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IMP Reference Guide  2.16.0
The Integrative Modeling Platform
class_example_index.md
1 Class Examples {#class_example_index}
2 ==============
3 
4 # Overview #
5 [TOC]
6 Examples that use a given class:
7 
8 See also [Factory Index](@ref factory_index), [Argument Index](@ref argument_index), [Class Examples](@ref class_example_index), [Function Examples](@ref function_example_index)
9 # IMP (kernel) # {#class_example_index_kernel}
10 <table><tr>
11 <th>Class</th><th>Examples</th></tr>
12 <tr><td>@ref IMP::ArgumentParser</td><td>[rotamer/rotamer_pdb2.py](rotamer_2rotamer_pdb2_8py-example.html), [rotamer/rotamer_pdb.py](rotamer_2rotamer_pdb_8py-example.html)</td></tr>
13 <tr><td>@ref IMP::Array</td><td>[atom/dope_and_excluded_volume.cpp](atom_2dope_and_excluded_volume_8cpp-example.html), [domino/marina_party.py](domino_2marina_party_8py-example.html)</td></tr>
14 <tr><td>@ref IMP::Container</td><td>[kernel/dependency_graph.py](kernel_2dependency_graph_8py-example.html)</td></tr>
15 <tr><td>@ref IMP::CreateLogContext</td><td>[log.py](log_8py-example.html)</td></tr>
16 <tr><td>@ref IMP::Decorator</td><td>[domino/marina_party.py](domino_2marina_party_8py-example.html)</td></tr>
17 <tr><td>@ref IMP::Flag</td><td>[flags.cpp](flags_8cpp-example.html)</td></tr>
18 <tr><td>@ref IMP::Index</td><td>[atom/dope_and_excluded_volume.cpp](atom_2dope_and_excluded_volume_8cpp-example.html), [core/simple.cpp](core_2simple_8cpp-example.html)</td></tr>
19 <tr><td>@ref IMP::Key</td><td>[container/filter_close_pairs.py](container_2filter_close_pairs_8py-example.html), [container/statistical.py](container_2statistical_8py-example.html), [domino/marina_party.py](domino_2marina_party_8py-example.html), [kernel/write_a_restraint.py](kernel_2write_a_restraint_8py-example.html), [kernel/write_an_optimizer_state.py](kernel_2write_an_optimizer_state_8py-example.html)</td></tr>
20 <tr><td>@ref IMP::Model</td><td>[BallMover.py](BallMover_8py-example.html), [atom/assess_dope.py](atom_2assess_dope_8py-example.html), [atom/cg_pdb.py](atom_2cg_pdb_8py-example.html), [atom/charmm_forcefield.py](atom_2charmm_forcefield_8py-example.html), [atom/charmm_forcefield_verbose.py](atom_2charmm_forcefield_verbose_8py-example.html), [atom/dope_and_excluded_volume.cpp](atom_2dope_and_excluded_volume_8cpp-example.html), [atom/edit_molecular_hierarchy.py](atom_2edit_molecular_hierarchy_8py-example.html), [atom/load_protein_restrain_bonds.py](atom_2load_protein_restrain_bonds_8py-example.html), [atom/markers.py](atom_2markers_8py-example.html), [atom/molecular_hierarchy.py](atom_2molecular_hierarchy_8py-example.html), [atom/multiresolution.py](atom_2multiresolution_8py-example.html), [atom/rigid_brownian_dynamics.py](atom_2rigid_brownian_dynamics_8py-example.html), [atom/score_protein_with_ligand.py](atom_2score_protein_with_ligand_8py-example.html), [atom/structure_from_sequence.py](atom_2structure_from_sequence_8py-example.html), [container/bipartite_nonbonded_interactions.py](container_2bipartite_nonbonded_interactions_8py-example.html), [container/connectivity.py](container_2connectivity_8py-example.html), [container/filter_close_pairs.py](container_2filter_close_pairs_8py-example.html), [container/nonbonded_interactions.py](container_2nonbonded_interactions_8py-example.html), [container/statistical.py](container_2statistical_8py-example.html), [core/XYZR_Decorator.py](core_2XYZR_Decorator_8py-example.html), [core/XYZ_Decorator.py](core_2XYZ_Decorator_8py-example.html), [core/connectivity_restraint.py](core_2connectivity_restraint_8py-example.html), [core/cover_particles.py](core_2cover_particles_8py-example.html), [core/custom_hierarchy.py](core_2custom_hierarchy_8py-example.html), [core/incremental_mc.py](core_2incremental_mc_8py-example.html), [core/ms_connectivity_restraint.py](core_2ms_connectivity_restraint_8py-example.html), [core/optimize_balls.py](core_2optimize_balls_8py-example.html), [core/randomize_rigid_body.py](core_2randomize_rigid_body_8py-example.html), [core/restrain_diameter.py](core_2restrain_diameter_8py-example.html), [core/restrain_in_sphere.py](core_2restrain_in_sphere_8py-example.html), [core/restrain_minimum_distance.py](core_2restrain_minimum_distance_8py-example.html), [core/rigid_bodies.py](core_2rigid_bodies_8py-example.html), [core/rigid_collisions.py](core_2rigid_collisions_8py-example.html), [core/simple.cpp](core_2simple_8cpp-example.html), [core/simple.py](core_2simple_8py-example.html), [core/symmetry.py](core_2symmetry_8py-example.html), [display/display_log.py](display_2display_log_8py-example.html), [display/displaying_ensembles.py](display_2displaying_ensembles_8py-example.html), [display/show_particles_as_spheres.py](display_2show_particles_as_spheres_8py-example.html), [domino/custom_filter.py](domino_2custom_filter_8py-example.html), [domino/domino_approach.py](domino_2domino_approach_8py-example.html), [domino/interactive.py](domino_2interactive_8py-example.html), [domino/interactive_with_containers.py](domino_2interactive_with_containers_8py-example.html), [domino/marina_party.py](domino_2marina_party_8py-example.html), [domino/merge_tree.py](domino_2merge_tree_8py-example.html), [domino/multiscale.py](domino_2multiscale_8py-example.html), [domino/restraint_cache.py](domino_2restraint_cache_8py-example.html), [domino/rigid_body_excluded_volume.py](domino_2rigid_body_excluded_volume_8py-example.html), [domino/save_assignments.py](domino_2save_assignments_8py-example.html), [domino/six_particles_optimization.py](domino_2six_particles_optimization_8py-example.html), [em2d/clustering_of_pdb_models.py](em2d_2clustering_of_pdb_models_8py-example.html), [em2d/collision_cross_section.py](em2d_2collision_cross_section_8py-example.html), [em2d/optimize_em2d_with_montecarlo.py](em2d_2optimize_em2d_with_montecarlo_8py-example.html), [em/analyze_convergence.py](em_2analyze_convergence_8py-example.html), [em/fit_restraint.py](em_2fit_restraint_8py-example.html), [em/generate_density_map_of_fixed_dimension.py](em_2generate_density_map_of_fixed_dimension_8py-example.html), [em/local_fitting.py](em_2local_fitting_8py-example.html), [em/pdb2density.py](em_2pdb2density_8py-example.html), [example/range_restriction.py](example_2range_restriction_8py-example.html), [gsl/simplex.py](gsl_2simplex_8py-example.html), [kernel/chain.py](kernel_2chain_8py-example.html), [kernel/dependency_graph.py](kernel_2dependency_graph_8py-example.html), [kernel/graph.py](kernel_2graph_8py-example.html), [kernel/setup.py](kernel_2setup_8py-example.html), [kernel/write_a_restraint.py](kernel_2write_a_restraint_8py-example.html), [kernel/write_an_optimizer_state.py](kernel_2write_an_optimizer_state_8py-example.html), [misc/decay.py](misc_2decay_8py-example.html), [modeller/imp_restraints_in_modeller.py](modeller_2imp_restraints_in_modeller_8py-example.html), [modeller/load_modeller_model.py](modeller_2load_modeller_model_8py-example.html), [modeller/modeller_restraints_in_imp.py](modeller_2modeller_restraints_in_imp_8py-example.html), [multistate.py](multistate_8py-example.html), [parallel/tasks.py](parallel_2tasks_8py-example.html), [pmi/ambiguity.py](pmi_2ambiguity_8py-example.html), [pmi/atomistic.py](pmi_2atomistic_8py-example.html), [pmi/automatic.py](pmi_2automatic_8py-example.html), [pmi/em.py](pmi_2em_8py-example.html), [pmi/ideal_helix.py](pmi_2ideal_helix_8py-example.html), [pmi/membrane.py](pmi_2membrane_8py-example.html), [pmi/multiscale.py](pmi_2multiscale_8py-example.html), [pmi/selection.py](pmi_2selection_8py-example.html), [pmi/symmetry.py](pmi_2symmetry_8py-example.html), [rmf/link.py](rmf_2link_8py-example.html), [rmf/multiresolution.py](rmf_2multiresolution_8py-example.html), [rmf/pdb.py](rmf_2pdb_8py-example.html), [rmf/simulation.py](rmf_2simulation_8py-example.html), [rotamer/rotamer_pdb2.py](rotamer_2rotamer_pdb2_8py-example.html), [rotamer/rotamer_pdb.py](rotamer_2rotamer_pdb_8py-example.html), [saxs/profile.py](saxs_2profile_8py-example.html), [saxs/profile_fit.py](saxs_2profile_fit_8py-example.html), [temperature_rem.py](temperature_rem_8py-example.html)</td></tr>
21 <tr><td>@ref IMP::ModelException</td><td>[core/rigid_collisions.py](core_2rigid_collisions_8py-example.html)</td></tr>
22 <tr><td>@ref IMP::Object</td><td>[log.py](log_8py-example.html)</td></tr>
23 <tr><td>@ref IMP::OptimizerState</td><td>[em2d/optimize_em2d_with_montecarlo.py](em2d_2optimize_em2d_with_montecarlo_8py-example.html), [kernel/write_an_optimizer_state.py](kernel_2write_an_optimizer_state_8py-example.html)</td></tr>
24 <tr><td>@ref IMP::PairPredicate</td><td>[container/filter_close_pairs.py](container_2filter_close_pairs_8py-example.html), [container/statistical.py](container_2statistical_8py-example.html)</td></tr>
25 <tr><td>@ref IMP::PairScore</td><td>[domino/marina_party.py](domino_2marina_party_8py-example.html)</td></tr>
