Class Examples

Examples that use a given class:

• IMP::algebra::BoundingBoxD:
  • algebra/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
  • em/analyze_convergence.py
  • em/cube.py
  • example/range_restriction.py
  • kernel/dock_with_crosslinks.py
  • kernel/nup84.py
  • kernel/setup.py
  • misc/decay.py
  • restrainer/rigid_body_and_excluded_volume_restraint.py
  • rmf/geometry.py
  • rmf/simulation.py
• IMP::algebra::Cylinder3D:
  • algebra/geometry.py
  • display/displaying_ensembles.py
• IMP::algebra::ReferenceFrame3D:
  • atom/cg_pdb.py
  • atom/rigid_brownian_dynamics.py
  • domino/rigid_body_excluded_volume.py
  • em/analyze_convergence.py
  • kernel/dock_with_crosslinks.py
  • restrainer/rigid_body_and_excluded_volume_restraint.py
• IMP::algebra::Segment3D:
  • algebra/geometry.py
  • display/displaying_ensembles.py
• IMP::algebra::SphereD:
  • 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
  • display/basic_geometry.py
  • domino/merge_tree.py
  • em/analyze_convergence.py
  • em/cube.py
  • kernel/setup.py
  • statistics/kmeans.py
• IMP::algebra::Transformation3D:
  • atom/cg_pdb.py
  • atom/markers.py
  • atom/rigid_brownian_dynamics.py
  • core/rigid_collisions.py
  • core/symmetry.py
  • domino/rigid_body_excluded_volume.py
  • em/local_fitting.py
  • kernel/dock_with_crosslinks.py
  • restrainer/rigid_body_and_excluded_volume_restraint.py
• IMP::algebra::VectorD:
  • algebra/grid_space.py
  • atom/cg_pdb.py
  • atom/dope_and_excluded_volume.cpp
  • atom/markers.py
  • atom/rigid_brownian_dynamics.py
  • container/filter_close_pairs.py
  • container/restrain_in_sphere.py
  • core/XYZR_Decorator.py
  • core/XYZ_Decorator.py
  • core/connectivity_restraint.py
  • core/incremental_mc.py
  • core/ms_connectivity_restraint.py
  • core/optimize_balls.py
  • core/rigid_collisions.py
  • core/symmetry.py
  • display/basic_geometry.py
  • domino/custom_filter.py
  • domino/domino_approach.py
  • domino/interactive.py
  • domino/interactive_with_containers.py
  • domino/multiscale.py
  • domino/restraint_cache.py
  • domino/rigid_body_excluded_volume.py
  • domino/six_particles_optimization.py
  • em/analyze_convergence.py
  • em/cube.py
  • example/range_restriction.py
  • gsl/simplex.py
  • kernel/dock_with_crosslinks.py
  • kernel/nup84.py
  • kernel/setup.py
  • misc/decay.py
  • parallel/tasks.py
  • restrainer/rigid_body_and_excluded_volume_restraint.py
  • rmf/geometry.py
  • rmf/simulation.py
  • statistics/kmeans.py
• IMP::atom::ATOMPDBSelector:
  • kernel/dependency_graph.py
  • kernel/nup84.py
• IMP::atom::AngleSingletonScore:
  • atom/charmm_forcefield_verbose.py
• IMP::atom::Atom:
  • atom/dope_and_excluded_volume.cpp
• IMP::atom::AtomType:
  • design_example
• IMP::atom::BondSingletonScore:
  • atom/charmm_forcefield_verbose.py
  • atom/load_protein_restrain_bonds.py
• IMP::atom::BondedPairFilter:
  • container/nonbonded_interactions.py
• IMP::atom::BrownianDynamics:
  • atom/rigid_brownian_dynamics.py
  • misc/decay.py
  • rmf/simulation.py
• IMP::atom::CAlphaPDBSelector:
  • display/displaying_ensembles.py
  • domino/rigid_body_excluded_volume.py
  • em/generate_density_map_of_fixed_dimension.py
  • em/local_fitting.py
  • kernel/dock_with_crosslinks.py
  • restrainer/simple_connectivity_on_rigid_bodies.py
  • restrainer/simple_excluded_volume.py
• IMP::atom::CHARMMStereochemistryRestraint:
  • atom/charmm_forcefield.py
• IMP::atom::CHARMMTopology:
  • atom/structure_from_sequence.py
• IMP::atom::Chain:
  • atom/cg_pdb.py
  • atom/dope_and_excluded_volume.cpp
