Torus3D::get_bounding_box()</a>, <a href="classIMP_1_1atom_1_1Hierarchy.html#a0b2a97a5d1d9906dd31d60a8ba588e5a">IMP::atom::Hierarchy::get_bounding_box()</a>, <a href="classIMP_1_1display_1_1BoundingBoxGeometry.html#ac2655fba9566ec3dc3e1063f8f29077d">IMP::display::BoundingBoxGeometry::get_geometry()</a>, <a href="classIMP_1_1em_1_1SampledDensityMap.html#a0aeeeba26e971ba0467c70a3ccdc21dc">IMP::em::SampledDensityMap::calculate_particles_bounding_box()</a>, <a href="classIMP_1_1statistics_1_1HistogramD.html#a1076a15bf53877cf192b36b1f7aa7b9f">IMP::statistics::HistogramD::get_bounding_box()</a>, <a href="namespaceIMP_1_1algebra.html#aecec6f9c6ca668315e6693773ac1c15f">IMP::algebra::get_cube_kd()</a>, <a href="namespaceIMP_1_1algebra.html#aec3bea2d24fbbf621216822517ca1593">IMP::algebra::get_transformed()</a>, <a href="namespaceIMP_1_1algebra.html#aa88ff22c3c9a9a857314e714d69dea62">IMP::algebra::get_unit_bounding_box_kd()</a>, <a href="namespaceIMP_1_1core.html#a0ba3b6f5fba01f4ecf8a3b8f18a311f2">IMP::core::get_bounding_box()</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></td></tr>
58 <tr><td>@ref IMP::algebra::Cone3D</td><td><a href="classIMP_1_1algebra_1_1Cone3D.html#a9408590e3b4ed9bea9901e0cc53f1039">IMP::algebra::Cone3D::get_cone_3d_geometry()</a></td></tr>
59 <tr><td>@ref IMP::algebra::Cylinder3D</td><td><a href="classIMP_1_1algebra_1_1Cylinder3D.html#a1f598fc535a050c3979cd2726732a552">IMP::algebra::Cylinder3D::get_cylinder_3d_geometry()</a>, <a href="classIMP_1_1core_1_1SurfaceGeometry.html#a46c142841b86dff45e9afac8d1cb7b80">IMP::core::SurfaceGeometry::get_cylinder()</a>, <a href="classIMP_1_1display_1_1CylinderGeometry.html#a68933bd92183b7af45927c57be378355">IMP::display::CylinderGeometry::get_geometry()</a>, <a href="classIMP_1_1npctransport_1_1SimulationData.html#ab0054d84562fce73f752add4c727654f">IMP::npctransport::SimulationData::get_cylinder()</a></td></tr>
60 <tr><td>@ref IMP::algebra::DenseGridStorageD</td><td><a href="classIMP_1_1algebra_1_1DenseGridStorageD.html#a5cd0208038b5008c73248047c91f38a7">IMP::algebra::DenseGridStorageD::operator=()</a>, <a href="namespaceIMP_1_1em.html#a9c72b01f6d6bbe0c84a0779fc08b809c">IMP::em::get_grid()</a></td></tr>
61 <tr><td>@ref IMP::algebra::Ellipsoid3D</td><td><a href="classIMP_1_1algebra_1_1Ellipsoid3D.html#a2fd68925f46292fc3f90454f7a34bded">IMP::algebra::Ellipsoid3D::get_ellipsoid_3d_geometry()</a>, <a href="classIMP_1_1display_1_1EllipsoidGeometry.html#a1286b6c9386a8f436b0170b13a1b638c">IMP::display::EllipsoidGeometry::get_geometry()</a></td></tr>
62 <tr><td>@ref IMP::algebra::ExtendedGridIndexD</td><td><a href="classIMP_1_1algebra_1_1BoundedGridRangeD.html#a737ab039ddae4cf86fe92044c15424e6">IMP::algebra::BoundedGridRangeD::get_extended_indexes()</a>, <a href="classIMP_1_1algebra_1_1BoundedGridRangeD.html#a61d03caf63e70aa0c0e6d6d74130c27c">IMP::algebra::BoundedGridRangeD::get_end_index()</a>, <a href="classIMP_1_1algebra_1_1BoundedGridRangeD.html#a395874afecb718cda8209087070b9aaa">IMP::algebra::BoundedGridRangeD::get_maximum_extended_index()</a>, <a href="classIMP_1_1algebra_1_1BoundedGridRangeD.html#a3630e2bb1873a86f4606a04b5bf7c847">IMP::algebra::BoundedGridRangeD::get_minimum_extended_index()</a>, <a href="classIMP_1_1algebra_1_1DefaultEmbeddingD.html#a7c5f5633d6495ade19fa00cca4dccff5">IMP::algebra::DefaultEmbeddingD::get_extended_index()</a>, <a href="classIMP_1_1algebra_1_1ExtendedGridIndexD.html#a950308f6221c222ca73d04480a595f4b">IMP::algebra::ExtendedGridIndexD::get_offset()</a>, <a href="classIMP_1_1algebra_1_1ExtendedGridIndexD.html#a68dba8692dbf509e79f7c884a030996e">IMP::algebra::ExtendedGridIndexD::get_uniform_offset()</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#a1f513a99898cd34a8f760b887b4f9220">IMP::algebra::GridD::get_extended_index()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#a333cca1384be415a4beb6423dc4e6273">IMP::algebra::LogEmbeddingD::get_extended_index()</a>, <a href="classIMP_1_1algebra_1_1UnboundedGridRangeD.html#ae36705377d9f2caf5c06984d1ce8bfaa">IMP::algebra::UnboundedGridRangeD::get_extended_indexes()</a></td></tr>
63 <tr><td>@ref IMP::algebra::FixedXYZ</td><td><a href="namespaceIMP_1_1algebra.html#a9ff9afb5d3b97dc0f5a1af70a0a6dde8">IMP::algebra::get_fixed_xyz_from_rotation()</a></td></tr>
64 <tr><td>@ref IMP::algebra::Gaussian3D</td><td><a href="classIMP_1_1core_1_1Gaussian.html#a0a35e7a5ed9a37fb6fd122c350f5f5e2">IMP::core::Gaussian::get_gaussian()</a>, <a href="namespaceIMP_1_1algebra.html#a059a34d24381984fa86ea77b026daa7e">IMP::algebra::get_gaussian_from_covariance()</a></td></tr>
65 <tr><td>@ref IMP::algebra::GridD</td><td><a href="namespaceIMP_1_1em.html#a9c72b01f6d6bbe0c84a0779fc08b809c">IMP::em::get_grid()</a></td></tr>
66 <tr><td>@ref IMP::algebra::GridIndexD</td><td><a href="classIMP_1_1algebra_1_1BoundedGridRangeD.html#a7a7bb6e98f48c2153626ad288340363f">IMP::algebra::BoundedGridRangeD::get_all_indexes()</a>, <a href="classIMP_1_1algebra_1_1BoundedGridRangeD.html#abfd54359550894c029defa77ead61ab8">IMP::algebra::BoundedGridRangeD::get_indexes()</a>, <a href="classIMP_1_1algebra_1_1BoundedGridRangeD.html#acf1f33b1c1d7957330f442f15d656ac9">IMP::algebra::BoundedGridRangeD::get_index()</a>, <a href="classIMP_1_1algebra_1_1DefaultEmbeddingD.html#ae4437a1c4ca95b4abbf58c9531209d02">IMP::algebra::DefaultEmbeddingD::get_index()</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#a24ba706b342d7dc7e3c5cb42ed64fccf">IMP::algebra::GridD::add_voxel()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#a09613ab4444befc995178b6b8a416358">IMP::algebra::LogEmbeddingD::get_index()</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#abcf4643d745ad8f61ac711026cb9a5cb">IMP::algebra::SparseGridStorageD::get_index()</a></td></tr>
67 <tr><td>@ref IMP::algebra::Line3D</td><td><a href="classIMP_1_1algebra_1_1Line3D.html#a4728fdd68054674a97088544ad173bfa">IMP::algebra::Line3D::get_opposite()</a>, <a href="classIMP_1_1algebra_1_1Line3D.html#afc6ba02a46de817baba50c58eab655e8">IMP::algebra::Line3D::get_line_3d_geometry()</a>, <a href="namespaceIMP_1_1algebra.html#a151019bab90b6cdc2f1755c6b7a92bdc">IMP::algebra::get_transformed()</a></td></tr>
68 <tr><td>@ref IMP::algebra::Plane3D</td><td><a href="classIMP_1_1algebra_1_1Cone3D.html#a9a39fe81e54ff2d233613fc1b6d92a56">IMP::algebra::Cone3D::get_base_plane()</a>, <a href="classIMP_1_1algebra_1_1Plane3D.html#aaccbebe65a7c6c14a0bde93ab9b91363">IMP::algebra::Plane3D::get_opposite()</a>, <a href="classIMP_1_1algebra_1_1Plane3D.html#ade3bebd378b15acf3e134236ccf4a894">IMP::algebra::Plane3D::get_plane_3d_geometry()</a>, <a href="classIMP_1_1algebra_1_1SpherePatch3D.html#abf412d5eb9224b9db29943be84bb5f69">IMP::algebra::SpherePatch3D::get_plane()</a>, <a href="classIMP_1_1core_1_1Surface.html#a47fd9412666171438d2dd25e9c7e4e6d">IMP::core::Surface::get_plane()</a></td></tr>
69 <tr><td>@ref IMP::algebra::ReferenceFrame3D</td><td><a href="classIMP_1_1algebra_1_1Ellipsoid3D.html#a64cdd46002ef8528e8583d5de98b749a">IMP::algebra::Ellipsoid3D::get_reference_frame()</a>, <a href="classIMP_1_1algebra_1_1Gaussian3D.html#a455df294c6db94bd0407f2b7fe56577a">IMP::algebra::Gaussian3D::get_reference_frame()</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_1algebra_1_1ReferenceFrame3D.html#a073f7afd1da412a31f5a357c0cc8a270">IMP::algebra::ReferenceFrame3D::operator=()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#ac13846a110676d06ea4baaa5530f4a49">IMP::core::RigidBody::get_reference_frame()</a>, <a href="classIMP_1_1core_1_1Surface.html#ac41c7cc9e54d559a3f6235b91b91a2d6">IMP::core::Surface::get_reference_frame()</a>, <a href="classIMP_1_1display_1_1ReferenceFrameGeometry.html#a78238ec0ea014903e5da1a323ace6fd2">IMP::display::ReferenceFrameGeometry::get_geometry()</a>, <a href="classIMP_1_1domino_1_1RigidBodyStates.html#accb521c129d1f71f3e5388e4a7d6aaa7">IMP::domino::RigidBodyStates::get_reference_frame()</a>, <a href="classIMP_1_1kinematics_1_1KinematicForest.html#ae9aea73c759c2ceeb7c88c46553fdc47">IMP::kinematics::KinematicForest::get_reference_frame_safe()</a>, <a href="namespaceIMP_1_1algebra.html#ad1ae16d9089296d2d7f458c2d667e587">IMP::algebra::get_transformed()</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></td></tr>
70 <tr><td>@ref IMP::algebra::Rotation2D</td><td><a href="classIMP_1_1algebra_1_1Rotation2D.html#a2f2b6db0f0898eb427c79f576c9e6b21">IMP::algebra::Rotation2D::get_inverse()</a>, <a href="classIMP_1_1algebra_1_1Transformation2D.html#a9c6b8c68d237c6327947db7f73df7a5f">IMP::algebra::Transformation2D::get_rotation()</a>, <a href="namespaceIMP_1_1algebra.html#a4ace4e3f3bb2f5d5fd442360945370a3">IMP::algebra::compose()</a>, <a href="namespaceIMP_1_1algebra.html#a34a359be279311b5284c4d2c56a62c65">IMP::algebra::get_identity_rotation_2d()</a>, <a href="namespaceIMP_1_1algebra.html#ac7ecfcd34e562d2b08fa9eb977e5f302">IMP::algebra::get_random_rotation_2d()</a>, <a href="namespaceIMP_1_1algebra.html#a491932b32722826e03b4e952444be4b0">IMP::algebra::get_rotation_to_x_axis()</a></td></tr>
71 <tr><td>@ref IMP::algebra::Rotation3D</td><td><a href="classIMP_1_1algebra_1_1Rotation3D.html#a64277befc08357d6768b5f8cba5fdf56">IMP::algebra::Rotation3D::get_inverse()</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#af38f7b53af59c4d73defebca22893b14">IMP::algebra::Transformation3D::get_rotation()</a>, <a href="classIMP_1_1atom_1_1BrownianDynamicsTAMD.html#af52b68ac46666de8213dda7600c58494">IMP::atom::BrownianDynamicsTAMD::compute_rotation_0()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#ac1209d4693e1c8e612865d923e269e6e">IMP::core::RigidBody::get_rotation()</a>, <a href="classIMP_1_1em2d_1_1GridStates.html#ac3e4528519d25658257b5f01a6bf10ce">IMP::em2d::GridStates::get_orientation()</a>, <a href="classIMP_1_1em2d_1_1ProjectionParameters.html#ae1773e9f6d26fced9d3511e6d8ffdca2">IMP::em2d::ProjectionParameters::get_rotation()</a>, <a href="classIMP_1_1em2d_1_1RegistrationResult.html#acd2c31e953d155a20d200440af0331e6">IMP::em2d::RegistrationResult::get_rotation()</a>, <a href="classIMP_1_1em_1_1PCAAligner.html#a717801d249ab2dd4b3b33eb5849be168">IMP::em::PCAAligner::get_rotation_matrix()</a>, <a href="namespaceIMP_1_1algebra.html#a50728b3c7c4674d610b353a58510b601">IMP::algebra::get_rotation_from_fixed_xyz()</a>, <a href="namespaceIMP_1_1algebra.html#a25e458f2015410be98a7805c50178c75">IMP::algebra::get_rotation_from_fixed_zxz()</a>, <a href="namespaceIMP_1_1algebra.html#a0d07cdae4fbf65960b6d02ecdc4501f6">IMP::algebra::get_rotation_from_fixed_zyz()</a>, <a href="namespaceIMP_1_1algebra.html#a216ec1243a72a2c3f9ddf6bd8bc22ece">IMP::algebra::compose()</a>, <a href="namespaceIMP_1_1algebra.html#a98a32dfffbb6b9f5f20a12dd479f1b9b">IMP::algebra::get_identity_rotation_3d()</a>, <a href="namespaceIMP_1_1algebra.html#aad56f25091896ce8e87f8e5f1098bf79">IMP::algebra::get_interpolated()</a>, <a href="namespaceIMP_1_1algebra.html#a139712da5a82968a06bb71b09196bc5b">IMP::algebra::get_random_rotation_3d()</a>, <a href="namespaceIMP_1_1algebra.html#abd23e8a25dda2d4acf8c00db35e2537f">IMP::algebra::get_random_rotation_3d()</a>, <a href="namespaceIMP_1_1algebra.html#a283f1463563e2c38fd3f4ae788c11484">IMP::algebra::get_rotation_about_axis()</a>, <a href="namespaceIMP_1_1algebra.html#ad96b1551c23f1f62de05e9ebbcbf3429">IMP::algebra::get_rotation_about_normalized_axis()</a>, <a href="namespaceIMP_1_1algebra.html#a28b2093fb8db4340e11cce11de658572">IMP::algebra::get_rotation_from_matrix()</a>, <a href="namespaceIMP_1_1algebra.html#a00a10a59dcf29a8947623a3fc69edb61">IMP::algebra::get_rotation_from_matrix()</a>, <a href="namespaceIMP_1_1algebra.html#a3003fd1a5254db165a8600f2979e7146">IMP::algebra::get_rotation_from_vector4d()</a>, <a href="namespaceIMP_1_1algebra.html#a010dd03d5d6e849ea7b0991f646d6b53">IMP::algebra::get_rotation_from_x_y_axes()</a>, <a href="namespaceIMP_1_1algebra.html#a6af4099df3f5babb4891be41ed215978">IMP::algebra::get_rotation_taking_first_to_second()</a>, <a href="namespaceIMP_1_1bayesianem.html#aabe932ba1e24530c42cd830ca3fe7368">IMP::bayesianem::get_rotation_matrix()</a></td></tr>
72 <tr><td>@ref IMP::algebra::Segment3D</td><td><a href="classIMP_1_1algebra_1_1Cylinder3D.html#a4b84e7480a5b89054d7f4a7e401b86be">IMP::algebra::Cylinder3D::get_segment()</a>, <a href="classIMP_1_1algebra_1_1Line3D.html#ab153c557e037c6cde16a6feb795e1094">IMP::algebra::Line3D::get_segment_starting_at()</a>, <a href="classIMP_1_1algebra_1_1Segment3D.html#af5c43b376efc839be7570ffa3ee7825b">IMP::algebra::Segment3D::get_segment_3d_geometry()</a>, <a href="classIMP_1_1core_1_1RigidBodyTorque.html#a799b8bbd20a5f67426fc210e634d1e2d">IMP::core::RigidBodyTorque::extract_geometry()</a>, <a href="classIMP_1_1core_1_1RigidBodyTorque.html#a85217a609822f7be1c0d223ee5915d6c">IMP::core::RigidBodyTorque::get_geometry()</a>, <a href="classIMP_1_1core_1_1SurfaceGeometry.html#aaa78fdc2c5da8633308fb2bfbbdb27fa">IMP::core::SurfaceGeometry::get_segment()</a>, <a href="classIMP_1_1display_1_1SegmentGeometry.html#a6a445735008db1fa269f7846dcd40943">IMP::display::SegmentGeometry::get_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#ae4a0378baab9f9cb01c824f2ec6abc51">IMP::algebra::get_projected()</a>, <a href="namespaceIMP_1_1algebra.html#aba7bf2d5c4d78a8bcd21d63ced9c30ad">IMP::algebra::get_segment_connecting_first_to_second()</a></td></tr>
73 <tr><td>@ref IMP::algebra::SphereD</td><td><a href="namespaceIMP_1_1algebra.html#a4834da35487ef0d191fbc1a9371724eb">IMP::algebra::get_unit_sphere_kd()</a></td></tr>
74 <tr><td>@ref IMP::algebra::SpherePatch3D</td><td><a href="classIMP_1_1algebra_1_1SpherePatch3D.html#ab64eeda4f1106781fd57c3635e593b12">IMP::algebra::SpherePatch3D::get_sphere_patch_3d_geometry()</a></td></tr>
75 <tr><td>@ref IMP::algebra::Torus3D</td><td><a href="classIMP_1_1algebra_1_1Torus3D.html#a87d58fbd0252feffafd1fe4cb8b3ff0e">IMP::algebra::Torus3D::get_torus_3d_geometry()</a></td></tr>
76 <tr><td>@ref IMP::algebra::Transformation2D</td><td><a href="classIMP_1_1algebra_1_1Transformation2D.html#a800d5df3b998086944f787ecc52f7961">IMP::algebra::Transformation2D::get_inverse()</a>, <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_1algebra_1_1Transformation2D.html#ae8df067f66b477d27cbe964ce79f2e47">IMP::algebra::Transformation2D::operator=()</a>, <a href="namespaceIMP_1_1algebra.html#a5d83cbee6a0e0af8738adf030f364f6d">IMP::algebra::compose()</a>, <a href="namespaceIMP_1_1algebra.html#aea1eef3d3cd259593cb46677dc510c29">IMP::algebra::get_identity_transformation_2d()</a>, <a href="namespaceIMP_1_1algebra.html#ae3383dcf150f2e7d76498fecbc55dde9">IMP::algebra::get_rotation_about_point()</a>, <a href="namespaceIMP_1_1algebra.html#a86f1249e8339878f8b0be5b73b031ad8">IMP::algebra::get_transformation_aligning_pair()</a></td></tr>
77 <tr><td>@ref IMP::algebra::Transformation3D</td><td><a href="classIMP_1_1algebra_1_1ReferenceFrame3D.html#a9a62f89fecbe2d134d417038a0272b47">IMP::algebra::ReferenceFrame3D::get_inverse()</a>, <a href="classIMP_1_1algebra_1_1ReferenceFrame3D.html#a0ea138451954b123f39698f67903f5ce">IMP::algebra::ReferenceFrame3D::get_transformation_from()</a>, <a href="classIMP_1_1algebra_1_1ReferenceFrame3D.html#a1e26b1d2ad062f25d54acdceb4566976">IMP::algebra::ReferenceFrame3D::get_transformation_to()</a>, <a href="classIMP_1_1algebra_1_1Transformation3D.html#a11749e8dd0e6454fa96ffb626b39949b">IMP::algebra::Transformation3D::get_inverse()</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_1algebra_1_1Transformation3D.html#aba2227aad6a22f1cc213435a5352c09d">IMP::algebra::Transformation3D::operator=()</a>, <a href="classIMP_1_1core_1_1RigidBodyMember.html#a1b2de56684ac4d70d7bf185f037e5a45">IMP::core::RigidBodyMember::get_internal_transformation()</a>, <a href="classIMP_1_1core_1_1SurfaceSymmetryConstraint.html#af08750bac7efbb396bfc2c145ec92c77">IMP::core::SurfaceSymmetryConstraint::get_transformation()</a>, <a href="classIMP_1_1core_1_1TransformationSymmetry.html#ac7d02396d4e224e33d0886c2e74c9aaf">IMP::core::TransformationSymmetry::get_internal_transformation()</a>, <a href="classIMP_1_1core_1_1TransformationSymmetry.html#acff2b23995b0f4b50c6e4bd4574f54d0">IMP::core::TransformationSymmetry::get_transformation()</a>, <a href="classIMP_1_1core_1_1TransformationSymmetryMover.html#a88aadb8c8524ef400fc313a1be0441fa">IMP::core::TransformationSymmetryMover::get_random_rotation_about_point()</a>, <a href="classIMP_1_1domino_1_1NestedRigidBodyStates.html#a12dda30d492ea96fa4ef79242abc9f8c">IMP::domino::NestedRigidBodyStates::get_transformation()</a>, <a href="classIMP_1_1em2d_1_1PCAFitRestraint.html#a3e2c1070df0792b34ee59339a1e83ba3">IMP::em2d::PCAFitRestraint::get_transformation()</a>, <a href="classIMP_1_1em_1_1EnvelopeFitRestraint.html#a0de188aa0a38a78ec85e898b09b763f8">IMP::em::EnvelopeFitRestraint::get_transformation()</a>, <a href="classIMP_1_1em_1_1FittingSolutions.html#a46b28b36a52016e65285fba309ae3d5b">IMP::em::FittingSolutions::get_transformation()</a>, <a href="classIMP_1_1kinematics_1_1Joint.html#a3e4b1f2fa4792d300278ebda6c091b5d">IMP::kinematics::Joint::get_transformation_child_to_parent()</a>, <a href="classIMP_1_1kinematics_1_1Joint.html#ac31f8b3fff9145b88f5f9bb4d7b4b021">IMP::kinematics::Joint::get_transformation_child_to_parent_no_checks()</a>, <a href="classIMP_1_1kinematics_1_1RevoluteJoint.html#a7b6f7b757bf908b57e23c481bbfd06bf">IMP::kinematics::RevoluteJoint::get_rotation_about_joint_in_parent_coordinates()</a>, <a href="classIMP_1_1multifit_1_1FittingSolutionRecord.html#a42ee92b9006f1854437cbd96d8a03223">IMP::multifit::FittingSolutionRecord::get_dock_transformation()</a>, <a href="classIMP_1_1multifit_1_1FittingSolutionRecord.html#ae71f26cdfc8fdb94a616687222cb3a69">IMP::multifit::FittingSolutionRecord::get_fit_transformation()</a>, <a href="classIMP_1_1pmi1_1_1TransformMover.html#a7483092a2062e0c41f9a4a645762a05b">IMP::pmi1::TransformMover::get_last_transformation()</a>, <a href="classIMP_1_1pmi_1_1TransformMover.html#ab67712fe16e54febec5c8411013a7138">IMP::pmi::TransformMover::get_last_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#ae23cbf48e7c15d087775ede2d0d5d03d">IMP::spb::TransformationSymmetry::get_transformation()</a>, <a href="namespaceIMP_1_1algebra.html#ac1d0008195a1cf08b39038c2d7dc44a8">IMP::algebra::get_transformation_aligning_first_to_second()</a>, <a href="namespaceIMP_1_1algebra.html#af2121b116324f67ee007e4aef258555c">IMP::algebra::compose()</a>, <a href="namespaceIMP_1_1algebra.html#a5c675979c1dfb0467246764a7e1e2cbf">IMP::algebra::get_identity_transformation_3d()</a>, <a href="namespaceIMP_1_1algebra.html#a1b3cdecd88bb99e7cf34d42117199775">IMP::algebra::get_random_local_transformation()</a>, <a href="namespaceIMP_1_1algebra.html#a07063149bf0d6fd24bd5a1116d6b5115">IMP::algebra::get_rotation_about_point()</a>, <a href="namespaceIMP_1_1algebra.html#a95b9c2466fd2ba29cddff88efc887aff">IMP::algebra::get_transformation_3d()</a>, <a href="namespaceIMP_1_1algebra.html#a2e7851e2cdd810e68bb3235699c0f5ba">IMP::algebra::get_transformation_from_first_to_second()</a>, <a href="namespaceIMP_1_1algebra.html#a40b9b1290fa21102bda8255d8eb3c4d8">IMP::algebra::get_transformation_from_first_triangle_to_second()</a>, <a href="namespaceIMP_1_1atom.html#a72ceba6f0fb3a05221086170a55f4d46">IMP::atom::get_transformation_aligning_first_to_second()</a>, <a href="namespaceIMP_1_1bayesianem.html#a2b1cbbee53f6277e776c525a0ea8ff09">IMP::bayesianem::get_transformation_aligning_first_to_second()</a>, <a href="namespaceIMP_1_1cnmultifit.html#a2e56b936c9db947d7febcc93a1389a2f">IMP::cnmultifit::calc_transformation_around_axis()</a>, <a href="namespaceIMP_1_1core.html#a805c9dce8eeee77af7354cec81a3991a">IMP::core::get_transformation_aligning_first_to_second()</a></td></tr>