26 <tr><td>@ref IMP::Particle</td><td>[atom/molecular_hierarchy.py](atom_2molecular_hierarchy_8py-example.html), [atom/rigid_brownian_dynamics.py](atom_2rigid_brownian_dynamics_8py-example.html), [core/XYZR_Decorator.py](core_2XYZR_Decorator_8py-example.html), [core/connectivity_restraint.py](core_2connectivity_restraint_8py-example.html), [core/custom_hierarchy.py](core_2custom_hierarchy_8py-example.html), [core/incremental_mc.py](core_2incremental_mc_8py-example.html), [core/ms_connectivity_restraint.py](core_2ms_connectivity_restraint_8py-example.html), [core/optimize_balls.py](core_2optimize_balls_8py-example.html), [core/randomize_rigid_body.py](core_2randomize_rigid_body_8py-example.html), [core/rigid_collisions.py](core_2rigid_collisions_8py-example.html), [core/symmetry.py](core_2symmetry_8py-example.html), [display/displaying_ensembles.py](display_2displaying_ensembles_8py-example.html), [domino/domino_approach.py](domino_2domino_approach_8py-example.html), [domino/interactive.py](domino_2interactive_8py-example.html), [domino/interactive_with_containers.py](domino_2interactive_with_containers_8py-example.html), [domino/marina_party.py](domino_2marina_party_8py-example.html), [domino/merge_tree.py](domino_2merge_tree_8py-example.html), [domino/multiscale.py](domino_2multiscale_8py-example.html), [domino/restraint_cache.py](domino_2restraint_cache_8py-example.html), [domino/save_assignments.py](domino_2save_assignments_8py-example.html), [em/analyze_convergence.py](em_2analyze_convergence_8py-example.html), [gsl/simplex.py](gsl_2simplex_8py-example.html), [kernel/dependency_graph.py](kernel_2dependency_graph_8py-example.html), [kernel/graph.py](kernel_2graph_8py-example.html), [kernel/setup.py](kernel_2setup_8py-example.html), [kernel/write_a_restraint.py](kernel_2write_a_restraint_8py-example.html), [parallel/tasks.py](parallel_2tasks_8py-example.html), [rmf/multiresolution.py](rmf_2multiresolution_8py-example.html), [rmf/simulation.py](rmf_2simulation_8py-example.html), [temperature_rem.py](temperature_rem_8py-example.html)</td></tr>
27 <tr><td>@ref IMP::Restraint</td><td>[kernel/dependency_graph.py](kernel_2dependency_graph_8py-example.html), [kernel/write_a_restraint.py](kernel_2write_a_restraint_8py-example.html)</td></tr>
28 <tr><td>@ref IMP::RestraintSet</td><td>[domino/domino_approach.py](domino_2domino_approach_8py-example.html), [em2d/optimize_em2d_with_montecarlo.py](em2d_2optimize_em2d_with_montecarlo_8py-example.html), [em/analyze_convergence.py](em_2analyze_convergence_8py-example.html), [kernel/write_an_optimizer_state.py](kernel_2write_an_optimizer_state_8py-example.html)</td></tr>
29 <tr><td>@ref IMP::ScopedSetAttribute</td><td>[core/optimize_balls.py](core_2optimize_balls_8py-example.html)</td></tr>
30 <tr><td>@ref IMP::ScoreState</td><td>[kernel/dependency_graph.py](kernel_2dependency_graph_8py-example.html)</td></tr>
31 <tr><td>@ref IMP::SetLogState</td><td>[domino/restraint_cache.py](domino_2restraint_cache_8py-example.html), [kernel/dependency_graph.py](kernel_2dependency_graph_8py-example.html), [log.py](log_8py-example.html)</td></tr>
32 <tr><td>@ref IMP::Vector</td><td>[atom/dope_and_excluded_volume.cpp](atom_2dope_and_excluded_volume_8cpp-example.html), [core/rigid_collisions.py](core_2rigid_collisions_8py-example.html), [em2d/clustering_of_pdb_models.py](em2d_2clustering_of_pdb_models_8py-example.html), [em/local_fitting.py](em_2local_fitting_8py-example.html), [saxs/profile_fit.py](saxs_2profile_fit_8py-example.html)</td></tr>
33 </table>
34 # IMP.algebra # {#class_example_index_algebra}
35 <table><tr>
36 <th>Class</th><th>Examples</th></tr>
37 <tr><td>@ref IMP::algebra::BoundingBoxD</td><td>[algebra/geometry.py](algebra_2geometry_8py-example.html), [container/filter_close_pairs.py](container_2filter_close_pairs_8py-example.html), [core/incremental_mc.py](core_2incremental_mc_8py-example.html), [core/optimize_balls.py](core_2optimize_balls_8py-example.html), [core/rigid_collisions.py](core_2rigid_collisions_8py-example.html), [display/basic_geometry.py](display_2basic_geometry_8py-example.html), [domino/merge_tree.py](domino_2merge_tree_8py-example.html), [domino/multiscale.py](domino_2multiscale_8py-example.html), [em2d/optimize_em2d_with_montecarlo.py](em2d_2optimize_em2d_with_montecarlo_8py-example.html), [em/analyze_convergence.py](em_2analyze_convergence_8py-example.html), [em/cube.py](em_2cube_8py-example.html), [example/range_restriction.py](example_2range_restriction_8py-example.html), [grid.cpp](grid_8cpp-example.html), [kernel/setup.py](kernel_2setup_8py-example.html), [misc/decay.py](misc_2decay_8py-example.html), [rmf/geometry.py](rmf_2geometry_8py-example.html), [rmf/simulation.py](rmf_2simulation_8py-example.html)</td></tr>
38 <tr><td>@ref IMP::algebra::Cylinder3D</td><td>[algebra/geometry.py](algebra_2geometry_8py-example.html), [display/displaying_ensembles.py](display_2displaying_ensembles_8py-example.html)</td></tr>
39 <tr><td>@ref IMP::algebra::GridD</td><td>[grid.cpp](grid_8cpp-example.html)</td></tr>
40 <tr><td>@ref IMP::algebra::ReferenceFrame3D</td><td>[atom/cg_pdb.py](atom_2cg_pdb_8py-example.html), [atom/multiresolution.py](atom_2multiresolution_8py-example.html), [atom/rigid_brownian_dynamics.py](atom_2rigid_brownian_dynamics_8py-example.html), [core/randomize_rigid_body.py](core_2randomize_rigid_body_8py-example.html), [domino/rigid_body_excluded_volume.py](domino_2rigid_body_excluded_volume_8py-example.html), [em/analyze_convergence.py](em_2analyze_convergence_8py-example.html)</td></tr>
41 <tr><td>@ref IMP::algebra::Segment3D</td><td>[algebra/geometry.py](algebra_2geometry_8py-example.html), [display/displaying_ensembles.py](display_2displaying_ensembles_8py-example.html)</td></tr>
42 <tr><td>@ref IMP::algebra::SphereD</td><td>[BallMover.py](BallMover_8py-example.html), [algebra/geometry.py](algebra_2geometry_8py-example.html), [algebra/grid_space.py](algebra_2grid_space_8py-example.html), [atom/rigid_brownian_dynamics.py](atom_2rigid_brownian_dynamics_8py-example.html), [container/filter_close_pairs.py](container_2filter_close_pairs_8py-example.html), [core/XYZR_Decorator.py](core_2XYZR_Decorator_8py-example.html), [core/connectivity_restraint.py](core_2connectivity_restraint_8py-example.html), [core/optimize_balls.py](core_2optimize_balls_8py-example.html), [core/restrain_in_sphere.py](core_2restrain_in_sphere_8py-example.html), [display/basic_geometry.py](display_2basic_geometry_8py-example.html), [domino/merge_tree.py](domino_2merge_tree_8py-example.html), [em/analyze_convergence.py](em_2analyze_convergence_8py-example.html), [em/cube.py](em_2cube_8py-example.html), [kernel/setup.py](kernel_2setup_8py-example.html), [statistics/kmeans.py](statistics_2kmeans_8py-example.html)</td></tr>
43 <tr><td>@ref IMP::algebra::Transformation3D</td><td>[BallMover.py](BallMover_8py-example.html), [atom/cg_pdb.py](atom_2cg_pdb_8py-example.html), [atom/markers.py](atom_2markers_8py-example.html), [atom/rigid_brownian_dynamics.py](atom_2rigid_brownian_dynamics_8py-example.html), [core/randomize_rigid_body.py](core_2randomize_rigid_body_8py-example.html), [core/rigid_collisions.py](core_2rigid_collisions_8py-example.html), [core/symmetry.py](core_2symmetry_8py-example.html), [domino/rigid_body_excluded_volume.py](domino_2rigid_body_excluded_volume_8py-example.html), [em2d/optimize_em2d_with_montecarlo.py](em2d_2optimize_em2d_with_montecarlo_8py-example.html), [em/local_fitting.py](em_2local_fitting_8py-example.html), [pmi/ambiguity.py](pmi_2ambiguity_8py-example.html)</td></tr>
44 </table>
45 # IMP.atom # {#class_example_index_atom}
46 <table><tr>
47 <th>Class</th><th>Examples</th></tr>
48 <tr><td>@ref IMP::atom::ATOMPDBSelector</td><td>[em2d/clustering_of_pdb_models.py](em2d_2clustering_of_pdb_models_8py-example.html), [em2d/collision_cross_section.py](em2d_2collision_cross_section_8py-example.html), [em2d/optimize_em2d_with_montecarlo.py](em2d_2optimize_em2d_with_montecarlo_8py-example.html), [kernel/dependency_graph.py](kernel_2dependency_graph_8py-example.html)</td></tr>
49 <tr><td>@ref IMP::atom::AngleSingletonScore</td><td>[atom/charmm_forcefield_verbose.py](atom_2charmm_forcefield_verbose_8py-example.html)</td></tr>
50 <tr><td>@ref IMP::atom::Atom</td><td>[atom/dope_and_excluded_volume.cpp](atom_2dope_and_excluded_volume_8cpp-example.html), [rotamer/rotamer_pdb.py](rotamer_2rotamer_pdb_8py-example.html)</td></tr>
51 <tr><td>@ref IMP::atom::BondSingletonScore</td><td>[atom/charmm_forcefield_verbose.py](atom_2charmm_forcefield_verbose_8py-example.html), [atom/load_protein_restrain_bonds.py](atom_2load_protein_restrain_bonds_8py-example.html)</td></tr>
52 <tr><td>@ref IMP::atom::BondedPairFilter</td><td>[container/nonbonded_interactions.py](container_2nonbonded_interactions_8py-example.html)</td></tr>
53 <tr><td>@ref IMP::atom::BrownianDynamics</td><td>[atom/rigid_brownian_dynamics.py](atom_2rigid_brownian_dynamics_8py-example.html), [misc/decay.py](misc_2decay_8py-example.html), [rmf/simulation.py](rmf_2simulation_8py-example.html)</td></tr>
