1 Function Examples {#function_example_index}
6 Examples that use a given
function:
8 See also [Factory Index](@ref factory_index), [Argument Index](@ref argument_index), [Class Examples](@
ref class_example_index)
9 # IMP (kernel) # {#function_example_index_kernel}
11 <th>Function</th><th>Examples</th></tr>
12 <tr><td>@ref
IMP::DependencyGraph()</td><td>[kernel/graph.py](kernel_2graph_8py-example.html)</td></tr>
13 <tr><td>@ref
IMP::Restraints()</td><td>[modeller/imp_restraints_in_modeller.py](modeller_2imp_restraints_in_modeller_8py-example.html)</td></tr>
14 <tr><td>@ref
IMP::add_bool_flag()</td><td>[example/range_restriction.py](example_2range_restriction_8py-example.html)</td></tr>
15 <tr><td>@ref
IMP::add_string_flag()</td><td>[kernel/flags.py](kernel_2flags_8py-example.html)</td></tr>
16 <tr><td>@ref
IMP::add_to_log()</td><td>[log.py](log_8py-example.html)</td></tr>
18 <tr><td>@ref
IMP::create_temporary_file_name()</td><td>[atom/rigid_brownian_dynamics.py](atom_2rigid_brownian_dynamics_8py-example.html), [core/incremental_mc.py](core_2incremental_mc_8py-example.html), [display/basic_geometry.py](display_2basic_geometry_8py-example.html), [domino/interactive_with_containers.py](domino_2interactive_with_containers_8py-example.html), [domino/restraint_cache.py](domino_2restraint_cache_8py-example.html), [domino/save_assignments.py](domino_2save_assignments_8py-example.html), [em/cube.py](em_2cube_8py-example.html), [misc/decay.py](misc_2decay_8py-example.html)</td></tr>
19 <tr><td>@ref
IMP::get_bool_flag()</td><td>[misc/decay.py](misc_2decay_8py-example.html), [rmf/multiresolution.py](rmf_2multiresolution_8py-example.html), [rotamer/rotamer_pdb2.py](rotamer_2rotamer_pdb2_8py-example.html), [rotamer/rotamer_pdb.py](rotamer_2rotamer_pdb_8py-example.html)</td></tr>
20 <tr><td>@ref
IMP::get_dependency_graph()</td><td>[kernel/dependency_graph.py](kernel_2dependency_graph_8py-example.html)</td></tr>
21 <tr><td>@ref
IMP::get_example_path()</td><td>[kernel/dependency_graph.py](kernel_2dependency_graph_8py-example.html)</td></tr>
22 <tr><td>@ref
IMP::get_indexes()</td><td>[domino/interactive.py](domino_2interactive_8py-example.html), [domino/interactive_with_containers.py](domino_2interactive_with_containers_8py-example.html)</td></tr>
23 <tr><td>@ref
IMP::get_is_quick_test()</td><td>[core/incremental_mc.py](core_2incremental_mc_8py-example.html), [core/
optimize_balls.py](core_2optimize_balls_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>
24 <tr><td>@ref
IMP::get_log_level()</td><td>[kernel/write_a_restraint.py](kernel_2write_a_restraint_8py-example.html)</td></tr>
26 <tr><td>@ref
IMP::get_particles()</td><td>[domino/marina_party.py](domino_2marina_party_8py-example.html), [kernel/basic_optimization.py](kernel_2basic_optimization_8py-example.html), [misc/decay.py](misc_2decay_8py-example.html)</td></tr>
28 <tr><td>@ref
IMP::get_relative_path()</td><td>[em2d/optimize_em2d_with_montecarlo.py](em2d_2optimize_em2d_with_montecarlo_8py-example.html)</td></tr>
29 <tr><td>@ref
IMP::get_string_flag()</td><td>[kernel/flags.py](kernel_2flags_8py-example.html)</td></tr>
30 <tr><td>@ref
IMP::set_check_level()</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/score_protein_with_ligand.py](atom_2score_protein_with_ligand_8py-example.html), [display/displaying_ensembles.py](display_2displaying_ensembles_8py-example.html), [em/local_fitting.py](em_2local_fitting_8py-example.html)</td></tr>
31 <tr><td>@ref
IMP::set_log_level()</td><td>[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/incremental_mc.py](core_2incremental_mc_8py-example.html), [core/restrain_diameter.py](core_2restrain_diameter_8py-example.html), [display/displaying_ensembles.py](display_2displaying_ensembles_8py-example.html), [domino/custom_filter.py](domino_2custom_filter_8py-example.html), [domino/merge_tree.py](domino_2merge_tree_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/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/fit_restraint.py](em_2fit_restraint_8py-example.html), [em/local_fitting.py](em_2local_fitting_8py-example.html), [kernel/chain.py](kernel_2chain_8py-example.html), [kmeans/kmeans_example.py](kmeans_2kmeans_example_8py-example.html), [log.py](log_8py-example.html), [misc/decay.py](misc_2decay_8py-example.html), [rotamer/rotamer_pdb2.py](rotamer_2rotamer_pdb2_8py-example.html), [rotamer/rotamer_pdb.py](rotamer_2rotamer_pdb_8py-example.html)</td></tr>
33 <tr><td>@ref
