Function Examples

Table of Contents

• IMP (kernel)
• IMP.algebra
• IMP.atom
• IMP.core
• IMP.display
• IMP.domino
• IMP.em
• IMP.em2d
• IMP.pmi
• IMP.rmf
• IMP.saxs
• IMP.statistics

Overview

Examples that use a given function:

See also Factory Index, Argument Index, Class Examples

IMP (kernel)

Function	Examples
IMP::DependencyGraph()	kernel/graph.py
IMP::Restraints()	modeller/imp_restraints_in_modeller.py
IMP::add_bool_flag()	example/range_restriction.py
IMP::add_string_flag()	kernel/flags.py
IMP::add_to_log()	log.py
IMP::create_temporary_file()	atom/cg_pdb.py
IMP::create_temporary_file_name()	atom/rigid_brownian_dynamics.py, core/move_aware_mc.py, display/basic_geometry.py, domino/interactive_with_containers.py, domino/restraint_cache.py, domino/save_assignments.py, em/cube.py, misc/decay.py
IMP::get_bool_flag()	misc/decay.py, rmf/multiresolution.py, rotamer/rotamer_pdb2.py, rotamer/rotamer_pdb.py
IMP::get_dependency_graph()	kernel/dependency_graph.py
IMP::get_example_path()	kernel/dependency_graph.py
IMP::get_indexes()	domino/interactive.py, domino/interactive_with_containers.py
IMP::get_is_quick_test()	core/move_aware_mc.py, core/optimize_balls.py, pmi/atomistic.py, pmi/automatic.py, pmi/membrane.py, pmi/multiscale.py, pmi/protein_residue_binding.py
IMP::get_log_level()	kernel/write_a_restraint.py
IMP::get_networkx_graph()	kernel/graph.py
IMP::get_particles()	domino/marina_party.py, kernel/basic_optimization.py, misc/decay.py
IMP::get_pruned_dependency_graph()	kernel/dependency_graph.py
IMP::get_relative_path()	em2d/optimize_em2d_with_montecarlo.py
IMP::get_string_flag()	kernel/flags.py
IMP::set_check_level()	atom/assess_dope.py, atom/charmm_forcefield.py, atom/charmm_forcefield_verbose.py, atom/score_protein_with_ligand.py, display/displaying_ensembles.py, em/local_fitting.py
IMP::set_log_level()	atom/rigid_brownian_dynamics.py, container/filter_close_pairs.py, core/move_aware_mc.py, core/restrain_diameter.py, display/displaying_ensembles.py, domino/custom_filter.py, domino/merge_tree.py, domino/rigid_body_excluded_volume.py, domino/save_assignments.py, domino/six_particles_optimization.py, em2d/collision_cross_section.py, em2d/optimize_em2d_with_montecarlo.py, em/fit_restraint.py, em/local_fitting.py, kernel/chain.py, kmeans/kmeans_example.py, log.py, misc/decay.py, rotamer/rotamer_pdb2.py, rotamer/rotamer_pdb.py
IMP::set_log_timer()	log.py
IMP::setup_from_argv()	BallMover.py, algebra/geometry.py, algebra/grid_space.py, atom/assess_dope.py, atom/brownian_statistics.py, atom/cg_pdb.py, atom/charmm_forcefield.py, atom/charmm_forcefield_verbose.py, atom/charmm_topology.py, atom/dope_and_excluded_volume.cpp, atom/edit_molecular_hierarchy.py, atom/load_protein_restrain_bonds.py, atom/markers.py, atom/molecular_hierarchy.py, atom/multiresolution.py, atom/rigid_brownian_dynamics.py, atom/score_protein_with_ligand.py, atom/structure_from_sequence.py, container/bipartite_nonbonded_interactions.py, container/connectivity.py, container/filter_close_pairs.py, container/nonbonded_interactions.py, container/restrain_in_sphere.py, container/statistical.py, core/XYZR_Decorator.py, core/XYZ_Decorator.py, core/connectivity_restraint.py, core/cover_particles.py, core/custom_hierarchy.py, core/excluded_volume.py, core/model_numpy.py, core/move_aware_mc.py, core/ms_connectivity_restraint.py, core/optimize_balls.py, core/pair_restraint.py, core/randomize_rigid_body.py, core/restrain_diameter.py, core/restrain_in_sphere.py, core/restrain_minimum_distance.py, core/rigid_bodies.py, core/rigid_collisions.py, core/simple.cpp, core/simple.py, core/symmetry.py, display/basic_geometry.py, display/display_log.py, display/displaying_ensembles.py, display/show_particles_as_spheres.py, domino/custom_filter.py, domino/domino_approach.py, domino/interactive.py, domino/interactive_with_containers.py, domino/marina_party.py, domino/merge_tree.py, domino/multiscale.py, domino/restraint_cache.py, domino/rigid_body_excluded_volume.py, domino/save_assignments.py, domino/six_particles_optimization.py, em2d/clustering_of_pdb_models.py, em2d/collision_cross_section.py, em2d/em_images_conversion.py, em2d/optimize_em2d_with_montecarlo.py, em/analyze_convergence.py, em/cube.py, em/fit_restraint.py, em/generate_density_map_of_fixed_dimension.py, em/local_fitting.py, em/numpy_data.py, em/pdb2density.py, example/range_restriction.py, flags.cpp, grid.cpp, gsl/simplex.py, kernel/basic_optimization.py, kernel/chain.py, kernel/dependency_graph.py, kernel/flags.py, kernel/graph.py, kernel/write_a_restraint.py, kernel/write_an_optimizer_state.py, kmeans/kmeans_example.py, log.py, misc/decay.py, modeller/imp_restraints_in_modeller.py, modeller/load_modeller_model.py, modeller/modeller_restraints_in_imp.py, multistate.py, parallel/local_distance.py, pmi/ambiguity.py, pmi/atomistic.py, pmi/automatic.py, pmi/em.py, pmi/ideal_helix.py, pmi/membrane.py, pmi/multiscale.py, pmi/protein_residue_binding.py, pmi/selection.py, pmi/symmetry.py, rmf/geometry.py, rmf/link.py, rmf/multiresolution.py, rmf/pdb.py, rmf/simulation.py, saxs/profile.py, saxs/profile_fit.py, statistics/kmeans.py, statistics/write_a_metric.py, temperature_rem.py
IMP::show_graphviz()	atom/edit_molecular_hierarchy.py, domino/interactive.py, domino/interactive_with_containers.py, kernel/dependency_graph.py, kernel/graph.py
IMP::show_restraint_hierarchy()	domino/restraint_cache.py
IMP::write_help()	kernel/flags.py

