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.algebra # {#class_example_index_algebra}
11 <th>Class</th><th>Examples</th></tr>
12 <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/nup84.py](kernel_2nup84_8py-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>
13 <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>
15 <tr><td>@ref
IMP::algebra::ReferenceFrame3D</td><td>[atom/cg_pdb.py](atom_2cg_pdb_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>
16 <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>
17 <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>
18 <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)</td></tr>
20 # IMP.atom # {#class_example_index_atom}
22 <th>Class</th><th>Examples</th></tr>
23 <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), [kernel/nup84.py](kernel_2nup84_8py-example.html)</td></tr>
25 <tr><td>@ref
IMP::atom::Atom</td><td>[atom/dope_and_excluded_volume.cpp](atom_2dope_and_excluded_volume_8cpp-example.html)</td></tr>
26 <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>
28 <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>
29 <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>
31 <tr><td>@ref
IMP::atom::CHARMMTopology</td><td>[atom/structure_from_sequence.py](atom_2structure_from_sequence_8py-example.html)</td></tr>
32 <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), [kernel/nup84.py](kernel_2nup84_8py-example.html)</td></tr>
35 <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>
37 <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>
39 <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>
40 <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), [saxs/profile.py](saxs_2profile_8py-example.html), [saxs/profile_fit.py](saxs_2profile_fit_8py-example.html)</td></tr>
43 <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), [multiresolution.py](multiresolution_8py-example.html), [rmf/multiresolution.py](rmf_2multiresolution_8py-example.html)</td></tr>
45 <tr><td>@ref
IMP::atom::Selection</td><td>[atom/markers.py](atom_2markers_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), [kernel/nup84.py](kernel_2nup84_8py-example.html), [multiresolution.py](multiresolution_8py-example.html), [multistate.py](multistate_8py-example.html)</td></tr>
50 # IMP.container # {#class_example_index_container}
52 <th>Class</th><th>Examples</th></tr>
53 <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>
54 <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), [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), [kernel/chain.py](kernel_2chain_8py-example.html)</td></tr>
60 <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>
61 <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), [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>
62 <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>
64 <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>
66 # IMP.core # {#class_example_index_core}
68 <th>Class</th><th>Examples</th></tr>
69 <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), [kernel/nup84.py](kernel_2nup84_8py-example.html), [temperature_rem.py](temperature_rem_8py-example.html)</td></tr>
70 <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>
72 <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>
75 <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>
76 <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>
78 <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>
81 <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/custom_filter.py](domino_2custom_filter_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>
83 <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>
84 <tr><td>@ref
IMP::core::HarmonicDistancePairScore</td><td>[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>
85 <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>
87 <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/custom_filter.py](domino_2custom_filter_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>
91 <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>
92 <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>
93 <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>
95 <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), [kernel/nup84.py](kernel_2nup84_8py-example.html), [temperature_rem.py](temperature_rem_8py-example.html)</td></tr>
96 <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>
97 <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), [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>
98 <tr><td>@ref
IMP::core::RigidBodyMover</td><td>[em2d/optimize_em2d_with_montecarlo.py](em2d_2optimize_em2d_with_montecarlo_8py-example.html), [kernel/nup84.py](kernel_2nup84_8py-example.html)</td></tr>
100 <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>
101 <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), [kernel/nup84.py](kernel_2nup84_8py-example.html), [temperature_rem.py](temperature_rem_8py-example.html)</td></tr>
103 <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>
104 <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), [kernel/nup84.py](kernel_2nup84_8py-example.html)</td></tr>
105 <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>
106 <tr><td>@ref
IMP::core::TableRefiner</td><td>[core/restrain_minimum_distance.py](core_2restrain_minimum_distance_8py-example.html), [em/analyze_convergence.py](em_2analyze_convergence_8py-example.html)</td></tr>
107 <tr><td>@ref