IMP::setup_from_argv()</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/assess_dope.py](atom_2assess_dope_8py-example.html), [atom/brownian_statistics.py](atom_2brownian_statistics_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/restrain_in_sphere.py](container_2restrain_in_sphere_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/excluded_volume.py](core_2excluded_volume_8py-example.html), [core/incremental_mc.py](core_2incremental_mc_8py-example.html), [core/model_numpy.py](core_2model_numpy_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/pair_restraint.py](core_2pair_restraint_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/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/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/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), [em/analyze_convergence.py](em_2analyze_convergence_8py-example.html), [em/cube.py](em_2cube_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), [example/range_restriction.py](example_2range_restriction_8py-example.html), [flags.cpp](flags_8cpp-example.html), [grid.cpp](grid_8cpp-example.html), [gsl/simplex.py](gsl_2simplex_8py-example.html), [kernel/basic_optimization.py](kernel_2basic_optimization_8py-example.html), [kernel/chain.py](kernel_2chain_8py-example.html), [kernel/dependency_graph.py](kernel_2dependency_graph_8py-example.html), [kernel/flags.py](kernel_2flags_8py-example.html), [kernel/graph.py](kernel_2graph_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), [kmeans/kmeans_example.py](kmeans_2kmeans_example_8py-example.html), [log.py](log_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/local_distance.py](parallel_2local_distance_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/geometry.py](rmf_2geometry_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), [saxs/profile.py](saxs_2profile_8py-example.html), [saxs/profile_fit.py](saxs_2profile_fit_8py-example.html), [statistics/kmeans.py](statistics_2kmeans_8py-example.html), [statistics/write_a_metric.py](statistics_2write_a_metric_8py-example.html), [temperature_rem.py](temperature_rem_8py-example.html)</td></tr>
34 <tr><td>@ref
IMP::show_graphviz()</td><td>[atom/edit_molecular_hierarchy.py](atom_2edit_molecular_hierarchy_8py-example.html), [domino/interactive.py](domino_2interactive_8py-example.html), [domino/interactive_with_containers.py](domino_2interactive_with_containers_8py-example.html), [kernel/dependency_graph.py](kernel_2dependency_graph_8py-example.html), [kernel/graph.py](kernel_2graph_8py-example.html)</td></tr>
36 <tr><td>@ref
IMP::write_help()</td><td>[kernel/flags.py](kernel_2flags_8py-example.html)</td></tr>
38 # IMP.algebra # {#function_example_index_algebra}
40 <th>Function</th><th>Examples</th></tr>
43 <tr><td>@ref
IMP::algebra::Vector2D()</td><td>[domino/multiscale.py](domino_2multiscale_8py-example.html)</td></tr>
44 <tr><td>@ref
IMP::algebra::Vector3D()</td><td>[BallMover.py](BallMover_8py-example.html), [algebra/grid_space.py](algebra_2grid_space_8py-example.html), [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/markers.py](atom_2markers_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), [container/restrain_in_sphere.py](container_2restrain_in_sphere_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/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_in_sphere.py](core_2restrain_in_sphere_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/basic_geometry.py](display_2basic_geometry_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/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), [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), [gsl/simplex.py](gsl_2simplex_8py-example.html), [kernel/setup.py](kernel_2setup_8py-example.html), [misc/decay.py](misc_2decay_8py-example.html), [parallel/tasks.py](parallel_2tasks_8py-example.html), [pmi/symmetry.py](pmi_2symmetry_8py-example.html), [rmf/geometry.py](rmf_2geometry_8py-example.html), [rmf/simulation.py](rmf_2simulation_8py-example.html), [statistics/kmeans.py](statistics_2kmeans_8py-example.html), [temperature_rem.py](temperature_rem_8py-example.html)</td></tr>
45 <tr><td>@ref
IMP::algebra::compose()</td><td>[core/randomize_rigid_body.py](core_2randomize_rigid_body_8py-example.html), [em2d/optimize_em2d_with_montecarlo.py](em2d_2optimize_em2d_with_montecarlo_8py-example.html)</td></tr>
46 <tr><td>@ref
IMP::algebra::get_bounding_box()</td><td>[algebra/geometry.py](algebra_2geometry_8py-example.html), [algebra/grid_space.py](algebra_2grid_space_8py-example.html)</td></tr>
47 <tr><td>@ref
IMP::algebra::get_distance()</td><td>[algebra/geometry.py](algebra_2geometry_8py-example.html), [algebra/grid_space.py](algebra_2grid_space_8py-example.html), [em2d/optimize_em2d_with_montecarlo.py](em2d_2optimize_em2d_with_montecarlo_8py-example.html), [grid.cpp](grid_8cpp-example.html)</td></tr>
52 <tr><td>@ref
IMP::algebra::get_random_rotation_3d()</td><td>[atom/cg_pdb.py](atom_2cg_pdb_8py-example.html), [atom/markers.py](atom_2markers_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), [em2d/optimize_em2d_with_montecarlo.py](em2d_2optimize_em2d_with_montecarlo_8py-example.html)</td></tr>
53 <tr><td>@ref
IMP::algebra::get_random_vector_in()</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/randomize_rigid_body.py](core_2randomize_rigid_body_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), [em2d/optimize_em2d_with_montecarlo.py](em2d_2optimize_em2d_with_montecarlo_8py-example.html), [em/local_fitting.py](em_2local_fitting_8py-example.html), [kernel/setup.py](kernel_2setup_8py-example.html), [rmf/simulation.py](rmf_2simulation_8py-example.html), [statistics/kmeans.py](statistics_2kmeans_8py-example.html)</td></tr>