IMP.algebra

Function	Examples
IMP::algebra::DenseFloatGrid3D()	domino/restraint_cache.py
IMP::algebra::SparseUnboundedIntGrid3D()	algebra/grid_space.py
IMP::algebra::Vector2D()	domino/multiscale.py
IMP::algebra::Vector3D()	BallMover.py, algebra/grid_space.py, atom/cg_pdb.py, atom/dope_and_excluded_volume.cpp, atom/markers.py, atom/rigid_brownian_dynamics.py, container/filter_close_pairs.py, container/restrain_in_sphere.py, core/XYZR_Decorator.py, core/XYZ_Decorator.py, core/connectivity_restraint.py, core/move_aware_mc.py, core/ms_connectivity_restraint.py, core/optimize_balls.py, core/restrain_in_sphere.py, core/rigid_collisions.py, core/simple.cpp, core/simple.py, core/symmetry.py, display/basic_geometry.py, domino/custom_filter.py, domino/domino_approach.py, domino/interactive.py, domino/interactive_with_containers.py, domino/multiscale.py, domino/restraint_cache.py, domino/rigid_body_excluded_volume.py, domino/six_particles_optimization.py, em2d/optimize_em2d_with_montecarlo.py, em/analyze_convergence.py, em/cube.py, example/range_restriction.py, grid.cpp, gsl/simplex.py, kernel/setup.py, misc/decay.py, parallel/tasks.py, pmi/symmetry.py, rmf/geometry.py, rmf/simulation.py, statistics/kmeans.py, temperature_rem.py
IMP::algebra::compose()	core/randomize_rigid_body.py, em2d/optimize_em2d_with_montecarlo.py
IMP::algebra::get_bounding_box()	algebra/geometry.py, algebra/grid_space.py
IMP::algebra::get_distance()	algebra/geometry.py, algebra/grid_space.py, em2d/optimize_em2d_with_montecarlo.py, grid.cpp
IMP::algebra::get_enclosing_sphere()	algebra/geometry.py
IMP::algebra::get_grid_interior_cover_by_spacing()	domino/multiscale.py
IMP::algebra::get_identity_rotation_3d()	em/local_fitting.py
IMP::algebra::get_linearly_interpolated()	grid.cpp
IMP::algebra::get_random_rotation_3d()	atom/cg_pdb.py, atom/markers.py, core/randomize_rigid_body.py, core/rigid_collisions.py, em2d/optimize_em2d_with_montecarlo.py
IMP::algebra::get_random_vector_in()	algebra/geometry.py, container/filter_close_pairs.py, core/move_aware_mc.py, core/optimize_balls.py, core/randomize_rigid_body.py, core/rigid_collisions.py, display/basic_geometry.py, domino/merge_tree.py, em2d/optimize_em2d_with_montecarlo.py, em/local_fitting.py, kernel/setup.py, rmf/simulation.py, statistics/kmeans.py
IMP::algebra::get_random_vector_on()	algebra/grid_space.py, em/local_fitting.py, rmf/simulation.py
IMP::algebra::get_rmsd()	em2d/clustering_of_pdb_models.py
IMP::algebra::get_rotation_about_axis()	core/symmetry.py, domino/rigid_body_excluded_volume.py, em/local_fitting.py, pmi/symmetry.py
IMP::algebra::get_rotation_about_point()	em2d/optimize_em2d_with_montecarlo.py, pmi/symmetry.py
IMP::algebra::get_transformation_aligning_first_to_second()	em2d/clustering_of_pdb_models.py
IMP::algebra::get_vertices()	em/cube.py