78 <tr><td>@ref IMP::algebra::Triangle3D</td><td><a href="classIMP_1_1display_1_1TriangleGeometry.html#a3fb7310b1377825c917fe57545de7c0a">IMP::display::TriangleGeometry::get_geometry()</a>, <a href="namespaceIMP_1_1algebra.html#a3619d60308d5ac5c78e601d1e6426dee">IMP::algebra::get_largest_triangle()</a>, <a href="namespaceIMP_1_1algebra.html#a8de5b9c2c7304487d384942301cdfde3">IMP::algebra::get_triangle_3d()</a></td></tr>
79 <tr><td>@ref IMP::algebra::UnitSimplexD_3-1_01_4</td><td><a href="classIMP_1_1isd_1_1Weight.html#a920b97218d9fd9e9c29439feb4209e04">IMP::isd::Weight::get_unit_simplex()</a></td></tr>
80 <tr><td>@ref IMP::algebra::VectorD</td><td><a href="classIMP_1_1algebra_1_1BoundingBoxD.html#aa31f8295a3ecc17ce469438df678617b">IMP::algebra::BoundingBoxD::get_corner()</a>, <a href="classIMP_1_1algebra_1_1DefaultEmbeddingD.html#a42f36edf378dc3cb21d8b8320b2262d9">IMP::algebra::DefaultEmbeddingD::get_center()</a>, <a href="classIMP_1_1algebra_1_1DefaultEmbeddingD.html#a584a87ad7db962f804e65beb46356e8a">IMP::algebra::DefaultEmbeddingD::get_center()</a>, <a href="classIMP_1_1algebra_1_1DefaultEmbeddingD.html#a339984d8e099583b0cadaad5e6bf47c8">IMP::algebra::DefaultEmbeddingD::get_origin()</a>, <a href="classIMP_1_1algebra_1_1DefaultEmbeddingD.html#a243f6b777d32aa49cc8e585edfaf79f6">IMP::algebra::DefaultEmbeddingD::get_unit_cell()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#a6f4d8f177ef76a4b4f05dbc3e26489f1">IMP::algebra::LogEmbeddingD::get_center()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#a5cb83dd94de983716f6591c717d1b47a">IMP::algebra::LogEmbeddingD::get_center()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#a3a3ab44f98c54855268ef87cb10080b9">IMP::algebra::LogEmbeddingD::get_origin()</a>, <a href="classIMP_1_1algebra_1_1LogEmbeddingD.html#adb20715e237723bf9de57872e11fb515">IMP::algebra::LogEmbeddingD::get_unit_cell()</a>, <a href="classIMP_1_1algebra_1_1PrincipalComponentAnalysisD.html#a514a16c972ceea192e39bb308896e28d">IMP::algebra::PrincipalComponentAnalysisD::get_centroid()</a>, <a href="classIMP_1_1algebra_1_1PrincipalComponentAnalysisD.html#a87432e5b75325d5988dddc9c69d0a0e9">IMP::algebra::PrincipalComponentAnalysisD::get_principal_component()</a>, <a href="classIMP_1_1algebra_1_1PrincipalComponentAnalysisD.html#a0ba09fe87df97ebef41f58c73ffaa710">IMP::algebra::PrincipalComponentAnalysisD::get_principal_components()</a>, <a href="classIMP_1_1algebra_1_1PrincipalComponentAnalysisD.html#a8bc34c872d7d80a7693bea12b91dc530">IMP::algebra::PrincipalComponentAnalysisD::get_principal_values()</a>, <a href="classIMP_1_1algebra_1_1SphereD.html#a66db928fc3b3bdcf01e891ba3507a3a0">IMP::algebra::SphereD::get_center()</a>, <a href="classIMP_1_1algebra_1_1UnitSimplexBaseD.html#a60cc3282f9f54822abad19cd7fc970ce">IMP::algebra::UnitSimplexBaseD::get_barycenter()</a>, <a href="classIMP_1_1algebra_1_1VectorD.html#ae812e3f853fb6b2aa3c28be0cac1068a">IMP::algebra::VectorD::get_unit_vector()</a>, <a href="classIMP_1_1algebra_1_1VectorD.html#a78101a1171a91a39f8fa48c21fc88b02">IMP::algebra::VectorD::operator*()</a>, <a href="classIMP_1_1algebra_1_1VectorD.html#a04bc1569ddb15624437312ac6dcea370">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#a465db28829855dc1e2b4130ccf4970ad">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_1algebra_1_1VectorD.html#a70fee54ca37221cefb8dd755d51dbd21">IMP::algebra::VectorD::operator/()</a>, <a href="classIMP_1_1algebra_1_1VectorD.html#a3e0204ea98d9a5067400d54e3e48029a">IMP::algebra::VectorD::operator/=()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#aa571733d4c574e3874777daef1f10d86">IMP::core::RigidBody::get_rotational_derivatives()</a>, <a href="classIMP_1_1example_1_1ExampleTemplateClassD.html#a86ede654e64072869b8c25f23bfde3d6">IMP::example::ExampleTemplateClassD::get_point()</a>, <a href="classIMP_1_1multifit_1_1GeometricHash.html#a27b2114018cc42b24e194589452e6e23">IMP::multifit::GeometricHash::from_bucket()</a>, <a href="classIMP_1_1statistics_1_1HistogramD.html#a3f95e629bfea515462d2554860205422">IMP::statistics::HistogramD::get_mean()</a>, <a href="classIMP_1_1statistics_1_1HistogramD.html#aa8f8a40723844f8f480074771dc3f0d2">IMP::statistics::HistogramD::get_standard_deviation()</a>, <a href="namespaceIMP_1_1algebra.html#a13112e2dae882f9c03a368a64986c198">IMP::algebra::get_random_vector_in()</a>, <a href="namespaceIMP_1_1algebra.html#a15788395c438b5a87b99281375c9e1e7">IMP::algebra::get_random_vector_on_unit_sphere()</a>, <a href="namespaceIMP_1_1algebra.html#a92b4877cc788e114ebc983c050f6218e">IMP::algebra::get_basis_vector_kd()</a>, <a href="namespaceIMP_1_1algebra.html#ab2737562aba5b6a92a38c231538ce2cc">IMP::algebra::get_ones_vector_kd()</a>, <a href="namespaceIMP_1_1algebra.html#aee99e2fdbca505bd36a478c9eb6ca171">IMP::algebra::get_zero_vector_kd()</a></td></tr>
81 </table>
82 # IMP.atom # {#factory_index_atom}
83 <table><tr>
84 <th>Class</th><th>Factories</th></tr>
85 <tr><td>@ref IMP::atom::Angle</td><td><a href="classIMP_1_1atom_1_1Angle.html#ac05c3945ed23762560f6d065d2626981">IMP::atom::Angle::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Angle.html#a17d8aa0a63057ee10bdea7d5df10e8a7">IMP::atom::Angle::setup_particle()</a></td></tr>
86 <tr><td>@ref IMP::atom::Atom</td><td><a href="classIMP_1_1atom_1_1Atom.html#a8673b3453596560cdbe50d3dbf4815a0">IMP::atom::Atom::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Atom.html#a19755ddf59764ee0ef0934fa6d5527f3">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_1Atom.html#ae6bddaeb0a8fd370d66c5a00414bcbf9">IMP::atom::Atom::setup_particle()</a>, <a href="classIMP_1_1atom_1_1CHARMMBondEndpoint.html#a5271a836eccdc72f7763d32a0af46573">IMP::atom::CHARMMBondEndpoint::get_atom()</a>, <a href="namespaceIMP_1_1atom.html#a899927712a6b9ae00aa8875407f5311a">IMP::atom::get_atom()</a>, <a href="namespaceIMP_1_1kinematics.html#a1d074d177f3e9b19fef1233c4c928f77">IMP::kinematics::find_atom()</a>, <a href="namespaceIMP_1_1kinematics.html#a43aefa0b49fa5b99d235cbcf1170d685">IMP::kinematics::get_ca_atom()</a></td></tr>
87 <tr><td>@ref IMP::atom::AtomType</td><td><a href="classIMP_1_1atom_1_1Atom.html#a867718443d203a8fdf69d0518b30fb1b">IMP::atom::Atom::get_atom_type()</a>, <a href="namespaceIMP_1_1atom.html#af4a6c11848aec861d0ef55068cf6261a">IMP::atom::get_atom_type()</a>, <a href="namespaceIMP_1_1atom.html#a02a38fbf0485b7d9642be56a9ee6bdc1">IMP::atom::add_atom_type()</a></td></tr>
88 <tr><td>@ref IMP::atom::Bond</td><td><a href="classIMP_1_1atom_1_1BondGraph.html#a323caace710dae515e4db435c6f65e3e">IMP::atom::BondGraph::get_bond()</a>, <a href="classIMP_1_1atom_1_1Bonded.html#ac6814fc8a4b9c0f53afe43fe02b1ea0b">IMP::atom::Bonded::get_bond()</a>, <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>, <a href="namespaceIMP_1_1kinematics.html#a1917c6e073639123db3b09d24d8b6dc6">IMP::kinematics::create_bond()</a></td></tr>
89 <tr><td>@ref IMP::atom::Bonded</td><td><a href="classIMP_1_1atom_1_1Bond.html#a8a5ba84484e72d168d03b0ab4c50c77e">IMP::atom::Bond::get_bonded()</a>, <a href="classIMP_1_1atom_1_1Bonded.html#a3c4e2968dfd4bd247f4661d874d63496">IMP::atom::Bonded::get_bonded()</a>, <a href="classIMP_1_1atom_1_1Bonded.html#ac867bddf7a6ae514918d98ef780f49df">IMP::atom::Bonded::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Bonded.html#a48b39e583b48f1dd403a80d6aac5e2f1">IMP::atom::Bonded::setup_particle()</a></td></tr>
90 <tr><td>@ref IMP::atom::BrownianDynamics</td><td><a href="classIMP_1_1npctransport_1_1SimulationData.html#a86c45294f3f86f28f66d0ec3d047e71b">IMP::npctransport::SimulationData::get_bd()</a></td></tr>
91 <tr><td>@ref IMP::atom::CHARMMAtom</td><td><a href="classIMP_1_1atom_1_1CHARMMAtom.html#a52d7b1b61cf3bd6ceb719f5c32e482e0">IMP::atom::CHARMMAtom::setup_particle()</a>, <a href="classIMP_1_1atom_1_1CHARMMAtom.html#abe9de32622eb206706e744ad97412084">IMP::atom::CHARMMAtom::setup_particle()</a></td></tr>
92 <tr><td>@ref IMP::atom::CHARMMAtomTopology</td><td><a href="classIMP_1_1atom_1_1CHARMMResidueTopologyBase.html#afadfc33ed67175c434cad952d0d11307">IMP::atom::CHARMMResidueTopologyBase::get_atom()</a>, <a href="classIMP_1_1atom_1_1CHARMMResidueTopologyBase.html#a91fff9329d2a36aa42719d443fb5fc35">IMP::atom::CHARMMResidueTopologyBase::get_atom()</a>, <a href="classIMP_1_1atom_1_1CHARMMResidueTopologyBase.html#a42f75fbdc90c3d0ffc6da888c8a05d26">IMP::atom::CHARMMResidueTopologyBase::get_atom()</a></td></tr>
93 <tr><td>@ref IMP::atom::CHARMMBondEndpoint</td><td><a href="classIMP_1_1atom_1_1CHARMMConnection.html#a5b2b5a53429c6cb8335145581de19850">IMP::atom::CHARMMConnection::get_endpoint()</a></td></tr>
94 <tr><td>@ref IMP::atom::CHARMMConnection</td><td><a href="classIMP_1_1atom_1_1CHARMMResidueTopologyBase.html#add4b79ec748e743f8c1517428af553a6">IMP::atom::CHARMMResidueTopologyBase::get_angle()</a>, <a href="classIMP_1_1atom_1_1CHARMMResidueTopologyBase.html#a55335589fdb6c359612a1fd37f8658e8">IMP::atom::CHARMMResidueTopologyBase::get_bond()</a>, <a href="classIMP_1_1atom_1_1CHARMMResidueTopologyBase.html#ade44e2c67bf8499b944f2574db441373">IMP::atom::CHARMMResidueTopologyBase::get_dihedral()</a>, <a href="classIMP_1_1atom_1_1CHARMMResidueTopologyBase.html#aa4f8390a6d5efc7d3a94689490a32808">IMP::atom::CHARMMResidueTopologyBase::get_improper()</a></td></tr>
95 <tr><td>@ref IMP::atom::CHARMMIdealResidueTopology</td><td><a href="classIMP_1_1atom_1_1CHARMMParameters.html#a93c5e6fbf6e839294e91ec2a179f74af">IMP::atom::CHARMMParameters::get_residue_topology()</a></td></tr>
96 <tr><td>@ref IMP::atom::CHARMMInternalCoordinate</td><td><a href="classIMP_1_1atom_1_1CHARMMResidueTopologyBase.html#ad610c4fa66857daaad66e9ab60c548c1">IMP::atom::CHARMMResidueTopologyBase::get_internal_coordinate()</a></td></tr>
97 <tr><td>@ref IMP::atom::CHARMMParameters</td><td><a href="classIMP_1_1atom_1_1CHARMMTopology.html#a82e86edc5d2515f3730f7e6b0bebfe9b">IMP::atom::CHARMMTopology::get_parameters()</a>, <a href="namespaceIMP_1_1atom.html#a7150f310d5f5da0275933bfbe4c68d1c">IMP::atom::get_all_atom_CHARMM_parameters()</a>, <a href="namespaceIMP_1_1atom.html#a4ab4248f452a6a9ccf43447d83f3e685">IMP::atom::get_heavy_atom_CHARMM_parameters()</a></td></tr>
98 <tr><td>@ref IMP::atom::CHARMMPatch</td><td><a href="classIMP_1_1atom_1_1CHARMMParameters.html#a7c83e58f1cea31a16484c15f8762635b">IMP::atom::CHARMMParameters::get_patch()</a></td></tr>
99 <tr><td>@ref IMP::atom::CHARMMResidueTopology</td><td><a href="classIMP_1_1atom_1_1CHARMMSegmentTopology.html#a8e36b0b1c1bf882994cc5c7b0cfc782f">IMP::atom::CHARMMSegmentTopology::get_residue()</a></td></tr>
100 <tr><td>@ref IMP::atom::CHARMMSegmentTopology</td><td><a href="classIMP_1_1atom_1_1CHARMMTopology.html#aae6f4e51cdf79001c102f679ebfc0a32">IMP::atom::CHARMMTopology::get_segment()</a></td></tr>
101 <tr><td>@ref IMP::atom::CHARMMTopology</td><td><a href="classIMP_1_1atom_1_1CHARMMParameters.html#aab56534fc18ba3715778af3f2aea8073">IMP::atom::CHARMMParameters::create_topology()</a></td></tr>
102 <tr><td>@ref IMP::atom::CenterOfMass</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#abb9e90bc8fa7641d313efc5f4d4d0007">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_1CenterOfMass.html#a7860b1329b505ca42e5fed2358c8c7ab">IMP::atom::CenterOfMass::setup_particle()</a></td></tr>
103 <tr><td>@ref IMP::atom::Chain</td><td><a href="classIMP_1_1atom_1_1Chain.html#a07e5b5a1bfa7e0c8ac52799bec365e30">IMP::atom::Chain::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Chain.html#a492ae12573ab53631b3322c0b07388b1">IMP::atom::Chain::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Chain.html#ade50cc0def80bf718f86eb89c2a9f53f">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 href="classIMP_1_1atom_1_1Chain.html#a83c2f2c4f3fa7a0a69d165700a2c26e1">IMP::atom::Chain::setup_particle()</a>, <a href="namespaceIMP_1_1atom.html#a13fb268fe2be9e83bbd9a1a2197499ef">IMP::atom::get_chain()</a></td></tr>
104 <tr><td>@ref IMP::atom::ChainType</td><td><a href="classIMP_1_1atom_1_1Chain.html#a4f4cd1aeab43eb3bc0959670616bae8c">IMP::atom::Chain::get_chain_type()</a></td></tr>
105 <tr><td>@ref IMP::atom::Charged</td><td><a href="classIMP_1_1atom_1_1Charged.html#adb5ce2ba7901a433614953e24551e988">IMP::atom::Charged::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Charged.html#a971711256a09256bcd41352da02036c8">IMP::atom::Charged::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Charged.html#a95980772fc84fe747b0b3565ed866967">IMP::atom::Charged::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Charged.html#a031ba65f4e81801e283a8b78d2e480a9">IMP::atom::Charged::setup_particle()</a></td></tr>
106 <tr><td>@ref IMP::atom::Copy</td><td><a href="classIMP_1_1atom_1_1Copy.html#a8c73c9318f588816caae8e805afa1cb0">IMP::atom::Copy::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Copy.html#a20efdc7696c33facc3afa285ecdb517a">IMP::atom::Copy::setup_particle()</a></td></tr>
107 <tr><td>@ref IMP::atom::Diffusion</td><td><a href="classIMP_1_1atom_1_1Diffusion.html#a0e3785a33c33251b7e61aa8cca9a6caa">IMP::atom::Diffusion::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Diffusion.html#a40959289e2ad022478caaebac5516477">IMP::atom::Diffusion::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Diffusion.html#ac6c7ca090143132139da1bc21398f3c7">IMP::atom::Diffusion::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Diffusion.html#a8b514700fd4a4024491d5ddca3755618">IMP::atom::Diffusion::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Diffusion.html#a25edd856dcbfe27bb6d3cbf197b30c66">IMP::atom::Diffusion::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Diffusion.html#a88b14a99695e62f4ff865850f12f3ab4">IMP::atom::Diffusion::setup_particle()</a></td></tr>
108 <tr><td>@ref IMP::atom::Dihedral</td><td><a href="classIMP_1_1atom_1_1Dihedral.html#aaac67bd8794d274653adce93501dca6c">IMP::atom::Dihedral::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Dihedral.html#aba8bf926754ed9a62e899e93f951b96c">IMP::atom::Dihedral::setup_particle()</a></td></tr>
109 <tr><td>@ref IMP::atom::Domain</td><td><a href="classIMP_1_1atom_1_1Domain.html#af7ac157cfb506e8ffb2d94311721aa09">IMP::atom::Domain::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Domain.html#a3a0129647c98c031a50340344fc708f2">IMP::atom::Domain::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Domain.html#aaeac693d6899512eb3b9e944c3e725f6">IMP::atom::Domain::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Domain.html#a5b65bdc3b41b2bd8be044f9b1181179b">IMP::atom::Domain::setup_particle()</a></td></tr>
110 <tr><td>@ref IMP::atom::ElementTable</td><td><a href="namespaceIMP_1_1atom.html#a5d562e4bead78d6882240505705d996e">IMP::atom::get_element_table()</a></td></tr>
111 <tr><td>@ref IMP::atom::Fragment</td><td><a href="classIMP_1_1atom_1_1Fragment.html#a337e229a5f80fbf81e2b2cdf2cb31d7b">IMP::atom::Fragment::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Fragment.html#abb3a0ce46df3dd4c46a27ffc678dc78d">IMP::atom::Fragment::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#abd1e359b8a8fe0538103a32c5e744ce3">IMP::atom::Fragment::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Fragment.html#ae0d090acdd339e0b89cc2f54d8bf2cf2">IMP::atom::Fragment::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Fragment.html#ab4aeeb70f31211becace2e0b5f8185be">IMP::atom::Fragment::setup_particle()</a></td></tr>
112 <tr><td>@ref IMP::atom::Hierarchy</td><td><a href="classIMP_1_1atom_1_1CHARMMTopology.html#a3d3e69d8d1d90294c5cedd6c0f33ca2c">IMP::atom::CHARMMTopology::create_hierarchy()</a>, <a href="classIMP_1_1atom_1_1Hierarchy.html#a4c26db6d0879ccf5d7fc72c30e9ec54e">IMP::atom::Hierarchy::get_child()</a>, <a href="classIMP_1_1atom_1_1Hierarchy.html#a3fa6740c3fcbf678ce64fb1db22a832e">IMP::atom::Hierarchy::get_parent()</a>, <a href="classIMP_1_1atom_1_1Hierarchy.html#a56ea228dde7abf072de82f4d9c82b629">IMP::atom::Hierarchy::setup_particle()</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#aea222a9dc8798d5ac1bcc492b73e72dd">IMP::atom::Hierarchy::create_fragment()</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_1Representation.html#af2cb8658482ff38369223b34bbb70d64">IMP::atom::Representation::get_representation()</a>, <a href="classIMP_1_1npctransport_1_1FGChain.html#a2c9f4671ad24c6175cf9f8f3aa8b4029">IMP::npctransport::FGChain::get_root()</a>, <a href="classIMP_1_1npctransport_1_1SimulationData.html#afd8b183920e29cec1950ab9e322b223d">IMP::npctransport::SimulationData::get_root()</a>, <a href="classIMP_1_1npctransport_1_1SimulationData.html#aa2c1343216d8134ade6e414c511440f8">IMP::npctransport::SimulationData::get_root_of_type()</a>, <a href="namespaceIMP_1_1atom.html#a1b4c863b0fefde1c1d95cdf6fed794a8">IMP::atom::create_simplified_along_backbone()</a>, <a href="namespaceIMP_1_1atom.html#af12315103e56599289223816dc3b3aeb">IMP::atom::create_simplified_along_backbone()</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#aaa55b95e08377207f065cbab8bec4399">IMP::atom::create_protein()</a>, <a href="namespaceIMP_1_1atom.html#a0d69cdcf058b017505e1b490054d48ff">IMP::atom::create_protein()</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#a2cadcc607aa4c1f8b1ec4c0c8d493312">IMP::atom::get_next_residue()</a>, <a href="namespaceIMP_1_1atom.html#ad329e5c66a8de2f49304492c5a690d90">IMP::atom::get_previous_residue()</a>, <a href="namespaceIMP_1_1atom.html#a2efb72426efcdea0d7566faa78d793ae">IMP::atom::read_mmcif()</a>, <a href="namespaceIMP_1_1atom.html#afa75d21223f20565d1cc585ec7ebc9af">IMP::atom::read_pdb_or_mmcif()</a>, <a href="namespaceIMP_1_1multifit.html#a3ae2f2b63f2b07f548e4fd095871d9b8">IMP::multifit::create_coarse_molecule_from_density()</a></td></tr>
113 <tr><td>@ref IMP::atom::LennardJones</td><td><a href="classIMP_1_1atom_1_1LennardJones.html#a851493748bc6faceacc22fb778cc1f74">IMP::atom::LennardJones::setup_particle()</a>, <a href="classIMP_1_1atom_1_1LennardJones.html#ac37550fd4cfdf388851c55ae21fcc249">IMP::atom::LennardJones::setup_particle()</a>, <a href="classIMP_1_1atom_1_1LennardJones.html#abce39f0dd97e7c13f9e614bbcec0852a">IMP::atom::LennardJones::setup_particle()</a>, <a href="classIMP_1_1atom_1_1LennardJones.html#a94fb9e0c9eeb99562203b1cf6e326929">IMP::atom::LennardJones::setup_particle()</a></td></tr>
114 <tr><td>@ref IMP::atom::Mass</td><td><a href="classIMP_1_1atom_1_1Mass.html#a5757986c617da8a3cb213859d3bd1550">IMP::atom::Mass::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Mass.html#a37c36c11794dfd6fd8e8e0d0f30cdbfd">IMP::atom::Mass::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Mass.html#a87a46b56fe6fab7402f2d4655bc0b04c">IMP::atom::Mass::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Mass.html#a4b111729975b621a095fe54baa1b0e52">IMP::atom::Mass::setup_particle()</a></td></tr>