54 <tr><td>@ref
IMP::algebra::get_random_vector_on()</td><td>[algebra/grid_space.py](algebra_2grid_space_8py-example.html), [em/local_fitting.py](em_2local_fitting_8py-example.html), [rmf/simulation.py](rmf_2simulation_8py-example.html)</td></tr>
55 <tr><td>@ref
IMP::algebra::get_rmsd()</td><td>[em2d/clustering_of_pdb_models.py](em2d_2clustering_of_pdb_models_8py-example.html)</td></tr>
56 <tr><td>@ref
IMP::algebra::get_rotation_about_axis()</td><td>[core/symmetry.py](core_2symmetry_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), [pmi/symmetry.py](pmi_2symmetry_8py-example.html)</td></tr>
57 <tr><td>@ref
IMP::algebra::get_rotation_about_point()</td><td>[em2d/optimize_em2d_with_montecarlo.py](em2d_2optimize_em2d_with_montecarlo_8py-example.html), [pmi/symmetry.py](pmi_2symmetry_8py-example.html)</td></tr>
61 # IMP.atom # {#function_example_index_atom}
63 <th>Function</th><th>Examples</th></tr>
64 <tr><td>@ref
IMP::atom::AT_CA()</td><td>[atom/dope_and_excluded_volume.cpp](atom_2dope_and_excluded_volume_8cpp-example.html)</td></tr>
65 <tr><td>@ref IMP::atom::Atom::get_is_setup()</td><td>[atom/assess_dope.py](atom_2assess_dope_8py-example.html)</td></tr>
70 <tr><td>@ref
IMP::atom::Fragment::setup_particle()</td><td>[atom/edit_molecular_hierarchy.py](atom_2edit_molecular_hierarchy_8py-example.html), [atom/rigid_brownian_dynamics.py](atom_2rigid_brownian_dynamics_8py-example.html), [core/connectivity_restraint.py](core_2connectivity_restraint_8py-example.html)</td></tr>
71 <tr><td>@ref
IMP::atom::Hierarchy::get_traits()</td><td>[core/connectivity_restraint.py](core_2connectivity_restraint_8py-example.html), [core/cover_particles.py](core_2cover_particles_8py-example.html), [display/displaying_ensembles.py](display_2displaying_ensembles_8py-example.html), [em/local_fitting.py](em_2local_fitting_8py-example.html)</td></tr>
72 <tr><td>@ref
IMP::atom::Hierarchy::setup_particle()</td><td>[atom/molecular_hierarchy.py](atom_2molecular_hierarchy_8py-example.html), [atom/multiresolution.py](atom_2multiresolution_8py-example.html), [core/connectivity_restraint.py](core_2connectivity_restraint_8py-example.html), [display/displaying_ensembles.py](display_2displaying_ensembles_8py-example.html), [domino/restraint_cache.py](domino_2restraint_cache_8py-example.html), [kernel/chain.py](kernel_2chain_8py-example.html), [kernel/dependency_graph.py](kernel_2dependency_graph_8py-example.html), [misc/decay.py](misc_2decay_8py-example.html), [multistate.py](multistate_8py-example.html), [rmf/multiresolution.py](rmf_2multiresolution_8py-example.html), [rmf/simulation.py](rmf_2simulation_8py-example.html)</td></tr>
74 <tr><td>@ref
IMP::atom::Mass::setup_particle()</td><td>[atom/rigid_brownian_dynamics.py](atom_2rigid_brownian_dynamics_8py-example.html), [domino/restraint_cache.py](domino_2restraint_cache_8py-example.html), [em/analyze_convergence.py](em_2analyze_convergence_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>
80 <tr><td>@ref
IMP::atom::add_bonds()</td><td>[atom/load_protein_restrain_bonds.py](atom_2load_protein_restrain_bonds_8py-example.html), [rmf/multiresolution.py](rmf_2multiresolution_8py-example.html)</td></tr>
81 <tr><td>@ref
IMP::atom::add_dope_score_data()</td><td>[atom/assess_dope.py](atom_2assess_dope_8py-example.html), [atom/dope_and_excluded_volume.cpp](atom_2dope_and_excluded_volume_8cpp-example.html)</td></tr>
83 <tr><td>@ref
IMP::atom::add_radii()</td><td>[atom/dope_and_excluded_volume.cpp](atom_2dope_and_excluded_volume_8cpp-example.html), [atom/structure_from_sequence.py](atom_2structure_from_sequence_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/fit_restraint.py](em_2fit_restraint_8py-example.html), [em/local_fitting.py](em_2local_fitting_8py-example.html), [em/pdb2density.py](em_2pdb2density_8py-example.html)</td></tr>
89 <tr><td>@ref
IMP::atom::create_custom_bond()</td><td>[container/nonbonded_interactions.py](container_2nonbonded_interactions_8py-example.html)</td></tr>
90 <tr><td>@ref
IMP::atom::create_distance_restraint()</td><td>[atom/rigid_brownian_dynamics.py](atom_2rigid_brownian_dynamics_8py-example.html), [kernel/dependency_graph.py](kernel_2dependency_graph_8py-example.html)</td></tr>
93 <tr><td>@ref
IMP::atom::create_protein()</td><td>[kernel/dependency_graph.py](kernel_2dependency_graph_8py-example.html)</td></tr>
94 <tr><td>@ref
IMP::atom::create_rigid_body()</td><td>[atom/cg_pdb.py](atom_2cg_pdb_8py-example.html), [atom/molecular_hierarchy.py](atom_2molecular_hierarchy_8py-example.html), [atom/multiresolution.py](atom_2multiresolution_8py-example.html), [core/rigid_bodies.py](core_2rigid_bodies_8py-example.html), [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), [kernel/dependency_graph.py](kernel_2dependency_graph_8py-example.html)</td></tr>
95 <tr><td>@ref
IMP::atom::create_simplified_along_backbone()</td><td>[atom/cg_pdb.py](atom_2cg_pdb_8py-example.html), [atom/molecular_hierarchy.py](atom_2molecular_hierarchy_8py-example.html), [atom/multiresolution.py](atom_2multiresolution_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>