  • atom/molecular_hierarchy.py
  • display/displaying_ensembles.py
  • kernel/dependency_graph.py
  • kernel/dock_with_crosslinks.py
  • kernel/nup84.py
• IMP::atom::DihedralSingletonScore:
  • atom/charmm_forcefield_verbose.py
• IMP::atom::DopePairScore:
  • atom/assess_dope.py
• IMP::atom::ForceSwitch:
  • atom/charmm_forcefield.py
  • atom/charmm_forcefield_verbose.py
• IMP::atom::Hierarchy:
  • core/rigid_bodies.py
  • design_example
• IMP::atom::HierarchyGeometry:
  • atom/markers.py
  • atom/rigid_brownian_dynamics.py
  • domino/rigid_body_excluded_volume.py
• IMP::atom::ImproperSingletonScore:
  • atom/charmm_forcefield_verbose.py
• IMP::atom::LangevinThermostatOptimizerState:
  • kernel/dock_with_crosslinks.py
• IMP::atom::LennardJonesPairScore:
  • atom/charmm_forcefield.py
  • atom/charmm_forcefield_verbose.py
• IMP::atom::MolecularDynamics:
  • kernel/dock_with_crosslinks.py
• IMP::atom::NonWaterNonHydrogenPDBSelector:
  • atom/assess_dope.py
  • atom/charmm_forcefield.py
  • atom/charmm_forcefield_verbose.py
  • saxs/profile.py
  • saxs/profile_fit.py
• IMP::atom::NonWaterPDBSelector:
  • em/fit_restraint.py
  • em/pdb2density.py
• IMP::atom::ProteinLigandAtomPairScore:
  • atom/score_protein_with_ligand.py
• IMP::atom::Residue:
  • atom/dope_and_excluded_volume.cpp
  • kernel/dock_with_crosslinks.py
  • rmf/multiresolution.py
• IMP::atom::SameResiduePairFilter:
  • atom/assess_dope.py
• IMP::atom::Selection:
  • atom/markers.py
  • atom/rigid_brownian_dynamics.py
  • display/displaying_ensembles.py
  • kernel/dependency_graph.py
  • kernel/dock_with_crosslinks.py
  • kernel/nup84.py
• IMP::atom::SelectionGeometry:
  • atom/markers.py
• IMP::atom::StereochemistryPairFilter:
  • atom/charmm_forcefield_verbose.py
• IMP::base::Array:
  • domino/marina_party.py
• IMP::base::CreateLogContext:
  • base/log.py
• IMP::base::Index:
  • atom/dope_and_excluded_volume.cpp
• IMP::base::ModelException:
  • core/rigid_collisions.py
• IMP::base::Object:
  • base/log.py
• IMP::base::SetLogState:
  • base/log.py
  • domino/restraint_cache.py
  • kernel/dependency_graph.py
• IMP::base::Vector:
  • atom/dope_and_excluded_volume.cpp
• IMP::container::CloseBipartitePairContainer:
  • container/bipartite_nonbonded_interactions.py
  • container/filter_close_pairs.py
  • kernel/dock_with_crosslinks.py
• IMP::container::ClosePairContainer:
  • atom/assess_dope.py
  • atom/charmm_forcefield.py
  • atom/charmm_forcefield_verbose.py
  • container/filter_close_pairs.py
  • container/nonbonded_interactions.py
  • core/excluded_volume.py
  • core/rigid_collisions.py
  • kernel/basic_optimization.py
  • kernel/chain.py
• IMP::container::ConnectingPairContainer:
  • container/connectivity.py
• IMP::container::ConsecutivePairContainer:
  • domino/restraint_cache.py
  • kernel/chain.py
• IMP::container::ConsecutivePairFilter:
  • kernel/chain.py
• IMP::container::ExclusiveConsecutivePairContainer:
  • core/optimize_balls.py
• IMP::container::ExclusiveConsecutivePairFilter:
  • core/optimize_balls.py
• IMP::container::ListPairContainer:
  • domino/custom_filter.py
  • domino/interactive.py
  • domino/interactive_with_containers.py
  • domino/merge_tree.py
  • domino/six_particles_optimization.py
• IMP::container::ListSingletonContainer:
  • atom/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
  • 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/dock_with_crosslinks.py
  • kernel/setup.py
• IMP::container::PairsRestraint:
  • atom/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::SingletonsConstraint:
  • example/range_restriction.py
