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IMP Reference Guide  develop.97bab1d8fd,2021/09/21
The Integrative Modeling Platform
Class Examples

Overview

Examples that use a given class:

See also Factory Index, Argument Index, Class Examples, Function Examples

IMP (kernel)

ClassExamples
IMP.ArgumentParserrotamer/rotamer_pdb2.py, rotamer/rotamer_pdb.py
IMP::Arrayatom/dope_and_excluded_volume.cpp, domino/marina_party.py
IMP::Containerkernel/dependency_graph.py
IMP::CreateLogContextlog.py
IMP::Decoratordomino/marina_party.py
IMP::Flagflags.cpp
IMP::Indexatom/dope_and_excluded_volume.cpp, core/simple.cpp
IMP::Keycontainer/filter_close_pairs.py, container/statistical.py, domino/marina_party.py, kernel/write_a_restraint.py, kernel/write_an_optimizer_state.py
IMP::ModelBallMover.py, atom/assess_dope.py, atom/cg_pdb.py, atom/charmm_forcefield.py, atom/charmm_forcefield_verbose.py, atom/dope_and_excluded_volume.cpp, atom/edit_molecular_hierarchy.py, atom/load_protein_restrain_bonds.py, atom/markers.py, atom/molecular_hierarchy.py, atom/multiresolution.py, atom/rigid_brownian_dynamics.py, atom/score_protein_with_ligand.py, atom/structure_from_sequence.py, container/bipartite_nonbonded_interactions.py, container/connectivity.py, container/filter_close_pairs.py, container/nonbonded_interactions.py, container/statistical.py, core/XYZR_Decorator.py, core/XYZ_Decorator.py, core/connectivity_restraint.py, core/cover_particles.py, core/custom_hierarchy.py, core/incremental_mc.py, core/ms_connectivity_restraint.py, core/optimize_balls.py, core/randomize_rigid_body.py, core/restrain_diameter.py, core/restrain_in_sphere.py, core/restrain_minimum_distance.py, core/rigid_bodies.py, core/rigid_collisions.py, core/simple.cpp, core/simple.py, core/symmetry.py, display/display_log.py, display/displaying_ensembles.py, display/show_particles_as_spheres.py, domino/custom_filter.py, domino/domino_approach.py, domino/interactive.py, domino/interactive_with_containers.py, domino/marina_party.py, domino/merge_tree.py, domino/multiscale.py, domino/restraint_cache.py, domino/rigid_body_excluded_volume.py, domino/save_assignments.py, domino/six_particles_optimization.py, em2d/clustering_of_pdb_models.py, em2d/collision_cross_section.py, em2d/optimize_em2d_with_montecarlo.py, em/analyze_convergence.py, em/fit_restraint.py, em/generate_density_map_of_fixed_dimension.py, em/local_fitting.py, em/pdb2density.py, example/range_restriction.py, gsl/simplex.py, kernel/chain.py, kernel/dependency_graph.py, kernel/graph.py, kernel/setup.py, kernel/write_a_restraint.py, kernel/write_an_optimizer_state.py, misc/decay.py, modeller/imp_restraints_in_modeller.py, modeller/load_modeller_model.py, modeller/modeller_restraints_in_imp.py, multistate.py, parallel/tasks.py, pmi/ambiguity.py, pmi/atomistic.py, pmi/automatic.py, pmi/em.py, pmi/ideal_helix.py, pmi/membrane.py, pmi/multiscale.py, pmi/selection.py, pmi/symmetry.py, rmf/link.py, rmf/multiresolution.py, rmf/pdb.py, rmf/simulation.py, rotamer/rotamer_pdb2.py, rotamer/rotamer_pdb.py, saxs/profile.py, saxs/profile_fit.py, temperature_rem.py
IMP::ModelExceptioncore/rigid_collisions.py
IMP::Objectlog.py
IMP::OptimizerStateem2d/optimize_em2d_with_montecarlo.py, kernel/write_an_optimizer_state.py
IMP::PairPredicatecontainer/filter_close_pairs.py, container/statistical.py
IMP::PairScoredomino/marina_party.py
IMP::Particleatom/molecular_hierarchy.py, atom/rigid_brownian_dynamics.py, core/XYZR_Decorator.py, core/connectivity_restraint.py, core/custom_hierarchy.py, core/incremental_mc.py, core/ms_connectivity_restraint.py, core/optimize_balls.py, core/randomize_rigid_body.py, core/rigid_collisions.py, core/symmetry.py, display/displaying_ensembles.py, domino/domino_approach.py, domino/interactive.py, domino/interactive_with_containers.py, domino/marina_party.py, domino/merge_tree.py, domino/multiscale.py, domino/restraint_cache.py, domino/save_assignments.py, em/analyze_convergence.py, gsl/simplex.py, kernel/dependency_graph.py, kernel/graph.py, kernel/setup.py, kernel/write_a_restraint.py, parallel/tasks.py, rmf/multiresolution.py, rmf/simulation.py, temperature_rem.py
IMP::Restraintkernel/dependency_graph.py, kernel/write_a_restraint.py
IMP::RestraintSetdomino/domino_approach.py, em2d/optimize_em2d_with_montecarlo.py, em/analyze_convergence.py, kernel/write_an_optimizer_state.py
IMP::ScopedSetAttributecore/optimize_balls.py
IMP::ScoreStatekernel/dependency_graph.py
IMP::SetLogStatedomino/restraint_cache.py, kernel/dependency_graph.py, log.py
IMP::Vectoratom/dope_and_excluded_volume.cpp, core/rigid_collisions.py, em2d/clustering_of_pdb_models.py, em/local_fitting.py, saxs/profile_fit.py