100 <tr><td>@ref
IMP::atom::get_example_path()</td><td>[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/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/score_protein_with_ligand.py](atom_2score_protein_with_ligand_8py-example.html), [multistate.py](multistate_8py-example.html)</td></tr>
101 <tr><td>@ref
IMP::atom::get_heavy_atom_CHARMM_parameters()</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>
102 <tr><td>@ref
IMP::atom::get_hierarchy_tree()</td><td>[atom/edit_molecular_hierarchy.py](atom_2edit_molecular_hierarchy_8py-example.html), [atom/molecular_hierarchy.py](atom_2molecular_hierarchy_8py-example.html)</td></tr>
103 <tr><td>@ref
IMP::atom::get_leaves()</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), [rmf/multiresolution.py](rmf_2multiresolution_8py-example.html), [rmf/pdb.py](rmf_2pdb_8py-example.html)</td></tr>
104 <tr><td>@ref
IMP::atom::get_residue()</td><td>[atom/molecular_hierarchy.py](atom_2molecular_hierarchy_8py-example.html)</td></tr>
105 <tr><td>@ref
IMP::atom::get_rmsd()</td><td>[em/local_fitting.py](em_2local_fitting_8py-example.html)</td></tr>
107 <tr><td>@ref
IMP::atom::read_mol2()</td><td>[atom/score_protein_with_ligand.py](atom_2score_protein_with_ligand_8py-example.html)</td></tr>
108 <tr><td>@ref
IMP::atom::read_pdb()</td><td>[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/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/score_protein_with_ligand.py](atom_2score_protein_with_ligand_8py-example.html), [core/cover_particles.py](core_2cover_particles_8py-example.html), [core/rigid_bodies.py](core_2rigid_bodies_8py-example.html), [display/displaying_ensembles.py](display_2displaying_ensembles_8py-example.html), [domino/rigid_body_excluded_volume.py](domino_2rigid_body_excluded_volume_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/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), [kernel/dependency_graph.py](kernel_2dependency_graph_8py-example.html), [multistate.py](multistate_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), [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)</td></tr>
111 <tr><td>@ref
IMP::atom::show_molecular_hierarchy()</td><td>[kernel/dependency_graph.py](kernel_2dependency_graph_8py-example.html), [rmf/pdb.py](rmf_2pdb_8py-example.html)</td></tr>
112 <tr><td>@ref
IMP::atom::show_with_representations()</td><td>[pmi/ambiguity.py](pmi_2ambiguity_8py-example.html), [pmi/em.py](pmi_2em_8py-example.html), [pmi/selection.py](pmi_2selection_8py-example.html)</td></tr>
113 <tr><td>@ref
IMP::atom::transform()</td><td>[atom/cg_pdb.py](atom_2cg_pdb_8py-example.html), [atom/markers.py](atom_2markers_8py-example.html)</td></tr>
114 <tr><td>@ref
IMP::atom::write_pdb()</td><td>[atom/cg_pdb.py](atom_2cg_pdb_8py-example.html), [atom/structure_from_sequence.py](atom_2structure_from_sequence_8py-example.html), [em2d/clustering_of_pdb_models.py](em2d_2clustering_of_pdb_models_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), [rotamer/rotamer_pdb2.py](rotamer_2rotamer_pdb2_8py-example.html), [rotamer/rotamer_pdb.py](rotamer_2rotamer_pdb_8py-example.html)</td></tr>
116 # IMP.core # {#function_example_index_core}
118 <th>Function</th><th>Examples</th></tr>
122 <tr><td>@ref
IMP::core::RigidBody::setup_particle()</td><td>[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), [core/rigid_collisions.py](core_2rigid_collisions_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)</td></tr>
124 <tr><td>@ref
IMP::core::XYZ::setup_particle()</td><td>[atom/dope_and_excluded_volume.cpp](atom_2dope_and_excluded_volume_8cpp-example.html), [core/XYZ_Decorator.py](core_2XYZ_Decorator_8py-example.html), [core/ms_connectivity_restraint.py](core_2ms_connectivity_restraint_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), [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/six_particles_optimization.py](domino_2six_particles_optimization_8py-example.html), [gsl/simplex.py](gsl_2simplex_8py-example.html), [parallel/tasks.py](parallel_2tasks_8py-example.html), [temperature_rem.py](temperature_rem_8py-example.html)</td></tr>
126 <tr><td>@ref
IMP::core::XYZR::setup_particle()</td><td>[BallMover.py](BallMover_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/cover_particles.py](core_2cover_particles_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_in_sphere.py](core_2restrain_in_sphere_8py-example.html), [core/symmetry.py](core_2symmetry_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), [em/analyze_convergence.py](em_2analyze_convergence_8py-example.html), [kernel/setup.py](kernel_2setup_8py-example.html), [misc/decay.py](misc_2decay_8py-example.html), [rmf/simulation.py](rmf_2simulation_8py-example.html), [saxs/profile_fit.py](saxs_2profile_fit_8py-example.html)</td></tr>
127 <tr><td>@ref