• IMP::container::SingletonsRestraint:
  • atom/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::BallMover:
  • core/incremental_mc.py
  • core/optimize_balls.py
  • core/restrain_minimum_distance.py
  • display/display_log.py
  • kernel/nup84.py
• IMP::core::ChildrenRefiner:
  • core/connectivity_restraint.py
  • core/cover_particles.py
• IMP::core::CoinFlipPairPredicate:
  • misc/decay.py
• IMP::core::ConjugateGradients:
  • container/bipartite_nonbonded_interactions.py
  • container/nonbonded_interactions.py
  • core/optimize_balls.py
  • core/restrain_diameter.py
  • core/rigid_collisions.py
  • core/symmetry.py
  • em/analyze_convergence.py
  • kernel/dock_with_crosslinks.py
• IMP::core::ConnectivityRestraint:
  • core/connectivity_restraint.py
  • restrainer/simple_connectivity_on_molecules.py
  • restrainer/simple_connectivity_on_rigid_bodies.py
• IMP::core::DiameterRestraint:
  • core/restrain_diameter.py
  • restrainer/simple_diameter.py
• IMP::core::DistancePairScore:
  • core/ms_connectivity_restraint.py
  • core/pair_restraint.py
  • kernel/basic_optimization.py
  • kernel/dock_with_crosslinks.py
• IMP::core::DistanceRestraint:
  • domino/domino_approach.py
  • gsl/simplex.py
  • modeller/imp_restraints_in_modeller.py
  • parallel/tasks.py
  • restrainer/simple_distance.py
• IMP::core::EdgePairsGeometry:
  • container/connectivity.py
• IMP::core::ExcludedVolumeRestraint:
  • atom/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
  • kernel/dock_with_crosslinks.py
  • misc/decay.py
  • restrainer/rigid_body_and_excluded_volume_restraint.py
  • restrainer/simple_excluded_volume.py
  • rmf/simulation.py
• IMP::core::GenericAttributeSingletonScore:
  • domino/multiscale.py
• IMP::core::GenericBoundingBox3DSingletonScore:
  • core/incremental_mc.py
  • core/optimize_balls.py
  • misc/decay.py
  • rmf/simulation.py
• IMP::core::GenericDistanceToSingletonScore:
  • container/restrain_in_sphere.py
  • domino/custom_filter.py
  • domino/multiscale.py
  • domino/six_particles_optimization.py
• IMP::core::GridClosePairsFinder:
  • domino/merge_tree.py
• IMP::core::Harmonic:
  • atom/charmm_forcefield_verbose.py
  • atom/load_protein_restrain_bonds.py
  • core/pair_restraint.py
  • domino/domino_approach.py
  • domino/multiscale.py
  • gsl/simplex.py
  • modeller/imp_restraints_in_modeller.py
  • parallel/tasks.py
• IMP::core::HarmonicDistancePairScore:
  • core/optimize_balls.py
  • domino/custom_filter.py
  • domino/interactive.py
  • domino/interactive_with_containers.py
  • domino/six_particles_optimization.py
  • kernel/chain.py
• IMP::core::HarmonicLowerBound:
  • container/bipartite_nonbonded_interactions.py
  • core/excluded_volume.py
  • core/rigid_collisions.py
  • kernel/basic_optimization.py
• IMP::core::HarmonicSphereDistancePairScore:
  • core/restrain_minimum_distance.py
  • domino/multiscale.py
• IMP::core::HarmonicUpperBound:
  • container/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
  • display/displaying_ensembles.py
  • domino/custom_filter.py
  • domino/six_particles_optimization.py
  • kernel/dock_with_crosslinks.py
  • misc/decay.py
  • rmf/simulation.py
• IMP::core::HarmonicUpperBoundSphereDistancePairScore:
  • domino/restraint_cache.py
  • misc/decay.py
  • rmf/simulation.py
• IMP::core::HierarchyTraits:
  • core/custom_hierarchy.py
• IMP::core::IncrementalScoringFunction:
  • core/incremental_mc.py
  • core/optimize_balls.py
  • kernel/nup84.py
• IMP::core::KClosePairsPairScore:
  • core/connectivity_restraint.py
  • core/restrain_minimum_distance.py