54 <tr><td>@ref IMP::atom::CAlphaPDBSelector</td><td>[display/displaying_ensembles.py](display_2displaying_ensembles_8py-example.html), [domino/rigid_body_excluded_volume.py](domino_2rigid_body_excluded_volume_8py-example.html), [em/generate_density_map_of_fixed_dimension.py](em_2generate_density_map_of_fixed_dimension_8py-example.html), [em/local_fitting.py](em_2local_fitting_8py-example.html)</td></tr>
55 <tr><td>@ref IMP::atom::CHARMMStereochemistryRestraint</td><td>[atom/charmm_forcefield.py](atom_2charmm_forcefield_8py-example.html)</td></tr>
56 <tr><td>@ref IMP::atom::CHARMMTopology</td><td>[atom/structure_from_sequence.py](atom_2structure_from_sequence_8py-example.html)</td></tr>
57 <tr><td>@ref IMP::atom::Chain</td><td>[atom/cg_pdb.py](atom_2cg_pdb_8py-example.html), [atom/dope_and_excluded_volume.cpp](atom_2dope_and_excluded_volume_8cpp-example.html), [atom/molecular_hierarchy.py](atom_2molecular_hierarchy_8py-example.html), [display/displaying_ensembles.py](display_2displaying_ensembles_8py-example.html), [kernel/dependency_graph.py](kernel_2dependency_graph_8py-example.html)</td></tr>
58 <tr><td>@ref IMP::atom::DihedralSingletonScore</td><td>[atom/charmm_forcefield_verbose.py](atom_2charmm_forcefield_verbose_8py-example.html)</td></tr>
59 <tr><td>@ref IMP::atom::DopePairScore</td><td>[atom/assess_dope.py](atom_2assess_dope_8py-example.html)</td></tr>
60 <tr><td>@ref IMP::atom::ForceSwitch</td><td>[atom/charmm_forcefield.py](atom_2charmm_forcefield_8py-example.html), [atom/charmm_forcefield_verbose.py](atom_2charmm_forcefield_verbose_8py-example.html)</td></tr>
61 <tr><td>@ref IMP::atom::Hierarchy</td><td>[core/rigid_bodies.py](core_2rigid_bodies_8py-example.html)</td></tr>
62 <tr><td>@ref IMP::atom::HierarchyGeometry</td><td>[atom/markers.py](atom_2markers_8py-example.html), [atom/rigid_brownian_dynamics.py](atom_2rigid_brownian_dynamics_8py-example.html), [domino/rigid_body_excluded_volume.py](domino_2rigid_body_excluded_volume_8py-example.html)</td></tr>
63 <tr><td>@ref IMP::atom::ImproperSingletonScore</td><td>[atom/charmm_forcefield_verbose.py](atom_2charmm_forcefield_verbose_8py-example.html)</td></tr>
64 <tr><td>@ref IMP::atom::LennardJonesPairScore</td><td>[atom/charmm_forcefield.py](atom_2charmm_forcefield_8py-example.html), [atom/charmm_forcefield_verbose.py](atom_2charmm_forcefield_verbose_8py-example.html)</td></tr>
65 <tr><td>@ref IMP::atom::NonWaterNonHydrogenPDBSelector</td><td>[atom/assess_dope.py](atom_2assess_dope_8py-example.html), [atom/charmm_forcefield.py](atom_2charmm_forcefield_8py-example.html), [atom/charmm_forcefield_verbose.py](atom_2charmm_forcefield_verbose_8py-example.html), [atom/multiresolution.py](atom_2multiresolution_8py-example.html), [saxs/profile.py](saxs_2profile_8py-example.html), [saxs/profile_fit.py](saxs_2profile_fit_8py-example.html)</td></tr>
66 <tr><td>@ref IMP::atom::NonWaterPDBSelector</td><td>[em/fit_restraint.py](em_2fit_restraint_8py-example.html), [em/pdb2density.py](em_2pdb2density_8py-example.html)</td></tr>
67 <tr><td>@ref IMP::atom::ProteinLigandAtomPairScore</td><td>[atom/score_protein_with_ligand.py](atom_2score_protein_with_ligand_8py-example.html)</td></tr>
68 <tr><td>@ref IMP::atom::Residue</td><td>[atom/dope_and_excluded_volume.cpp](atom_2dope_and_excluded_volume_8cpp-example.html), [atom/edit_molecular_hierarchy.py](atom_2edit_molecular_hierarchy_8py-example.html), [rmf/multiresolution.py](rmf_2multiresolution_8py-example.html), [rotamer/rotamer_pdb.py](rotamer_2rotamer_pdb_8py-example.html)</td></tr>
69 <tr><td>@ref IMP::atom::Selection</td><td>[atom/markers.py](atom_2markers_8py-example.html), [atom/multiresolution.py](atom_2multiresolution_8py-example.html), [atom/rigid_brownian_dynamics.py](atom_2rigid_brownian_dynamics_8py-example.html), [display/displaying_ensembles.py](display_2displaying_ensembles_8py-example.html), [kernel/dependency_graph.py](kernel_2dependency_graph_8py-example.html), [multistate.py](multistate_8py-example.html), [pmi/em.py](pmi_2em_8py-example.html), [pmi/selection.py](pmi_2selection_8py-example.html)</td></tr>
70 <tr><td>@ref IMP::atom::SelectionGeometry</td><td>[atom/markers.py](atom_2markers_8py-example.html)</td></tr>
71 <tr><td>@ref IMP::atom::StereochemistryPairFilter</td><td>[atom/charmm_forcefield_verbose.py](atom_2charmm_forcefield_verbose_8py-example.html)</td></tr>
72 <tr><td>@ref IMP::atom::WritePDBOptimizerState</td><td>[em2d/optimize_em2d_with_montecarlo.py](em2d_2optimize_em2d_with_montecarlo_8py-example.html)</td></tr>
73 </table>
74 # IMP.container # {#class_example_index_container}
75 <table><tr>
76 <th>Class</th><th>Examples</th></tr>
77 <tr><td>@ref IMP::container::CloseBipartitePairContainer</td><td>[container/bipartite_nonbonded_interactions.py](container_2bipartite_nonbonded_interactions_8py-example.html), [container/filter_close_pairs.py](container_2filter_close_pairs_8py-example.html)</td></tr>
78 <tr><td>@ref IMP::container::ClosePairContainer</td><td>[atom/assess_dope.py](atom_2assess_dope_8py-example.html), [atom/charmm_forcefield.py](atom_2charmm_forcefield_8py-example.html), [atom/charmm_forcefield_verbose.py](atom_2charmm_forcefield_verbose_8py-example.html), [container/filter_close_pairs.py](container_2filter_close_pairs_8py-example.html), [container/nonbonded_interactions.py](container_2nonbonded_interactions_8py-example.html), [container/statistical.py](container_2statistical_8py-example.html), [core/excluded_volume.py](core_2excluded_volume_8py-example.html), [core/model_numpy.py](core_2model_numpy_8py-example.html), [core/rigid_collisions.py](core_2rigid_collisions_8py-example.html), [kernel/basic_optimization.py](kernel_2basic_optimization_8py-example.html), [kernel/chain.py](kernel_2chain_8py-example.html)</td></tr>
79 <tr><td>@ref IMP::container::ConnectingPairContainer</td><td>[container/connectivity.py](container_2connectivity_8py-example.html)</td></tr>
80 <tr><td>@ref IMP::container::ConsecutivePairContainer</td><td>[domino/restraint_cache.py](domino_2restraint_cache_8py-example.html), [kernel/chain.py](kernel_2chain_8py-example.html)</td></tr>
81 <tr><td>@ref IMP::container::ConsecutivePairFilter</td><td>[kernel/chain.py](kernel_2chain_8py-example.html)</td></tr>
82 <tr><td>@ref IMP::container::ExclusiveConsecutivePairContainer</td><td>[core/optimize_balls.py](core_2optimize_balls_8py-example.html)</td></tr>
83 <tr><td>@ref IMP::container::ExclusiveConsecutivePairFilter</td><td>[core/optimize_balls.py](core_2optimize_balls_8py-example.html)</td></tr>
84 <tr><td>@ref IMP::container::ListPairContainer</td><td>[domino/custom_filter.py](domino_2custom_filter_8py-example.html), [domino/interactive.py](domino_2interactive_8py-example.html), [domino/interactive_with_containers.py](domino_2interactive_with_containers_8py-example.html), [domino/merge_tree.py](domino_2merge_tree_8py-example.html), [domino/six_particles_optimization.py](domino_2six_particles_optimization_8py-example.html)</td></tr>
85 <tr><td>@ref IMP::container::ListSingletonContainer</td><td>[atom/charmm_forcefield.py](atom_2charmm_forcefield_8py-example.html), [atom/charmm_forcefield_verbose.py](atom_2charmm_forcefield_verbose_8py-example.html), [atom/load_protein_restrain_bonds.py](atom_2load_protein_restrain_bonds_8py-example.html), [atom/rigid_brownian_dynamics.py](atom_2rigid_brownian_dynamics_8py-example.html), [container/bipartite_nonbonded_interactions.py](container_2bipartite_nonbonded_interactions_8py-example.html), [container/connectivity.py](container_2connectivity_8py-example.html), [container/filter_close_pairs.py](container_2filter_close_pairs_8py-example.html), [container/nonbonded_interactions.py](container_2nonbonded_interactions_8py-example.html), [container/statistical.py](container_2statistical_8py-example.html), [core/connectivity_restraint.py](core_2connectivity_restraint_8py-example.html), [core/incremental_mc.py](core_2incremental_mc_8py-example.html), [core/restrain_diameter.py](core_2restrain_diameter_8py-example.html), [core/rigid_collisions.py](core_2rigid_collisions_8py-example.html), [core/symmetry.py](core_2symmetry_8py-example.html), [display/display_log.py](display_2display_log_8py-example.html), [display/show_particles_as_spheres.py](display_2show_particles_as_spheres_8py-example.html), [domino/rigid_body_excluded_volume.py](domino_2rigid_body_excluded_volume_8py-example.html), [em2d/optimize_em2d_with_montecarlo.py](em2d_2optimize_em2d_with_montecarlo_8py-example.html), [example/range_restriction.py](example_2range_restriction_8py-example.html), [kernel/chain.py](kernel_2chain_8py-example.html), [kernel/setup.py](kernel_2setup_8py-example.html), [misc/decay.py](misc_2decay_8py-example.html)</td></tr>