IMP.algebra

ClassExamples
IMP::algebra::BoundingBoxDalgebra/geometry.py, container/filter_close_pairs.py, core/incremental_mc.py, core/optimize_balls.py, core/rigid_collisions.py, display/basic_geometry.py, domino/merge_tree.py, domino/multiscale.py, em2d/optimize_em2d_with_montecarlo.py, em/analyze_convergence.py, em/cube.py, example/range_restriction.py, grid.cpp, kernel/setup.py, misc/decay.py, rmf/geometry.py, rmf/simulation.py
IMP::algebra::Cylinder3Dalgebra/geometry.py, display/displaying_ensembles.py
IMP::algebra::GridDgrid.cpp
IMP::algebra::ReferenceFrame3Datom/cg_pdb.py, atom/multiresolution.py, atom/rigid_brownian_dynamics.py, core/randomize_rigid_body.py, domino/rigid_body_excluded_volume.py, em/analyze_convergence.py
IMP::algebra::Segment3Dalgebra/geometry.py, display/displaying_ensembles.py
IMP::algebra::SphereDBallMover.py, algebra/geometry.py, algebra/grid_space.py, atom/rigid_brownian_dynamics.py, container/filter_close_pairs.py, core/XYZR_Decorator.py, core/connectivity_restraint.py, core/optimize_balls.py, core/restrain_in_sphere.py, display/basic_geometry.py, domino/merge_tree.py, em/analyze_convergence.py, em/cube.py, kernel/setup.py, statistics/kmeans.py
IMP::algebra::Transformation3DBallMover.py, atom/cg_pdb.py, atom/markers.py, atom/rigid_brownian_dynamics.py, core/randomize_rigid_body.py, core/rigid_collisions.py, core/symmetry.py, domino/rigid_body_excluded_volume.py, em2d/optimize_em2d_with_montecarlo.py, em/local_fitting.py, pmi/ambiguity.py