IMP.atom

Function	Examples
IMP::atom::AT_CA()	atom/dope_and_excluded_volume.cpp
IMP::atom::Atom::get_is_setup()	atom/assess_dope.py
IMP::atom::Atom::setup_particle()	atom/dope_and_excluded_volume.cpp
IMP::atom::Bonded::setup_particle()	container/nonbonded_interactions.py
IMP::atom::Chain::setup_particle()	atom/dope_and_excluded_volume.cpp
IMP::atom::Diffusion::setup_particle()	misc/decay.py, rmf/simulation.py
IMP::atom::Fragment::setup_particle()	atom/edit_molecular_hierarchy.py, atom/rigid_brownian_dynamics.py, core/connectivity_restraint.py
IMP::atom::Hierarchy::get_traits()	core/connectivity_restraint.py, core/cover_particles.py, display/displaying_ensembles.py, em/local_fitting.py
IMP::atom::Hierarchy::setup_particle()	atom/molecular_hierarchy.py, atom/multiresolution.py, core/connectivity_restraint.py, display/displaying_ensembles.py, domino/restraint_cache.py, kernel/chain.py, kernel/dependency_graph.py, misc/decay.py, multistate.py, rmf/multiresolution.py, rmf/simulation.py
IMP::atom::Mass::get_mass_key()	em/local_fitting.py
IMP::atom::Mass::setup_particle()	atom/rigid_brownian_dynamics.py, domino/restraint_cache.py, em/analyze_convergence.py, kernel/chain.py, misc/decay.py, rmf/simulation.py
IMP::atom::Molecule::setup_particle()	atom/rigid_brownian_dynamics.py
IMP::atom::Representation::setup_particle()	atom/multiresolution.py
IMP::atom::Residue::setup_particle()	atom/dope_and_excluded_volume.cpp
IMP::atom::RigidBodyDiffusion::setup_particle()	atom/rigid_brownian_dynamics.py
IMP::atom::State::setup_particle()	multistate.py
IMP::atom::add_bonds()	atom/load_protein_restrain_bonds.py, rmf/multiresolution.py
IMP::atom::add_dope_score_data()	atom/assess_dope.py, atom/dope_and_excluded_volume.cpp
IMP::atom::add_protein_ligand_score_data()	atom/score_protein_with_ligand.py
IMP::atom::add_radii()	atom/dope_and_excluded_volume.cpp, atom/structure_from_sequence.py, em2d/collision_cross_section.py, em2d/optimize_em2d_with_montecarlo.py, em/fit_restraint.py, em/local_fitting.py, em/pdb2density.py
IMP::atom::create_compatible_rigid_body()	display/displaying_ensembles.py
IMP::atom::create_connectivity_restraint()	kernel/dependency_graph.py
IMP::atom::create_connectivity_restraint()()	core/connectivity_restraint.py
IMP::atom::create_cover()	atom/markers.py
IMP::atom::create_cover()()	atom/markers.py
IMP::atom::create_custom_bond()	container/nonbonded_interactions.py
IMP::atom::create_distance_restraint()	atom/rigid_brownian_dynamics.py, kernel/dependency_graph.py
IMP::atom::create_distance_restraint()()	core/restrain_minimum_distance.py
IMP::atom::create_excluded_volume_restraint()	kernel/dependency_graph.py
IMP::atom::create_protein()	kernel/dependency_graph.py