86 <tr><td>@ref IMP::container::PairsRestraint</td><td>[atom/assess_dope.py](atom_2assess_dope_8py-example.html), [atom/charmm_forcefield.py](atom_2charmm_forcefield_8py-example.html), [atom/charmm_forcefield_verbose.py](atom_2charmm_forcefield_verbose_8py-example.html), [container/bipartite_nonbonded_interactions.py](container_2bipartite_nonbonded_interactions_8py-example.html), [container/nonbonded_interactions.py](container_2nonbonded_interactions_8py-example.html), [core/excluded_volume.py](core_2excluded_volume_8py-example.html), [core/optimize_balls.py](core_2optimize_balls_8py-example.html), [core/rigid_collisions.py](core_2rigid_collisions_8py-example.html), [domino/custom_filter.py](domino_2custom_filter_8py-example.html), [domino/interactive.py](domino_2interactive_8py-example.html), [domino/interactive_with_containers.py](domino_2interactive_with_containers_8py-example.html), [domino/merge_tree.py](domino_2merge_tree_8py-example.html), [domino/restraint_cache.py](domino_2restraint_cache_8py-example.html), [domino/six_particles_optimization.py](domino_2six_particles_optimization_8py-example.html), [kernel/basic_optimization.py](kernel_2basic_optimization_8py-example.html), [kernel/chain.py](kernel_2chain_8py-example.html), [misc/decay.py](misc_2decay_8py-example.html), [rmf/simulation.py](rmf_2simulation_8py-example.html)</td></tr>
87 <tr><td>@ref IMP::container::PredicatePairsRestraint</td><td>[container/statistical.py](container_2statistical_8py-example.html)</td></tr>
88 <tr><td>@ref IMP::container::SingletonsConstraint</td><td>[example/range_restriction.py](example_2range_restriction_8py-example.html)</td></tr>
89 <tr><td>@ref IMP::container::SingletonsRestraint</td><td>[atom/charmm_forcefield_verbose.py](atom_2charmm_forcefield_verbose_8py-example.html), [atom/load_protein_restrain_bonds.py](atom_2load_protein_restrain_bonds_8py-example.html), [container/restrain_in_sphere.py](container_2restrain_in_sphere_8py-example.html), [core/incremental_mc.py](core_2incremental_mc_8py-example.html), [core/optimize_balls.py](core_2optimize_balls_8py-example.html), [misc/decay.py](misc_2decay_8py-example.html), [rmf/simulation.py](rmf_2simulation_8py-example.html)</td></tr>
90 </table>
91 # IMP.core # {#class_example_index_core}
92 <table><tr>
93 <th>Class</th><th>Examples</th></tr>
94 <tr><td>@ref IMP::core::BallMover</td><td>[BallMover.py](BallMover_8py-example.html), [core/incremental_mc.py](core_2incremental_mc_8py-example.html), [core/optimize_balls.py](core_2optimize_balls_8py-example.html), [core/restrain_minimum_distance.py](core_2restrain_minimum_distance_8py-example.html), [display/display_log.py](display_2display_log_8py-example.html), [temperature_rem.py](temperature_rem_8py-example.html)</td></tr>
95 <tr><td>@ref IMP::core::ChildrenRefiner</td><td>[core/connectivity_restraint.py](core_2connectivity_restraint_8py-example.html), [core/cover_particles.py](core_2cover_particles_8py-example.html)</td></tr>
96 <tr><td>@ref IMP::core::CoinFlipPairPredicate</td><td>[misc/decay.py](misc_2decay_8py-example.html)</td></tr>
97 <tr><td>@ref IMP::core::ConjugateGradients</td><td>[container/bipartite_nonbonded_interactions.py](container_2bipartite_nonbonded_interactions_8py-example.html), [container/nonbonded_interactions.py](container_2nonbonded_interactions_8py-example.html), [core/optimize_balls.py](core_2optimize_balls_8py-example.html), [core/restrain_diameter.py](core_2restrain_diameter_8py-example.html), [core/rigid_collisions.py](core_2rigid_collisions_8py-example.html), [core/simple.py](core_2simple_8py-example.html), [core/symmetry.py](core_2symmetry_8py-example.html), [em/analyze_convergence.py](em_2analyze_convergence_8py-example.html)</td></tr>
98 <tr><td>@ref IMP::core::ConnectivityRestraint</td><td>[core/connectivity_restraint.py](core_2connectivity_restraint_8py-example.html)</td></tr>
99 <tr><td>@ref IMP::core::DiameterRestraint</td><td>[core/restrain_diameter.py](core_2restrain_diameter_8py-example.html)</td></tr>
100 <tr><td>@ref IMP::core::DistancePairScore</td><td>[core/ms_connectivity_restraint.py](core_2ms_connectivity_restraint_8py-example.html), [core/pair_restraint.py](core_2pair_restraint_8py-example.html), [core/simple.py](core_2simple_8py-example.html), [kernel/basic_optimization.py](kernel_2basic_optimization_8py-example.html)</td></tr>
101 <tr><td>@ref IMP::core::DistanceRestraint</td><td>[domino/domino_approach.py](domino_2domino_approach_8py-example.html), [em2d/optimize_em2d_with_montecarlo.py](em2d_2optimize_em2d_with_montecarlo_8py-example.html), [gsl/simplex.py](gsl_2simplex_8py-example.html), [modeller/imp_restraints_in_modeller.py](modeller_2imp_restraints_in_modeller_8py-example.html), [parallel/tasks.py](parallel_2tasks_8py-example.html), [temperature_rem.py](temperature_rem_8py-example.html)</td></tr>
102 <tr><td>@ref IMP::core::EdgePairsGeometry</td><td>[container/connectivity.py](container_2connectivity_8py-example.html)</td></tr>
103 <tr><td>@ref IMP::core::ExcludedVolumeRestraint</td><td>[atom/rigid_brownian_dynamics.py](atom_2rigid_brownian_dynamics_8py-example.html), [core/excluded_volume.py](core_2excluded_volume_8py-example.html), [core/incremental_mc.py](core_2incremental_mc_8py-example.html), [core/optimize_balls.py](core_2optimize_balls_8py-example.html), [core/symmetry.py](core_2symmetry_8py-example.html), [display/display_log.py](display_2display_log_8py-example.html), [domino/rigid_body_excluded_volume.py](domino_2rigid_body_excluded_volume_8py-example.html), [misc/decay.py](misc_2decay_8py-example.html), [rmf/simulation.py](rmf_2simulation_8py-example.html)</td></tr>
104 <tr><td>@ref IMP::core::GenericAttributeSingletonScore</td><td>[domino/multiscale.py](domino_2multiscale_8py-example.html)</td></tr>
105 <tr><td>@ref IMP::core::GenericBoundingBox3DSingletonScore</td><td>[core/incremental_mc.py](core_2incremental_mc_8py-example.html), [core/optimize_balls.py](core_2optimize_balls_8py-example.html), [misc/decay.py](misc_2decay_8py-example.html), [rmf/simulation.py](rmf_2simulation_8py-example.html)</td></tr>
106 <tr><td>@ref IMP::core::GenericDistanceToSingletonScore</td><td>[container/restrain_in_sphere.py](container_2restrain_in_sphere_8py-example.html), [core/restrain_in_sphere.py](core_2restrain_in_sphere_8py-example.html), [core/simple.py](core_2simple_8py-example.html), [domino/multiscale.py](domino_2multiscale_8py-example.html), [domino/six_particles_optimization.py](domino_2six_particles_optimization_8py-example.html)</td></tr>
107 <tr><td>@ref IMP::core::GridClosePairsFinder</td><td>[domino/merge_tree.py](domino_2merge_tree_8py-example.html)</td></tr>
108 <tr><td>@ref IMP::core::Harmonic</td><td>[BallMover.py](BallMover_8py-example.html), [atom/charmm_forcefield_verbose.py](atom_2charmm_forcefield_verbose_8py-example.html), [atom/load_protein_restrain_bonds.py](atom_2load_protein_restrain_bonds_8py-example.html), [core/pair_restraint.py](core_2pair_restraint_8py-example.html), [core/simple.py](core_2simple_8py-example.html), [domino/domino_approach.py](domino_2domino_approach_8py-example.html), [domino/multiscale.py](domino_2multiscale_8py-example.html), [em2d/optimize_em2d_with_montecarlo.py](em2d_2optimize_em2d_with_montecarlo_8py-example.html), [gsl/simplex.py](gsl_2simplex_8py-example.html), [modeller/imp_restraints_in_modeller.py](modeller_2imp_restraints_in_modeller_8py-example.html), [parallel/tasks.py](parallel_2tasks_8py-example.html), [temperature_rem.py](temperature_rem_8py-example.html)</td></tr>
109 <tr><td>@ref IMP::core::HarmonicDistancePairScore</td><td>[container/statistical.py](container_2statistical_8py-example.html), [core/optimize_balls.py](core_2optimize_balls_8py-example.html), [domino/custom_filter.py](domino_2custom_filter_8py-example.html), [domino/interactive.py](domino_2interactive_8py-example.html), [domino/interactive_with_containers.py](domino_2interactive_with_containers_8py-example.html), [domino/six_particles_optimization.py](domino_2six_particles_optimization_8py-example.html), [kernel/chain.py](kernel_2chain_8py-example.html), [rotamer/rotamer_pdb2.py](rotamer_2rotamer_pdb2_8py-example.html)</td></tr>
110 <tr><td>@ref IMP::core::HarmonicLowerBound</td><td>[container/bipartite_nonbonded_interactions.py](container_2bipartite_nonbonded_interactions_8py-example.html), [core/excluded_volume.py](core_2excluded_volume_8py-example.html), [core/rigid_collisions.py](core_2rigid_collisions_8py-example.html), [kernel/basic_optimization.py](kernel_2basic_optimization_8py-example.html)</td></tr>
111 <tr><td>@ref IMP::core::HarmonicSphereDistancePairScore</td><td>[core/restrain_minimum_distance.py](core_2restrain_minimum_distance_8py-example.html), [domino/multiscale.py](domino_2multiscale_8py-example.html)</td></tr>
112 <tr><td>@ref IMP::core::HarmonicUpperBound</td><td>[container/restrain_in_sphere.py](container_2restrain_in_sphere_8py-example.html), [core/connectivity_restraint.py](core_2connectivity_restraint_8py-example.html), [core/incremental_mc.py](core_2incremental_mc_8py-example.html), [core/ms_connectivity_restraint.py](core_2ms_connectivity_restraint_8py-example.html), [core/optimize_balls.py](core_2optimize_balls_8py-example.html), [core/restrain_diameter.py](core_2restrain_diameter_8py-example.html), [core/restrain_in_sphere.py](core_2restrain_in_sphere_8py-example.html), [display/displaying_ensembles.py](display_2displaying_ensembles_8py-example.html), [domino/six_particles_optimization.py](domino_2six_particles_optimization_8py-example.html), [misc/decay.py](misc_2decay_8py-example.html), [rmf/simulation.py](rmf_2simulation_8py-example.html)</td></tr>