IMP.atom

ClassExamples
IMP::atom::ATOMPDBSelectorem2d/clustering_of_pdb_models.py, em2d/collision_cross_section.py, em2d/optimize_em2d_with_montecarlo.py, kernel/dependency_graph.py
IMP::atom::AngleSingletonScoreatom/charmm_forcefield_verbose.py
IMP::atom::Atomatom/dope_and_excluded_volume.cpp, rotamer/rotamer_pdb.py
IMP::atom::BondSingletonScoreatom/charmm_forcefield_verbose.py, atom/load_protein_restrain_bonds.py
IMP::atom::BondedPairFiltercontainer/nonbonded_interactions.py
IMP::atom::BrownianDynamicsatom/rigid_brownian_dynamics.py, misc/decay.py, rmf/simulation.py
IMP::atom::CAlphaPDBSelectordisplay/displaying_ensembles.py, domino/rigid_body_excluded_volume.py, em/generate_density_map_of_fixed_dimension.py, em/local_fitting.py
IMP::atom::CHARMMStereochemistryRestraintatom/charmm_forcefield.py
IMP::atom::CHARMMTopologyatom/structure_from_sequence.py
IMP::atom::Chainatom/cg_pdb.py, atom/dope_and_excluded_volume.cpp, atom/molecular_hierarchy.py, display/displaying_ensembles.py, kernel/dependency_graph.py
IMP::atom::DihedralSingletonScoreatom/charmm_forcefield_verbose.py
IMP::atom::DopePairScoreatom/assess_dope.py
IMP::atom::ForceSwitchatom/charmm_forcefield.py, atom/charmm_forcefield_verbose.py
IMP::atom::Hierarchycore/rigid_bodies.py
IMP::atom::HierarchyGeometryatom/markers.py, atom/rigid_brownian_dynamics.py, domino/rigid_body_excluded_volume.py
IMP::atom::ImproperSingletonScoreatom/charmm_forcefield_verbose.py
IMP::atom::LennardJonesPairScoreatom/charmm_forcefield.py, atom/charmm_forcefield_verbose.py
IMP::atom::NonWaterNonHydrogenPDBSelectoratom/assess_dope.py, atom/charmm_forcefield.py, atom/charmm_forcefield_verbose.py, atom/multiresolution.py, saxs/profile.py, saxs/profile_fit.py
IMP::atom::NonWaterPDBSelectorem/fit_restraint.py, em/pdb2density.py
IMP::atom::ProteinLigandAtomPairScoreatom/score_protein_with_ligand.py
IMP::atom::Residueatom/dope_and_excluded_volume.cpp, atom/edit_molecular_hierarchy.py, rmf/multiresolution.py, rotamer/rotamer_pdb.py
IMP::atom::Selectionatom/markers.py, atom/multiresolution.py, atom/rigid_brownian_dynamics.py, display/displaying_ensembles.py, kernel/dependency_graph.py, multistate.py, pmi/em.py, pmi/selection.py
IMP::atom::SelectionGeometryatom/markers.py
IMP::atom::StereochemistryPairFilteratom/charmm_forcefield_verbose.py
IMP::atom::WritePDBOptimizerStateem2d/optimize_em2d_with_montecarlo.py

IMP.container

ClassExamples
IMP::container::CloseBipartitePairContainercontainer/bipartite_nonbonded_interactions.py, container/filter_close_pairs.py
IMP::container::ClosePairContaineratom/assess_dope.py, atom/charmm_forcefield.py, atom/charmm_forcefield_verbose.py, container/filter_close_pairs.py, container/nonbonded_interactions.py, container/statistical.py, core/excluded_volume.py, core/model_numpy.py, core/rigid_collisions.py, kernel/basic_optimization.py, kernel/chain.py
IMP::container::ConnectingPairContainercontainer/connectivity.py
IMP::container::ConsecutivePairContainerdomino/restraint_cache.py, kernel/chain.py
IMP::container::ConsecutivePairFilterkernel/chain.py
IMP::container::ExclusiveConsecutivePairContainercore/optimize_balls.py
IMP::container::ExclusiveConsecutivePairFiltercore/optimize_balls.py
IMP::container::ListPairContainerdomino/custom_filter.py, domino/interactive.py, domino/interactive_with_containers.py, domino/merge_tree.py, domino/six_particles_optimization.py
IMP::container::ListSingletonContaineratom/charmm_forcefield.py, atom/charmm_forcefield_verbose.py, atom/load_protein_restrain_bonds.py, atom/rigid_brownian_dynamics.py, container/bipartite_nonbonded_interactions.py, container/connectivity.py, container/filter_close_pairs.py, container/nonbonded_interactions.py, container/statistical.py, core/connectivity_restraint.py, core/incremental_mc.py, core/restrain_diameter.py, core/rigid_collisions.py, core/symmetry.py, display/display_log.py, display/show_particles_as_spheres.py, domino/rigid_body_excluded_volume.py, em2d/optimize_em2d_with_montecarlo.py, example/range_restriction.py, kernel/chain.py, kernel/setup.py, misc/decay.py
IMP::container::PairsRestraintatom/assess_dope.py, atom/charmm_forcefield.py, atom/charmm_forcefield_verbose.py, container/bipartite_nonbonded_interactions.py, container/nonbonded_interactions.py, core/excluded_volume.py, core/optimize_balls.py, core/rigid_collisions.py, domino/custom_filter.py, domino/interactive.py, domino/interactive_with_containers.py, domino/merge_tree.py, domino/restraint_cache.py, domino/six_particles_optimization.py, kernel/basic_optimization.py, kernel/chain.py, misc/decay.py, rmf/simulation.py
IMP::container::PredicatePairsRestraintcontainer/statistical.py
IMP::container::SingletonsConstraintexample/range_restriction.py
IMP::container::SingletonsRestraintatom/charmm_forcefield_verbose.py, atom/load_protein_restrain_bonds.py, container/restrain_in_sphere.py, core/incremental_mc.py, core/optimize_balls.py, misc/decay.py, rmf/simulation.py