IMP::atom::create_rigid_body()	atom/cg_pdb.py, atom/molecular_hierarchy.py, atom/multiresolution.py, core/rigid_bodies.py, display/displaying_ensembles.py, domino/rigid_body_excluded_volume.py, em/local_fitting.py, kernel/dependency_graph.py
IMP::atom::create_simplified_along_backbone()	atom/cg_pdb.py, atom/molecular_hierarchy.py, atom/multiresolution.py, display/displaying_ensembles.py, kernel/dependency_graph.py
IMP::atom::get_all_atom_CHARMM_parameters()	atom/structure_from_sequence.py
IMP::atom::get_diffusion_angle()	atom/brownian_statistics.py
IMP::atom::get_diffusion_length()	atom/brownian_statistics.py
IMP::atom::get_einstein_diffusion_coefficient()	atom/brownian_statistics.py
IMP::atom::get_example_path()	atom/assess_dope.py, atom/cg_pdb.py, atom/charmm_forcefield.py, atom/charmm_forcefield_verbose.py, atom/edit_molecular_hierarchy.py, atom/load_protein_restrain_bonds.py, atom/markers.py, atom/molecular_hierarchy.py, atom/multiresolution.py, atom/score_protein_with_ligand.py, multistate.py
IMP::atom::get_heavy_atom_CHARMM_parameters()	atom/charmm_forcefield.py, atom/charmm_forcefield_verbose.py, atom/charmm_topology.py
IMP::atom::get_hierarchy_tree()	atom/edit_molecular_hierarchy.py, atom/molecular_hierarchy.py
IMP::atom::get_leaves()	em2d/clustering_of_pdb_models.py, em2d/collision_cross_section.py, rmf/multiresolution.py, rmf/pdb.py
IMP::atom::get_residue()	atom/molecular_hierarchy.py
IMP::atom::get_rmsd()	em/local_fitting.py
IMP::atom::get_state_index()	multistate.py
IMP::atom::read_mol2()	atom/score_protein_with_ligand.py
IMP::atom::read_pdb()	atom/assess_dope.py, atom/cg_pdb.py, atom/charmm_forcefield.py, atom/charmm_forcefield_verbose.py, atom/edit_molecular_hierarchy.py, atom/load_protein_restrain_bonds.py, atom/markers.py, atom/molecular_hierarchy.py, atom/multiresolution.py, atom/score_protein_with_ligand.py, core/cover_particles.py, core/rigid_bodies.py, display/displaying_ensembles.py, domino/rigid_body_excluded_volume.py, em2d/clustering_of_pdb_models.py, em2d/collision_cross_section.py, em2d/optimize_em2d_with_montecarlo.py, em/fit_restraint.py, em/generate_density_map_of_fixed_dimension.py, em/local_fitting.py, em/pdb2density.py, kernel/dependency_graph.py, multistate.py, rmf/link.py, rmf/multiresolution.py, rmf/pdb.py, rotamer/rotamer_pdb2.py, rotamer/rotamer_pdb.py, saxs/profile.py, saxs/profile_fit.py
IMP::atom::remove_charmm_untyped_atoms()	atom/charmm_forcefield_verbose.py
IMP::atom::setup_as_approximation()	rmf/multiresolution.py
IMP::atom::show_molecular_hierarchy()	kernel/dependency_graph.py, rmf/pdb.py
IMP::atom::show_with_representations()	pmi/ambiguity.py, pmi/em.py, pmi/selection.py
IMP::atom::transform()	atom/cg_pdb.py, atom/markers.py
IMP::atom::write_pdb()	atom/cg_pdb.py, atom/structure_from_sequence.py, em2d/clustering_of_pdb_models.py, em2d/optimize_em2d_with_montecarlo.py, em/local_fitting.py, rotamer/rotamer_pdb2.py, rotamer/rotamer_pdb.py