IMP::core::create_xyzr_particles()</td><td>[container/bipartite_nonbonded_interactions.py](container_2bipartite_nonbonded_interactions_8py-example.html), [container/connectivity.py](container_2connectivity_8py-example.html), [container/nonbonded_interactions.py](container_2nonbonded_interactions_8py-example.html), [container/statistical.py](container_2statistical_8py-example.html), [core/restrain_diameter.py](core_2restrain_diameter_8py-example.html), [core/restrain_minimum_distance.py](core_2restrain_minimum_distance_8py-example.html), [core/rigid_collisions.py](core_2rigid_collisions_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), [example/range_restriction.py](example_2range_restriction_8py-example.html), [kernel/chain.py](kernel_2chain_8py-example.html)</td></tr>
128 <tr><td>@ref
IMP::core::get_centroid()</td><td>[em/local_fitting.py](em_2local_fitting_8py-example.html)</td></tr>
129 <tr><td>@ref
IMP::core::get_distance()</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/XYZ_Decorator.py](core_2XYZ_Decorator_8py-example.html), [core/restrain_diameter.py](core_2restrain_diameter_8py-example.html), [core/restrain_minimum_distance.py](core_2restrain_minimum_distance_8py-example.html), [gsl/simplex.py](gsl_2simplex_8py-example.html)</td></tr>
131 <tr><td>@ref
IMP::core::get_example_path()</td><td>[core/cover_particles.py](core_2cover_particles_8py-example.html), [core/rigid_bodies.py](core_2rigid_bodies_8py-example.html)</td></tr>
132 <tr><td>@ref
IMP::core::get_leaves()</td><td>[em2d/optimize_em2d_with_montecarlo.py](em2d_2optimize_em2d_with_montecarlo_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), [pmi/ambiguity.py](pmi_2ambiguity_8py-example.html)</td></tr>
133 <tr><td>@ref
IMP::core::transform()</td><td>[core/randomize_rigid_body.py](core_2randomize_rigid_body_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>
135 # IMP.display # {#function_example_index_display}
137 <th>Function</th><th>Examples</th></tr>
138 <tr><td>@ref
IMP::display::Colored::setup_particle()</td><td>[core/
optimize_balls.py](core_2optimize_balls_8py-example.html), [domino/multiscale.py](domino_2multiscale_8py-example.html), [domino/restraint_cache.py](domino_2restraint_cache_8py-example.html), [misc/decay.py](misc_2decay_8py-example.html), [rmf/simulation.py](rmf_2simulation_8py-example.html)</td></tr>
139 <tr><td>@ref
IMP::display::get_display_color()</td><td>[core/
optimize_balls.py](core_2optimize_balls_8py-example.html), [display/basic_geometry.py](display_2basic_geometry_8py-example.html), [display/displaying_ensembles.py](display_2displaying_ensembles_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), [misc/decay.py](misc_2decay_8py-example.html), [rmf/simulation.py](rmf_2simulation_8py-example.html)</td></tr>
146 # IMP.domino # {#function_example_index_domino}
148 <th>Function</th><th>Examples</th></tr>
149 <tr><td>@ref
IMP::domino::get_example_path()</td><td>[domino/rigid_body_excluded_volume.py](domino_2rigid_body_excluded_volume_8py-example.html)</td></tr>
150 <tr><td>@ref
IMP::domino::get_interaction_graph()</td><td>[domino/domino_approach.py](domino_2domino_approach_8py-example.html), [domino/merge_tree.py](domino_2merge_tree_8py-example.html)</td></tr>
151 <tr><td>@ref
IMP::domino::get_junction_tree()</td><td>[domino/domino_approach.py](domino_2domino_approach_8py-example.html), [domino/merge_tree.py](domino_2merge_tree_8py-example.html)</td></tr>
152 <tr><td>@ref
IMP::domino::get_merge_tree()</td><td>[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)</td></tr>
153 <tr><td>@ref
IMP::domino::get_subsets()</td><td>[domino/domino_approach.py](domino_2domino_approach_8py-example.html)</td></tr>
156 <tr><td>@ref
IMP::domino::load_particle_states()</td><td>[domino/multiscale.py](domino_2multiscale_8py-example.html), [domino/restraint_cache.py](domino_2restraint_cache_8py-example.html)</td></tr>
158 # IMP.em # {#function_example_index_em}
160 <th>Function</th><th>Examples</th></tr>
162 <tr><td>@ref
IMP::em::create_density_header()</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)</td></tr>
166 <tr><td>@ref
IMP::em::get_example_path()</td><td>[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>
170 # IMP.em2d # {#function_example_index_em2d}
172 <th>Function</th><th>Examples</th></tr>
173 <tr><td>@ref
IMP::em2d::get_example_path()</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/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>
174 <tr><td>@ref
IMP::em2d::read_images()</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>
175 <tr><td>@ref
IMP::em2d::save_images()</td><td>[em2d/em_images_conversion.py](em2d_2em_images_conversion_8py-example.html)</td></tr>
177 # IMP.pmi # {#function_example_index_pmi}
179 <th>Function</th><th>Examples</th></tr>
180 <tr><td>@ref
IMP::pmi::get_example_path()</td><td>[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/multiscale.py](pmi_2multiscale_8py-example.html), [pmi/selection.py](pmi_2selection_8py-example.html)</td></tr>
183 <tr><td>@ref
IMP::pmi::tools::shuffle_configuration()</td><td>[pmi/ambiguity.py](pmi_2ambiguity_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>
185 # IMP.rmf # {#function_example_index_rmf}
187 <th>Function</th><th>Examples</th></tr>