113 <tr><td>@ref IMP::core::HarmonicUpperBoundSphereDistancePairScore</td><td>[domino/restraint_cache.py](domino_2restraint_cache_8py-example.html), [misc/decay.py](misc_2decay_8py-example.html), [rmf/simulation.py](rmf_2simulation_8py-example.html)</td></tr>
114 <tr><td>@ref IMP::core::HierarchyTraits</td><td>[core/custom_hierarchy.py](core_2custom_hierarchy_8py-example.html)</td></tr>
115 <tr><td>@ref IMP::core::IncrementalScoringFunction</td><td>[core/incremental_mc.py](core_2incremental_mc_8py-example.html), [core/optimize_balls.py](core_2optimize_balls_8py-example.html)</td></tr>
116 <tr><td>@ref IMP::core::KClosePairsPairScore</td><td>[core/connectivity_restraint.py](core_2connectivity_restraint_8py-example.html), [core/restrain_minimum_distance.py](core_2restrain_minimum_distance_8py-example.html), [display/displaying_ensembles.py](display_2displaying_ensembles_8py-example.html)</td></tr>
117 <tr><td>@ref IMP::core::LeavesRefiner</td><td>[display/displaying_ensembles.py](display_2displaying_ensembles_8py-example.html), [em/local_fitting.py](em_2local_fitting_8py-example.html)</td></tr>
118 <tr><td>@ref IMP::core::MCCGSampler</td><td>[kernel/basic_optimization.py](kernel_2basic_optimization_8py-example.html), [kernel/chain.py](kernel_2chain_8py-example.html)</td></tr>
119 <tr><td>@ref IMP::core::MSConnectivityRestraint</td><td>[core/ms_connectivity_restraint.py](core_2ms_connectivity_restraint_8py-example.html)</td></tr>
120 <tr><td>@ref IMP::core::MonteCarlo</td><td>[BallMover.py](BallMover_8py-example.html), [core/incremental_mc.py](core_2incremental_mc_8py-example.html), [core/optimize_balls.py](core_2optimize_balls_8py-example.html), [core/restrain_minimum_distance.py](core_2restrain_minimum_distance_8py-example.html), [display/display_log.py](display_2display_log_8py-example.html), [em2d/optimize_em2d_with_montecarlo.py](em2d_2optimize_em2d_with_montecarlo_8py-example.html), [temperature_rem.py](temperature_rem_8py-example.html)</td></tr>
121 <tr><td>@ref IMP::core::PairRestraint</td><td>[BallMover.py](BallMover_8py-example.html), [core/pair_restraint.py](core_2pair_restraint_8py-example.html), [core/restrain_minimum_distance.py](core_2restrain_minimum_distance_8py-example.html), [core/simple.py](core_2simple_8py-example.html), [domino/marina_party.py](domino_2marina_party_8py-example.html), [domino/multiscale.py](domino_2multiscale_8py-example.html), [kernel/chain.py](kernel_2chain_8py-example.html)</td></tr>
122 <tr><td>@ref IMP::core::RestraintsScoringFunction</td><td>[atom/charmm_forcefield.py](atom_2charmm_forcefield_8py-example.html), [atom/charmm_forcefield_verbose.py](atom_2charmm_forcefield_verbose_8py-example.html), [atom/rigid_brownian_dynamics.py](atom_2rigid_brownian_dynamics_8py-example.html), [container/statistical.py](container_2statistical_8py-example.html), [core/excluded_volume.py](core_2excluded_volume_8py-example.html), [core/optimize_balls.py](core_2optimize_balls_8py-example.html), [core/restrain_diameter.py](core_2restrain_diameter_8py-example.html), [core/rigid_collisions.py](core_2rigid_collisions_8py-example.html), [core/simple.py](core_2simple_8py-example.html), [core/symmetry.py](core_2symmetry_8py-example.html), [domino/custom_filter.py](domino_2custom_filter_8py-example.html), [domino/rigid_body_excluded_volume.py](domino_2rigid_body_excluded_volume_8py-example.html), [domino/six_particles_optimization.py](domino_2six_particles_optimization_8py-example.html), [em2d/optimize_em2d_with_montecarlo.py](em2d_2optimize_em2d_with_montecarlo_8py-example.html), [em/analyze_convergence.py](em_2analyze_convergence_8py-example.html), [kernel/basic_optimization.py](kernel_2basic_optimization_8py-example.html), [kernel/dependency_graph.py](kernel_2dependency_graph_8py-example.html), [modeller/imp_restraints_in_modeller.py](modeller_2imp_restraints_in_modeller_8py-example.html), [modeller/load_modeller_model.py](modeller_2load_modeller_model_8py-example.html), [modeller/modeller_restraints_in_imp.py](modeller_2modeller_restraints_in_imp_8py-example.html), [parallel/tasks.py](parallel_2tasks_8py-example.html), [rmf/simulation.py](rmf_2simulation_8py-example.html), [temperature_rem.py](temperature_rem_8py-example.html)</td></tr>
123 <tr><td>@ref IMP::core::RigidBodyMover</td><td>[em2d/optimize_em2d_with_montecarlo.py](em2d_2optimize_em2d_with_montecarlo_8py-example.html)</td></tr>
124 <tr><td>@ref IMP::core::RigidClosePairsFinder</td><td>[core/rigid_collisions.py](core_2rigid_collisions_8py-example.html)</td></tr>
125 <tr><td>@ref IMP::core::RigidMember</td><td>[display/displaying_ensembles.py](display_2displaying_ensembles_8py-example.html), [domino/rigid_body_excluded_volume.py](domino_2rigid_body_excluded_volume_8py-example.html), [em/local_fitting.py](em_2local_fitting_8py-example.html)</td></tr>
126 <tr><td>@ref IMP::core::SerialMover</td><td>[BallMover.py](BallMover_8py-example.html), [core/incremental_mc.py](core_2incremental_mc_8py-example.html), [core/optimize_balls.py](core_2optimize_balls_8py-example.html), [temperature_rem.py](temperature_rem_8py-example.html)</td></tr>
127 <tr><td>@ref IMP::core::SingletonConstraint</td><td>[core/symmetry.py](core_2symmetry_8py-example.html)</td></tr>
128 <tr><td>@ref IMP::core::SingletonRestraint</td><td>[core/restrain_in_sphere.py](core_2restrain_in_sphere_8py-example.html), [core/simple.py](core_2simple_8py-example.html), [domino/multiscale.py](domino_2multiscale_8py-example.html), [domino/six_particles_optimization.py](domino_2six_particles_optimization_8py-example.html)</td></tr>
129 <tr><td>@ref IMP::core::SoftSpherePairScore</td><td>[container/nonbonded_interactions.py](container_2nonbonded_interactions_8py-example.html), [core/optimize_balls.py](core_2optimize_balls_8py-example.html), [domino/merge_tree.py](domino_2merge_tree_8py-example.html), [kernel/chain.py](kernel_2chain_8py-example.html)</td></tr>
130 <tr><td>@ref IMP::core::SphereDistancePairScore</td><td>[BallMover.py](BallMover_8py-example.html), [container/bipartite_nonbonded_interactions.py](container_2bipartite_nonbonded_interactions_8py-example.html), [core/connectivity_restraint.py](core_2connectivity_restraint_8py-example.html), [core/excluded_volume.py](core_2excluded_volume_8py-example.html), [core/rigid_collisions.py](core_2rigid_collisions_8py-example.html), [display/displaying_ensembles.py](display_2displaying_ensembles_8py-example.html)</td></tr>
131 <tr><td>@ref IMP::core::TableRefiner</td><td>[core/restrain_minimum_distance.py](core_2restrain_minimum_distance_8py-example.html)</td></tr>
132 <tr><td>@ref IMP::core::Transform</td><td>[em2d/clustering_of_pdb_models.py](em2d_2clustering_of_pdb_models_8py-example.html)</td></tr>
133 <tr><td>@ref IMP::core::TransformationSymmetry</td><td>[core/symmetry.py](core_2symmetry_8py-example.html)</td></tr>
134 <tr><td>@ref IMP::core::XYZ</td><td>[atom/score_protein_with_ligand.py](atom_2score_protein_with_ligand_8py-example.html), [core/XYZR_Decorator.py](core_2XYZR_Decorator_8py-example.html), [core/restrain_diameter.py](core_2restrain_diameter_8py-example.html), [core/simple.cpp](core_2simple_8cpp-example.html), [core/symmetry.py](core_2symmetry_8py-example.html), [display/displaying_ensembles.py](display_2displaying_ensembles_8py-example.html), [domino/custom_filter.py](domino_2custom_filter_8py-example.html), [domino/six_particles_optimization.py](domino_2six_particles_optimization_8py-example.html), [pmi/ambiguity.py](pmi_2ambiguity_8py-example.html), [rmf/pdb.py](rmf_2pdb_8py-example.html), [rotamer/rotamer_pdb.py](rotamer_2rotamer_pdb_8py-example.html)</td></tr>
135 <tr><td>@ref IMP::core::XYZDerivativeGeometry</td><td>[em/analyze_convergence.py](em_2analyze_convergence_8py-example.html)</td></tr>
136 <tr><td>@ref IMP::core::XYZR</td><td>[BallMover.py](BallMover_8py-example.html), [atom/markers.py](atom_2markers_8py-example.html), [core/optimize_balls.py](core_2optimize_balls_8py-example.html), [display/show_particles_as_spheres.py](display_2show_particles_as_spheres_8py-example.html)</td></tr>
137 <tr><td>@ref IMP::core::XYZRGeometry</td><td>[atom/markers.py](atom_2markers_8py-example.html), [core/incremental_mc.py](core_2incremental_mc_8py-example.html), [core/optimize_balls.py](core_2optimize_balls_8py-example.html), [display/displaying_ensembles.py](display_2displaying_ensembles_8py-example.html), [domino/multiscale.py](domino_2multiscale_8py-example.html)</td></tr>
138 <tr><td>@ref IMP::core::XYZRsGeometry</td><td>[display/display_log.py](display_2display_log_8py-example.html), [display/show_particles_as_spheres.py](display_2show_particles_as_spheres_8py-example.html)</td></tr>
139 </table>
140 # IMP.display # {#class_example_index_display}
141 <table><tr>
142 <th>Class</th><th>Examples</th></tr>