IMP.core

ClassExamples
IMP::core::BallMoverBallMover.py, core/incremental_mc.py, core/optimize_balls.py, core/restrain_minimum_distance.py, display/display_log.py, temperature_rem.py
IMP::core::ChildrenRefinercore/connectivity_restraint.py, core/cover_particles.py
IMP::core::CoinFlipPairPredicatemisc/decay.py
IMP::core::ConjugateGradientscontainer/bipartite_nonbonded_interactions.py, container/nonbonded_interactions.py, core/optimize_balls.py, core/restrain_diameter.py, core/rigid_collisions.py, core/simple.py, core/symmetry.py, em/analyze_convergence.py
IMP::core::ConnectivityRestraintcore/connectivity_restraint.py
IMP::core::DiameterRestraintcore/restrain_diameter.py
IMP::core::DistancePairScorecore/ms_connectivity_restraint.py, core/pair_restraint.py, core/simple.py, kernel/basic_optimization.py
IMP::core::DistanceRestraintdomino/domino_approach.py, em2d/optimize_em2d_with_montecarlo.py, gsl/simplex.py, modeller/imp_restraints_in_modeller.py, parallel/tasks.py, temperature_rem.py
IMP::core::EdgePairsGeometrycontainer/connectivity.py
IMP::core::ExcludedVolumeRestraintatom/rigid_brownian_dynamics.py, core/excluded_volume.py, core/incremental_mc.py, core/optimize_balls.py, core/symmetry.py, display/display_log.py, domino/rigid_body_excluded_volume.py, misc/decay.py, rmf/simulation.py
IMP::core::GenericAttributeSingletonScoredomino/multiscale.py
IMP::core::GenericBoundingBox3DSingletonScorecore/incremental_mc.py, core/optimize_balls.py, misc/decay.py, rmf/simulation.py
IMP::core::GenericDistanceToSingletonScorecontainer/restrain_in_sphere.py, core/restrain_in_sphere.py, core/simple.py, domino/multiscale.py, domino/six_particles_optimization.py
IMP::core::GridClosePairsFinderdomino/merge_tree.py
IMP::core::HarmonicBallMover.py, atom/charmm_forcefield_verbose.py, atom/load_protein_restrain_bonds.py, core/pair_restraint.py, core/simple.py, domino/domino_approach.py, domino/multiscale.py, em2d/optimize_em2d_with_montecarlo.py, gsl/simplex.py, modeller/imp_restraints_in_modeller.py, parallel/tasks.py, temperature_rem.py
IMP::core::HarmonicDistancePairScorecontainer/statistical.py, core/optimize_balls.py, domino/custom_filter.py, domino/interactive.py, domino/interactive_with_containers.py, domino/six_particles_optimization.py, kernel/chain.py, rotamer/rotamer_pdb2.py
IMP::core::HarmonicLowerBoundcontainer/bipartite_nonbonded_interactions.py, core/excluded_volume.py, core/rigid_collisions.py, kernel/basic_optimization.py
IMP::core::HarmonicSphereDistancePairScorecore/restrain_minimum_distance.py, domino/multiscale.py
IMP::core::HarmonicUpperBoundcontainer/restrain_in_sphere.py, core/connectivity_restraint.py, core/incremental_mc.py, core/ms_connectivity_restraint.py, core/optimize_balls.py, core/restrain_diameter.py, core/restrain_in_sphere.py, display/displaying_ensembles.py, domino/six_particles_optimization.py, misc/decay.py, rmf/simulation.py
IMP::core::HarmonicUpperBoundSphereDistancePairScoredomino/restraint_cache.py, misc/decay.py, rmf/simulation.py
IMP::core::HierarchyTraitscore/custom_hierarchy.py
IMP::core::IncrementalScoringFunctioncore/incremental_mc.py, core/optimize_balls.py