115 <tr><td>@ref IMP::atom::Molecule</td><td><a href="classIMP_1_1atom_1_1Molecule.html#ace192fc31a17e97929f1949e361361a5">IMP::atom::Molecule::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Molecule.html#a9a912c3fcb8d6342c8981c02e9fcddc7">IMP::atom::Molecule::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#a53db57e350a92e258a5ea710a9c66c46">IMP::atom::Molecule::setup_particle()</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></td></tr>
116 <tr><td>@ref IMP::atom::PDBSelector</td><td><a href="namespaceIMP_1_1atom.html#af8a720ac93e90e948bd016b3e367663d">IMP::atom::get_default_pdb_selector()</a></td></tr>
117 <tr><td>@ref IMP::atom::Representation</td><td><a href="classIMP_1_1atom_1_1Representation.html#a76f87d9a914ba926d45f6cfc4914daf5">IMP::atom::Representation::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Representation.html#ab81427610a3cbd3ece06865f87aeebc2">IMP::atom::Representation::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Representation.html#a6cc5ba59d9368c4318d042ae181158a0">IMP::atom::Representation::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Representation.html#a068b43980eeac360524ab737999e5539">IMP::atom::Representation::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Representation.html#a841dbf09f7b35495a2611e57b423cf46">IMP::atom::Representation::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Representation.html#a4d969beb1d0fef460d6c8b10ad894838">IMP::atom::Representation::setup_particle()</a>, <a href="namespaceIMP_1_1atom.html#a48aba7ec117050a9a4d05f11266fa56d">IMP::atom::get_representation()</a></td></tr>
118 <tr><td>@ref IMP::atom::Residue</td><td><a href="classIMP_1_1atom_1_1Residue.html#aa8472267328ddc075dba74e16e71900b">IMP::atom::Residue::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Residue.html#aea91aaba26fc6ea760b049773023d484">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#a08896e883624f8b7472f2a121ec77e3c">IMP::atom::Residue::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Residue.html#ae6e37096c8b7bf5da10bf712ef93623a">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_1Residue.html#a9c559fdff64ef234dc191d4f49b8f94d">IMP::atom::Residue::setup_particle()</a>, <a href="classIMP_1_1atom_1_1Residue.html#ace3fac09ee49d5c1c13f4dde0d291783">IMP::atom::Residue::setup_particle()</a>, <a href="namespaceIMP_1_1atom.html#a1b9a562a6a9548c3e85047d8fe53183d">IMP::atom::get_residue()</a>, <a href="namespaceIMP_1_1kinematics.html#aecb446da0c7ec323296acebe02e5c644">IMP::kinematics::find_residue()</a></td></tr>
119 <tr><td>@ref IMP::atom::ResidueType</td><td><a href="classIMP_1_1atom_1_1CHARMMParameters.html#ad3151d18a8caed725aede9f667ea3a8d">IMP::atom::CHARMMParameters::parse_residue_line()</a>, <a href="classIMP_1_1atom_1_1Residue.html#ab4ca594e94407184dadbcf3f0fe4f9c7">IMP::atom::Residue::get_residue_type()</a>, <a href="namespaceIMP_1_1atom.html#a7bc45846fa709afb3ea73f2e9a3ad923">IMP::atom::get_residue_type()</a>, <a href="namespaceIMP_1_1atom.html#a4069a6db716b4d4a269df0aed8db5287">IMP::atom::get_residue_type()</a></td></tr>
120 <tr><td>@ref IMP::atom::RigidBodyDiffusion</td><td><a href="classIMP_1_1atom_1_1RigidBodyDiffusion.html#a0a3992fd48ae9e49202072809fe966b8">IMP::atom::RigidBodyDiffusion::setup_particle()</a>, <a href="classIMP_1_1atom_1_1RigidBodyDiffusion.html#a69475a1440fb159cd565aec4d0d623e0">IMP::atom::RigidBodyDiffusion::setup_particle()</a></td></tr>
121 <tr><td>@ref IMP::atom::SecondaryStructureResidue</td><td><a href="classIMP_1_1atom_1_1SecondaryStructureResidue.html#a092634d858d51527158116ce92a8036e">IMP::atom::SecondaryStructureResidue::setup_particle()</a>, <a href="classIMP_1_1atom_1_1SecondaryStructureResidue.html#a61bf918d96f0302c6030b00a16150d19">IMP::atom::SecondaryStructureResidue::setup_particle()</a>, <a href="classIMP_1_1atom_1_1SecondaryStructureResidue.html#aea26f9048af0cd495d711e7a5c842673">IMP::atom::SecondaryStructureResidue::setup_particle()</a>, <a href="namespaceIMP_1_1atom.html#a26d5bf29f960fc1cc1816a3d9fae4da5">IMP::atom::setup_coarse_secondary_structure_residue()</a></td></tr>
122 <tr><td>@ref IMP::atom::Selection</td><td><a href="classIMP_1_1atom_1_1Selection.html#ab6e1290b1f07537af66b8438e9423447">IMP::atom::Selection::create_clone()</a></td></tr>
123 <tr><td>@ref IMP::atom::Simulator</td><td><a href="classIMP_1_1npctransport_1_1ParticleTransportStatisticsOptimizerState.html#a65f5ee167a8b5382747947a1b5bb9412">IMP::npctransport::ParticleTransportStatisticsOptimizerState::get_owner()</a></td></tr>
124 <tr><td>@ref IMP::atom::SoapPairFilter</td><td><a href="classIMP_1_1atom_1_1OrientedSoapPairScore.html#a675428737e77f20be5bba87c8996d900">IMP::atom::OrientedSoapPairScore::get_pair_filter()</a></td></tr>
125 <tr><td>@ref IMP::atom::State</td><td><a href="classIMP_1_1atom_1_1State.html#a03f86cac6084d551031fcfa272a48f66">IMP::atom::State::setup_particle()</a>, <a href="classIMP_1_1atom_1_1State.html#a0a51d7b2bbd064658727d38e57b7bd1b">IMP::atom::State::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#a206f34ae39850d759e718200ccc35f8e">IMP::atom::State::setup_particle()</a></td></tr>
126 <tr><td>@ref IMP::atom::StereochemistryPairFilter</td><td><a href="classIMP_1_1atom_1_1CHARMMStereochemistryRestraint.html#ae0b7827cf358f1b32252b217af963637">IMP::atom::CHARMMStereochemistryRestraint::get_full_pair_filter()</a>, <a href="classIMP_1_1atom_1_1CHARMMStereochemistryRestraint.html#a96a84aff0d2d9ea0401ae5cfb15c561f">IMP::atom::CHARMMStereochemistryRestraint::get_pair_filter()</a></td></tr>
127 <tr><td>@ref IMP::atom::StructureSource</td><td><a href="classIMP_1_1atom_1_1StructureSource.html#abd4ead56962d212686113d174898c9b6">IMP::atom::StructureSource::setup_particle()</a>, <a href="classIMP_1_1atom_1_1StructureSource.html#a1d45e96d03ff8d5446553497818202bd">IMP::atom::StructureSource::setup_particle()</a></td></tr>
128 <tr><td>@ref IMP::atom::TAMDCentroid</td><td><a href="classIMP_1_1atom_1_1TAMDCentroid.html#a0798b30e5e80229807b08bbdcd8502a6">IMP::atom::TAMDCentroid::setup_particle()</a>, <a href="classIMP_1_1atom_1_1TAMDCentroid.html#a401b39dc58678d1960b6767d7328463c">IMP::atom::TAMDCentroid::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#ab1ba7b5fde2624f005631e0fbd2fb2fc">IMP::atom::TAMDCentroid::setup_particle()</a></td></tr>
129 <tr><td>@ref IMP::atom::TAMDParticle</td><td><a href="classIMP_1_1atom_1_1TAMDParticle.html#a33955f9318b82c7502ac2e3261846c5f">IMP::atom::TAMDParticle::setup_particle()</a>, <a href="classIMP_1_1atom_1_1TAMDParticle.html#a6cf72235c32b3575299182c2f3299db1">IMP::atom::TAMDParticle::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#a35e3a2c3b7658f1d93ad5518e4090adf">IMP::atom::TAMDParticle::setup_particle()</a></td></tr>
130 </table>
131 # IMP.container # {#factory_index_container}
132 <table><tr>
133 <th>Class</th><th>Factories</th></tr>
134 <tr><td>@ref IMP::container::DynamicListPairContainer</td><td><a href="classIMP_1_1container_1_1DistributePairsScoreState.html#a905137252f92c0e5df1ce56f59dcc8ef">IMP::container::DistributePairsScoreState::add_predicate()</a></td></tr>
135 <tr><td>@ref IMP::container::DynamicListQuadContainer</td><td><a href="classIMP_1_1container_1_1DistributeQuadsScoreState.html#a5fd9074e32c95ec367b06b5a40fd72ab">IMP::container::DistributeQuadsScoreState::add_predicate()</a></td></tr>
136 <tr><td>@ref IMP::container::DynamicListSingletonContainer</td><td><a href="classIMP_1_1container_1_1DistributeSingletonsScoreState.html#aace32527df07ef4c4e84dfd4f96ac46c">IMP::container::DistributeSingletonsScoreState::add_predicate()</a></td></tr>
137 <tr><td>@ref IMP::container::DynamicListTripletContainer</td><td><a href="classIMP_1_1container_1_1DistributeTripletsScoreState.html#a73b67981a22dc16bb6dc985ff85e26ae">IMP::container::DistributeTripletsScoreState::add_predicate()</a></td></tr>
138 <tr><td>@ref IMP::container::MinimumPairRestraint</td><td><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#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>
139 <tr><td>@ref IMP::container::PairContainerSet</td><td><a href="classIMP_1_1container_1_1PairContainerSet.html#ad73b337edcd61026138832c505587c47">IMP::container::PairContainerSet::get_set()</a></td></tr>
140 <tr><td>@ref IMP::container::PredicatePairsRestraint</td><td><a href="classIMP_1_1npctransport_1_1Scoring.html#a4652f839b606cd0de7efbe2220510a22">IMP::npctransport::Scoring::create_predicates_pair_restraint()</a>, <a href="classIMP_1_1npctransport_1_1Scoring.html#a44d0aff387c0e7dad1ad1c6c9e5985e0">IMP::npctransport::Scoring::get_predicates_pair_restraint()</a></td></tr>
141 <tr><td>@ref IMP::container::QuadContainerSet</td><td><a href="classIMP_1_1container_1_1QuadContainerSet.html#ac2a1a54aa5fed2f2d5394c0a4734229c">IMP::container::QuadContainerSet::get_set()</a></td></tr>
142 <tr><td>@ref IMP::container::SingletonContainerSet</td><td><a href="classIMP_1_1container_1_1SingletonContainerSet.html#a3053d32ea57216bae48fa420198bcf95">IMP::container::SingletonContainerSet::get_set()</a></td></tr>
143 <tr><td>@ref IMP::container::TripletContainerSet</td><td><a href="classIMP_1_1container_1_1TripletContainerSet.html#a5650d9c2999046961450a95b98d1ff26">IMP::container::TripletContainerSet::get_set()</a></td></tr>
144 </table>
145 # IMP.core # {#factory_index_core}
146 <table><tr>
147 <th>Class</th><th>Factories</th></tr>
148 <tr><td>@ref IMP::core::Centroid</td><td><a href="classIMP_1_1core_1_1Centroid.html#a71dff4dacdc4651833dcb63ed8eb5cab">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_1Centroid.html#aead8e0c785a7cc0e9ad18e1fb6391733">IMP::core::Centroid::setup_particle()</a>, <a href="classIMP_1_1core_1_1Centroid.html#a25fd05c17e081907c3059e5522c4db0e">IMP::core::Centroid::setup_particle()</a></td></tr>
149 <tr><td>@ref IMP::core::ClusterProvenance</td><td><a href="classIMP_1_1core_1_1ClusterProvenance.html#a6fcd618833c13657f737995b6f2d3e0e">IMP::core::ClusterProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1ClusterProvenance.html#ae7791d3b41ad5eecde6850eb9b2e8e40">IMP::core::ClusterProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1ClusterProvenance.html#addbd2f340c0408c64e44912f3b485781">IMP::core::ClusterProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1ClusterProvenance.html#aa29252602e26c8b37c675ab22448f344">IMP::core::ClusterProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1ClusterProvenance.html#a3e9c8cdb8f40757378436966d1e06b3c">IMP::core::ClusterProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1ClusterProvenance.html#aa6380944d4032f5a39ddd935a4597f5f">IMP::core::ClusterProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1ClusterProvenance.html#a58511719fbced1a3c8bbc825e986836d">IMP::core::ClusterProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1ClusterProvenance.html#a8bcfa300fc8ea8a70f93105572b0afe1">IMP::core::ClusterProvenance::setup_particle()</a></td></tr>
150 <tr><td>@ref IMP::core::CombineProvenance</td><td><a href="classIMP_1_1core_1_1CombineProvenance.html#aabbca68b96cabd237a38d20d5e148d07">IMP::core::CombineProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1CombineProvenance.html#afe1e1ec321f847898b30e1cc6a87233b">IMP::core::CombineProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1CombineProvenance.html#a6e3146d332826da64f5eb803b327d018">IMP::core::CombineProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1CombineProvenance.html#a03cf92b0778a2a99ecfe40102e480b2b">IMP::core::CombineProvenance::setup_particle()</a></td></tr>
151 <tr><td>@ref IMP::core::Cover</td><td><a href="classIMP_1_1core_1_1Cover.html#a645deb661b5a3cb58951bec80c25d38b">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_1Cover.html#a2ffc3b9b8ad6de417af9a329862e2216">IMP::core::Cover::setup_particle()</a>, <a href="classIMP_1_1core_1_1Cover.html#a18b4345f9d9ea754ab7d5dd909e1d85a">IMP::core::Cover::setup_particle()</a></td></tr>
152 <tr><td>@ref IMP::core::DataObject</td><td><a href="classIMP_1_1multifit_1_1ComplementarityRestraint.html#ad6aba49b9073b20c3338cd1542ae9500">IMP::multifit::ComplementarityRestraint::get_grid_object()</a></td></tr>
153 <tr><td>@ref IMP::core::Direction</td><td><a href="classIMP_1_1core_1_1Direction.html#a5daafe8c45336693253ed1b12a2f544b">IMP::core::Direction::setup_particle()</a>, <a href="classIMP_1_1core_1_1Direction.html#a4d99b93b94de25af8fb72841a6c4e919">IMP::core::Direction::setup_particle()</a>, <a href="classIMP_1_1core_1_1DirectionMover.html#a17b729e668ba035e43d643070d3138bc">IMP::core::DirectionMover::get_direction()</a></td></tr>
154 <tr><td>@ref IMP::core::DirectionAngle</td><td><a href="classIMP_1_1core_1_1DirectionAngle.html#ab6690f325dd3fdd9bb126d8c6afd31af">IMP::core::DirectionAngle::setup_particle()</a>, <a href="classIMP_1_1core_1_1DirectionAngle.html#ab4b663ebcf8e6fc6ea05bfe4787fd360">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_1DirectionAngle.html#ae8ebaf8c4ee5a1793b1bd42af368efd4">IMP::core::DirectionAngle::setup_particle()</a></td></tr>
155 <tr><td>@ref IMP::core::DistancePairScore</td><td><a href="namespaceIMP_1_1spb.html#a516ba1dc6020a084d8cfd0a36bc9e1f3">IMP::spb::get_pair_score()</a></td></tr>
156 <tr><td>@ref IMP::core::FilterProvenance</td><td><a href="classIMP_1_1core_1_1FilterProvenance.html#a5d380f53debdeb6dd8a3d9a9917467fc">IMP::core::FilterProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1FilterProvenance.html#a3b9bb1273235755c9210e3e404b3eaa0">IMP::core::FilterProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1FilterProvenance.html#a36dbeda7b2b26cb1fb50b85eb2597ef9">IMP::core::FilterProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1FilterProvenance.html#a22a1ef6b2b9d09e5f0e3892787974995">IMP::core::FilterProvenance::setup_particle()</a></td></tr>
157 <tr><td>@ref IMP::core::Gaussian</td><td><a href="classIMP_1_1core_1_1Gaussian.html#afd9cbab37963307598d28ebf3ab613b4">IMP::core::Gaussian::setup_particle()</a>, <a href="classIMP_1_1core_1_1Gaussian.html#ad4baf110be41f88988589ab34445b929">IMP::core::Gaussian::setup_particle()</a>, <a href="classIMP_1_1core_1_1Gaussian.html#a0b69d1b1dbe516bac468d716d1373427">IMP::core::Gaussian::setup_particle()</a>, <a href="classIMP_1_1core_1_1Gaussian.html#a67bd0085609920225b030817fb2f9079">IMP::core::Gaussian::setup_particle()</a></td></tr>
158 <tr><td>@ref IMP::core::Hierarchy</td><td><a href="classIMP_1_1core_1_1Hierarchy.html#a8a2f52cdcda06b1e473fbf15cf9eeb5e">IMP::core::Hierarchy::get_child()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#ac2fb4759f8f6c9b38e1a07f1e7fb5578">IMP::core::Hierarchy::get_parent()</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="namespaceIMP_1_1core.html#a4c078026c66398b7ae77eeb6f13ddcd0">IMP::core::get_root()</a></td></tr>
159 <tr><td>@ref IMP::core::HierarchyTraits</td><td><a href="classIMP_1_1atom_1_1Hierarchy.html#ab99b617e046d339ee51649f3eeb218e3">IMP::atom::Hierarchy::get_traits()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#a21ff4285e9aa013c1914f59a54f7b02c">IMP::core::Hierarchy::get_decorator_traits()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#ab576c86a2116587699523d583391824b">IMP::core::Hierarchy::get_traits()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#a0c6a95216a6e527ffee2f054faa8cdd6">IMP::core::Hierarchy::get_default_decorator_traits()</a>, <a href="classIMP_1_1core_1_1Hierarchy.html#aba2834d7467a9a41e0ba54d7f09044c5">IMP::core::Hierarchy::get_default_traits()</a></td></tr>
160 <tr><td>@ref IMP::core::IncrementalScoringFunction</td><td><a href="classIMP_1_1core_1_1MonteCarlo.html#a3276d3742cfacf2d09713a140cb5beeb">IMP::core::MonteCarlo::get_incremental_scoring_function()</a></td></tr>
161 <tr><td>@ref IMP::core::MonteCarlo</td><td><a href="namespaceIMP_1_1spb.html#ab58214204b446b5e3784249004b1ed9d">IMP::spb::setup_SPBMonteCarlo()</a></td></tr>
162 <tr><td>@ref IMP::core::MonteCarloMover</td><td><a href="classIMP_1_1core_1_1MonteCarlo.html#a0cb15cbadc52b3400fc71d9dba57114d">IMP::core::MonteCarlo::get_mover()</a></td></tr>
163 <tr><td>@ref IMP::core::NonRigidMember</td><td><a href="classIMP_1_1core_1_1NonRigidMember.html#a93d2f84385458c5ce71ed67788b8a6cd">IMP::core::NonRigidMember::operator=()</a></td></tr>
164 <tr><td>@ref IMP::core::OrderedTypePairPredicate</td><td><a href="classIMP_1_1npctransport_1_1Scoring.html#a5fc579835576dbc24ec3420691c47c32">IMP::npctransport::Scoring::get_ordered_type_pair_predicate()</a>, <a href="classIMP_1_1npctransport_1_1Scoring.html#a02a9279799eb9028568cb3048b1e229b">IMP::npctransport::Scoring::get_ordered_type_pair_predicate()</a></td></tr>
165 <tr><td>@ref IMP::core::Provenance</td><td><a href="classIMP_1_1core_1_1Provenance.html#a8d9aca624be1591b6a9dfd8d2c85f964">IMP::core::Provenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1Provenance.html#a76c47d7cbd7265c7096d2243dd18cc46">IMP::core::Provenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1Provenance.html#a015c8c87998debcdbee0272e9793e42d">IMP::core::Provenance::get_previous()</a>, <a href="classIMP_1_1core_1_1Provenanced.html#aa30e41dd38e3f2dc4ea11b3eb5f666ff">IMP::core::Provenanced::get_provenance()</a>, <a href="classIMP_1_1rmf_1_1HierarchyLoadLink.html#adb414343f11c2bf660fc4c2eb15cc85c">IMP::rmf::HierarchyLoadLink::create_one_provenance()</a>, <a href="namespaceIMP_1_1core.html#ab7597523d0b09bc8fa288b7261cedb69">IMP::core::create_clone()</a></td></tr>
166 <tr><td>@ref IMP::core::Provenanced</td><td><a href="classIMP_1_1core_1_1Provenanced.html#ad673bbc3c3472dc1a27217940fd719cd">IMP::core::Provenanced::setup_particle()</a>, <a href="classIMP_1_1core_1_1Provenanced.html#a975e54d208981493f518a3c27ef5003a">IMP::core::Provenanced::setup_particle()</a></td></tr>
167 <tr><td>@ref IMP::core::Reference</td><td><a href="classIMP_1_1core_1_1Reference.html#a83dc213faa437f37384eeabfa4923883">IMP::core::Reference::setup_particle()</a>, <a href="classIMP_1_1core_1_1Reference.html#a71b485271947fe268a60fe762642fb87">IMP::core::Reference::setup_particle()</a></td></tr>
168 <tr><td>@ref IMP::core::RigidBody</td><td><a href="classIMP_1_1core_1_1RigidBody.html#ac26218c9d04b5a21b5fa44687bc221e3">IMP::core::RigidBody::operator=()</a>, <a href="classIMP_1_1core_1_1RigidBody.html#a45be73e21f44d6246a31a1285aa1e6cf">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_1core_1_1RigidBody.html#a004eb894648f584c24039040b9c1b7d3">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_1RigidBodyMember.html#a37e8c45b0652cac4b1257e1773d9dc54">IMP::core::RigidBodyMember::get_rigid_body()</a>, <a href="classIMP_1_1kinematics_1_1Joint.html#a1c1015cacfabeb732fc45df58a914389">IMP::kinematics::Joint::get_child_node()</a>, <a href="classIMP_1_1kinematics_1_1Joint.html#a00109e3ad33f43ef6ab7b715ad529e9c">IMP::kinematics::Joint::get_parent_node()</a>, <a href="classIMP_1_1spb_1_1CellMover.html#a183acd439bf7dc9107feb68344f9fa74">IMP::spb::CellMover::get_rigid_bodies()</a>, <a href="classIMP_1_1spb_1_1PbcBoxedRigidBodyMover.html#acc877fb59301c3aa6cca9cf5fe93d547">IMP::spb::PbcBoxedRigidBodyMover::get_rigid_bodies()</a>, <a href="classIMP_1_1symmetry_1_1RigidBodyMover.html#ac2903b33221154299bb495fe40cf441b">IMP::symmetry::RigidBodyMover::get_rigid_bodies()</a>, <a href="namespaceIMP_1_1atom.html#a70ac55d293e6851c67b45d7fd55a3163">IMP::atom::create_compatible_rigid_body()</a>, <a href="namespaceIMP_1_1atom.html#a1b72819ad85249bfe290fe31b4084e9e">IMP::atom::create_rigid_body()</a>, <a href="namespaceIMP_1_1atom.html#a40da5b3553d98acf020078b4e435b12a">IMP::atom::create_rigid_body()</a>, <a href="namespaceIMP_1_1spb.html#a767148a9e5c40841aa2c91221389e67e">IMP::spb::get_rigid_bodies()</a></td></tr>