IMP.core

Function	Examples
IMP::core::Cover::setup_particle()	core/cover_particles.py
IMP::core::Hierarchy::setup_particle()	core/custom_hierarchy.py
IMP::core::Reference::setup_particle()	core/symmetry.py
IMP::core::RigidBody::setup_particle()	atom/multiresolution.py, atom/rigid_brownian_dynamics.py, core/randomize_rigid_body.py, core/rigid_collisions.py, em2d/optimize_em2d_with_montecarlo.py, em/analyze_convergence.py
IMP::core::XYZ::get_xyz_keys()	domino/multiscale.py
IMP::core::XYZ::setup_particle()	atom/dope_and_excluded_volume.cpp, core/XYZ_Decorator.py, core/ms_connectivity_restraint.py, core/simple.cpp, core/simple.py, core/symmetry.py, domino/custom_filter.py, domino/domino_approach.py, domino/interactive.py, domino/interactive_with_containers.py, domino/six_particles_optimization.py, gsl/simplex.py, parallel/tasks.py, temperature_rem.py
IMP::core::XYZR::get_radius_key()	core/optimize_balls.py
IMP::core::XYZR::setup_particle()	BallMover.py, atom/rigid_brownian_dynamics.py, container/filter_close_pairs.py, core/XYZR_Decorator.py, core/connectivity_restraint.py, core/cover_particles.py, core/move_aware_mc.py, core/optimize_balls.py, core/restrain_in_sphere.py, core/symmetry.py, domino/merge_tree.py, domino/multiscale.py, domino/restraint_cache.py, em/analyze_convergence.py, kernel/setup.py, misc/decay.py, rmf/simulation.py, saxs/profile_fit.py
IMP::core::create_xyzr_particles()	container/bipartite_nonbonded_interactions.py, container/connectivity.py, container/nonbonded_interactions.py, container/statistical.py, core/restrain_diameter.py, core/restrain_minimum_distance.py, core/rigid_collisions.py, display/display_log.py, display/show_particles_as_spheres.py, example/range_restriction.py, kernel/chain.py
IMP::core::get_centroid()	em/local_fitting.py
IMP::core::get_distance()	atom/score_protein_with_ligand.py, core/XYZR_Decorator.py, core/XYZ_Decorator.py, core/restrain_diameter.py, core/restrain_minimum_distance.py, gsl/simplex.py
IMP::core::get_enclosing_sphere()	kernel/basic_optimization.py
IMP::core::get_example_path()	core/cover_particles.py, core/rigid_bodies.py
IMP::core::get_leaves()	em2d/optimize_em2d_with_montecarlo.py, em/fit_restraint.py, em/generate_density_map_of_fixed_dimension.py, em/local_fitting.py, em/pdb2density.py, pmi/ambiguity.py
IMP::core::transform()	core/randomize_rigid_body.py, em2d/optimize_em2d_with_montecarlo.py, em/local_fitting.py, pmi/ambiguity.py

IMP.display

Function	Examples
IMP::display::Colored::setup_particle()	core/optimize_balls.py, domino/multiscale.py, domino/restraint_cache.py, misc/decay.py, rmf/simulation.py
IMP::display::get_display_color()	core/optimize_balls.py, display/basic_geometry.py, display/displaying_ensembles.py, domino/multiscale.py, domino/rigid_body_excluded_volume.py, misc/decay.py, rmf/simulation.py
IMP::display::get_example_path()	display/displaying_ensembles.py
IMP::display::get_gray_color()	em/analyze_convergence.py
IMP::display::get_hot_color()	em/analyze_convergence.py
IMP::display::get_interpolated_rgb()	display/displaying_ensembles.py
IMP::display::get_jet_color()	domino/restraint_cache.py