143 <tr><td>@ref IMP::display::BoundingBoxGeometry</td><td>[core/optimize_balls.py](core_2optimize_balls_8py-example.html), [display/basic_geometry.py](display_2basic_geometry_8py-example.html), [misc/decay.py](misc_2decay_8py-example.html), [rmf/geometry.py](rmf_2geometry_8py-example.html), [rmf/simulation.py](rmf_2simulation_8py-example.html)</td></tr>
144 <tr><td>@ref IMP::display::Color</td><td>[atom/markers.py](atom_2markers_8py-example.html), [display/display_log.py](display_2display_log_8py-example.html), [display/displaying_ensembles.py](display_2displaying_ensembles_8py-example.html), [display/show_particles_as_spheres.py](display_2show_particles_as_spheres_8py-example.html), [domino/multiscale.py](domino_2multiscale_8py-example.html)</td></tr>
145 <tr><td>@ref IMP::display::CylinderGeometry</td><td>[display/displaying_ensembles.py](display_2displaying_ensembles_8py-example.html)</td></tr>
146 <tr><td>@ref IMP::display::PointGeometry</td><td>[domino/multiscale.py](domino_2multiscale_8py-example.html)</td></tr>
147 <tr><td>@ref IMP::display::PymolWriter</td><td>[atom/markers.py](atom_2markers_8py-example.html), [atom/rigid_brownian_dynamics.py](atom_2rigid_brownian_dynamics_8py-example.html), [core/incremental_mc.py](core_2incremental_mc_8py-example.html), [core/optimize_balls.py](core_2optimize_balls_8py-example.html), [display/basic_geometry.py](display_2basic_geometry_8py-example.html), [display/display_log.py](display_2display_log_8py-example.html), [display/displaying_ensembles.py](display_2displaying_ensembles_8py-example.html), [display/show_particles_as_spheres.py](display_2show_particles_as_spheres_8py-example.html), [domino/multiscale.py](domino_2multiscale_8py-example.html), [domino/rigid_body_excluded_volume.py](domino_2rigid_body_excluded_volume_8py-example.html), [em/analyze_convergence.py](em_2analyze_convergence_8py-example.html)</td></tr>
148 <tr><td>@ref IMP::display::ReferenceFrameGeometry</td><td>[display/displaying_ensembles.py](display_2displaying_ensembles_8py-example.html)</td></tr>
149 <tr><td>@ref IMP::display::SphereGeometry</td><td>[display/basic_geometry.py](display_2basic_geometry_8py-example.html), [em/analyze_convergence.py](em_2analyze_convergence_8py-example.html), [em/cube.py](em_2cube_8py-example.html)</td></tr>
150 <tr><td>@ref IMP::display::WriteOptimizerState</td><td>[display/display_log.py](display_2display_log_8py-example.html)</td></tr>
151 </table>
152 # IMP.domino # {#class_example_index_domino}
153 <table><tr>
154 <th>Class</th><th>Examples</th></tr>
155 <tr><td>@ref IMP::domino::Assignment</td><td>[domino/save_assignments.py](domino_2save_assignments_8py-example.html)</td></tr>
156 <tr><td>@ref IMP::domino::BranchAndBoundAssignmentsTable</td><td>[domino/custom_filter.py](domino_2custom_filter_8py-example.html), [domino/interactive_with_containers.py](domino_2interactive_with_containers_8py-example.html), [domino/rigid_body_excluded_volume.py](domino_2rigid_body_excluded_volume_8py-example.html), [domino/six_particles_optimization.py](domino_2six_particles_optimization_8py-example.html)</td></tr>
157 <tr><td>@ref IMP::domino::DominoSampler</td><td>[domino/custom_filter.py](domino_2custom_filter_8py-example.html), [domino/domino_approach.py](domino_2domino_approach_8py-example.html), [domino/interactive.py](domino_2interactive_8py-example.html), [domino/marina_party.py](domino_2marina_party_8py-example.html), [domino/multiscale.py](domino_2multiscale_8py-example.html), [domino/restraint_cache.py](domino_2restraint_cache_8py-example.html), [domino/rigid_body_excluded_volume.py](domino_2rigid_body_excluded_volume_8py-example.html), [domino/six_particles_optimization.py](domino_2six_particles_optimization_8py-example.html)</td></tr>
158 <tr><td>@ref IMP::domino::ExclusionSubsetFilterTable</td><td>[domino/custom_filter.py](domino_2custom_filter_8py-example.html), [domino/interactive_with_containers.py](domino_2interactive_with_containers_8py-example.html), [domino/marina_party.py](domino_2marina_party_8py-example.html), [domino/restraint_cache.py](domino_2restraint_cache_8py-example.html), [domino/rigid_body_excluded_volume.py](domino_2rigid_body_excluded_volume_8py-example.html), [domino/six_particles_optimization.py](domino_2six_particles_optimization_8py-example.html)</td></tr>
159 <tr><td>@ref IMP::domino::ListSubsetFilterTable</td><td>[domino/marina_party.py](domino_2marina_party_8py-example.html), [domino/multiscale.py](domino_2multiscale_8py-example.html)</td></tr>
160 <tr><td>@ref IMP::domino::ParticleStates</td><td>[domino/marina_party.py](domino_2marina_party_8py-example.html)</td></tr>
161 <tr><td>@ref IMP::domino::ParticleStatesTable</td><td>[domino/custom_filter.py](domino_2custom_filter_8py-example.html), [domino/domino_approach.py](domino_2domino_approach_8py-example.html), [domino/interactive.py](domino_2interactive_8py-example.html), [domino/interactive_with_containers.py](domino_2interactive_with_containers_8py-example.html), [domino/marina_party.py](domino_2marina_party_8py-example.html), [domino/merge_tree.py](domino_2merge_tree_8py-example.html), [domino/multiscale.py](domino_2multiscale_8py-example.html), [domino/restraint_cache.py](domino_2restraint_cache_8py-example.html), [domino/rigid_body_excluded_volume.py](domino_2rigid_body_excluded_volume_8py-example.html), [domino/six_particles_optimization.py](domino_2six_particles_optimization_8py-example.html)</td></tr>
162 <tr><td>@ref IMP::domino::ReadAssignmentContainer</td><td>[domino/save_assignments.py](domino_2save_assignments_8py-example.html)</td></tr>
163 <tr><td>@ref IMP::domino::ReadHDF5AssignmentContainer</td><td>[domino/interactive_with_containers.py](domino_2interactive_with_containers_8py-example.html)</td></tr>
164 <tr><td>@ref IMP::domino::RestraintCache</td><td>[domino/custom_filter.py](domino_2custom_filter_8py-example.html), [domino/interactive_with_containers.py](domino_2interactive_with_containers_8py-example.html), [domino/multiscale.py](domino_2multiscale_8py-example.html), [domino/restraint_cache.py](domino_2restraint_cache_8py-example.html), [domino/rigid_body_excluded_volume.py](domino_2rigid_body_excluded_volume_8py-example.html), [domino/six_particles_optimization.py](domino_2six_particles_optimization_8py-example.html)</td></tr>
165 <tr><td>@ref IMP::domino::RestraintScoreSubsetFilterTable</td><td>[domino/custom_filter.py](domino_2custom_filter_8py-example.html), [domino/interactive_with_containers.py](domino_2interactive_with_containers_8py-example.html), [domino/multiscale.py](domino_2multiscale_8py-example.html), [domino/restraint_cache.py](domino_2restraint_cache_8py-example.html), [domino/rigid_body_excluded_volume.py](domino_2rigid_body_excluded_volume_8py-example.html), [domino/six_particles_optimization.py](domino_2six_particles_optimization_8py-example.html)</td></tr>
166 <tr><td>@ref IMP::domino::RigidBodyStates</td><td>[domino/rigid_body_excluded_volume.py](domino_2rigid_body_excluded_volume_8py-example.html)</td></tr>
167 <tr><td>@ref IMP::domino::Subset</td><td>[domino/multiscale.py](domino_2multiscale_8py-example.html), [domino/restraint_cache.py](domino_2restraint_cache_8py-example.html), [domino/save_assignments.py](domino_2save_assignments_8py-example.html)</td></tr>
168 <tr><td>@ref IMP::domino::SubsetFilter</td><td>[domino/custom_filter.py](domino_2custom_filter_8py-example.html)</td></tr>
169 <tr><td>@ref IMP::domino::SubsetFilterTable</td><td>[domino/custom_filter.py](domino_2custom_filter_8py-example.html)</td></tr>
170 <tr><td>@ref IMP::domino::WriteAssignmentContainer</td><td>[domino/save_assignments.py](domino_2save_assignments_8py-example.html)</td></tr>
171 <tr><td>@ref IMP::domino::WriteHDF5AssignmentContainer</td><td>[domino/interactive_with_containers.py](domino_2interactive_with_containers_8py-example.html)</td></tr>
172 <tr><td>@ref IMP::domino::XYZStates</td><td>[domino/custom_filter.py](domino_2custom_filter_8py-example.html), [domino/domino_approach.py](domino_2domino_approach_8py-example.html), [domino/interactive.py](domino_2interactive_8py-example.html), [domino/interactive_with_containers.py](domino_2interactive_with_containers_8py-example.html), [domino/merge_tree.py](domino_2merge_tree_8py-example.html), [domino/multiscale.py](domino_2multiscale_8py-example.html), [domino/restraint_cache.py](domino_2restraint_cache_8py-example.html), [domino/six_particles_optimization.py](domino_2six_particles_optimization_8py-example.html)</td></tr>
173 </table>
174 # IMP.em # {#class_example_index_em}
175 <table><tr>
176 <th>Class</th><th>Examples</th></tr>
177 <tr><td>@ref IMP::em::FitRestraint</td><td>[em/analyze_convergence.py](em_2analyze_convergence_8py-example.html), [em/fit_restraint.py](em_2fit_restraint_8py-example.html)</td></tr>
178 <tr><td>@ref IMP::em::MRCReaderWriter</td><td>[em/analyze_convergence.py](em_2analyze_convergence_8py-example.html), [em/fit_restraint.py](em_2fit_restraint_8py-example.html), [em/generate_density_map_of_fixed_dimension.py](em_2generate_density_map_of_fixed_dimension_8py-example.html), [em/local_fitting.py](em_2local_fitting_8py-example.html), [em/numpy_data.py](em_2numpy_data_8py-example.html), [em/pdb2density.py](em_2pdb2density_8py-example.html)</td></tr>