IMP::core::Transform</td><td>[em2d/clustering_of_pdb_models.py](em2d_2clustering_of_pdb_models_8py-example.html)</td></tr>
109 <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), [kernel/nup84.py](kernel_2nup84_8py-example.html), [rmf/pdb.py](rmf_2pdb_8py-example.html), [rotamer/rotamer_pdb.py](rotamer_2rotamer_pdb_8py-example.html)</td></tr>
111 <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), [kernel/nup84.py](kernel_2nup84_8py-example.html)</td></tr>
112 <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>
113 <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>
115 # IMP.display # {#class_example_index_display}
117 <th>Class</th><th>Examples</th></tr>
118 <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>
119 <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>
122 <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>
124 <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>
127 # IMP.domino # {#class_example_index_domino}
129 <th>Class</th><th>Examples</th></tr>
130 <tr><td>@ref
IMP::domino::Assignment</td><td>[domino/save_assignments.py](domino_2save_assignments_8py-example.html)</td></tr>
131 <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>
132 <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>
133 <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>
136 <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>
139 <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>
140 <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>
141 <tr><td>@ref
IMP::domino::RigidBodyStates</td><td>[domino/rigid_body_excluded_volume.py](domino_2rigid_body_excluded_volume_8py-example.html)</td></tr>
142 <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>
143 <tr><td>@ref
IMP::domino::SubsetFilter</td><td>[domino/custom_filter.py](domino_2custom_filter_8py-example.html)</td></tr>
147 <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>
149 # IMP.em # {#class_example_index_em}
151 <th>Class</th><th>Examples</th></tr>
152 <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>
153 <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/pdb2density.py](em_2pdb2density_8py-example.html)</td></tr>
154 <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>
156 # IMP.em2d # {#class_example_index_em2d}
158 <th>Class</th><th>Examples</th></tr>
160 <tr><td>@ref
IMP::em2d::EM2DScore</td><td>[em2d/optimize_em2d_with_montecarlo.py](em2d_2optimize_em2d_with_montecarlo_8py-example.html)</td></tr>
161 <tr><td>@ref
IMP::em2d::Em2DRestraint</td><td>[em2d/optimize_em2d_with_montecarlo.py](em2d_2optimize_em2d_with_montecarlo_8py-example.html)</td></tr>
163 <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>
166 # IMP.example # {#class_example_index_example}
168 <th>Class</th><th>Examples</th></tr>
171 # IMP.gsl # {#class_example_index_gsl}
173 <th>Class</th><th>Examples</th></tr>
174 <tr><td>@ref
IMP::gsl::Simplex</td><td>[gsl/simplex.py](gsl_2simplex_8py-example.html)</td></tr>
176 # IMP.kernel # {#class_example_index_kernel}
178 <th>Class</th><th>Examples</th></tr>
179 <tr><td>@ref IMP::kernel::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>
180 <tr><td>@ref IMP::kernel::ConfigurationSet</td><td>[kernel/nup84.py](kernel_2nup84_8py-example.html)</td></tr>
181 <tr><td>@ref IMP::kernel::Container</td><td>[kernel/dependency_graph.py](kernel_2dependency_graph_8py-example.html)</td></tr>
182 <tr><td>@ref IMP::kernel::CreateLogContext</td><td>[log.py](log_8py-example.html)</td></tr>
183 <tr><td>@ref IMP::kernel::Decorator</td><td>[domino/marina_party.py](domino_2marina_party_8py-example.html)</td></tr>
184 <tr><td>@ref IMP::kernel::Flag</td><td>[flags.cpp](flags_8cpp-example.html)</td></tr>
185 <tr><td>@ref IMP::kernel::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>
186 <tr><td>@ref IMP::kernel::Key</td><td>[container/filter_close_pairs.py](container_2filter_close_pairs_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>
187 <tr><td>@ref IMP::kernel::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/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), [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/nup84.py](kernel_2nup84_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), [multiresolution.py](multiresolution_8py-example.html), [multistate.py](multistate_8py-example.html), [parallel/tasks.py](parallel_2tasks_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>
188 <tr><td>@ref IMP::kernel::ModelException</td><td>[core/rigid_collisions.py](core_2rigid_collisions_8py-example.html)</td></tr>
189 <tr><td>@ref IMP::kernel::Object</td><td>[log.py](log_8py-example.html)</td></tr>
190 <tr><td>@ref IMP::kernel::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>
191 <tr><td>@ref IMP::kernel::OptionParser</td><td>[rotamer/rotamer_pdb2.py](rotamer_2rotamer_pdb2_8py-example.html), [rotamer/rotamer_pdb.py](rotamer_2rotamer_pdb_8py-example.html)</td></tr>
192 <tr><td>@ref IMP::kernel::PairPredicate</td><td>[container/filter_close_pairs.py](container_2filter_close_pairs_8py-example.html)</td></tr>
193 <tr><td>@ref IMP::kernel::PairScore</td><td>[domino/marina_party.py](domino_2marina_party_8py-example.html)</td></tr>
194 <tr><td>@ref IMP::kernel::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/nup84.py](kernel_2nup84_8py-example.html), [kernel/setup.py](kernel_2setup_8py-example.html), [kernel/write_a_restraint.py](kernel_2write_a_restraint_8py-example.html), [multiresolution.py](multiresolution_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>