IMP.domino

Function	Examples
IMP::domino::get_example_path()	domino/rigid_body_excluded_volume.py
IMP::domino::get_interaction_graph()	domino/domino_approach.py, domino/merge_tree.py
IMP::domino::get_junction_tree()	domino/domino_approach.py, domino/merge_tree.py
IMP::domino::get_merge_tree()	domino/interactive.py, domino/interactive_with_containers.py, domino/merge_tree.py
IMP::domino::get_subsets()	domino/domino_approach.py
IMP::domino::load_leaf_assignments()	domino/interactive_with_containers.py
IMP::domino::load_merged_assignments()	domino/interactive_with_containers.py
IMP::domino::load_particle_states()	domino/multiscale.py, domino/restraint_cache.py

IMP.em

Function	Examples
IMP::em::compute_fitting_score()	em/fit_restraint.py
IMP::em::create_density_header()	em/analyze_convergence.py, em/generate_density_map_of_fixed_dimension.py
IMP::em::create_density_map()	em/cube.py
IMP::em::get_bounding_box()	em/cube.py
IMP::em::get_coarse_cc_coefficient()	em/local_fitting.py
IMP::em::get_example_path()	em/fit_restraint.py, em/generate_density_map_of_fixed_dimension.py, em/local_fitting.py, em/numpy_data.py, em/pdb2density.py
IMP::em::local_rigid_fitting()	em/local_fitting.py
IMP::em::particles2density()	em/pdb2density.py

IMP.em2d

Function	Examples
IMP::em2d::get_example_path()	em2d/clustering_of_pdb_models.py, em2d/collision_cross_section.py, em2d/em_images_conversion.py, em2d/optimize_em2d_with_montecarlo.py
IMP::em2d::read_images()	em2d/em_images_conversion.py, em2d/optimize_em2d_with_montecarlo.py
IMP::em2d::save_images()	em2d/em_images_conversion.py

IMP.pmi

Function	Examples
IMP::pmi::get_example_path()	pmi/atomistic.py, pmi/automatic.py, pmi/em.py, pmi/multiscale.py, pmi/protein_residue_binding.py, pmi/selection.py
IMP.pmi.io.parse_dssp()	pmi/atomistic.py
IMP.pmi.tools.display_bonds()	pmi/multiscale.py
IMP.pmi.tools.shuffle_configuration()	pmi/ambiguity.py, pmi/automatic.py, pmi/membrane.py, pmi/multiscale.py, pmi/protein_residue_binding.py

IMP.rmf

Function	Examples
IMP::rmf::add_geometries()	misc/decay.py
IMP::rmf::add_geometry()	container/connectivity.py, em/cube.py, rmf/geometry.py, rmf/simulation.py
IMP::rmf::add_hierarchies()	misc/decay.py, rmf/link.py, rmf/multiresolution.py, rmf/pdb.py
IMP::rmf::add_hierarchy()	domino/restraint_cache.py, kernel/chain.py, rmf/simulation.py
IMP::rmf::add_restraints()	domino/restraint_cache.py, misc/decay.py, rmf/simulation.py
IMP::rmf::create_geometries()	rmf/geometry.py
IMP::rmf::create_hierarchies()	rmf/pdb.py
IMP::rmf::get_example_path()	rmf/link.py, rmf/multiresolution.py, rmf/pdb.py
IMP::rmf::link_hierarchies()	rmf/link.py
IMP::rmf::load_frame()	rmf/geometry.py, rmf/link.py, rmf/pdb.py
IMP::rmf::save_frame()	container/connectivity.py, domino/restraint_cache.py, em/cube.py, kernel/chain.py, rmf/geometry.py, rmf/link.py, rmf/pdb.py

IMP.saxs

Function	Examples
IMP::saxs::get_default_form_factor_table()	saxs/profile_fit.py
IMP::saxs::get_example_path()	saxs/profile.py, saxs/profile_fit.py

IMP.statistics

Function	Examples
IMP::statistics::create_centrality_clustering()	statistics/write_a_metric.py
IMP::statistics::create_lloyds_kmeans()	kernel/basic_optimization.py, statistics/kmeans.py