179 <tr><td>@ref IMP::em::SampledDensityMap</td><td>[em/analyze_convergence.py](em_2analyze_convergence_8py-example.html), [em/generate_density_map_of_fixed_dimension.py](em_2generate_density_map_of_fixed_dimension_8py-example.html), [em/local_fitting.py](em_2local_fitting_8py-example.html)</td></tr>
180 </table>
181 # IMP.em2d # {#class_example_index_em2d}
182 <table><tr>
183 <th>Class</th><th>Examples</th></tr>
184 <tr><td>@ref IMP::em2d::CollisionCrossSection</td><td>[em2d/collision_cross_section.py](em2d_2collision_cross_section_8py-example.html)</td></tr>
185 <tr><td>@ref IMP::em2d::EM2DScore</td><td>[em2d/optimize_em2d_with_montecarlo.py](em2d_2optimize_em2d_with_montecarlo_8py-example.html)</td></tr>
186 <tr><td>@ref IMP::em2d::Em2DRestraint</td><td>[em2d/optimize_em2d_with_montecarlo.py](em2d_2optimize_em2d_with_montecarlo_8py-example.html)</td></tr>
187 <tr><td>@ref IMP::em2d::Em2DRestraintParameters</td><td>[em2d/optimize_em2d_with_montecarlo.py](em2d_2optimize_em2d_with_montecarlo_8py-example.html)</td></tr>
188 <tr><td>@ref IMP::em2d::SpiderImageReaderWriter</td><td>[em2d/em_images_conversion.py](em2d_2em_images_conversion_8py-example.html), [em2d/optimize_em2d_with_montecarlo.py](em2d_2optimize_em2d_with_montecarlo_8py-example.html)</td></tr>
189 <tr><td>@ref IMP::em2d::TIFFImageReaderWriter</td><td>[em2d/em_images_conversion.py](em2d_2em_images_conversion_8py-example.html)</td></tr>
190 </table>
191 # IMP.example # {#class_example_index_example}
192 <table><tr>
193 <th>Class</th><th>Examples</th></tr>
194 <tr><td>@ref IMP::example::ExampleSingletonModifier</td><td>[example/range_restriction.py](example_2range_restriction_8py-example.html)</td></tr>
195 </table>
196 # IMP.gsl # {#class_example_index_gsl}
197 <table><tr>
198 <th>Class</th><th>Examples</th></tr>
199 <tr><td>@ref IMP::gsl::Simplex</td><td>[gsl/simplex.py](gsl_2simplex_8py-example.html)</td></tr>
200 </table>
201 # IMP.kmeans # {#class_example_index_kmeans}
202 <table><tr>
203 <th>Class</th><th>Examples</th></tr>
204 <tr><td>@ref IMP::kmeans::KMeans</td><td>[kmeans/kmeans_example.py](kmeans_2kmeans_example_8py-example.html)</td></tr>
205 </table>
206 # IMP.misc # {#class_example_index_misc}
207 <table><tr>
208 <th>Class</th><th>Examples</th></tr>
209 <tr><td>@ref IMP::misc::DecayPairContainerOptimizerState</td><td>[misc/decay.py](misc_2decay_8py-example.html)</td></tr>
210 </table>
211 # IMP.modeller # {#class_example_index_modeller}
212 <table><tr>
213 <th>Class</th><th>Examples</th></tr>
214 <tr><td>@ref IMP::modeller::IMPRestraints</td><td>[modeller/imp_restraints_in_modeller.py](modeller_2imp_restraints_in_modeller_8py-example.html)</td></tr>
215 <tr><td>@ref IMP::modeller::ModelLoader</td><td>[modeller/imp_restraints_in_modeller.py](modeller_2imp_restraints_in_modeller_8py-example.html), [modeller/load_modeller_model.py](modeller_2load_modeller_model_8py-example.html), [modeller/modeller_restraints_in_imp.py](modeller_2modeller_restraints_in_imp_8py-example.html)</td></tr>
216 <tr><td>@ref IMP::modeller::ModellerRestraints</td><td>[modeller/modeller_restraints_in_imp.py](modeller_2modeller_restraints_in_imp_8py-example.html)</td></tr>
217 </table>
218 # IMP.mpi # {#class_example_index_mpi}
219 <table><tr>
220 <th>Class</th><th>Examples</th></tr>
221 <tr><td>@ref IMP::mpi::ReplicaExchange</td><td>[temperature_rem.py](temperature_rem_8py-example.html)</td></tr>
222 </table>
223 # IMP.parallel # {#class_example_index_parallel}
224 <table><tr>
225 <th>Class</th><th>Examples</th></tr>
226 <tr><td>@ref IMP::parallel::LocalWorker</td><td>[parallel/local_distance.py](parallel_2local_distance_8py-example.html)</td></tr>
227 <tr><td>@ref IMP::parallel::Manager</td><td>[parallel/local_distance.py](parallel_2local_distance_8py-example.html)</td></tr>
228 </table>
229 # IMP.pmi # {#class_example_index_pmi}
230 <table><tr>
231 <th>Class</th><th>Examples</th></tr>
232 <tr><td>@ref IMP::pmi::dof::DegreesOfFreedom</td><td>[pmi/ambiguity.py](pmi_2ambiguity_8py-example.html), [pmi/atomistic.py](pmi_2atomistic_8py-example.html), [pmi/membrane.py](pmi_2membrane_8py-example.html), [pmi/multiscale.py](pmi_2multiscale_8py-example.html), [pmi/selection.py](pmi_2selection_8py-example.html), [pmi/symmetry.py](pmi_2symmetry_8py-example.html)</td></tr>
233 <tr><td>@ref IMP::pmi::macros::BuildSystem</td><td>[pmi/automatic.py](pmi_2automatic_8py-example.html)</td></tr>
234 <tr><td>@ref IMP::pmi::macros::ReplicaExchange0</td><td>[pmi/ambiguity.py](pmi_2ambiguity_8py-example.html), [pmi/atomistic.py](pmi_2atomistic_8py-example.html), [pmi/automatic.py](pmi_2automatic_8py-example.html), [pmi/membrane.py](pmi_2membrane_8py-example.html), [pmi/multiscale.py](pmi_2multiscale_8py-example.html)</td></tr>
235 <tr><td>@ref IMP::pmi::output::Output</td><td>[pmi/ideal_helix.py](pmi_2ideal_helix_8py-example.html), [pmi/symmetry.py](pmi_2symmetry_8py-example.html)</td></tr>
236 <tr><td>@ref IMP::pmi::topology::Sequences</td><td>[pmi/atomistic.py](pmi_2atomistic_8py-example.html), [pmi/em.py](pmi_2em_8py-example.html), [pmi/multiscale.py](pmi_2multiscale_8py-example.html), [pmi/selection.py](pmi_2selection_8py-example.html)</td></tr>
237 <tr><td>@ref IMP::pmi::topology::System</td><td>[pmi/ambiguity.py](pmi_2ambiguity_8py-example.html), [pmi/atomistic.py](pmi_2atomistic_8py-example.html), [pmi/em.py](pmi_2em_8py-example.html), [pmi/ideal_helix.py](pmi_2ideal_helix_8py-example.html), [pmi/membrane.py](pmi_2membrane_8py-example.html), [pmi/multiscale.py](pmi_2multiscale_8py-example.html), [pmi/selection.py](pmi_2selection_8py-example.html), [pmi/symmetry.py](pmi_2symmetry_8py-example.html)</td></tr>
238 <tr><td>@ref IMP::pmi::topology::TopologyReader</td><td>[pmi/automatic.py](pmi_2automatic_8py-example.html)</td></tr>
239 </table>
240 # IMP.rmf # {#class_example_index_rmf}
241 <table><tr>
242 <th>Class</th><th>Examples</th></tr>
243 <tr><td>@ref IMP::rmf::SaveOptimizerState</td><td>[misc/decay.py](misc_2decay_8py-example.html), [rmf/simulation.py](rmf_2simulation_8py-example.html)</td></tr>
244 </table>
245 # IMP.rotamer # {#class_example_index_rotamer}
246 <table><tr>
247 <th>Class</th><th>Examples</th></tr>
248 <tr><td>@ref IMP::rotamer::RotamerCalculator</td><td>[rotamer/rotamer_pdb2.py](rotamer_2rotamer_pdb2_8py-example.html), [rotamer/rotamer_pdb.py](rotamer_2rotamer_pdb_8py-example.html)</td></tr>
249 <tr><td>@ref IMP::rotamer::RotamerLibrary</td><td>[rotamer/rotamer_pdb2.py](rotamer_2rotamer_pdb2_8py-example.html), [rotamer/rotamer_pdb.py](rotamer_2rotamer_pdb_8py-example.html)</td></tr>
250 </table>
251 # IMP.saxs # {#class_example_index_saxs}
252 <table><tr>
253 <th>Class</th><th>Examples</th></tr>
254 <tr><td>@ref IMP::saxs::Profile</td><td>[saxs/profile.py](saxs_2profile_8py-example.html), [saxs/profile_fit.py](saxs_2profile_fit_8py-example.html)</td></tr>
255 <tr><td>@ref IMP::saxs::RadialDistributionFunction</td><td>[saxs/profile.py](saxs_2profile_8py-example.html)</td></tr>
256 <tr><td>@ref IMP::saxs::SolventAccessibleSurface</td><td>[saxs/profile_fit.py](saxs_2profile_fit_8py-example.html)</td></tr>
257 </table>
258 # IMP.score_functor # {#class_example_index_score_functor}
259 <table><tr>
260 <th>Class</th><th>Examples</th></tr>
261 <tr><td>@ref IMP::score_functor::AddScores</td><td>[atom/dope_and_excluded_volume.cpp](atom_2dope_and_excluded_volume_8cpp-example.html)</td></tr>
262 <tr><td>@ref IMP::score_functor::DistancePairScore</td><td>[atom/dope_and_excluded_volume.cpp](atom_2dope_and_excluded_volume_8cpp-example.html)</td></tr>
263 <tr><td>@ref IMP::score_functor::Dope</td><td>[atom/dope_and_excluded_volume.cpp](atom_2dope_and_excluded_volume_8cpp-example.html)</td></tr>
264 <tr><td>@ref IMP::score_functor::HarmonicLowerBound</td><td>[atom/dope_and_excluded_volume.cpp](atom_2dope_and_excluded_volume_8cpp-example.html)</td></tr>
265 <tr><td>@ref IMP::score_functor::SphereDistance</td><td>[atom/dope_and_excluded_volume.cpp](atom_2dope_and_excluded_volume_8cpp-example.html)</td></tr>
266 </table>
267 # IMP.statistics # {#class_example_index_statistics}
268 <table><tr>
269 <th>Class</th><th>Examples</th></tr>
270 <tr><td>@ref IMP::statistics::ConfigurationSetXYZEmbedding</td><td>[kernel/basic_optimization.py](kernel_2basic_optimization_8py-example.html), [statistics/kmeans.py](statistics_2kmeans_8py-example.html)</td></tr>
271 <tr><td>@ref IMP::statistics::Metric</td><td>[statistics/write_a_metric.py](statistics_2write_a_metric_8py-example.html)</td></tr>
272 <tr><td>@ref IMP::statistics::ParticleEmbedding</td><td>[statistics/kmeans.py](statistics_2kmeans_8py-example.html)</td></tr>
273 <tr><td>@ref IMP::statistics::VectorDEmbedding</td><td>[statistics/kmeans.py](statistics_2kmeans_8py-example.html)</td></tr>
274 </table>
275 # IMP.symmetry # {#class_example_index_symmetry}
276 <table><tr>
277 <th>Class</th><th>Examples</th></tr>
278 <tr><td>@ref IMP::symmetry::BallMover</td><td>[BallMover.py](BallMover_8py-example.html)</td></tr>
279 </table>
Applies a SingletonScore to each Singleton in a list.