  • display/displaying_ensembles.py
• IMP::core::LeavesRefiner:
  • display/displaying_ensembles.py
  • em/local_fitting.py
• IMP::core::MCCGSampler:
  • kernel/basic_optimization.py
  • kernel/chain.py
• IMP::core::MSConnectivityRestraint:
  • core/ms_connectivity_restraint.py
• IMP::core::MonteCarlo:
  • core/incremental_mc.py
  • core/optimize_balls.py
  • core/restrain_minimum_distance.py
  • display/display_log.py
  • kernel/dock_with_crosslinks.py
  • kernel/nup84.py
• IMP::core::PairRestraint:
  • core/pair_restraint.py
  • core/restrain_minimum_distance.py
  • domino/multiscale.py
  • kernel/chain.py
  • kernel/dock_with_crosslinks.py
• IMP::core::RestraintsScoringFunction:
  • core/optimize_balls.py
  • rmf/simulation.py
• IMP::core::RigidBody:
  • restrainer/rigid_body_and_excluded_volume_restraint.py
• IMP::core::RigidBodyMover:
  • kernel/dock_with_crosslinks.py
  • kernel/nup84.py
• IMP::core::RigidClosePairsFinder:
  • core/rigid_collisions.py
• IMP::core::RigidMember:
  • display/displaying_ensembles.py
  • domino/rigid_body_excluded_volume.py
  • em/local_fitting.py
  • kernel/dock_with_crosslinks.py
• IMP::core::SerialMover:
  • core/incremental_mc.py
  • core/optimize_balls.py
  • kernel/nup84.py
• IMP::core::SingletonConstraint:
  • core/symmetry.py
• IMP::core::SingletonRestraint:
  • domino/multiscale.py
  • domino/six_particles_optimization.py
• IMP::core::SoftSpherePairScore:
  • container/nonbonded_interactions.py
  • core/optimize_balls.py
  • domino/merge_tree.py
  • kernel/chain.py
  • kernel/nup84.py
• IMP::core::SphereDistancePairScore:
  • container/bipartite_nonbonded_interactions.py
  • core/connectivity_restraint.py
  • core/excluded_volume.py
  • core/rigid_collisions.py
  • display/displaying_ensembles.py
• IMP::core::TableRefiner:
  • core/restrain_minimum_distance.py
  • em/analyze_convergence.py
• IMP::core::TransformationSymmetry:
  • core/symmetry.py
• IMP::core::TypedPairScore:
  • design_example
• IMP::core::XYZ:
  • atom/score_protein_with_ligand.py
  • core/restrain_diameter.py
  • core/symmetry.py
  • display/displaying_ensembles.py
  • domino/custom_filter.py
  • domino/six_particles_optimization.py
  • kernel/nup84.py
  • rmf/pdb.py
  • rotamer/rotamer_pdb.py
• IMP::core::XYZDerivativeGeometry:
  • em/analyze_convergence.py
• IMP::core::XYZR:
  • atom/markers.py
  • core/optimize_balls.py
  • display/show_particles_as_spheres.py
  • kernel/dock_with_crosslinks.py
  • kernel/nup84.py
• IMP::core::XYZRGeometry:
  • atom/markers.py
  • core/incremental_mc.py
  • core/optimize_balls.py
  • display/displaying_ensembles.py
  • domino/multiscale.py
  • kernel/chain.py
• IMP::core::XYZRsGeometry:
  • display/display_log.py
  • display/show_particles_as_spheres.py
• IMP::display::BoundingBoxGeometry:
  • core/optimize_balls.py
  • display/basic_geometry.py
  • misc/decay.py
  • rmf/geometry.py
  • rmf/simulation.py
• IMP::display::ChimeraWriter:
  • container/connectivity.py
  • display/display_log.py
  • display/show_particles_as_spheres.py
  • em/cube.py
  • kernel/chain.py
• IMP::display::Color:
  • atom/markers.py
  • display/display_log.py
  • display/displaying_ensembles.py
  • display/show_particles_as_spheres.py
  • domino/multiscale.py
• IMP::display::CylinderGeometry:
  • display/displaying_ensembles.py
• IMP::display::PointGeometry:
  • domino/multiscale.py
• IMP::display::PymolWriter:
  • atom/markers.py
  • atom/rigid_brownian_dynamics.py
  • core/incremental_mc.py
  • core/optimize_balls.py
  • display/basic_geometry.py
  • display/displaying_ensembles.py
  • domino/multiscale.py