IMP::core::KClosePairsPairScorecore/connectivity_restraint.py, core/restrain_minimum_distance.py, display/displaying_ensembles.py
IMP::core::LeavesRefinerdisplay/displaying_ensembles.py, em/local_fitting.py
IMP::core::MCCGSamplerkernel/basic_optimization.py, kernel/chain.py
IMP::core::MSConnectivityRestraintcore/ms_connectivity_restraint.py
IMP::core::MonteCarloBallMover.py, core/incremental_mc.py, core/optimize_balls.py, core/restrain_minimum_distance.py, display/display_log.py, em2d/optimize_em2d_with_montecarlo.py, temperature_rem.py
IMP::core::PairRestraintBallMover.py, core/pair_restraint.py, core/restrain_minimum_distance.py, core/simple.py, domino/marina_party.py, domino/multiscale.py, kernel/chain.py
IMP::core::RestraintsScoringFunctionatom/charmm_forcefield.py, atom/charmm_forcefield_verbose.py, atom/rigid_brownian_dynamics.py, container/statistical.py, core/excluded_volume.py, core/optimize_balls.py, core/restrain_diameter.py, core/rigid_collisions.py, core/simple.py, core/symmetry.py, domino/custom_filter.py, domino/rigid_body_excluded_volume.py, domino/six_particles_optimization.py, em2d/optimize_em2d_with_montecarlo.py, em/analyze_convergence.py, kernel/basic_optimization.py, kernel/dependency_graph.py, modeller/imp_restraints_in_modeller.py, modeller/load_modeller_model.py, modeller/modeller_restraints_in_imp.py, parallel/tasks.py, rmf/simulation.py, temperature_rem.py
IMP::core::RigidBodyMoverem2d/optimize_em2d_with_montecarlo.py
IMP::core::RigidClosePairsFindercore/rigid_collisions.py
IMP::core::RigidMemberdisplay/displaying_ensembles.py, domino/rigid_body_excluded_volume.py, em/local_fitting.py
IMP::core::SerialMoverBallMover.py, core/incremental_mc.py, core/optimize_balls.py, temperature_rem.py
IMP::core::SingletonConstraintcore/symmetry.py
IMP::core::SingletonRestraintcore/restrain_in_sphere.py, core/simple.py, domino/multiscale.py, domino/six_particles_optimization.py
IMP::core::SoftSpherePairScorecontainer/nonbonded_interactions.py, core/optimize_balls.py, domino/merge_tree.py, kernel/chain.py
IMP::core::SphereDistancePairScoreBallMover.py, container/bipartite_nonbonded_interactions.py, core/connectivity_restraint.py, core/excluded_volume.py, core/rigid_collisions.py, display/displaying_ensembles.py
IMP::core::TableRefinercore/restrain_minimum_distance.py
IMP::core::Transformem2d/clustering_of_pdb_models.py
IMP::core::TransformationSymmetrycore/symmetry.py
IMP::core::XYZatom/score_protein_with_ligand.py, core/XYZR_Decorator.py, core/restrain_diameter.py, core/simple.cpp, core/symmetry.py, display/displaying_ensembles.py, domino/custom_filter.py, domino/six_particles_optimization.py, pmi/ambiguity.py, rmf/pdb.py, rotamer/rotamer_pdb.py
IMP::core::XYZDerivativeGeometryem/analyze_convergence.py
IMP::core::XYZRBallMover.py, atom/markers.py, core/optimize_balls.py, display/show_particles_as_spheres.py
IMP::core::XYZRGeometryatom/markers.py, core/incremental_mc.py, core/optimize_balls.py, display/displaying_ensembles.py, domino/multiscale.py
IMP::core::XYZRsGeometrydisplay/display_log.py, display/show_particles_as_spheres.py