169 <tr><td>@ref IMP::core::RigidBodyMember</td><td><a href="classIMP_1_1core_1_1RigidBodyMember.html#a3fe7b1bff38121bf91b972bea625f484">IMP::core::RigidBodyMember::operator=()</a></td></tr>
170 <tr><td>@ref IMP::core::RigidMember</td><td><a href="classIMP_1_1core_1_1RigidMember.html#ac53a96061483b5228c2fa10c1b14e64f">IMP::core::RigidMember::operator=()</a></td></tr>
171 <tr><td>@ref IMP::core::SampleProvenance</td><td><a href="classIMP_1_1core_1_1SampleProvenance.html#ac9f2f1b32dd4fc7353f9e58aef555134">IMP::core::SampleProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1SampleProvenance.html#a9e4d57ea67f0b701fcaf1391d1c2dbd1">IMP::core::SampleProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1SampleProvenance.html#a6b60b02aecf3d234a9cf7124986dcc54">IMP::core::SampleProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1SampleProvenance.html#ae58bc3939e285eb5d78ff427010e228c">IMP::core::SampleProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1SampleProvenance.html#a178dbb7a6a1acf8893c4a273a76c81d1">IMP::core::SampleProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1SampleProvenance.html#af02b0b8650e58bf9aae34b7b61557283">IMP::core::SampleProvenance::setup_particle()</a></td></tr>
172 <tr><td>@ref IMP::core::ScriptProvenance</td><td><a href="classIMP_1_1core_1_1ScriptProvenance.html#a626325de0e441b9cebb7855633c1307b">IMP::core::ScriptProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1ScriptProvenance.html#a5fbee0521c2214e2580ef2d1ef3f5929">IMP::core::ScriptProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1ScriptProvenance.html#a720500fc75ca95d5db25545a2e790a40">IMP::core::ScriptProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1ScriptProvenance.html#a248401f9e74c426ff1b66c0c724da23a">IMP::core::ScriptProvenance::setup_particle()</a></td></tr>
173 <tr><td>@ref IMP::core::SoftwareProvenance</td><td><a href="classIMP_1_1core_1_1SoftwareProvenance.html#a7e594d1afc2a39053e0e5a9bf3c5b43f">IMP::core::SoftwareProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1SoftwareProvenance.html#a2740e3e81caed401cc58f05df2e1a238">IMP::core::SoftwareProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1SoftwareProvenance.html#a2d54fbf32f195a5c26a4ed8f3a613720">IMP::core::SoftwareProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1SoftwareProvenance.html#a3f5dd1f507dd6187510c00565573593a">IMP::core::SoftwareProvenance::setup_particle()</a></td></tr>
174 <tr><td>@ref IMP::core::SphereDistancePairScore</td><td><a href="namespaceIMP_1_1spb.html#a89502a2252250f76a5b47192552165ae">IMP::spb::get_sphere_pair_score()</a>, <a href="namespaceIMP_1_1spb.html#a42be0ddd8e2e7d54844fd1eb2aca5601">IMP::spb::get_sphere_pair_score()</a></td></tr>
175 <tr><td>@ref IMP::core::StructureProvenance</td><td><a href="classIMP_1_1core_1_1StructureProvenance.html#abe84c4f8061427510ebbe5bc4761f9fa">IMP::core::StructureProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1StructureProvenance.html#aa95e692760b11064d53ef4cf4358a87c">IMP::core::StructureProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1StructureProvenance.html#a27ee0875bac2c8755df775a837213d23">IMP::core::StructureProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1StructureProvenance.html#a992e115c0685aaa29b4dc27c5a8d02c7">IMP::core::StructureProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1StructureProvenance.html#ac758f523bea1201de4d1b0f96331fb37">IMP::core::StructureProvenance::setup_particle()</a>, <a href="classIMP_1_1core_1_1StructureProvenance.html#aaf11a4f9558d13560cbc87ea306ebf8a">IMP::core::StructureProvenance::setup_particle()</a></td></tr>
176 <tr><td>@ref IMP::core::Surface</td><td><a href="classIMP_1_1core_1_1Surface.html#a3edff8afcb062c7d3239dbb04f28ae97">IMP::core::Surface::setup_particle()</a>, <a href="classIMP_1_1core_1_1Surface.html#abe8433079e5a76903106a2ced2dd0aa7">IMP::core::Surface::setup_particle()</a>, <a href="classIMP_1_1core_1_1Surface.html#a353d17efbba58c5667408f1692cb51ed">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#aa1dadcaf371ed3a2fe46f3e0e6895ca3">IMP::core::Surface::setup_particle()</a>, <a href="classIMP_1_1core_1_1Surface.html#add65d020138b1f36ab5500de75730b46">IMP::core::Surface::setup_particle()</a>, <a href="classIMP_1_1core_1_1Surface.html#aaf1c408984ac409151d5df944e3de185">IMP::core::Surface::setup_particle()</a>, <a href="classIMP_1_1core_1_1Surface.html#a04863c0756eaa91980149e00f1dc343f">IMP::core::Surface::setup_particle()</a>, <a href="classIMP_1_1core_1_1SurfaceGeometry.html#afcd83b2ec6ce2a0446a61b37ff7250b2">IMP::core::SurfaceGeometry::get_geometry()</a>, <a href="classIMP_1_1core_1_1SurfaceGeometryConstraint.html#a5fc8271c902740f68b79cc497fcdebc7">IMP::core::SurfaceGeometryConstraint::get_surface()</a>, <a href="classIMP_1_1core_1_1SurfaceMover.html#ae7f0f384e0206c26800aaa0dbc763ba3">IMP::core::SurfaceMover::get_surface()</a></td></tr>
177 <tr><td>@ref IMP::core::SurfaceGeometry</td><td><a href="classIMP_1_1core_1_1SurfaceGeometryConstraint.html#a9d41c3987fc1ff140e9075ea372d7095">IMP::core::SurfaceGeometryConstraint::get_geometry()</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></td></tr>
178 <tr><td>@ref IMP::core::Typed</td><td><a href="classIMP_1_1core_1_1Typed.html#abe2ff709d939e3c09abd4160022a9779">IMP::core::Typed::setup_particle()</a>, <a href="classIMP_1_1core_1_1Typed.html#a39616e4ceda219518cf1808c6a332957">IMP::core::Typed::setup_particle()</a></td></tr>
179 <tr><td>@ref IMP::core::XYZ</td><td><a href="classIMP_1_1core_1_1XYZ.html#a0b8f68f0622a3076e17cb1ccbe773a53">IMP::core::XYZ::setup_particle()</a>, <a href="classIMP_1_1core_1_1XYZ.html#ac78d4427211401f07c317207a1e740c1">IMP::core::XYZ::setup_particle()</a>, <a href="classIMP_1_1core_1_1XYZ.html#a32b3dcc08f430fc0403441b3ac1ac87f">IMP::core::XYZ::setup_particle()</a>, <a href="classIMP_1_1core_1_1XYZ.html#a55c3249309694fa15ee83e09541ca5f8">IMP::core::XYZ::setup_particle()</a>, <a href="classIMP_1_1kinematics_1_1DihedralAngleRevoluteJoint.html#a49f28730d11a9ae0fd7fba4c3dd069c6">IMP::kinematics::DihedralAngleRevoluteJoint::get_a()</a>, <a href="classIMP_1_1kinematics_1_1DihedralAngleRevoluteJoint.html#a0cd877be8bb2068c442ab972291cd705">IMP::kinematics::DihedralAngleRevoluteJoint::get_b()</a>, <a href="classIMP_1_1kinematics_1_1DihedralAngleRevoluteJoint.html#a8cf4011fcc06c2d764c414eca9bde7ff">IMP::kinematics::DihedralAngleRevoluteJoint::get_c()</a>, <a href="classIMP_1_1kinematics_1_1DihedralAngleRevoluteJoint.html#abed30c005a1b240c142aa3192324c99c">IMP::kinematics::DihedralAngleRevoluteJoint::get_d()</a></td></tr>
180 <tr><td>@ref IMP::core::XYZR</td><td><a href="classIMP_1_1core_1_1XYZR.html#a2972fe8c69de14cce2a4261f52c635a1">IMP::core::XYZR::setup_particle()</a>, <a href="classIMP_1_1core_1_1XYZR.html#ae7fde5a611ede0831d8230356a6ad34d">IMP::core::XYZR::setup_particle()</a>, <a href="classIMP_1_1core_1_1XYZR.html#af8286a027e59710bd5f26099a0986196">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_1core_1_1XYZR.html#a4c297dfccc564490ba9315f65b56a25b">IMP::core::XYZR::setup_particle()</a>, <a href="namespaceIMP_1_1atom.html#aed5950befd1610327f1bc9bc737de49f">IMP::atom::create_cover()</a></td></tr>
181 </table>
182 # IMP.display # {#factory_index_display}
183 <table><tr>
184 <th>Class</th><th>Factories</th></tr>
185 <tr><td>@ref IMP::display::BoundingBoxGeometry</td><td><a href="namespaceIMP_1_1display.html#a788545ff045770aea75e72b5568aba1d">IMP::display::create_geometry()</a></td></tr>
186 <tr><td>@ref IMP::display::Color</td><td><a href="classIMP_1_1display_1_1Color.html#a518c467a7e1ceb7e475ae704e2f499fb">IMP::display::Color::operator=()</a>, <a href="classIMP_1_1display_1_1Colored.html#af4eb5de7d7025ed94a665ad53e22521c">IMP::display::Colored::get_color()</a>, <a href="classIMP_1_1display_1_1Geometry.html#a1812713ecd15573825afeca59b69e570">IMP::display::Geometry::get_color()</a>, <a href="classIMP_1_1display_1_1PairGeometry.html#a146c1739a6706a2db5aec125a6f77ed6">IMP::display::PairGeometry::get_color()</a>, <a href="classIMP_1_1display_1_1SingletonGeometry.html#ae39aa0314faa864735c1d78aed0130ba">IMP::display::SingletonGeometry::get_color()</a>, <a href="namespaceIMP_1_1display.html#a8873da49642f951ec86570656e98e908">IMP::display::get_jet_color()</a>, <a href="namespaceIMP_1_1display.html#ae15042a6bb4f4548ec2876ceddfd3165">IMP::display::get_hot_color()</a>, <a href="namespaceIMP_1_1display.html#a3ea1c11940d14e4ac022768e96514dff">IMP::display::get_rgb_color()</a>, <a href="namespaceIMP_1_1display.html#abd278fa3123b329c7fe1784b02f4ca31">IMP::display::get_gray_color()</a>, <a href="namespaceIMP_1_1display.html#ad982e4a6182db9aa8157f3fc020da33f">IMP::display::get_gnuplot_color()</a>, <a href="namespaceIMP_1_1display.html#a7139e3c2ffdf998ca304a7f01e6e237e">IMP::display::get_display_color()</a>, <a href="namespaceIMP_1_1display.html#ada2a3156a15dd0217840bfc8675724d8">IMP::display::get_interpolated_rgb()</a></td></tr>
187 <tr><td>@ref IMP::display::Colored</td><td><a href="classIMP_1_1display_1_1Colored.html#a1f682cba5427be0068b38d6c126da974">IMP::display::Colored::setup_particle()</a>, <a href="classIMP_1_1display_1_1Colored.html#aba3bd220eae85bc31513237dafc78649">IMP::display::Colored::setup_particle()</a></td></tr>
188 <tr><td>@ref IMP::display::CylinderGeometry</td><td><a href="namespaceIMP_1_1display.html#a418acde3993b51a25f3ba4311f4c9b74">IMP::display::create_geometry()</a></td></tr>
189 <tr><td>@ref IMP::display::EllipsoidGeometry</td><td><a href="namespaceIMP_1_1display.html#acbb9389b216a0e7f8c4d9794075ccbf8">IMP::display::create_geometry()</a></td></tr>
190 <tr><td>@ref IMP::display::Geometry</td><td><a href="classIMP_1_1display_1_1WriteOptimizerState.html#ab7308b24bd03e46f14de9693ab613535">IMP::display::WriteOptimizerState::get_geometry()</a>, <a href="classIMP_1_1npctransport_1_1SimulationData.html#a9e57336bb6c67d20ba952bdf7e2b606d">IMP::npctransport::SimulationData::get_static_geometry()</a></td></tr>
191 <tr><td>@ref IMP::display::PointGeometry</td><td><a href="namespaceIMP_1_1display.html#ae2f3fba6f3395b1bb19444ba9907314f">IMP::display::create_geometry()</a></td></tr>
192 <tr><td>@ref IMP::display::PolygonGeometry</td><td><a href="namespaceIMP_1_1display.html#aa60c5d366f71d009a94cb7911503ab3d">IMP::display::create_geometry()</a></td></tr>
193 <tr><td>@ref IMP::display::ReferenceFrameGeometry</td><td><a href="namespaceIMP_1_1display.html#a7e059bdeb2a7290b1260cab6923bdd29">IMP::display::create_geometry()</a></td></tr>
194 <tr><td>@ref IMP::display::SegmentGeometry</td><td><a href="namespaceIMP_1_1display.html#a071ef8e162f88294b235de620e423d2c">IMP::display::create_geometry()</a></td></tr>
195 <tr><td>@ref IMP::display::SphereGeometry</td><td><a href="namespaceIMP_1_1display.html#ad9d90b0ae0f1f0c079a9f3b4a11d1d77">IMP::display::create_geometry()</a></td></tr>
196 <tr><td>@ref IMP::display::TriangleGeometry</td><td><a href="namespaceIMP_1_1display.html#a54a071369efd0709c091051cd6355e67">IMP::display::create_geometry()</a></td></tr>
197 <tr><td>@ref IMP::display::Writer</td><td><a href="classIMP_1_1display_1_1WriterAdaptor.html#afe4e8faa43b0dcc21116c1b0e2c4b252">IMP::display::WriterAdaptor::get_writer()</a>, <a href="classIMP_1_1display_1_1WriterAdaptor.html#a108d1a11ac10a1f30477d9209779f9d6">IMP::display::WriterAdaptor::operator->()</a>, <a href="namespaceIMP_1_1display.html#a55414a3681ffd79c126fabdbf13abb2d">IMP::display::create_writer()</a></td></tr>
198 </table>
199 # IMP.domino # {#factory_index_domino}
200 <table><tr>
201 <th>Class</th><th>Factories</th></tr>
202 <tr><td>@ref IMP::domino::Assignment</td><td><a href="classIMP_1_1domino_1_1AssignmentContainer.html#aa81ef13a668c41da618439be20b6f2aa">IMP::domino::AssignmentContainer::get_assignment()</a>, <a href="classIMP_1_1domino_1_1CappedAssignmentContainer.html#a70d2a417f44ffa5c2b9398f922d68476">IMP::domino::CappedAssignmentContainer::get_assignment()</a>, <a href="classIMP_1_1domino_1_1HeapAssignmentContainer.html#a75b4c6590290622f2a591526c2d7d980">IMP::domino::HeapAssignmentContainer::get_assignment()</a>, <a href="classIMP_1_1domino_1_1ListAssignmentContainer.html#aecff7e9b8b9b160d4600acca18476325">IMP::domino::ListAssignmentContainer::get_assignment()</a>, <a href="classIMP_1_1domino_1_1Order.html#a5073cfaca05e214fb48cc38d76f2df51">IMP::domino::Order::get_subset_ordered()</a>, <a href="classIMP_1_1domino_1_1PackedAssignmentContainer.html#ac30fa155daac1182b10eac73092776bf">IMP::domino::PackedAssignmentContainer::get_assignment()</a>, <a href="classIMP_1_1domino_1_1RangeViewAssignmentContainer.html#a4873660d67875ee0555ade12a5d27cef">IMP::domino::RangeViewAssignmentContainer::get_assignment()</a>, <a href="classIMP_1_1domino_1_1ReadAssignmentContainer.html#a1c63b2c726878bd81ba1892f8631ee3c">IMP::domino::ReadAssignmentContainer::get_assignment()</a>, <a href="classIMP_1_1domino_1_1ReadHDF5AssignmentContainer.html#ae4005d10d8c190ca20ef7348b0e79ad5">IMP::domino::ReadHDF5AssignmentContainer::get_assignment()</a>, <a href="classIMP_1_1domino_1_1SampleAssignmentContainer.html#afe0a0b8954b75b9ce2f5441eda1cbf74">IMP::domino::SampleAssignmentContainer::get_assignment()</a>, <a href="classIMP_1_1domino_1_1Slice.html#ab3c699a06268f2fa405c296149c4515b">IMP::domino::Slice::get_sliced()</a>, <a href="classIMP_1_1domino_1_1WriteAssignmentContainer.html#a8536920e0d6d48f1b9724aff7d96abdd">IMP::domino::WriteAssignmentContainer::get_assignment()</a>, <a href="classIMP_1_1domino_1_1WriteHDF5AssignmentContainer.html#aaf256614cd8a08a899a9573dfbaece17">IMP::domino::WriteHDF5AssignmentContainer::get_assignment()</a>, <a href="namespaceIMP_1_1domino.html#abd8a69ba2cc2b8fea2f49c99189d8711">IMP::domino::get_nearest_assignment()</a></td></tr>
203 <tr><td>@ref IMP::domino::AssignmentsTable</td><td><a href="classIMP_1_1domino_1_1DiscreteSampler.html#a4e75f4975c1009934c6c594f93ca31e1">IMP::domino::DiscreteSampler::get_assignments_table_to_use()</a></td></tr>
204 <tr><td>@ref IMP::domino::ParticleStates</td><td><a href="classIMP_1_1domino_1_1ParticleStatesTable.html#aeeaf96e9b2425dae382e391e2a0dfa01">IMP::domino::ParticleStatesTable::get_particle_states()</a></td></tr>
205 <tr><td>@ref IMP::domino::ParticleStatesTable</td><td><a href="classIMP_1_1domino_1_1DiscreteSampler.html#add8262de16a05f7912617cb655f37831">IMP::domino::DiscreteSampler::get_particle_states_table()</a>, <a href="classIMP_1_1multifit_1_1ProteomicsEMAlignmentAtomic.html#af4484a70172a58bed5eedfe9a42a0705">IMP::multifit::ProteomicsEMAlignmentAtomic::set_particle_states_table()</a></td></tr>
206 <tr><td>@ref IMP::domino::Slice</td><td><a href="classIMP_1_1domino_1_1RestraintCache.html#a15f1f5513308176b4eaccc9e411277f2">IMP::domino::RestraintCache::get_slice()</a>, <a href="namespaceIMP_1_1domino.html#a619c0aea6816fda8b69b08cf5e57876d">IMP::domino::get_slice()</a></td></tr>
207 <tr><td>@ref IMP::domino::Subset</td><td><a href="classIMP_1_1domino_1_1ParticleStatesTable.html#ad199188132a371bdf4d086cc82ad2735">IMP::domino::ParticleStatesTable::get_subset()</a>, <a href="classIMP_1_1domino_1_1RestraintCache.html#abfeee91ee10e51b2dcf53e0daaf3fd37">IMP::domino::RestraintCache::get_subset()</a>, <a href="classIMP_1_1domino_1_1Slice.html#a2f4e028d276be06d17293141b9a472c1">IMP::domino::Slice::get_sliced()</a>, <a href="namespaceIMP_1_1domino.html#a1e91ca287b91fd6144aeeff14960c14a">IMP::domino::get_difference()</a>, <a href="namespaceIMP_1_1domino.html#a399d7344a0696fbab4a6ca6c2796157b">IMP::domino::get_intersection()</a>, <a href="namespaceIMP_1_1domino.html#adc940e96eb944fe259a8fba40830a251">IMP::domino::get_union()</a></td></tr>
208 <tr><td>@ref IMP::domino::SubsetFilter</td><td><a href="classIMP_1_1domino_1_1EqualitySubsetFilterTable.html#aef78c6e898fd5b501286176dddb83761">IMP::domino::EqualitySubsetFilterTable::get_subset_filter()</a>, <a href="classIMP_1_1domino_1_1EquivalenceAndExclusionSubsetFilterTable.html#aac5555f7a73f683982044b8bd2f5e489">IMP::domino::EquivalenceAndExclusionSubsetFilterTable::get_subset_filter()</a>, <a href="classIMP_1_1domino_1_1EquivalenceSubsetFilterTable.html#af1a3292d922681436e7e80e3078e539e">IMP::domino::EquivalenceSubsetFilterTable::get_subset_filter()</a>, <a href="classIMP_1_1domino_1_1ExclusionSubsetFilterTable.html#a615f62ddb2a41e8724181b494c8ccc95">IMP::domino::ExclusionSubsetFilterTable::get_subset_filter()</a>, <a href="classIMP_1_1domino_1_1ListSubsetFilterTable.html#a48920d6f207daebabf6ed311fd0db0e8">IMP::domino::ListSubsetFilterTable::get_subset_filter()</a>, <a href="classIMP_1_1domino_1_1MinimumRestraintScoreSubsetFilterTable.html#a1dce7f872d7a7e502d0503c81d116d2d">IMP::domino::MinimumRestraintScoreSubsetFilterTable::get_subset_filter()</a>, <a href="classIMP_1_1domino_1_1PairListSubsetFilterTable.html#a17b25f81495da3b10c33f9fe76756bee">IMP::domino::PairListSubsetFilterTable::get_subset_filter()</a>, <a href="classIMP_1_1domino_1_1ProbabilisticSubsetFilterTable.html#ab1c4966fc3fa5058840da7e95dea553d">IMP::domino::ProbabilisticSubsetFilterTable::get_subset_filter()</a>, <a href="classIMP_1_1domino_1_1RestraintScoreSubsetFilterTable.html#a605ca12686b3b5e03eb90bdd9ad9dd8e">IMP::domino::RestraintScoreSubsetFilterTable::get_subset_filter()</a>, <a href="classIMP_1_1domino_1_1SubsetFilterTable.html#ac455bb060804addf2274c8304a2aa5fd">IMP::domino::SubsetFilterTable::get_subset_filter()</a>, <a href="classIMP_1_1em2d_1_1DistanceFilterTable.html#a486ca77a43af6e29b51637a633e09c9d">IMP::em2d::DistanceFilterTable::get_subset_filter()</a>, <a href="classIMP_1_1example_1_1ExampleSubsetFilterTable.html#a4fd0328dc1039a8ec541abb8fa4990ac">IMP::example::ExampleSubsetFilterTable::get_subset_filter()</a></td></tr>
209 <tr><td>@ref IMP::domino::SubsetFilterTable</td><td><a href="classIMP_1_1domino_1_1DiscreteSampler.html#ae77e8ad6a8313ae2970f192df444cf85">IMP::domino::DiscreteSampler::get_subset_filter_table()</a></td></tr>
210 </table>
211 # IMP.em # {#factory_index_em}
212 <table><tr>
213 <th>Class</th><th>Factories</th></tr>
214 <tr><td>@ref IMP::em::DensityHeader</td><td><a href="classIMP_1_1em_1_1DensityMap.html#a4675217cca898418d497226772210c9a">IMP::em::DensityMap::get_header()</a>, <a href="classIMP_1_1em_1_1DensityMap.html#af1705e5ebf5aa3d9fc5a84c897e2ebb8">IMP::em::DensityMap::get_header_writable()</a>, <a href="namespaceIMP_1_1em.html#a11f40ffc07e7b3d9dde0711015f3e97e">IMP::em::create_density_header()</a></td></tr>