Return the hierarchy children of a particle.
Simplify creation of constraints and movers for an IMP Hierarchy.
Select non water and non hydrogen atoms.
Definition: pdb.h:245
Abstract class for scoring object(s) of type ParticleIndexPair.
Definition: PairScore.h:42
Embed a configuration using the XYZ coordinates of a set of particles.
Definition: embeddings.h:28
A harmonic upper bound on the distance between two spheres.
A Monte Carlo optimizer.
Definition: MonteCarlo.h:45
Simple 3D transformation class.
A class to implement Hamiltonian Replica Exchange.
Lower bound harmonic function (non-zero when feature < mean)
Represent an RGB color.
Definition: Color.h:24
Enforce CHARMM stereochemistry on the given Hierarchy.
Score the angle based on a UnaryFunction,.
Apply a SingletonFunction to a SingletonContainer to maintain an invariant.
Apply a score to a fixed number of close pairs from the two sets.
Set the coordinates of a particle to be a transformed version of a reference.
Definition: core/symmetry.h:76
Return the hierarchy leaves under a particle.
Definition: LeavesRefiner.h:25
A Modeller restraint which evaluates an IMP scoring function.
Maintain an explicit list of what states each particle is allowed to have.
Upper bound harmonic function (non-zero when feature > mean)
A class to store an fixed array of same-typed values.
Definition: Array.h:33
Display a Selection.
Definition: Selection.h:348
Move a particle and keep it in the primitive cell of a periodic lattice.
A class storing a whole rotamer library read from a file.
A typed index.
Definition: Index.h:25
Applies a PairScore to each Pair in a list based on a predicate.
Display an IMP::SingletonContainer of IMP::core::XYZR particles as balls.
Definition: XYZR.h:151
A container which contains all consecutive particle pairs from an input list.
Modify the transformation of a rigid body.
A voxel grid in d-dimensional space.
Definition: GridD.h:79
Maintain a pair container with a decaying list of pairs.
Simple conjugate gradients optimizer.
Sample best solutions using Domino.
Definition: DominoSampler.h:32
Represent a cylinder in 3D.
Definition: Cylinder3D.h:26
A harmonic score on the distance between two spheres.
Filter a configuration of the subset using the Model thresholds.
Apply a SingletonFunction to a Singleton.
Represent a subset of the particles being optimized.
Definition: Subset.h:33
Create a scoring function on a list of restraints.
Store the assignments in an HDF5DataSet.
A score on the distance between the surfaces of two spheres.
Move continuous particle variables by perturbing them within a ball.
A macro to build a IMP::pmi::topology::System based on a TopologyReader object.
Definition: macros.py:566
Return all close unordered pairs of particles taken from the SingletonContainer.
Return all spatially-proximals pairs of particles (a,b) from the two SingletonContainers A and B...
Represent the root node of the global IMP.atom.Hierarchy.
Distance restraint between two particles.
Create efficient distance-based pair scores.
Score particles based on how far outside a box they are.
A more IMP-like version of the std::vector.
Definition: Vector.h:40
An IMP restraint using all defined Modeller restraints.
A reference frame in 3D.
Object used to hold a set of restraints.
Definition: RestraintSet.h:37
Class for storing model, its restraints, constraints, and particles.
Definition: Model.h:73
Do not allow two particles to be in the same state.
Store a list of ParticleIndexPairs.
Class for sampling a density map from particles.
Select all non-alternative ATOM records.
Definition: pdb.h:64
Simple Brownian dynamics simulator.
Lennard-Jones score between a pair of particles.
The standard decorator for manipulating molecular structures.
Common base class for heavy weight IMP objects.
Definition: Object.h:106
Store a list of ParticleIndexes.
A worker running on the same machine as the manager.
A simplex optimizer taken from GSL.
Definition: Simplex.h:27
A lookup based particle refiner.
Definition: TableRefiner.h:21
A decorator for a particle representing an atom.
Definition: atom/Atom.h:234
ScoreStates maintain invariants in the Model.
Definition: ScoreState.h:54
A class performing the rotations of atoms in the residues.
A class to change and restore log state.
Definition: SetLogState.h:31
A container which keeps a set of pairs that connect a set of spheres.
Restrain the diameter of a set of points.
Definition: Flag.h:36
Define the type for a type of hierarchy.
Score the improper dihedral based on a UnaryFunction,.
void optimize_balls(Model *m, const ParticleIndexes &pis, const RestraintsTemp &rs=RestraintsTemp(), const PairPredicates &excluded=PairPredicates(), const OptimizerStates &opt_states=OptimizerStates(), LogLevel ll=DEFAULT)
Ensure that a set of particles remains connected with one another.
Apply a function to the distance to a fixed point.
A decorator for a particle with x,y,z coordinates.
Definition: XYZ.h:30
Apply a transformation to a passed particle.
Definition: Transform.h:20
A base class for Keys.
Definition: Key.h:44
Class for easy writing of PDBs, RMFs, and stat files.
Definition: output.py:201
Score the bond based on a UnaryFunction,.
A simple sampler.
Definition: MCCGSampler.h:40
An axis-aligned bounding box.
Definition: BoundingBoxD.h:27
Interface to specialized Particle types (e.g. atoms)
Definition: Decorator.h:118
IMP-specific subclass of argparse.ArgumentParser.
Definition: __init__.py:10642
Find all nearby pairs by testing all pairs.
Simple implementation of segments in 3D.
Definition: Segment3D.h:24
A decorator for a residue.
Definition: Residue.h:137
Periodically dump the state of all associated objects into the RMF file.
Abstract predicate function.
Definition: PairPredicate.h:31
Read the assignments from binary data on disk.
Parameters used by Em2DRestraint and ProjectionFinder.
Store a configuration of a subset.
Definition: Assignment.h:32
Calculate score based on fit to EM map.
Definition: FitRestraint.h:39
Automatically setup Sytem and Degrees of Freedom with a formatted text file.
Display a segment for each pair in a IMP::PairContainer.
Definition: XYZR.h:170
Shared optimizer state that is invoked upon commitment of new coordinates.
Select all non-water non-alternative ATOM and HETATM records.
Definition: pdb.h:287
A filter that excludes bonds, angles and dihedrals.
Prevent a set of particles and rigid bodies from inter-penetrating.
Read a Modeller model into IMP.
Class to handle individual particles of a Model object.
Definition: Particle.h:41
Determine the collision cross section for some projections of particles.
Write a CGO file with the geometry.
Definition: PymolWriter.h:34
Score pair of atoms based on DOPE.
Definition: Dope.h:32
Store info for a chain of a protein.
Definition: Chain.h:61
Store the assignments on disk as binary data.
Applies a PairScore to a Pair.
Definition: PairRestraint.h:29
Score the model efficiently when a small number of particles are changed.
Store the assignments in an HDF5DataSet.
Select all CA ATOM records.
Definition: pdb.h:77
The topology of a complete CHARMM model.
A macro to help setup and run replica exchange.
Definition: macros.py:58
A dictionary-like wrapper for reading and storing sequence data.
Score pair of atoms based on DOPE.
Definition: DopePairScore.h:36
An exception which is thrown when the Model has attributes with invalid values.
Definition: exception.h:189
Smooth interaction scores by switching the derivatives (force switch).
Create a new log context.
Ensure that a set of particles remains connected with one another.
Select hierarchy particles identified by the biological name.
Definition: Selection.h:66
Abstract class for containers of particles.
Applies a SingletonScore to a Singleton.
Applies a list of movers one at a time.
Definition: SerialMover.h:23
Represent a sphere in D-dimensions.
Definition: SphereD.h:25
Management of reading/writing TIFF images.
Applies a PairScore to each Pair in a list.
A filter for bonds.
Display an IMP::atom::Hierarchy particle as balls.
Perform more efficient close pair finding when rigid bodies are involved.
Display an IMP::core::XYZR particle as a ball.
Definition: XYZR.h:151
A restraint is a term in an IMP ScoringFunction.
Definition: Restraint.h:54
Simply return the coordinates of a VectorD.
Definition: embeddings.h:79
Harmonic function (symmetric about the mean)
Definition: core/Harmonic.h:24
Manages workers and contexts.
Store data to be clustered for distance metric based algorithms.
Definition: Metric.h:25
A decorator for a particle with x,y,z coordinates and a radius.
Definition: XYZR.h:27