  • domino/rigid_body_excluded_volume.py
  • em/analyze_convergence.py
• IMP::display::ReferenceFrameGeometry:
  • display/displaying_ensembles.py
• IMP::display::SphereGeometry:
  • display/basic_geometry.py
  • em/analyze_convergence.py
  • em/cube.py
• IMP::display::WriteOptimizerState:
  • display/display_log.py
• IMP::display::Writer:
  • display/show_particles_as_spheres.py
• IMP::domino::Assignment:
  • domino/save_assignments.py
• IMP::domino::BranchAndBoundAssignmentsTable:
  • domino/custom_filter.py
  • domino/interactive_with_containers.py
  • domino/rigid_body_excluded_volume.py
  • domino/six_particles_optimization.py
• IMP::domino::DominoSampler:
  • domino/custom_filter.py
  • domino/domino_approach.py
  • domino/interactive.py
  • domino/multiscale.py
  • domino/restraint_cache.py
  • domino/rigid_body_excluded_volume.py
  • domino/six_particles_optimization.py
• IMP::domino::ExclusionSubsetFilterTable:
  • domino/custom_filter.py
  • domino/interactive_with_containers.py
  • domino/restraint_cache.py
  • domino/rigid_body_excluded_volume.py
  • domino/six_particles_optimization.py
• IMP::domino::ListSubsetFilterTable:
  • domino/multiscale.py
• IMP::domino::ParticleStatesTable:
  • domino/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/rigid_body_excluded_volume.py
  • domino/six_particles_optimization.py
• IMP::domino::ReadAssignmentContainer:
  • domino/save_assignments.py
• IMP::domino::ReadHDF5AssignmentContainer:
  • domino/interactive_with_containers.py
• IMP::domino::RestraintCache:
  • domino/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::RestraintScoreSubsetFilterTable:
  • domino/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::RigidBodyStates:
  • domino/rigid_body_excluded_volume.py
• IMP::domino::Subset:
  • domino/multiscale.py
  • domino/restraint_cache.py
  • domino/save_assignments.py
• IMP::domino::SubsetFilter:
  • domino/custom_filter.py
• IMP::domino::SubsetFilterTable:
  • domino/custom_filter.py
• IMP::domino::WriteAssignmentContainer:
  • domino/save_assignments.py
• IMP::domino::WriteHDF5AssignmentContainer:
  • domino/interactive_with_containers.py
• IMP::domino::XYZStates:
  • domino/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::em2d::EM2DScore:
  • em2d/optimize_em2d_with_montecarlo.py
• IMP::em2d::Em2DRestraint:
  • em2d/optimize_em2d_with_montecarlo.py
• IMP::em::FitRestraint:
  • em/analyze_convergence.py
  • em/fit_restraint.py
  • restrainer/em_restraint.py
  • restrainer/simple_em_fit.py
• IMP::em::MRCReaderWriter:
  • em/analyze_convergence.py
  • em/fit_restraint.py
  • em/generate_density_map_of_fixed_dimension.py
  • em/local_fitting.py
  • em/pdb2density.py
• IMP::em::SampledDensityMap:
  • em/analyze_convergence.py
  • em/generate_density_map_of_fixed_dimension.py
  • em/local_fitting.py
• IMP::example::ExampleSingletonModifier:
  • example/range_restriction.py
• IMP::gsl::Simplex:
  • gsl/simplex.py
• IMP::kernel::ConfigurationSet:
  • kernel/nup84.py
• IMP::kernel::Decorator:
  • domino/marina_party.py
• IMP::kernel::Key:
  • container/filter_close_pairs.py
  • domino/marina_party.py
  • kernel/write_a_restraint.py
  • kernel/write_an_optimizer_state.py
  • restrainer/simple_distance.py
  • restrainer/simple_em_fit.py
• IMP::kernel::Model:
  • atom/assess_dope.py
  • atom/cg_pdb.py
  • atom/charmm_forcefield.py
  • atom/charmm_forcefield_verbose.py
  • atom/dope_and_excluded_volume.cpp
  • atom/load_protein_restrain_bonds.py
  • atom/markers.py
  • atom/molecular_hierarchy.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