215 <tr><td>@ref IMP::em::DensityMap</td><td><a href="classIMP_1_1em_1_1DensityMap.html#a3cbce8f549241438b9e02fbcc5e9f47f">IMP::em::DensityMap::get_cropped()</a>, <a href="classIMP_1_1em_1_1DensityMap.html#a22a4b07290dee25e91a77157ebf4393d">IMP::em::DensityMap::get_cropped()</a>, <a href="classIMP_1_1em_1_1DensityMap.html#a152abc77a04a0eddaedca4a61643c7e4">IMP::em::DensityMap::get_cropped()</a>, <a href="classIMP_1_1em_1_1DensityMap.html#a8f5c966aab9fb6fa41e89500efc7f7e3">IMP::em::DensityMap::pad_margin()</a>, <a href="classIMP_1_1em_1_1DensityMap.html#a38ed273d99248a3258e9ed33676cd2d6">IMP::em::DensityMap::create_density_map()</a>, <a href="classIMP_1_1em_1_1DensityMap.html#ae4349c6f32dd2bd503c4d1bc0dffbb2f">IMP::em::DensityMap::create_density_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#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#aa7ad31965184a36215f80816a2749662">IMP::em::DensityMap::read_map()</a>, <a href="classIMP_1_1em_1_1DensityMap.html#a1e7a07ba713fd32af20b67ca694cc35f">IMP::em::DensityMap::read_map()</a>, <a href="classIMP_1_1multifit_1_1FFTFitting.html#a37d65339d5125709922ec82eba2ce9ed">IMP::multifit::FFTFitting::crop_margin()</a>, <a href="namespaceIMP_1_1bayesianem.html#aac1c7654b58f288053040fd246060d07">IMP::bayesianem::get_masked_map()</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_1em.html#a7e08fd743778d6b18b8e759bea705454">IMP::em::bayesem3d_get_density_from_particle()</a>, <a href="namespaceIMP_1_1em.html#a1c88424c8b24a5802ef048175e22787b">IMP::em::binarize()</a>, <a href="namespaceIMP_1_1em.html#aa873c569e58e5c5d66dac1c0420f3e6c">IMP::em::create_density_map()</a>, <a href="namespaceIMP_1_1em.html#ad6586b38abb58a2ebc6b64b10f60f734">IMP::em::create_density_map()</a>, <a href="namespaceIMP_1_1em.html#ace9a6d63b63146fcaac428d8995ade7b">IMP::em::create_density_map()</a>, <a href="namespaceIMP_1_1em.html#ae7eacf1de1781ba22d2169b635d87753">IMP::em::get_max_map()</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#a3078e4c77b9e81fa61b8222934185d1e">IMP::em::get_threshold_map()</a>, <a href="namespaceIMP_1_1em.html#a7ca59d2a3aa688060c280efa250d80a7">IMP::em::interpolate_map()</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#a3359231b0601df5803958afcd8d93184">IMP::multifit::create_hit_map()</a>, <a href="namespaceIMP_1_1multifit.html#ae2668faf165711107665d494a73351a2">IMP::multifit::grid2map()</a>, <a href="namespaceIMP_1_1multifit.html#a8528245410468cfc40ab674d0ef64d70">IMP::multifit::remove_background()</a></td></tr>
216 <tr><td>@ref IMP::em::FittingSolutions</td><td><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#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#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_1multifit.html#a2a2ca63805bc102fbf07209c85e2ce44">IMP::multifit::convert_multifit_to_em_format()</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></td></tr>
217 <tr><td>@ref IMP::em::ImageHeader</td><td><a href="classIMP_1_1em2d_1_1Image.html#a22c35720b110b90c7725b31926902d9b">IMP::em2d::Image::get_header()</a></td></tr>
218 <tr><td>@ref IMP::em::KernelParameters</td><td><a href="classIMP_1_1em_1_1SampledDensityMap.html#a583657d98547c95dceb6130ea3bf1e02">IMP::em::SampledDensityMap::get_kernel_params()</a></td></tr>
219 <tr><td>@ref IMP::em::SampledDensityMap</td><td><a href="classIMP_1_1em_1_1FitRestraint.html#a2f978d1d053deab1b5ea26317c33d6d0">IMP::em::FitRestraint::get_model_dens_map()</a>, <a href="namespaceIMP_1_1em.html#a12121a1c9d4ec3f58b959b1b8c136ecb">IMP::em::particles2binarized_density()</a>, <a href="namespaceIMP_1_1em.html#af47d3d5898cb50aecaf7b8cf5a40d167">IMP::em::particles2density()</a></td></tr>
220 <tr><td>@ref IMP::em::SurfaceShellDensityMap</td><td><a href="namespaceIMP_1_1em.html#a4c18a8d1e939db80e5767b8b3e9c040f">IMP::em::particles2surface()</a></td></tr>
221 <tr><td>@ref IMP::em::Voxel</td><td><a href="classIMP_1_1em_1_1Voxel.html#af56f556902db8b0ab8731eebce3c12a3">IMP::em::Voxel::setup_particle()</a>, <a href="classIMP_1_1em_1_1Voxel.html#a3131b8aa6d6fa12e1226054df4a291df">IMP::em::Voxel::setup_particle()</a></td></tr>
222 </table>
223 # IMP.em2d # {#factory_index_em2d}
224 <table><tr>
225 <th>Class</th><th>Factories</th></tr>
226 <tr><td>@ref IMP::em2d::Image</td><td><a href="classIMP_1_1em2d_1_1ProjectionStates.html#ad7a92de7b4d0453d5cf58c001ce1a1f0">IMP::em2d::ProjectionStates::get_projection()</a></td></tr>
227 <tr><td>@ref IMP::em2d::ProjectionParameters</td><td><a href="classIMP_1_1em2d_1_1ProjectionParameters.html#a1564012d89842dc7c01c785bbaf92b91">IMP::em2d::ProjectionParameters::setup_particle()</a>, <a href="classIMP_1_1em2d_1_1ProjectionParameters.html#a7608632f3765376047d0a20deb5d0fbc">IMP::em2d::ProjectionParameters::setup_particle()</a></td></tr>
228 </table>
229 # IMP.example # {#factory_index_example}
230 <table><tr>
231 <th>Class</th><th>Factories</th></tr>
232 <tr><td>@ref IMP::example::ExampleDecorator</td><td><a href="classIMP_1_1example_1_1ExampleDecorator.html#af8dcc04f322c06a8873d069a62c886c0">IMP::example::ExampleDecorator::setup_particle()</a>, <a href="classIMP_1_1example_1_1ExampleDecorator.html#a173127079675cb7866584f44d127edeb">IMP::example::ExampleDecorator::setup_particle()</a></td></tr>
233 </table>
234 # IMP.isd # {#factory_index_isd}
235 <table><tr>
236 <th>Class</th><th>Factories</th></tr>
237 <tr><td>@ref IMP::isd::FretRestraint</td><td><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></td></tr>
238 <tr><td>@ref IMP::isd::MolecularDynamics</td><td><a href="classIMP_1_1isd_1_1HybridMonteCarlo.html#a126896181fdc35049811f2a1cd3d9980">IMP::isd::HybridMonteCarlo::get_md()</a>, <a href="classIMP_1_1isd_1_1MolecularDynamicsMover.html#a8536ffc5917d63f065ee68239b450e93">IMP::isd::MolecularDynamicsMover::get_md()</a></td></tr>
239 <tr><td>@ref IMP::isd::Nuisance</td><td><a href="classIMP_1_1isd_1_1Nuisance.html#ac86cd1243edb27bf5836913a7ee47c1f">IMP::isd::Nuisance::setup_particle()</a>, <a href="classIMP_1_1isd_1_1Nuisance.html#aabf6195915b7373bad22698c0f0cbfd8">IMP::isd::Nuisance::setup_particle()</a>, <a href="classIMP_1_1isd_1_1Nuisance.html#a5389f5dd742255e89ad0f6169b21d0c5">IMP::isd::Nuisance::setup_particle()</a>, <a href="classIMP_1_1isd_1_1Nuisance.html#a0e8e2a9e009a51ec26838fee36ca1814">IMP::isd::Nuisance::setup_particle()</a></td></tr>
240 <tr><td>@ref IMP::isd::Scale</td><td><a href="classIMP_1_1isd_1_1NormalSigmaPCRestraint.html#adf3b95ea8a55efa3f1133500538cb575">IMP::isd::NormalSigmaPCRestraint::get_sigma()</a>, <a href="classIMP_1_1isd_1_1Scale.html#aadab22db4f26f34f6623348be012dbb6">IMP::isd::Scale::setup_particle()</a>, <a href="classIMP_1_1isd_1_1Scale.html#a8d621153a696a891d3541d4e7d31b101">IMP::isd::Scale::setup_particle()</a>, <a href="classIMP_1_1isd_1_1Scale.html#a10900f39652f84d5f017a02bf95218bb">IMP::isd::Scale::setup_particle()</a>, <a href="classIMP_1_1isd_1_1Scale.html#a0314030a246fa5d3520b8f5d2b75fd3f">IMP::isd::Scale::setup_particle()</a></td></tr>
241 <tr><td>@ref IMP::isd::Switching</td><td><a href="classIMP_1_1isd_1_1Switching.html#a42235fccf7f0610cd78f330ed558545d">IMP::isd::Switching::setup_particle()</a>, <a href="classIMP_1_1isd_1_1Switching.html#a36ee737a6372bea9c105a99172fde250">IMP::isd::Switching::setup_particle()</a>, <a href="classIMP_1_1isd_1_1Switching.html#ab3eec443cb4610e92bdbd8d0025454f1">IMP::isd::Switching::setup_particle()</a>, <a href="classIMP_1_1isd_1_1Switching.html#a8c6c00ef202c3cd73d1a03d71dddfcc4">IMP::isd::Switching::setup_particle()</a></td></tr>
242 <tr><td>@ref IMP::isd::Weight</td><td><a href="classIMP_1_1isd_1_1Weight.html#ad65d141fc4f7dc06e2c5b6dc841f00e0">IMP::isd::Weight::setup_particle()</a>, <a href="classIMP_1_1isd_1_1Weight.html#af2db650ff6cf15033745008b9af1d4d2">IMP::isd::Weight::setup_particle()</a>, <a href="classIMP_1_1isd_1_1Weight.html#ab0e3254cf9b6d9b59dbf4ec6f1807211">IMP::isd::Weight::setup_particle()</a>, <a href="classIMP_1_1isd_1_1Weight.html#a444c8c0b694dc51c882ae3f116dfa4f2">IMP::isd::Weight::setup_particle()</a>, <a href="classIMP_1_1isd_1_1Weight.html#a4430bddeaede83941b07c56b88bd6a4c">IMP::isd::Weight::setup_particle()</a>, <a href="classIMP_1_1isd_1_1Weight.html#ab67a7c287aa12e9505039ded8d82a5eb">IMP::isd::Weight::setup_particle()</a></td></tr>
243 </table>
244 # IMP.kinematics # {#factory_index_kinematics}
245 <table><tr>
246 <th>Class</th><th>Factories</th></tr>
247 <tr><td>@ref IMP::kinematics::DOF</td><td><a href="classIMP_1_1kinematics_1_1DOFsSampler.html#a4e374b3d8393b057c5ce60cbc7c1fad2">IMP::kinematics::DOFsSampler::get_dof()</a></td></tr>
248 <tr><td>@ref IMP::kinematics::DOFValues</td><td><a href="classIMP_1_1kinematics_1_1DOFsSampler.html#a6b23a655042253363991b7f1ecad808b">IMP::kinematics::DOFsSampler::get_sample()</a>, <a href="classIMP_1_1kinematics_1_1DOFsSampler.html#ad2f36b799915187b7e3b1b5178f45258">IMP::kinematics::DOFsSampler::do_get_sample()</a>, <a href="classIMP_1_1kinematics_1_1DirectionalDOF.html#a377501664554376eb3c305654a66d434">IMP::kinematics::DirectionalDOF::get_dofs_values()</a>, <a href="classIMP_1_1kinematics_1_1FibrilSampler.html#ae5773a0413984366a73b086fee4cfb0f">IMP::kinematics::FibrilSampler::do_get_sample()</a>, <a href="classIMP_1_1kinematics_1_1LocalPlanner.html#aa3e2c3f33045da082ccbc0c57cf98fae">IMP::kinematics::LocalPlanner::plan()</a>, <a href="classIMP_1_1kinematics_1_1PathLocalPlanner.html#a99c61f10809fe09bbbd15625d5c44009">IMP::kinematics::PathLocalPlanner::plan()</a>, <a href="classIMP_1_1kinematics_1_1RRT_1_1RRTNode.html#a854857cf2007eff341b7a608d55854b5">IMP::kinematics::RRT::RRTNode::get_DOFValues()</a>, <a href="classIMP_1_1kinematics_1_1UniformBackboneSampler.html#a604b6449f693a3b7784ed313350bbd63">IMP::kinematics::UniformBackboneSampler::do_get_sample()</a></td></tr>
249 <tr><td>@ref IMP::kinematics::DihedralAngleRevoluteJoint</td><td><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#a175fe14ea73c95932e547b64dcd6c032">IMP::kinematics::ProteinKinematics::get_phi_joint()</a>, <a href="classIMP_1_1kinematics_1_1ProteinKinematics.html#a3bfc396bdc667f1d73df79025a3e9292">IMP::kinematics::ProteinKinematics::get_psi_joint()</a></td></tr>
250 <tr><td>@ref IMP::kinematics::Joint</td><td><a href="classIMP_1_1kinematics_1_1KinematicForest.html#a4f4f75ae4464f9238edbd4f9f53da211">IMP::kinematics::KinematicForest::add_edge()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#a40ad561042d38de8f17e9732deeac344">IMP::kinematics::KinematicNode::get_in_joint()</a></td></tr>
251 <tr><td>@ref IMP::kinematics::KinematicForest</td><td><a href="classIMP_1_1kinematics_1_1Joint.html#ace40f33493218a6909b5c5ec3747210e">IMP::kinematics::Joint::get_owner_kf()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#afb08a98ef2a09bbfde3f86f65d886eb6">IMP::kinematics::KinematicNode::get_owner()</a>, <a href="classIMP_1_1kinematics_1_1ProteinKinematics.html#a7d362a387254728e698107b187ccabc9">IMP::kinematics::ProteinKinematics::get_kinematic_forest()</a></td></tr>
252 <tr><td>@ref IMP::kinematics::KinematicNode</td><td><a href="classIMP_1_1kinematics_1_1KinematicNode.html#abfb20ad6959f6bd74156061302f47700">IMP::kinematics::KinematicNode::setup_particle()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#aa41da78d70027959c88b3b8f1429d809">IMP::kinematics::KinematicNode::setup_particle()</a>, <a href="classIMP_1_1kinematics_1_1KinematicNode.html#ac4a27e38b4e2e40f53c27b5622a24db8">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#a61f5a6a83beae853f7a8b2e01cec0941">IMP::kinematics::KinematicNode::setup_particle()</a></td></tr>
253 <tr><td>@ref IMP::kinematics::RRT::RRTNode</td><td><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#ae53fc915b7bebd5809c99ffda6719f5c">IMP::kinematics::RRT::RRTNode::get_edges()</a></td></tr>
254 </table>
255 # IMP.misc # {#factory_index_misc}
256 <table><tr>
257 <th>Class</th><th>Factories</th></tr>
258 <tr><td>@ref IMP::misc::CustomXYZR</td><td><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>
259 </table>
260 # IMP.multifit # {#factory_index_multifit}
261 <table><tr>
262 <th>Class</th><th>Factories</th></tr>
263 <tr><td>@ref IMP::multifit::AnchorsData</td><td><a href="classIMP_1_1multifit_1_1ProteinsAnchorsSamplingSpace.html#a749cb63890e572b59c9b0b5e5e4075c1">IMP::multifit::ProteinsAnchorsSamplingSpace::get_anchors()</a>, <a href="namespaceIMP_1_1multifit.html#aedc64c26eefe139ef34e5cce89d13a51">IMP::multifit::molecule2anchors()</a>, <a href="namespaceIMP_1_1multifit.html#a1311b5448ea5d757a085c959a77e5fc2">IMP::multifit::read_anchors_data()</a></td></tr>
264 <tr><td>@ref IMP::multifit::AssemblyHeader</td><td><a href="classIMP_1_1multifit_1_1SettingsData.html#ab907ede30470a45d77126d0ed631868e">IMP::multifit::SettingsData::get_assembly_header()</a></td></tr>
265 <tr><td>@ref IMP::multifit::ComponentHeader</td><td><a href="classIMP_1_1multifit_1_1SettingsData.html#a64cd483a817da67778deb9fbbb0d90a9">IMP::multifit::SettingsData::get_component_header()</a></td></tr>
266 <tr><td>@ref IMP::multifit::Ensemble</td><td><a href="namespaceIMP_1_1multifit.html#a990fc248adf46233d96011ab77130eec">IMP::multifit::load_ensemble()</a></td></tr>
267 <tr><td>@ref IMP::multifit::FFTFittingOutput</td><td><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></td></tr>
268 <tr><td>@ref IMP::multifit::ProteinsAnchorsSamplingSpace</td><td><a href="namespaceIMP_1_1multifit.html#a1cc01cbbbb1cf9bb7f226524e0616e12">IMP::multifit::get_part_of_sampling_space()</a>, <a href="namespaceIMP_1_1multifit.html#adbd924144aee36a0b6dd9789ca164da8">IMP::multifit::read_protein_anchors_mapping()</a></td></tr>
269 <tr><td>@ref IMP::multifit::ProteomicsData</td><td><a href="classIMP_1_1multifit_1_1ProteinsAnchorsSamplingSpace.html#ab6cfebe16d6ea30f264e390f01e73890">IMP::multifit::ProteinsAnchorsSamplingSpace::get_proteomics_data()</a>, <a href="namespaceIMP_1_1multifit.html#aac05dae9e06cb11ef27e820cf54be014">IMP::multifit::get_partial_proteomics_data()</a>, <a href="namespaceIMP_1_1multifit.html#ae4470dd25cd94e09c145556b62fd54b7">IMP::multifit::read_proteomics_data()</a></td></tr>
270 <tr><td>@ref IMP::multifit::SettingsData</td><td><a href="namespaceIMP_1_1multifit.html#a3746dc39094e607667c55bde5aca85e6">IMP::multifit::get_partial_assembly_setting_data()</a>, <a href="namespaceIMP_1_1multifit.html#a90e0fd8875d0cdb56efa7419f51fc67e">IMP::multifit::read_settings()</a></td></tr>
271 </table>
272 # IMP.npctransport # {#factory_index_npctransport}
273 <table><tr>
274 <th>Class</th><th>Factories</th></tr>
275 <tr><td>@ref IMP::npctransport::FGChain</td><td><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_1npctransport.html#ae7a91516eb510beba957bd253626e22b">IMP::npctransport::get_fg_chain()</a></td></tr>
276 <tr><td>@ref IMP::npctransport::RelaxingSpring</td><td><a href="classIMP_1_1npctransport_1_1RelaxingSpring.html#a64df0f0064fcd7d14990458ec3b048fe">IMP::npctransport::RelaxingSpring::setup_particle()</a>, <a href="classIMP_1_1npctransport_1_1RelaxingSpring.html#a0af5978ddc8840ca5576953425ca8ded">IMP::npctransport::RelaxingSpring::setup_particle()</a></td></tr>
277 <tr><td>@ref IMP::npctransport::Scoring</td><td><a href="classIMP_1_1npctransport_1_1SimulationData.html#aa141e3e041963a194dfce3bef9f0f85d">IMP::npctransport::SimulationData::get_scoring()</a>, <a href="classIMP_1_1npctransport_1_1SimulationData.html#ab6bf77374a57f8c472ac8a5adcea5655">IMP::npctransport::SimulationData::get_scoring()</a></td></tr>
278 <tr><td>@ref IMP::npctransport::SimulationData</td><td><a href="classIMP_1_1npctransport_1_1ParticleFactory.html#ab742c4c31ef9ff7015a9385990bb6b19">IMP::npctransport::ParticleFactory::get_simulation_data()</a>, <a href="classIMP_1_1npctransport_1_1Scoring.html#a9d9a6424679119d6f30b3ed4adcdad46">IMP::npctransport::Scoring::get_sd()</a>, <a href="classIMP_1_1npctransport_1_1Scoring.html#a8e6ed2b0c1ce9659942227f412be20c5">IMP::npctransport::Scoring::get_sd()</a>, <a href="classIMP_1_1npctransport_1_1Statistics.html#aa3d25ade5a201d984d0d3e1ce338bdc5">IMP::npctransport::Statistics::get_sd()</a>, <a href="classIMP_1_1npctransport_1_1Statistics.html#a39e3581c4eb09bf4c5b2a75883988fd9">IMP::npctransport::Statistics::get_sd()</a>, <a href="namespaceIMP_1_1npctransport.html#a2af95d49ecd90f72d94b6122fec8d405">IMP::npctransport::startup()</a></td></tr>
279 <tr><td>@ref IMP::npctransport::SlabWithCylindricalPore</td><td><a href="classIMP_1_1npctransport_1_1SlabWithCylindricalPore.html#ab7769e4e0926ac132d52799e5bbe9f61">IMP::npctransport::SlabWithCylindricalPore::setup_particle()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithCylindricalPore.html#ae301271e74499f0d8647fdb74b363eb7">IMP::npctransport::SlabWithCylindricalPore::setup_particle()</a></td></tr>
280 <tr><td>@ref IMP::npctransport::SlabWithPore</td><td><a href="classIMP_1_1npctransport_1_1SlabWithPore.html#af5cb3804ddf53f76ddb8db8086a039d2">IMP::npctransport::SlabWithPore::setup_particle()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithPore.html#ac03d4e35c9c772fff4d300d4155d23f1">IMP::npctransport::SlabWithPore::setup_particle()</a></td></tr>
281 <tr><td>@ref IMP::npctransport::SlabWithToroidalPore</td><td><a href="classIMP_1_1npctransport_1_1SlabWithToroidalPore.html#aaf307e24380fdacb3c205d5073d0144a">IMP::npctransport::SlabWithToroidalPore::setup_particle()</a>, <a href="classIMP_1_1npctransport_1_1SlabWithToroidalPore.html#abf6f1001e8f575785dae808b9f84dd6a">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_1SlabWithToroidalPore.html#a8a9c2131c40596728442f99734f76485">IMP::npctransport::SlabWithToroidalPore::setup_particle()</a></td></tr>
282 <tr><td>@ref IMP::npctransport::Statistics</td><td><a href="classIMP_1_1npctransport_1_1SimulationData.html#a2bab690e0137e2750c1458baef9acef2">IMP::npctransport::SimulationData::get_statistics()</a>, <a href="classIMP_1_1npctransport_1_1SimulationData.html#aebad5e9d8afb447e8c788aae93a7ef62">IMP::npctransport::SimulationData::get_statistics()</a></td></tr>
283 <tr><td>@ref IMP::npctransport::Transporting</td><td><a href="classIMP_1_1npctransport_1_1Transporting.html#adaa01fc8072a868df076503486fa4eaa">IMP::npctransport::Transporting::setup_particle()</a>, <a href="classIMP_1_1npctransport_1_1Transporting.html#a4040a253b333196bd955a5945a079283">IMP::npctransport::Transporting::setup_particle()</a></td></tr>
284 </table>
285 # IMP.pmi # {#factory_index_pmi}
286 <table><tr>
287 <th>Class</th><th>Factories</th></tr>
288 <tr><td>@ref IMP::pmi::Resolution</td><td><a href="classIMP_1_1pmi_1_1Resolution.html#afe33425fc9b6e30f6fef08e644ae23d6">IMP::pmi::Resolution::setup_particle()</a>, <a href="classIMP_1_1pmi_1_1Resolution.html#a84a147a105e3ddbb62ce6f357584eb3f">IMP::pmi::Resolution::setup_particle()</a></td></tr>
289 <tr><td>@ref IMP::pmi::Symmetric</td><td><a href="classIMP_1_1pmi_1_1Symmetric.html#ae95167db885a60e540bcf7b66abbdaac">IMP::pmi::Symmetric::setup_particle()</a>, <a href="classIMP_1_1pmi_1_1Symmetric.html#ad0242a6a4a42aee2d0e9624e3786f8c9">IMP::pmi::Symmetric::setup_particle()</a></td></tr>
290 <tr><td>@ref IMP::pmi::Uncertainty</td><td><a href="classIMP_1_1pmi_1_1Uncertainty.html#ab5afc06397b7e14477e106a2475d3706">IMP::pmi::Uncertainty::setup_particle()</a>, <a href="classIMP_1_1pmi_1_1Uncertainty.html#a3e69a9051e1acc2054c11ef0c731a805">IMP::pmi::Uncertainty::setup_particle()</a></td></tr>
291 </table>
