1 Class Examples {#class_example_index}
6 Examples that use a given
class:
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}
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>
16 <tr><td>@ref
IMP::Decorator</td><td>[domino/marina_party.py](domino_2marina_party_8py-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>
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>
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>
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>
34 # IMP.algebra # {#class_example_index_algebra}
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>
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>
45 # IMP.atom # {#class_example_index_atom}
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>
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>
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>
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>
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>
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>
74 # IMP.container # {#class_example_index_container}
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>
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>
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>
91 # IMP.core # {#class_example_index_core}
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
140 # IMP.display # {#class_example_index_display}
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>
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>
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>
152 # IMP.domino # {#class_example_index_domino}
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>
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>
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>
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>
174 # IMP.em # {#class_example_index_em}
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>
181 # IMP.em2d # {#class_example_index_em2d}
183 <th>Class</th><th>Examples</th></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>
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>
191 # IMP.example # {#class_example_index_example}
193 <th>Class</th><th>Examples</th></tr>
196 # IMP.gsl # {#class_example_index_gsl}
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>
201 # IMP.kmeans # {#class_example_index_kmeans}
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>
206 # IMP.misc # {#class_example_index_misc}
208 <th>Class</th><th>Examples</th></tr>
211 # IMP.modeller # {#class_example_index_modeller}
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>
218 # IMP.mpi # {#class_example_index_mpi}
220 <th>Class</th><th>Examples</th></tr>
223 # IMP.parallel # {#class_example_index_parallel}
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>
229 # IMP.pmi # {#class_example_index_pmi}
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>
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>
240 # IMP.rmf # {#class_example_index_rmf}
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>
245 # IMP.rotamer # {#class_example_index_rotamer}
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>
251 # IMP.saxs # {#class_example_index_saxs}
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>
258 # IMP.score_functor # {#class_example_index_score_functor}
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>
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>
267 # IMP.statistics # {#class_example_index_statistics}
269 <th>Class</th><th>Examples</th></tr>
271 <tr><td>@ref
IMP::statistics::Metric</td><td>[statistics/write_a_metric.py](statistics_2write_a_metric_8py-example.html)</td></tr>
275 # IMP.symmetry # {#class_example_index_symmetry}
277 <th>Class</th><th>Examples</th></tr>
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.
Abstract class for scoring object(s) of type ParticleIndexPair.
Embed a configuration using the XYZ coordinates of a set of particles.
A harmonic upper bound on the distance between two spheres.
A class to implement Hamiltonian Replica Exchange.
Lower bound harmonic function (non-zero when feature < mean)
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.
Return the hierarchy leaves under a particle.
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.
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.
Applies a PairScore to each Pair in a list based on a predicate.
Display an IMP::SingletonContainer of IMP::core::XYZR particles as balls.
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.
Maintain a pair container with a decaying list of pairs.
Simple conjugate gradients optimizer.
Sample best solutions using Domino.
Represent a cylinder in 3D.
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.
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.
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.
An IMP restraint using all defined Modeller restraints.
Object used to hold a set of restraints.
Class for storing model, its restraints, constraints, and particles.
Do not allow two particles to be in the same state.
Store a list of ParticleIndexPairs.
Display a reference frame.
Class for sampling a density map from particles.
Select all non-alternative ATOM records.
An example singleton modifier.
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.
Store a list of ParticleIndexes.
A worker running on the same machine as the manager.
A simplex optimizer taken from GSL.
A lookup based particle refiner.
A decorator for a particle representing an atom.
ScoreStates maintain invariants in the Model.
A class performing the rotations of atoms in the residues.
A class to change and restore log state.
A container which keeps a set of pairs that connect a set of spheres.
Restrain the diameter of a set of points.
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.
Class for easy writing of PDBs, RMFs, and stat files.
Score the bond based on a UnaryFunction,.
An axis-aligned bounding box.
Interface to specialized Particle types (e.g. atoms)
IMP-specific subclass of argparse.ArgumentParser.
Find all nearby pairs by testing all pairs.
Simple implementation of segments in 3D.
A decorator for a residue.
Periodically dump the state of all associated objects into the RMF file.
Abstract predicate function.
Read the assignments from binary data on disk.
Parameters used by Em2DRestraint and ProjectionFinder.
Store a configuration of a subset.
Calculate score based on fit to EM map.
Automatically setup Sytem and Degrees of Freedom with a formatted text file.
Display a segment for each pair in a IMP::PairContainer.
Shared optimizer state that is invoked upon commitment of new coordinates.
Select all non-water non-alternative ATOM and HETATM records.
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.
Determine the collision cross section for some projections of particles.
Write a CGO file with the geometry.
Score pair of atoms based on DOPE.
Store info for a chain of a protein.
Store the assignments on disk as binary data.
Applies a PairScore to a Pair.
Score the model efficiently when a small number of particles are changed.
Store the assignments in an HDF5DataSet.
Select all CA ATOM records.
The topology of a complete CHARMM model.
A macro to help setup and run replica exchange.
A dictionary-like wrapper for reading and storing sequence data.
Score pair of atoms based on DOPE.
An exception which is thrown when the Model has attributes with invalid values.
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.
Abstract class for containers of particles.
Applies a SingletonScore to a Singleton.
Applies a list of movers one at a time.
Represent a sphere in D-dimensions.
Apply a function to an attribute.
Management of reading/writing TIFF images.
Applies a PairScore to each Pair in a list.
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.
Score the dihedral angle.
A restraint is a term in an IMP ScoringFunction.
Simply return the coordinates of a VectorD.
Harmonic function (symmetric about the mean)
Manages workers and contexts.
Store data to be clustered for distance metric based algorithms.
A decorator for a particle with x,y,z coordinates and a radius.