195 <tr><td>@ref IMP::kernel::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>
196 <tr><td>@ref IMP::kernel::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>
197 <tr><td>@ref IMP::kernel::ScopedSetAttribute</td><td>[core/
optimize_balls.py](core_2optimize_balls_8py-example.html)</td></tr>
198 <tr><td>@ref IMP::kernel::ScoreState</td><td>[kernel/dependency_graph.py](kernel_2dependency_graph_8py-example.html)</td></tr>
199 <tr><td>@ref IMP::kernel::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>
200 <tr><td>@ref IMP::kernel::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>
202 # IMP.kmeans # {#class_example_index_kmeans}
204 <th>Class</th><th>Examples</th></tr>
205 <tr><td>@ref
IMP::kmeans::KMeans</td><td>[kmeans/kmeans_example.py](kmeans_2kmeans_example_8py-example.html)</td></tr>
207 # IMP.misc # {#class_example_index_misc}
209 <th>Class</th><th>Examples</th></tr>
212 # IMP.modeller # {#class_example_index_modeller}
214 <th>Class</th><th>Examples</th></tr>
215 <tr><td>@ref
IMP::modeller::IMPRestraints</td><td>[modeller/imp_restraints_in_modeller.py](modeller_2imp_restraints_in_modeller_8py-example.html)</td></tr>
216 <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>
219 # IMP.mpi # {#class_example_index_mpi}
221 <th>Class</th><th>Examples</th></tr>
224 # IMP.parallel # {#class_example_index_parallel}
226 <th>Class</th><th>Examples</th></tr>
227 <tr><td>@ref
IMP::parallel::LocalSlave</td><td>[parallel/local_distance.py](parallel_2local_distance_8py-example.html)</td></tr>
230 # IMP.rmf # {#class_example_index_rmf}
232 <th>Class</th><th>Examples</th></tr>
233 <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>
235 # IMP.rotamer # {#class_example_index_rotamer}
237 <th>Class</th><th>Examples</th></tr>
238 <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>
239 <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>
241 # IMP.saxs # {#class_example_index_saxs}
243 <th>Class</th><th>Examples</th></tr>
244 <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>
248 # IMP.score_functor # {#class_example_index_score_functor}
250 <th>Class</th><th>Examples</th></tr>
251 <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>
253 <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>
257 # IMP.statistics # {#class_example_index_statistics}
259 <th>Class</th><th>Examples</th></tr>
261 <tr><td>@ref
IMP::statistics::Metric</td><td>[statistics/write_a_metric.py](statistics_2write_a_metric_8py-example.html)</td></tr>
265 # IMP.symmetry # {#class_example_index_symmetry}
267 <th>Class</th><th>Examples</th></tr>
Applies a SingletonScore to each Singleton in a list.
Return the hierarchy children of a particle.
Select non water and non hydrogen atoms.
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.
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)
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.
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 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.
A score on the distance between the surfaces of two spheres.
Modify a set of continuous variables by perturbing them within a ball.
Return all close unordered pairs of particles taken from the SingletonContainer.
Return all close ordered pairs of particles taken from the two SingletonContainers.
Distance restraint between two particles.
Create efficient distance-based pair scores.
Score particles based on how far outside a box they are.
An IMP restraint using all defined Modeller restraints.
void optimize_balls(const ParticlesTemp &ps, const RestraintsTemp &rs=RestraintsTemp(), const PairPredicates &excluded=PairPredicates(), const OptimizerStates &opt_states=OptimizerStates(), LogLevel ll=DEFAULT)
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 modifer.
Simple Brownian dynamics simulator.
Lennard-Jones score between a pair of particles.
The standard decorator for manipulating molecular structures.
Store a list of ParticleIndexes.
A simplex optimizer taken from GSL.
A lookup based particle refiner.
A decorator for a particle representing an atom.
A class performing the rotations of atoms in the residues.
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,.
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.
Score the bond based on a UnaryFunction,.
An axis-aligned bounding box.
Find all nearby pairs by testing all pairs.
Simple implementation of segments in 3D.
A decorator for a residue.
Parameters used by Em2DRestraint and ProjectionFinder.
Store a configuration of a subset.
Calculate score based on fit to EM map.
Display a segment for each pair in a IMP::PairContainer.
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.
Determine the collision cross section for some projections of particles.
Write a CGO file with the geometry.
Store info for a chain of a protein.
Applies a PairScore to a Pair.
Select all CA ATOM records.
The topology of a complete CHARMM model.
Smooth interaction scores by switching the derivatives (force switch).
Ensure that a set of particles remains connected with one another.
Select hierarchy particles identified by the biological name.
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.
Simply return the coordinates of a VectorD.
Harmonic function (symmetric about the mean)
Manages slaves and contexts.
Store data to be clustered for distance metric based algorithms.
A slave running on the same machine as the master.
A decorator for a particle with x,y,z coordinates and a radius.