292 # IMP.pmi1 # {#factory_index_pmi1}
293 <table><tr>
294 <th>Class</th><th>Factories</th></tr>
295 <tr><td>@ref IMP::pmi1::Resolution</td><td><a href="classIMP_1_1pmi1_1_1Resolution.html#a62ad0268fee3b17322401ca59937bc40">IMP::pmi1::Resolution::setup_particle()</a>, <a href="classIMP_1_1pmi1_1_1Resolution.html#a5355960e431eab4a7297ba993b900c18">IMP::pmi1::Resolution::setup_particle()</a></td></tr>
296 <tr><td>@ref IMP::pmi1::Symmetric</td><td><a href="classIMP_1_1pmi1_1_1Symmetric.html#a14e50dfbe30e8c3b38a9bba3b723bc9c">IMP::pmi1::Symmetric::setup_particle()</a>, <a href="classIMP_1_1pmi1_1_1Symmetric.html#a845729a7199d5724547652b7ca8170ee">IMP::pmi1::Symmetric::setup_particle()</a></td></tr>
297 <tr><td>@ref IMP::pmi1::Uncertainty</td><td><a href="classIMP_1_1pmi1_1_1Uncertainty.html#a27aa0f2676642cf2ec2d02285519684c">IMP::pmi1::Uncertainty::setup_particle()</a>, <a href="classIMP_1_1pmi1_1_1Uncertainty.html#addf4e0aa7e2f2a210ab57678f1dd01ae">IMP::pmi1::Uncertainty::setup_particle()</a></td></tr>
298 </table>
299 # IMP.rmf # {#factory_index_rmf}
300 <table><tr>
301 <th>Class</th><th>Factories</th></tr>
302 <tr><td>@ref IMP::rmf::SaveOptimizerState</td><td><a href="classIMP_1_1npctransport_1_1SimulationData.html#a6d48a4a0c2690d6d89ff537edfa2b85f">IMP::npctransport::SimulationData::get_rmf_sos_writer()</a></td></tr>
303 </table>
304 # IMP.rotamer # {#factory_index_rotamer}
305 <table><tr>
306 <th>Class</th><th>Factories</th></tr>
307 <tr><td>@ref IMP::rotamer::ResidueRotamer</td><td><a href="classIMP_1_1rotamer_1_1RotamerCalculator.html#a87f7878daf288370734d78479eaea929">IMP::rotamer::RotamerCalculator::get_rotamer()</a></td></tr>
308 </table>
309 # IMP.saxs # {#factory_index_saxs}
310 <table><tr>
311 <th>Class</th><th>Factories</th></tr>
312 <tr><td>@ref IMP::saxs::DeltaDistributionFunction</td><td><a href="classIMP_1_1saxs_1_1DerivativeCalculator.html#a9ebc76cc8dbdb3d16457bc4870f76a5e">IMP::saxs::DerivativeCalculator::precompute_derivative_helpers()</a></td></tr>
313 <tr><td>@ref IMP::saxs::FitParameters</td><td><a href="classIMP_1_1saxs_1_1ProfileFitter.html#afaa5cad2558d184e54d2255880ab156e">IMP::saxs::ProfileFitter::fit_profile()</a>, <a href="classIMP_1_1saxs_1_1ProfileFitter.html#aac32d65c66c88a72e95c19661698ed90">IMP::saxs::ProfileFitter::search_fit_parameters()</a></td></tr>
314 <tr><td>@ref IMP::saxs::FormFactorTable</td><td><a href="namespaceIMP_1_1saxs.html#a4376a2c676c4c92975cbb4df0cb6d294">IMP::saxs::get_default_form_factor_table()</a></td></tr>
315 <tr><td>@ref IMP::saxs::Profile</td><td><a href="classIMP_1_1saxs_1_1ProfileFitter.html#a99a3500f4b707258b6ee239500d74fea">IMP::saxs::ProfileFitter::get_profile()</a>, <a href="namespaceIMP_1_1saxs.html#a3088d29b90d6cefe75a9cf2bd68f340b">IMP::saxs::compute_profile()</a></td></tr>
316 <tr><td>@ref IMP::saxs::WeightedFitParameters</td><td><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#aa28fdf86378765d2cb980f811196a94e">IMP::multi_state::MultiStateModelScore::get_fit_parameters()</a>, <a href="classIMP_1_1multi__state_1_1SAXSMultiCombinationScore.html#aebebb3b7df28c7f9c61ecdc12dbb0ded">IMP::multi_state::SAXSMultiCombinationScore::get_fit_parameters()</a>, <a href="classIMP_1_1multi__state_1_1SAXSMultiCombinationScore.html#a7b23abb9e9677a63c80bc60078febc45">IMP::multi_state::SAXSMultiCombinationScore::get_fit_parameters()</a>, <a href="classIMP_1_1multi__state_1_1SAXSMultiStateModelScore.html#a5065007424e91c197ef31f8f199e1848">IMP::multi_state::SAXSMultiStateModelScore::get_fit_parameters()</a>, <a href="classIMP_1_1multi__state_1_1SAXSMultiStateModelScore.html#ad2127ecfecbf553e81fefbb3ee55f1a5">IMP::multi_state::SAXSMultiStateModelScore::get_fit_parameters()</a>, <a href="classIMP_1_1saxs_1_1WeightedProfileFitter.html#ac48627aa0a274cc70594d4ebc01195e8">IMP::saxs::WeightedProfileFitter::fit_profile()</a>, <a href="classIMP_1_1saxs_1_1WeightedProfileFitter.html#aa7fe6fec9fccc23b98b3c3c1742556f5">IMP::saxs::WeightedProfileFitter::search_fit_parameters()</a></td></tr>
317 </table>
318 # IMP.spb # {#factory_index_spb}
319 <table><tr>
320 <th>Class</th><th>Factories</th></tr>
321 <tr><td>@ref IMP::spb::EM2DRestraint</td><td><a href="namespaceIMP_1_1spb.html#ae9d0b23db782452a116f737439adcd0f">IMP::spb::em2d_restraint()</a>, <a href="namespaceIMP_1_1spb.html#a381a514f0f058cbd0c02028c3f2654ca">IMP::spb::em2d_restraint()</a></td></tr>
322 <tr><td>@ref IMP::spb::HelixDecorator</td><td><a href="classIMP_1_1spb_1_1HelixDecorator.html#a3bdcdea309db55d9a67bc6d2ed12a5ea">IMP::spb::HelixDecorator::setup_particle()</a></td></tr>
323 </table>
324 # IMP.statistics # {#factory_index_statistics}
325 <table><tr>
326 <th>Class</th><th>Factories</th></tr>
327 <tr><td>@ref IMP::statistics::HistogramD</td><td><a href="classIMP_1_1statistics_1_1HistogramD.html#ac2495b2cae91eceb541a71d405a8910a">IMP::statistics::HistogramD::get_frequencies()</a>, <a href="classIMP_1_1statistics_1_1HistogramD.html#a86b8234abcce13c45107b89edddda2c1">IMP::statistics::HistogramD::get_probability_distribution_function()</a></td></tr>
328 <tr><td>@ref IMP::statistics::PartitionalClustering</td><td><a href="classIMP_1_1statistics_1_1RecursivePartitionalClusteringEmbedding.html#ad985a95838650906b20fab33bf23b3ea">IMP::statistics::RecursivePartitionalClusteringEmbedding::create_full_clustering()</a>, <a href="classIMP_1_1statistics_1_1RecursivePartitionalClusteringMetric.html#a298cc8279d3029e200a24ce9fb247942">IMP::statistics::RecursivePartitionalClusteringMetric::create_full_clustering()</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#a19eae7a22f877948e0582872cb42e760">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>
329 <tr><td>@ref IMP::statistics::PartitionalClusteringWithCenter</td><td><a href="namespaceIMP_1_1statistics.html#a2ccc84a060553c450d17b18bce708436">IMP::statistics::create_bin_based_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></td></tr>
330 </table>
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
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
const SpherePatch3D & get_sphere_patch_3d_geometry(const SpherePatch3D &g)
Definition: SpherePatch3D.h:55
algebra::Segment3D get_segment_starting_at(const Vector3D &v, double d) const
Get segment of a given length starting at a point.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
static Symmetric setup_particle(Model *m, ParticleIndex pi, Float symmetric)
Definition: /Symmetric.h:44
Particle * get_particle(ParticleIndex p) const
Get the particle from an index.
Definition: Model.h:463
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
algebra::Rotation3D get_orientation(unsigned int i) const
Returns the orientation corresponding to the state i.
static Switching setup_particle(Model *m, ParticleIndex pi)
Definition: Switching.h:34
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
AtomType add_atom_type(std::string name, Element e)
Create a new AtomType.
An ensemble of fitting solutions.
PartitionalClusteringWithCenter * create_lloyds_kmeans(Embedding *embedding, unsigned int k, unsigned int iterations)
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Rotation3D get_rotation_about_normalized_axis(const Vector3D &axis_norm, double angle)
Definition: Rotation3D.h:410
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Particles create_dihedrals(Particles bonds) const
Auto-generate Dihedral particles from the passed list of Bond particles.
IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: PCAAligner.h:49
static Nuisance setup_particle(Model *m, ParticleIndex pi)
Definition: Nuisance.h:33
Rotation2D get_inverse() const
Return the matrix for the inverse rotation.
Definition: Rotation2D.h:62
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Add mass to a particle.
Definition: Mass.h:23
ParticleIndexes get_all_possible_indexes() const
Get contained particles.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Restraint * create_decomposition() const
Decompose this restraint into constituent terms.
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.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Abstract class for scoring object(s) of type ParticleIndexPair.
Definition: PairScore.h:44
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
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:248
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
A shared container for Pairs.
Definition: PairContainer.h:39
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const override
Transformation2D get_transformation_aligning_pair(const Vector2Ds &set_from, const Vector2Ds &set_to)
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
static CHARMMAtom setup_particle(Model *m, ParticleIndex pi, String charmm_type)
Create a decorator with the passed CHARMM type.
Definition: CHARMMAtom.h:37
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: CoverBond.h:35
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
static Charged setup_particle(Model *m, ParticleIndex pi, Float charge)
Definition: Charged.h:46
static Resolution setup_particle(Model *m, ParticleIndex pi, Float resolution)
Definition: /Resolution.h:45
CHARMMParameters * get_heavy_atom_CHARMM_parameters()
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
WeakPointer< IMP::atom::Simulator > get_owner() const
returns the simulator that was declared in the constructor or by
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const override
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: SettingsData.h:165
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
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.
static StructureSource setup_particle(Model *m, ParticleIndex pi, std::string source_id, std::string source_chain_id)
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: pdb.h:617
algebra::Transformation3D get_transformation_aligning_first_to_second(XYZsOrVector3ds a, XYZsOrVector3ds b)
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: pdb.h:405
A Monte Carlo optimizer.
Definition: MonteCarlo.h:45
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: NormalMover.h:55
Simple 3D transformation class.
const DensityHeader * get_header() const
Returns a read-only pointer to the header of the map.
Definition: DensityMap.h:245
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: GammaPrior.h:36
A decorator to associate a particle with a part of a protein.
Definition: Domain.h:21
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: predicates.h:131
static Provenance setup_particle(Model *m, ParticleIndex pi)
Definition: provenance.h:74
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
atom::Hierarchies get_fg_chains() const
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
static CenterOfMass setup_particle(Model *m, ParticleIndex pi, ParticleIndexesAdaptor members)
Definition: CenterOfMass.h:81
static Dihedral setup_particle(Model *m, ParticleIndex pi, core::XYZ a, core::XYZ b, core::XYZ c, core::XYZ d)
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: core/Harmonic.h:43
ExtendedGridIndexD< D > get_end_index() const
Get the past-end voxel.
Definition: grid_ranges.h:142
Add weights to a particle.
Definition: Weight.h:29
Chain get_chain(Hierarchy h)
Get the containing chain or Chain() if there is none.
Hierarchy get_parent() const
Get the parent particle.
static CustomXYZR setup_particle(Model *m, ParticleIndex pi, DecoratorTraits tr=get_default_decorator_traits())
Definition: CustomXYZR.h:49
atom::Hierarchy get_root_of_type(core::ParticleType type) const
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
static Transporting setup_particle(Model *m, ParticleIndex pi, bool is_last_entry_from_top=false)
Definition: Transporting.h:63
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Represent an RGB color.
Definition: Color.h:25
A decorator to associate a particle with a part of a protein/DNA/RNA.
Definition: Fragment.h:20
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: pdb.h:163
Key & operator++()
Definition: Key.h:239
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Vector< AtomTypes > get_chi_dihedral_atom_types(ResidueType rt)
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: Simplex.h:67
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: GeometrySet.h:29
ExtendedGridIndexD< D > get_maximum_extended_index() const
Return the index of the maximal cell.
Definition: grid_ranges.h:270
ParticlesTemp get_non_optimizable_beads()
static Gaussian setup_particle(Model *m, ParticleIndex pi)
Definition: core/Gaussian.h:65
Atoms get_phi_dihedral_atoms(Residue rd)
Return the atoms comprising the phi dihedral.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: embeddings.h:42
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: pdb.h:337
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.
Simple implementation of lines in 3D.
Definition: Line3D.h:29
Particle * get_slab_particle() const
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual std::vector< DOFValues > plan(DOFValues q_from, DOFValues q_rand, ScoringFunction *sf) override
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: QuasiNewton.h:49
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: pdb.h:244
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: TableRefiner.h:45
Particles density2particles(DensityMap *dmap, Float threshold, Model *m, int step=1)
Convert a density grid to a set of particles.
Direction get_direction() const
Get the surface being moved.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Score based on the min or max PairScore over a set.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: XYZR.h:158
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const override
IMP::PairScore const * get_predicate_pair_score(core::ParticleType t1, core::ParticleType t2) const
returns the pair score for particles of types t1 and t2 */
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
static RigidBodyDiffusion setup_particle(Model *m, ParticleIndex pi)
Definition: Diffusion.h:157
Track creation of a system fragment from running some software.
Definition: provenance.h:562
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
const Vector< double > & get_form_factors(Particle *p, FormFactorType ff_type=HEAVY_ATOMS) const
full form factor for reciprocal space profile calculation
Rotation3D get_rotation_from_x_y_axes(const Vector3D &x, const Vector3D &y)
const VectorD< D > & get_corner(unsigned int i) const
For 0 return lower corner and for 1, the upper corner.
Definition: BoundingBoxD.h:140
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: SitesGeometry.h:36
const Transformation3D & get_transformation_from() const
Return the transformation from global to local coordinates.
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)
virtual ParticleIndexes get_indexes() const =0
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
BoundingBoxD< 3 > get_bounding_box(const Plane3D &g)
Definition: Plane3D.h:86
ParticlesTemp create_particles(RMF::FileConstHandle fh, Model *m)
algebra::BoundingBoxD< 3 > get_bounding_box(const DensityMap *m, Float threshold)
Get the bounding box for a map.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
atom::Hierarchies create_hierarchies(RMF::FileConstHandle fh, Model *m)
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const override
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: Linear.h:41
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: em/embedding.h:28
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Hierarchy create_clone(Hierarchy d)
Clone the Hierarchy.
Particles add_bonds(Hierarchy hierarchy) const
Add bonds to the given Hierarchy using this topology, and return them.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
DensityMap * bayesem3d_get_density_from_particle(DensityMap *em, const IMP::ParticlesTemp &ps, double resolution, const double window_size=1.0)
ParticleIndexes get_all_possible_indexes() const override
Get contained particles.
A decorator for an angle between two directions.
Definition: direction.h:84
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
static const HierarchyTraits & get_default_traits()
Get the default hierarchy traits.
Hierarchy create_simplified_from_volume(Hierarchy h, double resolution)
A connection (bond, angle, dihedral) between some number of endpoints.
Rotation3D get_rotation_from_fixed_xyz(double xr, double yr, double zr)
Initialize a rotation in x-y-z order from three angles.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: SettingsData.h:114
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
DensityMap * pad_margin(int mrg_x, int mrg_y, int mrg_z, float val=0.0)
Create a new padded map.
A member of a rigid body, it has internal (local) coordinates.
Definition: rigid_bodies.h:634
IMP::Particle * create(std::string name="")
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: pdb.h:188
virtual RestraintInfo * get_static_info() const
Definition: Restraint.h:178
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Add resolution to a particle.
Definition: /Resolution.h:24
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
algebra::BoundingBoxD< 3 > get_bounding_box(const Hierarchy &h)
Get a bounding box for the Hierarchy.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Represent an ellipsoid in 3D.
Definition: Ellipsoid3D.h:23
VectorD< 3 > get_random_vector_on_unit_sphere()
A decorator for a particle with x,y,z coordinates and a radius.
Definition: CustomXYZR.h:24
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
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:246
RestraintInfo * get_static_info() const override
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Simple RRT node implementation.
Definition: RRT.h:35
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Vector< char > write_particles_to_buffer(const ParticlesTemp &particles, const FloatKeys &keys)
return a binary buffer with the data
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
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 ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: pdb.h:258
static Fragment setup_particle(Model *m, ParticleIndex pi)
Definition: Fragment.h:67
const Vector< double > & get_water_dummy_form_factors() const
full water dummy form factor
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Particles add_dihedrals(Hierarchy hierarchy) const
Add dihedrals to the given Hierarchy using this topology, and return them.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Represent a rotation in 2D space.
Definition: Rotation2D.h:37
const Rotation2D get_rotation() const
Return the rotation.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: pdb.h:63
A particle that has an associated reference particle.
Definition: core/symmetry.h:23
Parameters of a fit, from ProfileFitter.
Definition: FitParameters.h:16
VectorD< D > get_zero_vector_kd(int Di)
Return a dynamically sized vector of zeros.
Definition: VectorD.h:280
Calculates and stores Gaussian kernel parameters.
static Weight setup_particle(Model *m, ParticleIndex pi)
Set up an empty Weight.