IMP.display

ClassExamples
IMP::display::BoundingBoxGeometrycore/optimize_balls.py, display/basic_geometry.py, misc/decay.py, rmf/geometry.py, rmf/simulation.py
IMP::display::Coloratom/markers.py, display/display_log.py, display/displaying_ensembles.py, display/show_particles_as_spheres.py, domino/multiscale.py
IMP::display::CylinderGeometrydisplay/displaying_ensembles.py
IMP::display::PointGeometrydomino/multiscale.py
IMP::display::PymolWriteratom/markers.py, atom/rigid_brownian_dynamics.py, core/incremental_mc.py, core/optimize_balls.py, display/basic_geometry.py, display/display_log.py, display/displaying_ensembles.py, display/show_particles_as_spheres.py, domino/multiscale.py, domino/rigid_body_excluded_volume.py, em/analyze_convergence.py
IMP::display::ReferenceFrameGeometrydisplay/displaying_ensembles.py
IMP::display::SphereGeometrydisplay/basic_geometry.py, em/analyze_convergence.py, em/cube.py
IMP::display::WriteOptimizerStatedisplay/display_log.py

IMP.domino

ClassExamples
IMP::domino::Assignmentdomino/save_assignments.py
IMP::domino::BranchAndBoundAssignmentsTabledomino/custom_filter.py, domino/interactive_with_containers.py, domino/rigid_body_excluded_volume.py, domino/six_particles_optimization.py
IMP::domino::DominoSamplerdomino/custom_filter.py, domino/domino_approach.py, domino/interactive.py, domino/marina_party.py, domino/multiscale.py, domino/restraint_cache.py, domino/rigid_body_excluded_volume.py, domino/six_particles_optimization.py
IMP::domino::ExclusionSubsetFilterTabledomino/custom_filter.py, domino/interactive_with_containers.py, domino/marina_party.py, domino/restraint_cache.py, domino/rigid_body_excluded_volume.py, domino/six_particles_optimization.py
IMP::domino::ListSubsetFilterTabledomino/marina_party.py, domino/multiscale.py
IMP::domino::ParticleStatesdomino/marina_party.py
IMP::domino::ParticleStatesTabledomino/custom_filter.py, domino/domino_approach.py, domino/interactive.py, domino/interactive_with_containers.py, domino/marina_party.py, domino/merge_tree.py, domino/multiscale.py, domino/restraint_cache.py, domino/rigid_body_excluded_volume.py, domino/six_particles_optimization.py
IMP::domino::ReadAssignmentContainerdomino/save_assignments.py
IMP::domino::ReadHDF5AssignmentContainerdomino/interactive_with_containers.py
IMP::domino::RestraintCachedomino/custom_filter.py, domino/interactive_with_containers.py, domino/multiscale.py, domino/restraint_cache.py, domino/rigid_body_excluded_volume.py, domino/six_particles_optimization.py
IMP::domino::RestraintScoreSubsetFilterTabledomino/custom_filter.py, domino/interactive_with_containers.py, domino/multiscale.py, domino/restraint_cache.py, domino/rigid_body_excluded_volume.py, domino/six_particles_optimization.py
IMP::domino::RigidBodyStatesdomino/rigid_body_excluded_volume.py
IMP::domino::Subsetdomino/multiscale.py, domino/restraint_cache.py, domino/save_assignments.py
IMP::domino::SubsetFilterdomino/custom_filter.py
IMP::domino::SubsetFilterTabledomino/custom_filter.py
IMP::domino::WriteAssignmentContainerdomino/save_assignments.py
IMP::domino::WriteHDF5AssignmentContainerdomino/interactive_with_containers.py
IMP::domino::XYZStatesdomino/custom_filter.py, domino/domino_approach.py, domino/interactive.py, domino/interactive_with_containers.py, domino/merge_tree.py, domino/multiscale.py, domino/restraint_cache.py, domino/six_particles_optimization.py

IMP.em

ClassExamples
IMP::em::FitRestraintem/analyze_convergence.py, em/fit_restraint.py
IMP::em::MRCReaderWriterem/analyze_convergence.py, em/fit_restraint.py, em/generate_density_map_of_fixed_dimension.py, em/local_fitting.py, em/numpy_data.py, em/pdb2density.py
IMP::em::SampledDensityMapem/analyze_convergence.py, em/generate_density_map_of_fixed_dimension.py, em/local_fitting.py