189 <tr><td>@ref
IMP::rmf::add_geometry()</td><td>[container/connectivity.py](container_2connectivity_8py-example.html), [em/cube.py](em_2cube_8py-example.html), [rmf/geometry.py](rmf_2geometry_8py-example.html), [rmf/simulation.py](rmf_2simulation_8py-example.html)</td></tr>
190 <tr><td>@ref
IMP::rmf::add_hierarchies()</td><td>[misc/decay.py](misc_2decay_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)</td></tr>
191 <tr><td>@ref
IMP::rmf::add_hierarchy()</td><td>[domino/restraint_cache.py](domino_2restraint_cache_8py-example.html), [kernel/chain.py](kernel_2chain_8py-example.html), [rmf/simulation.py](rmf_2simulation_8py-example.html)</td></tr>
192 <tr><td>@ref
IMP::rmf::add_restraints()</td><td>[domino/restraint_cache.py](domino_2restraint_cache_8py-example.html), [misc/decay.py](misc_2decay_8py-example.html), [rmf/simulation.py](rmf_2simulation_8py-example.html)</td></tr>
195 <tr><td>@ref
IMP::rmf::get_example_path()</td><td>[rmf/link.py](rmf_2link_8py-example.html), [rmf/multiresolution.py](rmf_2multiresolution_8py-example.html), [rmf/pdb.py](rmf_2pdb_8py-example.html)</td></tr>
197 <tr><td>@ref
IMP::rmf::load_frame()</td><td>[rmf/geometry.py](rmf_2geometry_8py-example.html), [rmf/link.py](rmf_2link_8py-example.html), [rmf/pdb.py](rmf_2pdb_8py-example.html)</td></tr>
198 <tr><td>@ref
IMP::rmf::save_frame()</td><td>[container/connectivity.py](container_2connectivity_8py-example.html), [domino/restraint_cache.py](domino_2restraint_cache_8py-example.html), [em/cube.py](em_2cube_8py-example.html), [kernel/chain.py](kernel_2chain_8py-example.html), [rmf/geometry.py](rmf_2geometry_8py-example.html), [rmf/link.py](rmf_2link_8py-example.html), [rmf/pdb.py](rmf_2pdb_8py-example.html)</td></tr>
200 # IMP.saxs # {#function_example_index_saxs}
202 <th>Function</th><th>Examples</th></tr>
204 <tr><td>@ref
IMP::saxs::get_example_path()</td><td>[saxs/profile.py](saxs_2profile_8py-example.html), [saxs/profile_fit.py](saxs_2profile_fit_8py-example.html)</td></tr>
206 # IMP.statistics # {#function_example_index_statistics}
208 <th>Function</th><th>Examples</th></tr>
210 <tr><td>@ref
IMP::statistics::create_lloyds_kmeans()</td><td>[kernel/basic_optimization.py](kernel_2basic_optimization_8py-example.html), [statistics/kmeans.py](statistics_2kmeans_8py-example.html)</td></tr>
display::Geometries create_geometries(RMF::FileConstHandle parent)
Create geometry objects for the geometry nodes found in the file.
PartitionalClusteringWithCenter * create_lloyds_kmeans(Embedding *embedding, unsigned int k, unsigned int iterations)
Grid3D< float, DenseGridStorage3D< float > > DenseFloatGrid3D
CHARMMParameters * get_heavy_atom_CHARMM_parameters()
VectorD< D > get_random_vector_on(const BoundingBoxD< D > &bb)
Generate a random vector on a box with uniform density.
static FloatKey get_mass_key()
void show_molecular_hierarchy(Hierarchy h)
Print out the molecular hierarchy.
static RigidBodyDiffusion setup_particle(Model *m, ParticleIndex pi)
Grid3D< int, SparseGridStorage3D< int, UnboundedGridStorage3D > > SparseUnboundedIntGrid3D
void remove_charmm_untyped_atoms(Hierarchy hierarchy)
Remove any atom from the Hierarchy that does not have a CHARMM type.
algebra::BoundingBoxD< 3 > get_bounding_box(const DensityMap *m, Float threshold)
Get the bounding box for a map.
atom::Hierarchies create_hierarchies(RMF::FileConstHandle fh, Model *m)
RMF::FrameID save_frame(RMF::FileHandle file, std::string name="")
Save the current state of the linked objects as a new RMF frame.
DependencyGraph get_dependency_graph(Model *m)
void show_with_representations(Hierarchy h, std::ostream &out=std::cout)
Traverse through the tree and show atom info, including representations.
static Atom setup_particle(Model *m, ParticleIndex pi, Atom other)
static FloatKey get_radius_key()
Get the key for the radius.
double get_coarse_cc_coefficient(const DensityMap *grid1, const DensityMap *grid2, double grid2_voxel_data_threshold, bool allow_padding=false, FloatPair norm_factors=FloatPair(0., 0.))
Calculates the cross correlation coefficient between two maps.
static Fragment setup_particle(Model *m, ParticleIndex pi)
BoundingBoxD< 3 > get_bounding_box(const Geometry &)
Compute the bounding box of any geometric object.
Rotation2D compose(const Rotation2D &a, const Rotation2D &b)
Compose two rotations a and b.
Sphere3D get_enclosing_sphere(const Sphere3Ds &ss)
Return a sphere containing the listed spheres.
static XYZR setup_particle(Model *m, ParticleIndex pi)
IMP::core::RigidBody create_compatible_rigid_body(Hierarchy h, Hierarchy reference)
Rigidify a molecule or collection of molecules.
Hierarchy create_simplified_along_backbone(Hierarchy input, int num_res, bool keep_detailed=false)
boost::graph DependencyGraph
Directed graph on the interactions between the various objects in the model.
XYZRs create_xyzr_particles(Model *m, unsigned int num, Float radius, Float box_side=10)
Create a set of particles with random coordinates.
def parse_dssp
Read a DSSP file, and return secondary structure elements (SSEs).