Definition: Weight.h:48
ParticleIndexes get_simulation_particle_indexes() const
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Rotation2D compose(const Rotation2D &a, const Rotation2D &b)
Compose two rotations a and b.
Definition: Rotation2D.h:121
static Symmetric setup_particle(Model *m, ParticleIndex pi, Float symmetric)
Definition: Symmetric.h:44
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: BoxedMover.h:39
static XYZR setup_particle(Model *m, ParticleIndex pi)
Definition: XYZR.h:48
The base class for geometry.
static Direction setup_particle(Model *m, ParticleIndex pi, algebra::Vector3D v)
Definition: direction.h:29
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
IMP::core::RigidBody create_compatible_rigid_body(Hierarchy h, Hierarchy reference)
Rigidify a molecule or collection of molecules.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: MCCGSampler.h:120
A decorator for a particle which has bonds.
Hierarchy create_simplified_along_backbone(Hierarchy input, int num_res, bool keep_detailed=false)
An exception for an invalid type being passed to IMP.
Definition: exception.h:146
XYZRs create_xyzr_particles(Model *m, unsigned int num, Float radius, Float box_side=10)
Create a set of particles with random coordinates.
algebra::Transformation3D get_transformation(unsigned int i) const
Get the score of the i'th solution.
Definition: rigid_fitting.h:61
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.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
An exception that signifies some event occurred.
Definition: exception.h:203
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: predicates.h:59
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
A class to store a fixed array of same-typed values.
Definition: Array.h:35
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: DensityMap.h:431
IMP::ScoringFunction * get_scoring_function(bool force_update=false)
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
IMP::algebra::Rotation3D get_rotation() const
Definition: rigid_bodies.h:208
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
ReferenceFrame3D get_local_reference_frame(const ReferenceFrame3D &v) const
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
VectorD< D > get_barycenter() const
Get center of mass on simplex in embedded coordinates.
Definition: UnitSimplexD.h:36
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Restraint * create_bounding_volume_restraint(SingletonContainerAdaptor beads) const
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Line3D get_opposite() const
Get the line in the opposite direction.
Definition: Line3D.h:62
virtual RestraintInfo * get_dynamic_info() const
Definition: Restraint.h:190
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Rotation3D operator/(const Rotation3D &r) const
Compute the rotation which when composed with r gives this.
Definition: Rotation3D.h:259
IMP::ParticleIndexPair make_unordered_particle_index_pair(IMP::ParticleIndex pi0, IMP::ParticleIndex pi1)
Definition: typedefs.h:45
A single atom in a CHARMM topology.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
const Vector< double > & get_vacuum_form_factors(Particle *p, FormFactorType ff_type=HEAVY_ATOMS) const
for reciprocal space profile calculation
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.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Represent a real cell in a grid (one within the bounding box)
Definition: grid_indexes.h:170
IMP::npctransport::SimulationData * startup(int argc, char *argv[])
IMP::Particle * get_bead(unsigned int i) const
get the i'th bead in the chain (assume valid root)
Definition: FGChain.h:128
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
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
A simple class for returning XYZ Euler angles.
Definition: Rotation3D.h:592
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
static LennardJones setup_particle(Model *m, ParticleIndex pi)
Definition: LennardJones.h:36
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: pdb.h:104
RestraintInfo * get_static_info() const override
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: embeddings.h:101
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Storage of anchors (points and edges)
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
atom::Hierarchies get_fg_chain_roots() const
Triangle3D get_largest_triangle(const Vector3Ds &points)
Return the largest triangle defined by 3 points from the input.
Transformation2D get_inverse() const
Return the inverse transformation.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
ParticlesTemp get_obstacle_particles() const
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: SettingsData.h:56
An exception for an invalid usage of IMP.
Definition: exception.h:122
RestraintInfo * get_static_info() const override
A decorator for a particle that represents a direction in 3D.
Definition: direction.h:23
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: ChiScore.h:34
static StructureProvenance setup_particle(Model *m, ParticleIndex pi, std::string filename, std::string chain_id, int residue_offset)
Definition: provenance.h:157
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Model * get_model() const
Returns the Model containing the particle.
Definition: Decorator.h:214
Color get_rgb_color(double f)
Return the color for f from the RGB color map.
A particle that is the geometric centroid of other particles.
virtual ScoringFunction * create_scoring_function(double weight=1.0, double max=NO_MAX) const
Create a scoring function with only this restraint.
IMP::Restraint * create_z_bias_restraint(SingletonContainerAdaptor ps, double k) const
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
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.
Gaussian3D get_gaussian_from_covariance(const Eigen::Matrix3d &covariance, const Vector3D &center)
Return a Gaussian centered at the origin from a covariance matrix.
DensityMap * mask_and_norm(em::DensityMap *dmap, em::DensityMap *mask)
Return a masked density, and normalize the output map within the mask region.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: pdb.h:90
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
An index in an infinite grid on space.
Definition: grid_indexes.h:31
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Applies a PairScore to each Pair in a list based on a predicate.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: SerialMover.h:54
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
A voxel grid in d-dimensional space.
Definition: GridD.h:79
Stores a set of SingletonContainers.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: pdb.h:323
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
stores the anchors sampling space for each protein
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: ExampleObject.h:50
Provenance create_clone(Provenance p)
Clone provenance (including previous provenance)
virtual ParticleIndexes const & get_refined_indexes_by_ref(Model *m, ParticleIndex pi) const override
Return the indexes of the particles returned by get_refined()
Definition: FixedRefiner.h:61
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: MonteCarlo.h:268
Vector< double > get_solvent_accessibility(const core::XYZRs &points, double probe_radius=1.8, double density=5.0)
estimate surface accessibility of each atom.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: core/symmetry.h:68
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: Model.h:617
algebra::Plane3D get_plane() const
Get a plane that lies along the surface.
Definition: Surface.h:117
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:224
RestraintInfo * get_dynamic_info() const override
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
A decorator for a particle transporting through a barrier.
Definition: Transporting.h:23
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 ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: UniformPrior.h:46
Display a Surface particle as a cylindrical disk.
Definition: Surface.h:169
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
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
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
A simple list of fitting solutions.
Definition: rigid_fitting.h:43
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Atoms get_omega_dihedral_atoms(Residue rd)
Return the atoms comprising the omega dihedral.
const ParticleIndexes & get_neighbors(ParticleIndex pi) const
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
DensityMap * get_threshold_map(const DensityMap *orig_map, float threshold)
Return a map with 0 for all voxels below the threshold.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
DensityMap * get_segment_by_masking(DensityMap *map_to_segment, DensityMap *mask, float mas_threshold)
Get a segment of the map covered by another map.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Transformation3D get_transformation_from_first_triangle_to_second(Triangle3D first_tri, Triangle3D second_tri)
Return a transformation between two triangles.
ParticleIndexes get_all_possible_indexes() const override
Get contained particles.
Add symmetric attribute to a particle.
Definition: Symmetric.h:23
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const override
Assignment get_nearest_assignment(const Subset &s, const algebra::VectorKD &embedding, ParticleStatesTable *pst)
Return the nearest assignment from an embedding.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
DensityMap * create_density_map(algebra::DenseGrid3D< float > &grid)
Return a density map with the values taken from the grid.
static State setup_particle(Model *m, ParticleIndex pi, unsigned int index)
Definition: State.h:39
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: Particle.h:50
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Base class for writing geometry to a file.
Definition: Writer.h:28
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: Selection.h:361
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
ChainType get_chain_type() const
Return the chain type.
Definition: Chain.h:122
ParticlesTemp get_particles(Model *m, const ParticleIndexes &ps)
Get the particles from a list of indexes.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ParticleIndexes get_range_indexes() const =0
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Represent a cylinder in 3D.
Definition: Cylinder3D.h:27
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
ParticleIndexes get_all_possible_indexes() const override
Get contained particles.
BoundingBoxD< 3 > get_bounding_box(const Cylinder3D &g)
Definition: Cylinder3D.h:85
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Bond get_bond(unsigned int i) const
Get a Bond of the ith bond.
IMP::ParticlesTemp get_beads() const
get the beads of the chain (assume valid root)
Definition: FGChain.h:124
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const override
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
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.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: KinkPairScore.h:36
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.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: FitRestraint.h:73
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
ExtendedGridIndexD< D > get_extended_index(const VectorD< D > &o) const
Return the index that would contain the voxel if the grid extended there.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Add scale parameter to particle.
Definition: Scale.h:24
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
static SlabWithPore setup_particle(Model *m, ParticleIndex pi, double thickness, double pore_radius)
Definition: SlabWithPore.h:70
Represent a subset of the particles being optimized.
Definition: Subset.h:33
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: pdb.h:229
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
The type of an atom.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: metrics.h:30
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: FGChain.h:186
static Surface setup_particle(Model *m, ParticleIndex pi)
Definition: Surface.h:45
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Add uncertainty to a particle.
Definition: Uncertainty.h:24
A score on the distance between the surfaces of two spheres.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Atoms get_charmm_untyped_atoms(Hierarchy hierarchy)
Get all atoms in the Hierarchy that do not have CHARMM types.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
RestraintSet * get_restraint_set()
Get the restraints set up by add_all_restraints().
Statistics and order parameters about the simulations.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
FormFactorTable * get_default_form_factor_table()
RestraintInfo * get_static_info() const override
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)
algebra::ReferenceFrame3D get_reference_frame() const
Get surface orientation as a reference frame.
const Plane3D & get_plane_3d_geometry(const Plane3D &g)
Definition: Plane3D.h:86
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Hierarchy create_fragment(const Hierarchies &ps)
Create a fragment containing the specified nodes.
virtual ParticleIndexes get_all_possible_indexes() const override
Get contained particles.
PartitionalClustering * create_gromos_clustering(Metric *d, double cutoff)
em::ImageHeader & get_header()
Definition: Image.h:94
static Domain setup_particle(Model *m, ParticleIndex pi, Domain other)
Definition: Domain.h:61
DynamicListTripletContainer * add_predicate(TripletPredicate *predicate, int value)
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:151
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Color get_hot_color(double f)
Return the color for f from the hot color map.
Atom get_atom(Residue rd, AtomType at)
Return a particle atom from the residue.
Add helix parameters to a particle.
RestraintInfo * get_static_info() const override
Represent a triangle in 3D.
Definition: Triangle3D.h:24
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Surface get_surface() const
Get the surface being moved.
Definition: SurfaceMover.h:71
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Stores a set of QuadContainers.
static XYZ setup_particle(Model *m, ParticleIndex pi)
Definition: XYZ.h:51
ParticleIndexPair get_contribution_particle_indexes(int i) const
Get the particle indexes from a contribution.
RestraintInfo * get_static_info() const override
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Hierarchies get_children() const
Return the children in the order they were added.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
SampledDensityMap * get_model_dens_map() const
Return the predicted density map of the model.
Definition: FitRestraint.h:67
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Restraint * create_excluded_volume(Model *m, const ParticleIndexes &ps, double k, std::string name)
virtual const ParticlesTemp get_refined(Particle *) const override
Refine the passed particle into a set of particles.
A more IMP-like version of the std::vector.
Definition: Vector.h:42
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: RestraintSet.h:68
TextOutput create_temporary_file(std::string prefix="imp_temp", std::string suffix="")
Create a temporary file. The path can be extracted from the TextOutput.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: pdb.h:177
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.
The end of a bond, angle, dihedral, improper, or internal coordinate.
A class storing the rotated coordinates of the atoms in the residue.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: QuadRestraint.h:60
VectorD< D > get_basis_vector_kd(int Di, unsigned int coordinate)
Return the basis vector for the given coordinate.
Definition: VectorD.h:240
Plane3D get_base_plane() const
Get the plane supporting the base of the cone.
UnaryFunction * get_function(unsigned int i)
Get function at index.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Restraint * get_bounding_volume_restraint(bool update=false)
static Uncertainty setup_particle(Model *m, ParticleIndex pi, Float uncertainty)
Definition: Uncertainty.h:45
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
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.
ParticlesTemp get_output_particles(const ModelObjectsTemp &mos)
Return all the output particles for a given ModelObject.
virtual const ParticlesTemp get_refined(Particle *p) const override
Returns the fixed set of particles.
RestraintInfo * get_static_info() const override
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
ParticleIndexPair get_contribution(int i) const
Get the particles in a contribution.
static SlabWithCylindricalPore setup_particle(Model *m, ParticleIndex pi, double thickness, double radius)
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
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:99
A reference frame in 3D.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Add switching parameter to particle.
Definition: Switching.h:23
Add resolution to a particle.
Definition: Resolution.h:24
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: pdb.h:149
CHARMM force field parameters.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: pdb.h:203
static Centroid setup_particle(Model *m, ParticleIndex pi, ParticleIndexesAdaptor members)
VectorD< D > get_ones_vector_kd(unsigned int Di, double v=1)
Return a vector of ones (or another constant)
Definition: VectorD.h:313
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Object used to hold a set of restraints.
Definition: RestraintSet.h:41
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 ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Implement a constraint on the Model.
Definition: Constraint.h:49
A particle which covers a set of other particles.
Definition: CoverRefined.h:72
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
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.
Rotation3D get_rotation_about_axis(const Vector3D &axis, double angle)
Generate a Rotation3D object from a rotation around an axis.
Definition: Rotation3D.h:436
SphereGeometry * create_geometry(const algebra::Sphere3D &t, std::string name="algebra::Sphere3D"+"%1""%")
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: Joint.h:33
Class for storing model, its restraints, constraints, and particles.
Definition: Model.h:86
Filter atom pairs for SOAP.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: PairRestraint.h:60
Segment3D get_shortest_segment(const Segment3D &s, const Vector3D &p)
DOF const * get_dof(unsigned int i) const
Returns the i'th dof over which this sampler works.
Definition: DOFsSampler.h:59
An input/output exception.
Definition: exception.h:173
Object * get_data(ModelKey mk) const
Get back some data stored in the model.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
A decorator for a point particle that has an electrostatic charge.
Definition: Charged.h:31
ModelObjectsTemps get_interactions() const
Get the interacting sets induced by this ModelObject.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: FStudentT.h:149
static SlabWithToroidalPore setup_particle(Model *m, ParticleIndex pi, double thickness, double major_radius)
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
A simple decorator which adds a name to a particle.
Hierarchies read_multimodel_mmcif(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector())
Read all models from the mmCIF file.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
ParticleIndexes get_particle_indexes_value(unsigned i) const
Get the value for the ith ParticleIndexes mapping.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: DihedralMover.h:36
RestraintInfo * get_static_info() const override
Restraint * create_current_decomposition() const
Decompose this restraint into constituent terms for the current conf.
const Rotation3D & get_rotation() const
Return the rotation associated with this transformation.
Class for handling density maps.
Definition: DensityMap.h:95
Store a subset of a subset or assignment.
Definition: Slice.h:30
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
IMP::algebra::BoundingBoxD< 3 > calculate_particles_bounding_box(const Particles &ps)
Calculate the parameters of the particles bounding box.
ParticlesTemp get_selected_particles(bool with_representation=true) const
Get the selected particles.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
IMP::algebra::Transformation3D get_transformation_aligning_first_to_second(const Vector3DsOrXYZs0 &source, const Vector3DsOrXYZs1 &target)
Compute the rigid transform bringing the first point set to the second.
Transformation2D get_rotation_about_point(const Vector2D &point, const Rotation2D &rotation)
Generate a Transformation2D object from a rotation around a point.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Base class for a simple primitive-like type.
Definition: Value.h:23
Add uncertainty to a particle.
Definition: /Uncertainty.h:24
A Gaussian distribution in 3D.
Definition: Gaussian3D.h:25
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: predicates.h:98
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Provenance get_previous() const
Definition: provenance.h:45
Class for sampling a density map from particles.
DynamicListPairContainer * add_predicate(PairPredicate *predicate, int value)
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Representation of one degree of freedom (DOF).
Definition: DOF.h:31
A decorator for keeping track of copies of a molecule.
Definition: Copy.h:28
The class represents a molecule as shells of distance from the surface.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
ReferenceFrame3D get_global_reference_frame(const ReferenceFrame3D &v) const
virtual RestraintInfo * get_static_info() const override
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: DOFsSampler.h:18
Abstract class for scoring object(s) of type ParticleIndexQuad.
Definition: QuadScore.h:44
Bonds get_internal_bonds(Hierarchy mhd)
Get the bonds internal to this tree.
RestraintInfo * get_static_info() const override
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: Image.h:155
Store strings describing the source of this structure fragment.
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.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: SubsetMover.h:59
Rotation3D get_random_rotation_3d()
Pick a rotation at random from all possible rotations.
algebra::Transformation3D get_transformation(unsigned int image_number) const
Get transformation that best places the model on the image.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
DensityMap * get_resampled(DensityMap *input, double scaling)
Get a resampled version of the map.
BoundingBoxD< 3 > get_bounding_box(const Segment3D &g)
Definition: Segment3D.h:53
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Particle * get_particle(unsigned int i) const
Get ith direction particle.
Vector2D operator*(const Vector2D &v) const
Perform the transformation on a 2D vector.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: pdb.h:358
Scoring associated with a SimulationData object.
Definition: Scoring.h:47
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: WeightedSum.h:76
Simple Brownian dynamics simulator.
ParticleIndexPair get_contribution_sigma_indexes(int i) const
Get the sigma particle indexes from a contribution.
Image * get_projection(unsigned int i) const
Returns the projection corresponding to the state i;.
PartitionalClustering * create_diameter_clustering(Metric *d, double maximum_diameter)
ParticlesTemp get_non_optimizable_particles(ParticlesTemp const &particles)
Hierarchy get_root(Hierarchy h)
Return the root of the hierarchy.
static FilterProvenance setup_particle(Model *m, ParticleIndex pi, std::string method, double threshold, int frames)
Definition: provenance.h:416
Restraint * create_slab_restraint(SingletonContainerAdaptor beads) const
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Hierarchy get_parent() const
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
A decorator for a representation.
core::XYZR create_cover(const Selection &s, std::string name=std::string())
A particle that describes an angle between three particles.
UnaryFunction * get_function(unsigned int i)
Get function at index.
Definition: WeightedSum.h:71
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: embeddings.h:75
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
const Cone3D & get_cone_3d_geometry(const Cone3D &g)
Definition: Cone3D.h:71
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const override
The standard decorator for manipulating molecular structures.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
A Cartesian vector in D-dimensions.
Definition: VectorD.h:56
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
RestraintSet * create_elastic_network(const Particles &ps, Float dist_cutoff, Float strength)
Create an elastic network restraint set.
Definition: pmi/utilities.h:26
Common base class for heavy weight IMP objects.
Definition: Object.h:111
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
DensityMap * multiply(const DensityMap *m1, const DensityMap *m2)
Return a density map for which voxel i contains the result of m1[i]*m2[i].
ExtendedGridIndexD< D > get_minimum_extended_index() const
Return the ExtendedGridIndexD of all zeros.
Definition: grid_ranges.h:262
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
IMP::algebra::Transformation3D get_rotation_about_joint_in_parent_coordinates() const
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.
ParticleIndexes get_particle_indexes(ParticlesTemp const &particles)
StereochemistryPairFilter * get_full_pair_filter()
Get a PairFilter including everything from original topology.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: RMSDMetric.h:34
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()
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
PairScore * get_pair_score() const
Return the pair score used for scoring.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
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:238
Abstract class for scoring object(s) of type ParticleIndex.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual const ParticlesTemp get_refined(Particle *) const override
Refine the passed particle into a set of particles.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: pdb.h:300
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: EzRestraint.h:40
ScoreStates maintain invariants in the Model.
Definition: ScoreState.h:56
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
ParticlesTemp get_order(const Subset &s, const SubsetFilterTables &sft)
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: spb/Gaussian.h:49
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
static Mass setup_particle(Model *m, ParticleIndex pi, Float mass)
Definition: Mass.h:48
ExtendedGridIndexD< D > get_extended_index(const VectorD< D > &o) const
Return the index that would contain the voxel if the grid extended there.
Bond create_bond(Bonded a, Bonded b, Int t)
Connect the two wrapped particles by a bond.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
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.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Rotation2D get_identity_rotation_2d()
Build an identity rotation in 2D.
Definition: Rotation2D.h:103
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: StateAdaptor.h:31
Plane3D get_opposite() const
Return the plane with the opposite normal.
Definition: Plane3D.h:54
const IMP::algebra::VectorD< D > & get_point(unsigned int i) const
Get one of the endpoints.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Track creation of a system fragment by filtering.
Definition: provenance.h:340
PartitionalClustering * create_connectivity_clustering(Metric *metric, double dist)
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Add nuisance parameter to particle.
Definition: Nuisance.h:27
Rotation3D get_inverse() const
Return the rotation which undoes this rotation.
Definition: Rotation3D.h:234
SimulationData * get_sd()
Definition: Scoring.h:436
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
DensityHeader create_density_header(const algebra::BoundingBoxD< 3 > &bb, float spacing)
Create a header from a bounding box in 3D.
A base class for classes which perturb particles.
Storage of the results from an FFT fit.
Hierarchy get_residue(Hierarchy mhd, unsigned int index)
Get the residue with the specified index.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
ParticleIndexes get_selected_particle_indexes(bool with_representation=true) const
Get the indexes of the selected particles.
static Model * get_by_unique_id(uint32_t id)
Return the Model with the given unique ID.
Definition: Model.h:613
Base class for all optimizers.
Definition: Optimizer.h:48
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
BoundingBoxD< 3 > get_bounding_box(const Cone3D &g)
Definition: Cone3D.h:71
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
static Bonded setup_particle(Model *m, ParticleIndex pi)
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
static Hierarchy setup_particle(Model *m, ParticleIndex pi, DecoratorTraits tr=get_default_decorator_traits())
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
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
RestraintInfo * get_static_info() const override
const Transformation3D & get_transformation_to() const
Return transformation from local to global coordinates.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: LeavesRefiner.h:40
const VectorD< D > & get_unit_cell() const
Return the unit cell, relative to the origin.
The type for a residue.
SurfaceGeometry * create_geometry(const Surface s, std::string name=std::string("SurfaceGeometry%1%"))
Create a geometry from a Surface.
Definition: Surface.h:191
container::PredicatePairsRestraint * get_predicates_pair_restraint(bool update=false)
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: Flag.h:36
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Represent a cone in 3D.
Definition: Cone3D.h:32
const Cylinder3D & get_cylinder_3d_geometry(const Cylinder3D &g)
Definition: Cylinder3D.h:85
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Define the type for a type of hierarchy.
Rotation3D get_rotation_from_fixed_zyz(double Rot, double Tilt, double Psi)
Generate a rotation object from Euler Angles.
Restraint * get_slab_restraint(bool update=false)
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: PbcBoxedMover.h:39
algebra::BoundingBoxD< 3 > get_bounding_box(const XYZRs &ps)
Get the bounding box.
An exception for a request for an invalid member of a container.
Definition: exception.h:156
A class that holds DOF values for DOFs.
Definition: DOFValues.h:23
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Hierarchy get_previous_residue(Residue rd)
Return the residue from the same chain with one lower index.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
static ExampleDecorator setup_particle(Model *m, ParticleIndex pi, std::string name)
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Class for adding up scores during ScoringFunction evaluation.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
PairScore * get_pair_score() const
Return the pair score used for scoring.