IMP.em2d

ClassExamples
IMP::em2d::CollisionCrossSectionem2d/collision_cross_section.py
IMP::em2d::EM2DScoreem2d/optimize_em2d_with_montecarlo.py
IMP::em2d::Em2DRestraintem2d/optimize_em2d_with_montecarlo.py
IMP::em2d::Em2DRestraintParametersem2d/optimize_em2d_with_montecarlo.py
IMP::em2d::SpiderImageReaderWriterem2d/em_images_conversion.py, em2d/optimize_em2d_with_montecarlo.py
IMP::em2d::TIFFImageReaderWriterem2d/em_images_conversion.py

IMP.example

ClassExamples
IMP::example::ExampleSingletonModifierexample/range_restriction.py

IMP.gsl

ClassExamples
IMP::gsl::Simplexgsl/simplex.py

IMP.kmeans

ClassExamples
IMP::kmeans::KMeanskmeans/kmeans_example.py

IMP.misc

ClassExamples
IMP::misc::DecayPairContainerOptimizerStatemisc/decay.py

IMP.modeller

ClassExamples
IMP.modeller.IMPRestraintsmodeller/imp_restraints_in_modeller.py
IMP.modeller.ModelLoadermodeller/imp_restraints_in_modeller.py, modeller/load_modeller_model.py, modeller/modeller_restraints_in_imp.py
IMP.modeller.ModellerRestraintsmodeller/modeller_restraints_in_imp.py

IMP.mpi

ClassExamples
IMP::mpi::ReplicaExchangetemperature_rem.py

IMP.parallel

ClassExamples
IMP.parallel.LocalWorkerparallel/local_distance.py
IMP.parallel.Managerparallel/local_distance.py

IMP.pmi

ClassExamples
IMP.pmi.dof.DegreesOfFreedompmi/ambiguity.py, pmi/atomistic.py, pmi/membrane.py, pmi/multiscale.py, pmi/selection.py, pmi/symmetry.py
IMP.pmi.macros.BuildSystempmi/automatic.py
IMP.pmi.macros.ReplicaExchange0pmi/ambiguity.py, pmi/atomistic.py, pmi/automatic.py, pmi/membrane.py, pmi/multiscale.py
IMP.pmi.output.Outputpmi/ideal_helix.py, pmi/symmetry.py
IMP.pmi.topology.Sequencespmi/atomistic.py, pmi/em.py, pmi/multiscale.py, pmi/selection.py
IMP.pmi.topology.Systempmi/ambiguity.py, pmi/atomistic.py, pmi/em.py, pmi/ideal_helix.py, pmi/membrane.py, pmi/multiscale.py, pmi/selection.py, pmi/symmetry.py
IMP.pmi.topology.TopologyReaderpmi/automatic.py

IMP.rmf

ClassExamples
IMP::rmf::SaveOptimizerStatemisc/decay.py, rmf/simulation.py

IMP.rotamer

ClassExamples
IMP::rotamer::RotamerCalculatorrotamer/rotamer_pdb2.py, rotamer/rotamer_pdb.py
IMP::rotamer::RotamerLibraryrotamer/rotamer_pdb2.py, rotamer/rotamer_pdb.py

IMP.saxs

ClassExamples
IMP::saxs::Profilesaxs/profile.py, saxs/profile_fit.py
IMP::saxs::RadialDistributionFunctionsaxs/profile.py
IMP::saxs::SolventAccessibleSurfacesaxs/profile_fit.py

IMP.score_functor

ClassExamples
IMP::score_functor::AddScoresatom/dope_and_excluded_volume.cpp
IMP::score_functor::DistancePairScoreatom/dope_and_excluded_volume.cpp
IMP::score_functor::Dopeatom/dope_and_excluded_volume.cpp
IMP::score_functor::HarmonicLowerBoundatom/dope_and_excluded_volume.cpp
IMP::score_functor::SphereDistanceatom/dope_and_excluded_volume.cpp

IMP.statistics

ClassExamples
IMP::statistics::ConfigurationSetXYZEmbeddingkernel/basic_optimization.py, statistics/kmeans.py
IMP::statistics::Metricstatistics/write_a_metric.py
IMP::statistics::ParticleEmbeddingstatistics/kmeans.py
IMP::statistics::VectorDEmbeddingstatistics/kmeans.py

IMP.symmetry

ClassExamples
IMP::symmetry::BallMoverBallMover.py