Function Examples

Examples that use a given function:

• IMP::Container():
  • kernel/dependency_graph.py
• IMP::DependencyGraph():
  • kernel/graph.py
• IMP::IntKey():
  • design_example
• IMP::Model():
  • atom/dope_and_excluded_volume.cpp
• IMP::PairScore():
  • design_example
• IMP::Particle():
  • kernel/dependency_graph.py
• IMP::Restraint():
  • kernel/dependency_graph.py
• IMP::ScoreState():
  • kernel/dependency_graph.py
• IMP::algebra::DenseFloatGrid3D():
  • domino/restraint_cache.py
• IMP::algebra::SparseUnboundedIntGrid3D():
  • algebra/grid_space.py
• IMP::algebra::get_ball_radius_from_volume_3d():
  • kernel/dock_with_crosslinks.py
• IMP::algebra::get_bounding_box():
  • algebra/geometry.py
• IMP::algebra::get_distance():
  • algebra/geometry.py
• 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_random_rotation_3d():
  • atom/cg_pdb.py
  • atom/markers.py
  • core/randomize_rigid_body.py
  • core/rigid_collisions.py
  • kernel/dock_with_crosslinks.py
  • restrainer/rigid_body_and_excluded_volume_restraint.py
• IMP::algebra::get_random_vector_in():
  • algebra/geometry.py
  • container/filter_close_pairs.py
  • core/incremental_mc.py
  • core/optimize_balls.py
  • core/randomize_rigid_body.py
  • core/rigid_collisions.py
  • display/basic_geometry.py
  • domino/merge_tree.py
  • em/local_fitting.py
  • kernel/dock_with_crosslinks.py
  • kernel/nup84.py
  • kernel/setup.py
  • misc/decay.py
  • restrainer/rigid_body_and_excluded_volume_restraint.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_rotation_about_axis():
  • core/symmetry.py
  • domino/rigid_body_excluded_volume.py
  • em/local_fitting.py
• IMP::algebra::get_transformation_aligning_first_to_second():
  • em2d/clustering_of_pdb_models.py
• IMP::atom::Atom::particle_is_instance():
  • 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::Diffusion::setup_particle():
  • misc/decay.py
  • rmf/simulation.py
• IMP::atom::Fragment::setup_particle():
  • 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
  • core/connectivity_restraint.py
  • display/displaying_ensembles.py
  • domino/restraint_cache.py
  • kernel/dependency_graph.py
  • kernel/nup84.py
  • misc/decay.py
  • restrainer/simple_connectivity_on_molecules.py
  • restrainer/simple_em_fit.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
  • misc/decay.py
  • rmf/simulation.py
• IMP::atom::Molecule::setup_particle():
  • atom/rigid_brownian_dynamics.py
• IMP::atom::Residue::setup_particle():
  • atom/dope_and_excluded_volume.cpp
• IMP::atom::RigidBodyDiffusion::setup_particle():
  • atom/rigid_brownian_dynamics.py
• IMP::atom::add_atom_type()():
  • design_example
• 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
  • em/fit_restraint.py
  • em/local_fitting.py
  • em/pdb2density.py
  • restrainer/simple_connectivity_on_rigid_bodies.py
• IMP::atom::create_compatible_rigid_body():
  • display/displaying_ensembles.py
• IMP::atom::create_connectivity_restraint():
  • kernel/dependency_graph.py
  • kernel/nup84.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
  • kernel/nup84.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
  • kernel/nup84.py
• IMP::atom::create_rigid_body():
  • atom/cg_pdb.py
  • atom/molecular_hierarchy.py
  • core/rigid_bodies.py
  • display/displaying_ensembles.py
  • domino/rigid_body_excluded_volume.py
  • em/local_fitting.py
  • kernel/dependency_graph.py
  • kernel/dock_with_crosslinks.py
  • kernel/nup84.py
• IMP::atom::create_simplified_along_backbone():
  • atom/cg_pdb.py
  • atom/molecular_hierarchy.py
  • display/displaying_ensembles.py
  • kernel/dependency_graph.py
  • kernel/nup84.py
• IMP::atom::destroy():
  • atom/cg_pdb.py
  • atom/molecular_hierarchy.py
  • display/displaying_ensembles.py
  • kernel/dependency_graph.py
  • kernel/nup84.py
• IMP::atom::get_all_atom_CHARMM_parameters():
  • atom/structure_from_sequence.py
• IMP::atom::get_bounding_box():
  • em/generate_density_map_of_fixed_dimension.py
• IMP::atom::get_by_type():
  • atom/assess_dope.py
  • atom/cg_pdb.py
  • atom/charmm_forcefield.py
  • atom/charmm_forcefield_verbose.py
  • atom/molecular_hierarchy.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
  • kernel/dependency_graph.py
  • kernel/dock_with_crosslinks.py
  • kernel/nup84.py
  • modeller/imp_restraints_in_modeller.py
  • modeller/modeller_restraints_in_imp.py
  • rmf/multiresolution.py
  • rotamer/rotamer_pdb.py
  • saxs/profile.py
  • saxs/profile_fit.py
• IMP::atom::get_example_path():
  • atom/assess_dope.py
  • atom/cg_pdb.py
  • atom/charmm_forcefield.py
  • atom/charmm_forcefield_verbose.py
  • atom/load_protein_restrain_bonds.py
  • atom/markers.py
  • atom/molecular_hierarchy.py
  • atom/score_protein_with_ligand.py
• IMP::atom::get_heavy_atom_CHARMM_parameters():
  • atom/charmm_forcefield.py
  • atom/charmm_forcefield_verbose.py
• IMP::atom::get_hierarchy_tree():