  • 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_minimum_distance.py
  • core/rigid_bodies.py
  • core/rigid_collisions.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/dock_with_crosslinks.py
  • kernel/graph.py
  • kernel/nup84.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
  • parallel/tasks.py
  • restrainer/simple_connectivity_on_molecules.py
  • restrainer/simple_connectivity_on_rigid_bodies.py
  • restrainer/simple_diameter.py
  • restrainer/simple_distance.py
  • restrainer/simple_em_fit.py
  • restrainer/simple_excluded_volume.py
  • rmf/link.py
  • rmf/multiresolution.py
  • rmf/pdb.py
  • rmf/simulation.py
  • rotamer/rotamer_pdb.py
  • saxs/profile.py
  • saxs/profile_fit.py
• IMP::kernel::OptimizerState:
  • em2d/optimize_em2d_with_montecarlo.py
  • kernel/write_an_optimizer_state.py
• IMP::kernel::PairPredicate:
  • container/filter_close_pairs.py
• IMP::kernel::PairScore:
  • domino/marina_party.py
• IMP::kernel::Particle:
  • atom/molecular_hierarchy.py
  • atom/rigid_brownian_dynamics.py
  • container/filter_close_pairs.py
  • core/XYZR_Decorator.py
  • core/XYZ_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/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/save_assignments.py
  • domino/six_particles_optimization.py
  • em/analyze_convergence.py
  • gsl/simplex.py
  • kernel/dependency_graph.py
  • kernel/dock_with_crosslinks.py
  • kernel/graph.py
  • kernel/nup84.py
  • kernel/setup.py
  • kernel/write_a_restraint.py
  • misc/decay.py
  • parallel/tasks.py
  • restrainer/simple_distance.py
  • restrainer/simple_em_fit.py
  • rmf/multiresolution.py
  • rmf/simulation.py
• IMP::kernel::Restraint:
  • kernel/write_a_restraint.py
• IMP::kernel::RestraintSet:
  • core/optimize_balls.py
  • em2d/optimize_em2d_with_montecarlo.py
  • em/analyze_convergence.py
  • kernel/dock_with_crosslinks.py
• IMP::kernel::ScopedSetAttribute:
  • core/optimize_balls.py
• IMP::kmeans::KMeans:
  • kmeans_example
• IMP::misc::DecayPairContainerOptimizerState:
  • misc/decay.py
• IMP::modeller::IMPRestraints:
  • modeller/imp_restraints_in_modeller.py
• IMP::modeller::ModelLoader:
  • modeller/imp_restraints_in_modeller.py
  • modeller/load_modeller_model.py
  • modeller/modeller_restraints_in_imp.py
• IMP::modeller::ModellerRestraints:
  • modeller/modeller_restraints_in_imp.py
• IMP::parallel::LocalSlave:
  • parallel/local_distance.py
• IMP::parallel::Manager:
  • parallel/local_distance.py
• IMP::rmf::SaveOptimizerState:
  • misc/decay.py
  • rmf/simulation.py
• IMP::rotamer::RotamerCalculator:
  • rotamer/rotamer_pdb.py
• IMP::rotamer::RotamerLibrary:
  • rotamer/rotamer_pdb.py
• IMP::saxs::Profile:
  • saxs/profile.py
  • saxs/profile_fit.py
• IMP::saxs::RadialDistributionFunction:
  • saxs/profile.py
• IMP::saxs::Restraint:
  • restrainer/saxs_restraint.py
• IMP::saxs::SolventAccessibleSurface:
  • saxs/profile_fit.py
• IMP::score_functor::AddScores:
  • atom/dope_and_excluded_volume.cpp
• IMP::score_functor::DistancePairScore:
  • atom/dope_and_excluded_volume.cpp
• IMP::score_functor::Dope:
  • atom/dope_and_excluded_volume.cpp
• IMP::score_functor::HarmonicLowerBound:
  • atom/dope_and_excluded_volume.cpp
• IMP::score_functor::SphereDistance:
  • atom/dope_and_excluded_volume.cpp
• IMP::statistics::ConfigurationSetXYZEmbedding:
  • kernel/basic_optimization.py
  • statistics/kmeans.py
• IMP::statistics::Metric:
  • statistics/write_a_metric.py
• IMP::statistics::ParticleEmbedding:
  • statistics/kmeans.py
• IMP::statistics::VectorDEmbedding:
  • statistics/kmeans.py