SubsetGraph get_junction_tree(const InteractionGraph &ig)
Vector< VectorD< D > > get_vertices(const BoundingBoxD< D > &bb)
Return a list of the 2^D bounding points for the bounding box.
void add_radii(Hierarchy d, const ForceFieldParameters *ffp=get_all_atom_CHARMM_parameters(), FloatKey radius_key=FloatKey("radius"))
bool get_bool_flag(std::string name)
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
static Cover setup_particle(Model *m, ParticleIndex pi, ParticleIndexesAdaptor members)
void write_pdb(const Selection &mhd, TextOutput out, unsigned int model=1)
void setup_as_approximation(Particle *h, const ParticlesTemp &other)
static State setup_particle(Model *m, ParticleIndex pi, unsigned int index)
ParticlesTemp get_particles(Model *m, const ParticleIndexes &ps)
Get the particles from a list of indexes.
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
Subsets get_subsets(const SubsetGraph &g)
Gets all of the Subsets of a SubsetGraph.
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
SampledDensityMap * particles2density(const ParticlesTemp &ps, Float resolution, Float apix, int sig_cutoff=3, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key())
Resample a set of particles into a density grid.
algebra::Vector3D get_centroid(const XYZs &ps)
Get the centroid.
HierarchyTree get_hierarchy_tree(Hierarchy h)
Get a graph for the passed Hierarchy.
FormFactorTable * get_default_form_factor_table()
void add_string_flag(std::string name, std::string default_value, std::string description)
static Residue setup_particle(Model *m, ParticleIndex pi, ResidueType t, int index, int insertion_code)
static Representation setup_particle(Model *m, ParticleIndex pi)
LogLevel get_log_level()
Get the currently active global log level.
void add_hierarchies(RMF::FileHandle fh, const atom::Hierarchies &hs)
GenericHierarchies get_leaves(Hierarchy mhd)
Get all the leaves of the bit of hierarchy.
Color get_interpolated_rgb(const Color &a, const Color &b, double f)
Return a color interpolated between a and b in RGB space.
Color get_hot_color(double f)
Return the color for f from the hot color map.
static XYZ setup_particle(Model *m, ParticleIndex pi)
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
TextOutput create_temporary_file(std::string prefix="imp_temp", std::string suffix="")
Create a temporary file. The path can be extracted from the TextOutput.
InteractionGraph get_interaction_graph(ScoringFunctionAdaptor rs, const ParticleStatesTable *pst)
static Molecule setup_particle(Model *m, ParticleIndex pi)
Restraint * create_excluded_volume_restraint(const Hierarchies &hs, double resolution=-1)
Bond create_custom_bond(Bonded a, Bonded b, Float length, Float stiffness=-1)
Connect the two wrapped particles by a custom bond.
Rotation3D get_rotation_about_axis(const Vector3D &axis, double angle)
Generate a Rotation3D object from a rotation around an axis.
void write_help(std::ostream &out=std::cerr)
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
MergeTree get_merge_tree(ScoringFunctionAdaptor input, const ParticleStatesTable *pst)
double get_diffusion_angle(double D, double dtfs)
IMP::algebra::Transformation3D get_transformation_aligning_first_to_second(const Vector3DsOrXYZs0 &source, const Vector3DsOrXYZs1 &target)
Compute the rigid transform bringing the first point set to the second.
Transformation2D get_rotation_about_point(const Vector2D &point, const Rotation2D &rotation)
Generate a Transformation2D object from a rotation around a point.
static Hierarchy setup_particle(Model *m, ParticleIndex pi, ParticleIndexesAdaptor children=ParticleIndexesAdaptor())
Create a Hierarchy of level t by adding the needed attributes.
Rotation3D get_random_rotation_3d()
Pick a rotation at random from all possible rotations.
void add_hierarchy(RMF::FileHandle fh, atom::Hierarchy hs)
void transform(Hierarchy h, const algebra::Transformation3D &tr)
Transform a hierarchy. This is aware of rigid bodies.
core::XYZR create_cover(const Selection &s, std::string name=std::string())
Hierarchy create_protein(Model *m, std::string name, double target_radius, int number_of_residues, int first_residue_index=0, double volume=-1)
Create a coarse grained molecule.
static Mass setup_particle(Model *m, ParticleIndex pi, Float mass)
void load_leaf_assignments(const Subset &subset, AssignmentsTable *at, AssignmentContainer *ac)
Fill in assignments for a leaf.
DensityHeader create_density_header(const algebra::BoundingBoxD< 3 > &bb, float spacing)
Create a header from a bounding box in 3D.
void load_merged_assignments(const Subset &first_subset, AssignmentContainer *first, const Subset &second_subset, AssignmentContainer *second, const SubsetFilterTablesTemp &filters, AssignmentContainer *ret)
Fill in assignments for an internal node.
static Bonded setup_particle(Model *m, ParticleIndex pi)
static Hierarchy setup_particle(Model *m, ParticleIndex pi, DecoratorTraits tr=get_default_decorator_traits())
Images read_images(const Strings &names, const ImageReaderWriter *rw)
void add_restraints(RMF::FileHandle fh, const Restraints &hs)
double get_rmsd(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2)
Float compute_fitting_score(const ParticlesTemp &ps, DensityMap *em_map, FloatKey wei_key=atom::Mass::get_mass_key())
Compute fitting scores for a given set of rigid transformations.
void add_to_log(LogLevel level, std::string to_write)
Write a string to the log, for Python.