SecondaryStructureResidue setup_coarse_secondary_structure_residue(const Particles &ssr_ps, Model *mdl, bool winner_takes_all_per_res=false)
Coarsen some SecondaryStructureResidues.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
const ParticleIndexes & get_member_particle_indexes() const
Definition: rigid_bodies.h:139
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
A sphere patch is defined as all points above the plane and on the sphere.
Definition: SpherePatch3D.h:19
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
VectorD< D > get_random_vector_in(const BoundingBoxD< D > &bb)
Generate a random vector in a box with uniform density.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
const Transformation2D & operator*=(const Transformation2D &o)
See help for operator*.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
DynamicListQuadContainer * add_predicate(QuadPredicate *predicate, int value)
BoundingBoxD<-1 > get_unit_bounding_box_kd(unsigned int d)
Box with radius one.
Definition: BoundingBoxD.h:194
RestraintInfo * get_static_info() const override
PartitionalClusteringWithCenter * create_bin_based_clustering(Embedding *embed, double side)
Simple 2D transformation class.
virtual ParticleIndexes get_refined_indexes(Model *m, ParticleIndex pi) const
Return the indexes of the particles returned by get_refined()
GridIndexD< D > get_index(const ExtendedGridIndexD< D > &i) const
requires get_has_index(i) is true.
Hierarchy read_mol2(TextInput mol2_file, Model *model, Mol2Selector *mol2sel=nullptr)
Create a hierarchy from a Mol2 file.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: pdb.h:126
static TAMDCentroid setup_particle(Model *m, ParticleIndex pi, ParticleIndexesAdaptor members)
Definition: TAMDCentroid.h:63
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: RRT.h:31
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Track creation of a system fragment from a PDB file.
Definition: provenance.h:86
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Color get_display_color(unsigned int i)
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Version and module information for Objects.
Definition: VersionInfo.h:29
Hierarchy create_clone_one(Hierarchy d)
Clone the node in the Hierarchy.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: Surface.h:232
static RelaxingSpring setup_particle(Model *m, ParticleIndex pi, ParticleIndex bonded_pi0, ParticleIndex bonded_pi1, double equilibrium_rest_length_factor, double rest_length_diffusion_coefficient)
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const override
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.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: Surface.h:188
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
RestraintInfo * get_static_info() const override
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: Transform.h:42
Holds header data for optimization.
Definition: SettingsData.h:135
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
A class to store a set of configurations of a model.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
A decorator for a particle with x,y,z coordinates.
Definition: XYZ.h:30
Stores a set of TripletContainers.
static Angle setup_particle(Model *m, ParticleIndex pi, core::XYZ a, core::XYZ b, core::XYZ c)
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: XYZR.h:158
A shared container for Quads.
Definition: QuadContainer.h:39
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
static Scale setup_particle(Model *m, ParticleIndex pi)
Definition: Scale.h:30
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: Scoring.h:727
ExtendedGridIndexD< D > get_extended_index(const GridIndexD< D > &index) const
Convert an index back to an extended index.
Definition: GridD.h:247
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: NOERestraint.h:48
static KinematicNode setup_particle(Model *m, ParticleIndex pi, KinematicForest *owner)
Definition: KinematicNode.h:36
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
DensityMap * get_max_map(DensityMaps maps)
Return a map where each voxel is the maximum value from the input maps.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
DensityMap * create_density_map(const DensityMap *other)
Create a copy of another map.
Bonded get_bonded(unsigned int i) const
Get the atom i of the bond.
A base class for Keys.
Definition: Key.h:45
DensityHeader * get_header_writable()
Returns a pointer to the header of the map in a writable version.
Definition: DensityMap.h:248
Restraint * create_internal_connectivity_restraint(const Selection &s, double k, std::string name="Connectivity%1%")
Create a restraint connecting the selection.
ProteomicsData * read_proteomics_data(const char *proteomics_fn)
Proteomics reader.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: Cosine.h:44
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:53
Holds data about the assembly density needed for optimization.
Definition: SettingsData.h:76
A shared container for Singletons.
A decorator for a particle that has a Lennard-Jones potential well.
Definition: LennardJones.h:26
Rotation3D get_interpolated(const Rotation3D &a, const Rotation3D &b, double f)
Interpolate between two rotations.
Definition: Rotation3D.h:630
static Voxel setup_particle(Model *m, ParticleIndex pi, algebra::Vector3D position, Float radius, Float density)
Definition: Voxel.h:39
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
The type for a chain.
Hierarchy get_child(unsigned int i) const
Get the ith child based on the order they were added.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
static SoftwareProvenance setup_particle(Model *m, ParticleIndex pi, std::string name, std::string version, std::string location)
Definition: provenance.h:627
Rotation3D get_rotation_from_vector4d(const VectorD< 4 > &v)
Compute a rotation from an unnormalized quaternion.
Definition: Rotation3D.h:503
BoundingBoxD<-1 > get_cube_kd(unsigned int d, double radius)
Cube with radius of length side.
Definition: BoundingBoxD.h:208
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
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
Rotation3D get_rotation_taking_first_to_second(const Vector3D &v1, const Vector3D &v2)
Create a rotation from the first vector to the second one.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
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 ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: anchor_graph.h:58
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Transformation3D operator/(const Transformation3D &b) const
Compute the transformation which, when composed with b, gives *this.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
static Colored setup_particle(Model *m, ParticleIndex pi, Color color)
Definition: Colored.h:62
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
DensityMap * get_binarized_interior(DensityMap *dmap)
Return a binarized map with 1 for voxels that are internal in the input map.
Report key:value information on restraints.
Definition: RestraintInfo.h:47
virtual const ParticlesTemp get_refined(Particle *a) const =0
Refine the passed particle into a set of particles.
Represent a torus in 3D.
Definition: Torus3D.h:26
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: FNormal.h:91
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: vonMises.h:64
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
const Vector< double > & get_water_vacuum_form_factors() const
full water vacuum form factor
ParticleIndexes get_all_possible_indexes() const
Get contained particles.
Rotation2D get_rotation_to_x_axis(const Vector2D &v)
Definition: Rotation2D.h:113
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
A CHARMM patch residue.
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
A decorator for a spring particle connecting two diffusing particles.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const override
Writer * create_writer(std::string filename)
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: WormLikeChain.h:42
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
A decorator for a particle that is part of a rigid body but not rigid.
Definition: rigid_bodies.h:768
Color get_gnuplot_color(double f)
Return colors using the gnuplot default color map.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: XYZR.h:151
static const IMP::core::HierarchyTraits & get_traits()
Get the molecular hierarchy HierarchyTraits.
Stores a set of PairContainers.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
static Resolution setup_particle(Model *m, ParticleIndex pi, Float resolution)
Definition: Resolution.h:45
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
A decorator for a particle that represents a surface, its coordinates, and orientation.
Definition: Surface.h:35
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
A particle that describes a dihedral angle between four particles.
static DirectionAngle setup_particle(Model *m, ParticleIndex pi, ParticleIndexPair ds)
Definition: direction.h:95
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: pdb.h:280
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: predicates.h:37
virtual ParticleIndexes get_refined_indexes(Model *m, ParticleIndex) const override
Returns the fixed set of particles, as indexes.
Definition: FixedRefiner.h:52
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
ParticleIndexes get_movable_particles() const
Particle * get_particle() const
Returns the particle decorated by this decorator.
Definition: Decorator.h:194
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)
RestraintInfo * get_static_info() const override
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: metrics.h:57
Store all parameters for a simulation.
static Uncertainty setup_particle(Model *m, ParticleIndex pi, Float uncertainty)
Definition: /Uncertainty.h:45
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
An axis-aligned bounding box.
Definition: BoundingBoxD.h:28
Transformation2D operator/(const Transformation2D &b) const
Compute the transformation d which, when composed with b, gives this one.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: PymolWriter.h:66
static Copy setup_particle(Model *m, ParticleIndex pi, Int number)
Create a decorator for the numberth copy.
Definition: Copy.h:42
3D rotation class.
Definition: Rotation3D.h:52
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Vector< Atoms > get_chi_dihedral_atoms(Residue rd)
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Transformation3D get_identity_transformation_3d()
Return a transformation that does not do anything.
const Segment3D & get_segment_3d_geometry(const Segment3D &g)
Definition: Segment3D.h:53
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
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 ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Joint that is parameterized as a dihedral angle between two planes.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: scores2D.h:67
Simple implementation of segments in 3D.
Definition: Segment3D.h:25
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
const Vector< double > & get_water_form_factors() const
full water form factor
RestraintInfo * get_dynamic_info() const override
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
RestraintSet * create_elastic_network(const Particles &ps, Float dist_cutoff, Float strength)
Create an elastic network restraint set.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
const Ellipsoid3D & get_ellipsoid_3d_geometry(const Ellipsoid3D &g)
Definition: Ellipsoid3D.h:53
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
A decorator for a residue with probability of secondary structure.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
ParticlesTemp get_optimizable_particles(ParticlesTemp const &particles)
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Use this to add an advanced flag to the program.
Definition: Flag.h:53
ParticlesTemp get_input_particles(const ModelObjectsTemp &mos)
Return all the input particles for a given ModelObject.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
HistogramD< D > get_probability_distribution_function() const
Definition: HistogramD.h:53
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Parameters of a weighted fit, from WeightedProfileFitter.
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.
SimulationData * get_simulation_data()
return SimulationData object associated with this factory
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
A decorator for a residue.
Definition: Residue.h:137
A rigid body that is connected by a joint to other rigid bodies.
Definition: KinematicNode.h:26
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ParticleIndexes get_all_possible_indexes() const =0
Get contained particles.
IMP::ScoringFunction * get_custom_scoring_function(const RestraintsTemp &extra_restraints, SingletonContainerAdaptor non_optimizable_beads, SingletonContainerAdaptor optimizable_beads, bool is_attr_interactions_on=true) const
Periodically dump the state of all associated objects into the RMF file.
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)
Rotation3D get_rotation_from_matrix(double m00, double m01, double m02, double m10, double m11, double m12, double m20, double m21, double m22)
Generate a Rotation3D object from a rotation matrix.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual const ParticlesTemp get_refined(Particle *) const override
Refine the passed particle into a set of particles.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Transformation3D get_transformation_3d(const Transformation2D &t2d)
Build a 3D transformation from a 2D one.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
RestraintInfo * get_static_info() const override
Vector3D operator*(const Vector3D &v) const
Apply transformation (rotate and then translate)
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Represents a scoring function on the model.
Base class for joints between rigid bodies in a kinematic tree.
Definition: Joint.h:29
RestraintInfo * get_dynamic_info() const override
Hierarchies read_multimodel_pdb(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector())
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Store a configuration of a subset.
Definition: Assignment.h:35
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
static CombineProvenance setup_particle(Model *m, ParticleIndex pi, int runs, int frames)
Definition: provenance.h:325
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
IMP::PairContainer * create_close_beads_container(SingletonContainerAdaptor non_optimiziable_beads, SingletonContainerAdaptor optimizable_beads) const
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
ParticlesTemp get_simulation_particles() const
Returns the set of particles used in the simulation.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
RestraintInfo * get_static_info() const override
atom::Hierarchies create_hierarchies_with_sites(RMF::FileConstHandle fh, Model *m)
The general base class for IMP exceptions.
Definition: exception.h:48
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Associate an integer "state" index with a hierarchy node.
Definition: State.h:27
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: CrossLinkData.h:64
static SecondaryStructureResidue setup_particle(Model *m, ParticleIndex pi, Float prob_helix, Float prob_strand, Float prob_coil)
algebra::Rotation3D get_rotation() const
Returns the rotation for the 3 projection angles.
Hierarchies get_hierarchies() const
Return the hierarchies that the Selection was constructed with.
Hierarchy get_representation(double resolution, RepresentationType type=BALLS)
Get children at the resolution closest to resolution of the passed type.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: LogWrapper.h:56
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
const Line3D & get_line_3d_geometry(const Line3D &g)
Definition: Line3D.h:77
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
const Transformation2D & operator/=(const Transformation2D &o)
See help for operator/.
RestraintInfo * get_static_info() const override
static Diffusion setup_particle(Model *m, ParticleIndex pi, Float D)
Setup the particle with the specified diffusion coefficient.
Definition: Diffusion.h:76
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
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.
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
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual VersionInfo get_version_info() const
Get information about the module and version of the object.
Definition: Object.h:206
static TAMDParticle setup_particle(Model *m, ParticleIndex pi, ParticleIndex pi_ref, Float tsf, Float fsf)
Definition: TAMDParticle.h:80
WeightedFitParameters fit_profile(ProfilesTemp partial_profiles, 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
fit profiles by optimization of c1/c2 and weights
algebra::VectorD< 4 > get_rotational_derivatives() const
Get the derivatives of the quaternion.
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.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Residue get_residue(Atom d, bool nothrow=false)
Return the Residue containing this atom.
Shared optimizer state that is invoked upon commitment of new coordinates.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: ChiScoreLog.h:43
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const override
Hierarchy get_root(Hierarchy h)
Return the root of the hierarchy.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: EnvelopeScore.h:63
Track creation of a system fragment from clustering.
Definition: provenance.h:426
A filter that excludes bonds, angles and dihedrals.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
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.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
static Reference setup_particle(Model *m, ParticleIndex pi, ParticleIndexAdaptor reference)
Definition: core/symmetry.h:32
Rotation3D get_identity_rotation_3d()
Return a rotation that does not do anything.
Definition: Rotation3D.h:371
BoundingBoxD< 3 > get_bounding_box(const Torus3D &g)
Definition: Torus3D.h:61
Color get_gray_color(double f)
Return the a grayscale value for f.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Class to handle individual particles of a Model object.
Definition: Particle.h:43
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
const VectorD< D > & get_unit_cell() const
Return the unit cell, relative to the origin.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: pdb.h:76
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
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.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Bond get_bond(Bonded a, Bonded b)
Get the bond between two particles.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: Profile.h:252
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
ParticleIndexes get_indexes(int predicate_value) const
Molecular dynamics optimizer on 1-D and 3-D particles.
Restraint * create_distance_restraint(const Selection &n0, const Selection &n1, double x0, double k, std::string name="Distance%1%")
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Add symmetric attribute to a particle.
Definition: /Symmetric.h:23
Hierarchies get_representations(RepresentationType type=BALLS)
Return all children at all resolutions.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ParticleIndexes get_all_possible_indexes() const override
Get contained particles.
Representation get_representation(Hierarchy h, bool nothrow=false)
Return the Representation object containing this hierarchy.
ParticleIndexes get_all_possible_indexes() const
Get contained particles.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: WeightMover.h:34
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
The topology of a single CHARMM segment in a model.
Color get_jet_color(double f)
Return the color for f from the jet color map.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: XYZR.h:170
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: FretData.h:58
ParticleIndexes get_particle_indexes()
Get all particle indexes.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: FixedRefiner.h:76
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.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: Configuration.h:46
A decorator for classifying particles in your system.
Definition: Typed.h:34
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: CellMover.h:35
static Key< ID > add_alias(Key< ID > old_key, std::string new_name)
Make new_name an alias for old_key.
Definition: Key.h:200
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
IMP::PairContainer * get_close_beads_container(bool update=false)
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
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 const ParticlesTemp get_refined(Particle *) const override
Refine the passed particle into a set of particles.
algebra::UnitSimplexKD get_unit_simplex() const
Get unit simplex on which weight vector lies.
virtual const IMP::algebra::Transformation3D & get_transformation_child_to_parent() const
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: HarmonicWell.h:61
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
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.
Store info for a chain of a protein.
Definition: Chain.h:61
const Vector< double > & get_dummy_form_factors(Particle *p, FormFactorType ff_type=HEAVY_ATOMS) const
for reciprocal space profile calculation
Bonded get_bonded(unsigned int i) const
Get a Bonded of the ith bonded particle.
virtual const ParticlesTemp get_refined(Particle *) const override
Refine the passed particle into a set of particles.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
RestraintInfo * get_static_info() const override
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Restraint * create_chain_restraint(Model *m, const ParticleIndexes &ps, double length_factor, double k, std::string name)
A decorator for helping deal with a generalized hierarchy.
ParticleIndexes get_member_indexes() const
Definition: rigid_bodies.h:165
ParticleIndexes get_all_possible_indexes() const override
Get contained particles.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
algebra::Gaussian3D get_gaussian() const
create Gaussian3D from these attributes
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: DOF.h:32
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
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.
Selection create_clone()
Make a clone of this Selection.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
A decorator for a diffusing particle with a diffusion coefficient.
Definition: Diffusion.h:36
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Track how parts of the system were created.
Definition: provenance.h:31
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.
const ParticleIndexes & get_body_member_particle_indexes() const
Definition: rigid_bodies.h:152
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
A decorator for a rigid body.
Definition: rigid_bodies.h:82
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: CoverRefined.h:61
The topology of a complete CHARMM model.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: MonteCarlo.h:250
BoundingBoxD< 3 > get_bounding_box(const Line3D &g)
Definition: Line3D.h:77
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: MonteCarlo.h:52
Dynamically build a histogram embedded in D-dimensional space.
Definition: HistogramD.h:27
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
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.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
DynamicListSingletonContainer * add_predicate(SingletonPredicate *predicate, int value)
Represent a plane in 3D.
Definition: Plane3D.h:21
virtual const IMP::algebra::Transformation3D & get_transformation_child_to_parent_no_checks() const
Definition: Joint.h:74
SoapPairFilter * get_pair_filter()
Get a filter that returns pairs that this score should use.
Hierarchies get_by_type(Hierarchy mhd, GetByType t)
Gather all the molecular particles of a certain level in the hierarchy.
algebra::Transformation3D get_internal_transformation() const
Definition: rigid_bodies.h:686
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: DominoSampler.h:46
StereochemistryPairFilter * get_pair_filter()
Get a PairFilter that excludes all stereochemical pairs.
Subset get_subset() const
Return the subset corresponding to all the particles.
ResidueRotamer get_rotamer(const IMP::atom::Residue &rd, double thr) const
get the coordinates of the residue atoms
An exception which is thrown when the Model has attributes with invalid values.
Definition: exception.h:188
Hierarchy create_simplified_assembly_from_volume(Hierarchy h, double resolution)
FGChain * get_fg_chain(atom::Hierarchy root)
Define and manipulate a kinematic structure over a model.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
container::PredicatePairsRestraint * create_predicates_pair_restraint(PairContainer *bead_pairs, bool is_attr_interactions_on=true) const
Abstract class for scoring object(s) of type ParticleIndexTriplet.
Definition: TripletScore.h:44
IMP::core::RigidBody create_rigid_body(const Hierarchies &h, std::string name=std::string("created rigid body"))
Rigidify a molecule or collection of molecules.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Tag part of the system to track how it was created.
Definition: provenance.h:632
Hierarchies get_leaves(Hierarchy h)
static Chain setup_particle(Model *m, ParticleIndex pi, std::string id)
Definition: Chain.h:81
CHARMMParameters * get_all_atom_CHARMM_parameters()
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ParticleIndexes get_all_possible_indexes() const override
Get contained particles.
Hierarchies get_leaves(const Selection &h)
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
An exception for an invalid value being passed to IMP.
Definition: exception.h:136
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.
Select which atoms to read from a PDB file.
Definition: pdb.h:43
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
PartitionalClustering * create_centrality_clustering(Metric *d, double far, int k)
A decorator for a molecule.
Definition: Molecule.h:24
ParticleIndexPair get_contribution_sigmas(int i) const
Get the sigma nuisances in a contribution.
static ScriptProvenance setup_particle(Model *m, ParticleIndex pi, std::string filename)
Definition: provenance.h:548
Select hierarchy particles identified by the biological name.
Definition: Selection.h:70
DOFValues get_sample() const
Definition: DOFsSampler.h:28
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
atom::BrownianDynamics * get_bd(bool recreate=false)
virtual ParticleIndexes get_all_possible_indexes() const override
Get contained particles.
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.
Helper class to aid in output of IMP classes to streams.
Definition: Showable.h:25
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
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.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: SurfaceMover.h:77
static RigidBody setup_particle(Model *m, ParticleIndex pi, ParticleIndexesAdaptor ps)
Definition: rigid_bodies.h:180
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const override
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
RestraintInfo * get_dynamic_info() const override
Slice get_slice(Restraint *r, const Subset &s) const
Return the slice for that restraint given the subset.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Rotation3D get_rotation_from_fixed_zxz(double phi, double theta, double psi)
Initialize a rotation from Euler angles.
ScoringFunction * get_scoring_function() const
Return the scoring function that is being used.
Definition: Sampler.h:42
Represent a sphere in D-dimensions.
Definition: SphereD.h:26
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: XYZR.h:151
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
GridIndexD< D > add_voxel(const ExtendedGridIndexD< D > &i, const VT &gi)
Add a voxel to the storage, this voxel will now have a GridIndex3D.
virtual ModelObjectsTemps do_get_interactions() const
Hierarchy get_next_residue(Residue rd)
Return the residue from the same chain with one higher index.
RestraintInfo * get_static_info() const override
const Profile * get_profile() const
Abstract single variable functor class for score functions.
Definition: UnaryFunction.h:27
CHARMMTopology * create_topology(Hierarchy hierarchy) const
Create topology that corresponds to the primary sequence of the Hierarchy.
rmf::SaveOptimizerState * get_rmf_sos_writer()
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: Surface.h:280
Restraint * create_connectivity_restraint(const Selections &s, double k, std::string name="Connectivity%1%")
Create a restraint connecting the selections.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Track creation of a system fragment from running a script.
Definition: provenance.h:511
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: pdb.h:428
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.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
ParticleIndexes get_all_possible_indexes() const override
Get contained particles.
Class for adding derivatives from restraints to the model.
static Vector< std::string > get_all_strings()
Get a list of all of the keys of this type.
A particle that is the center of mass of other particles.
Definition: CenterOfMass.h:33
A decorator for an atom that has a defined CHARMM type.
Definition: CHARMMAtom.h:24
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: SitesGeometry.h:52
Model * get_model()
return model associated with this factory
Transformation3D get_random_local_transformation(Vector3D origin, double max_translation=5., double max_angle_in_rad=0.26)
Get a local transformation.
2D Electron Microscopy images in IMP
Definition: Image.h:27
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Transformation2D get_identity_transformation_2d()
Return a transformation that does not do anything.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: pdb.h:381
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: XYZR.h:170
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Definition: LogPairScore.h:35
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
BoundingBoxD< 3 > get_bounding_box(const SpherePatch3D &g)
Definition: SpherePatch3D.h:55
A base class for clustering results where each item is in one cluster.
IMP::algebra::ReferenceFrame3D get_reference_frame() const
Definition: rigid_bodies.h:215
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
A restraint is a term in an IMP ScoringFunction.
Definition: Restraint.h:56
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
Slice get_slice(Subset outer, Subset inner, const Subsets &excluded)
Definition: Slice.h:76
Rotation2D get_random_rotation_2d()
Build an identity rotation in 2D.
Definition: Rotation2D.h:106
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
ScoringFunction * get_scoring_function() const
Return the scoring function that is being used.
Definition: Optimizer.h:106
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.
A particle with a color.
Definition: Colored.h:23
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
A decorator for a particle with x,y,z coordinates and a radius.
Definition: XYZR.h:27