VectorD< D > get_random_vector_in(const BoundingBoxD< D > &bb)
Generate a random vector in a box with uniform density.
void optimize_balls(Model *m, const ParticleIndexes &pis, const RestraintsTemp &rs=RestraintsTemp(), const PairPredicates &excluded=PairPredicates(), const OptimizerStates &opt_states=OptimizerStates(), LogLevel ll=DEFAULT)
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
Hierarchy read_mol2(TextInput mol2_file, Model *model, Mol2Selector *mol2sel=nullptr)
Create a hierarchy from a Mol2 file.
Color get_display_color(unsigned int i)
std::string get_relative_path(std::string base, std::string relative)
Return a path to a file relative to another file.
void load_frame(RMF::FileConstHandle file, RMF::FrameID frame)
Load the given RMF frame into the state of the linked objects.
DensityMap * create_density_map(const DensityMap *other)
Create a copy of another map.
Hierarchy read_pdb(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector(), bool select_first_model=true)
Read all the molecules in the first model of the PDB file.
int get_state_index(Hierarchy h)
Walk up the hierarchy to find the current state.
static Colored setup_particle(Model *m, ParticleIndex pi, Color color)
void save_images(Images images, const Strings &names, const ImageReaderWriter *rw)
static const IMP::core::HierarchyTraits & get_traits()
Get the molecular hierarchy HierarchyTraits.
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
void add_protein_ligand_score_data(Hierarchy h)
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
void set_log_level(LogLevel l)
Set the current global log level.
algebra::Sphere3D get_enclosing_sphere(const XYZs &v)
Get a sphere enclosing the set of XYZRs.
FittingSolutions local_rigid_fitting(Particle *p, Refiner *refiner, const FloatKey &weight_key, DensityMap *dmap, OptimizerStates display_log, Int number_of_optimization_runs=5, Int number_of_mc_steps=10, Int number_of_cg_steps=100, Float max_translation=2., Float max_rotation=.3, bool fast=true)
Local rigid fitting of a rigid body.
Value get_linearly_interpolated(const GridD< D, Storage, Value, Embedding > &g, const VectorD< D > &pt)
Get the value from the grid with linear interpolation.
double get_rmsd(const core::XYZs &s0, const core::XYZs &s1)
void set_log_timer(bool tb)
Set whether log messages are tagged with the current log time.
void show_restraint_hierarchy(ScoringFunctionAdaptor rs, std::ostream &out=std::cout)
Print the hierarchy of restraints.
DependencyGraph get_pruned_dependency_graph(Model *m)
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
static Diffusion setup_particle(Model *m, ParticleIndex pi, Float D)
Residue get_residue(Atom d, bool nothrow=false)
Return the Residue containing this atom.
static Reference setup_particle(Model *m, ParticleIndex pi, ParticleIndexAdaptor reference)
Rotation3D get_identity_rotation_3d()
Return a rotation that does not do anything.
Color get_gray_color(double f)
Return the a grayscale value for f.
void link_hierarchies(RMF::FileConstHandle fh, const atom::Hierarchies &hs)
void add_dope_score_data(atom::Hierarchy h)
std::string show_graphviz(Graph g)
Restraint * create_distance_restraint(const Selection &n0, const Selection &n1, double x0, double k, std::string name="Distance%1%")
std::string get_string_flag(std::string name)
networkx::DiGraph get_networkx_graph(Graph g)
void transform(RigidBody a, const algebra::Transformation3D &tr)
Transform a rigid body.
Color get_jet_color(double f)
Return the color for f from the jet color map.
Vector< VectorD< D > > get_grid_interior_cover_by_spacing(const BoundingBoxD< D > &bb, double s)
void add_geometry(RMF::FileHandle file, display::Geometry *r)
Add a single geometry to the file.
static const FloatKeys & get_xyz_keys()
Get a vector containing the keys for x,y,z.
void add_geometries(RMF::FileHandle file, const display::GeometriesTemp &r)
Add geometries to the file.
void load_particle_states(const Subset &s, const Assignment &ss, const ParticleStatesTable *pst)
Load the appropriate state for each particle in a Subset.
IMP::core::RigidBody create_rigid_body(const Hierarchies &h, std::string name=std::string("created rigid body"))
Rigidify a molecule or collection of molecules.
void setup_from_argv(int argc, char **argv, std::string description)
Parse the command line flags and return the positional arguments.
static Chain setup_particle(Model *m, ParticleIndex pi, std::string id)
CHARMMParameters * get_all_atom_CHARMM_parameters()
void add_bool_flag(std::string name, std::string description)
Hierarchies get_leaves(const Selection &h)
double get_einstein_diffusion_coefficient(double r, double temp=-1)
PartitionalClustering * create_centrality_clustering(Metric *d, double far, int k)
double get_distance(const Surface &s, const XYZR &d)
Get distance from sphere to surface.
ParticleIndexes get_indexes(const ParticlesTemp &ps)
Get the indexes from a list of particles.
static RigidBody setup_particle(Model *m, ParticleIndex pi, ParticleIndexesAdaptor ps)
Restraint * create_connectivity_restraint(const Selections &s, double k, std::string name="Connectivity%1%")
Create a restraint connecting the selections.
double get_distance(const Line3D &s, const Vector3D &p)
Get closest distance between a line and a point.
void add_bonds(Hierarchy d, const ForceFieldParameters *ffp=get_all_atom_CHARMM_parameters())
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
double get_diffusion_length(double D, double t)
std::string create_temporary_file_name(std::string prefix="imp_temp", std::string suffix="")
Create a temporary file.