  • atom/molecular_hierarchy.py
• IMP::atom::get_internal_bonds():
  • atom/load_protein_restrain_bonds.py
• IMP::atom::get_leaves():
  • display/displaying_ensembles.py
  • em2d/collision_cross_section.py
  • kernel/dependency_graph.py
  • kernel/dock_with_crosslinks.py
  • kernel/nup84.py
  • rmf/multiresolution.py
  • rmf/pdb.py
• IMP::atom::get_residue():
  • atom/molecular_hierarchy.py
• IMP::atom::get_rmsd():
  • em2d/clustering_of_pdb_models.py
  • em/local_fitting.py
• IMP::atom::get_volume_from_residue_type():
  • kernel/dock_with_crosslinks.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/load_protein_restrain_bonds.py
  • atom/markers.py
  • atom/molecular_hierarchy.py
  • atom/score_protein_with_ligand.py
  • core/cover_particles.py
  • core/rigid_bodies.py
  • design_example
  • display/displaying_ensembles.py
  • domino/rigid_body_excluded_volume.py
  • em/fit_restraint.py
  • em/generate_density_map_of_fixed_dimension.py
  • em/local_fitting.py
  • em/pdb2density.py
  • kernel/dependency_graph.py
  • kernel/dock_with_crosslinks.py
  • kernel/nup84.py
  • restrainer/simple_connectivity_on_rigid_bodies.py
  • restrainer/simple_excluded_volume.py
  • rmf/link.py
  • rmf/multiresolution.py
  • rmf/pdb.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::transform():
  • atom/cg_pdb.py
  • atom/markers.py
• IMP::atom::write_pdb():
  • atom/cg_pdb.py
  • atom/structure_from_sequence.py
  • em/local_fitting.py
  • kernel/dock_with_crosslinks.py
  • rotamer/rotamer_pdb.py
• IMP::base::add_bool_flag():
  • example/range_restriction.py
  • kernel/nup84.py
• IMP::base::add_to_log():
  • base/log.py
• IMP::base::create_temporary_file_name():
  • atom/rigid_brownian_dynamics.py
  • core/incremental_mc.py
  • kernel/nup84.py
  • misc/decay.py
  • rmf/multiresolution.py
  • rmf/simulation.py
• IMP::base::get_bool_flag():
  • kernel/dock_with_crosslinks.py
  • kernel/nup84.py
  • misc/decay.py
  • rmf/multiresolution.py
• IMP::base::get_relative_path():
  • em2d/optimize_em2d_with_montecarlo.py
• IMP::base::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
  • kernel/dock_with_crosslinks.py
• IMP::base::set_log_level():
  • atom/rigid_brownian_dynamics.py
  • base/log.py
  • container/filter_close_pairs.py
  • core/incremental_mc.py
  • core/optimize_balls.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
  • kernel/write_an_optimizer_state.py
  • misc/decay.py
  • restrainer/nup84_complex_in_bead_representation.py
  • rotamer/rotamer_pdb.py
• IMP::base::set_log_timer():
  • base/log.py
• IMP::base::setup_from_argv():
  • atom/dope_and_excluded_volume.cpp
  • example/range_restriction.py
  • kernel/dock_with_crosslinks.py
  • kernel/nup84.py
  • misc/decay.py
  • rmf/multiresolution.py
• 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::particle_is_instance():
  • kernel/nup84.py
• IMP::core::RigidBody::setup_particle():
  • atom/rigid_brownian_dynamics.py
  • core/randomize_rigid_body.py
  • core/rigid_collisions.py
  • em/analyze_convergence.py
  • kernel/dock_with_crosslinks.py
• IMP::core::RigidBody::teardown_particle():
  • kernel/dock_with_crosslinks.py
• IMP::core::TypedPairScore::set_pair_score()():
  • design_example
• IMP::core::XYZ::decorate_particle():
  • core/XYZR_Decorator.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/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
• IMP::core::XYZR::get_radius_key():
  • core/optimize_balls.py
• IMP::core::XYZR::setup_particle():
  • atom/rigid_brownian_dynamics.py
  • container/filter_close_pairs.py
  • core/XYZR_Decorator.py
  • core/connectivity_restraint.py
  • core/cover_particles.py
  • core/incremental_mc.py
  • core/optimize_balls.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
  • 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
  • restrainer/simple_connectivity_on_molecules.py
  • restrainer/simple_diameter.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():
  • em/fit_restraint.py
  • em/generate_density_map_of_fixed_dimension.py
  • em/local_fitting.py
  • em/pdb2density.py
• IMP::core::transform():
  • core/randomize_rigid_body.py
  • em/local_fitting.py
  • kernel/nup84.py
• 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_grey_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::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::CoarseCC::cross_correlation_coefficient():
  • em/local_fitting.py
• 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_example_path():
  • em/fit_restraint.py
  • em/generate_density_map_of_fixed_dimension.py
  • em/local_fitting.py
  • em/pdb2density.py
• IMP::em::local_rigid_fitting():
  • em/local_fitting.py
• IMP::em::particles2density():
  • em/pdb2density.py
• IMP::em::read_map():
  • em/fit_restraint.py
  • em/local_fitting.py
• IMP::em::write_map():
  • em/analyze_convergence.py
  • em/cube.py
  • em/generate_density_map_of_fixed_dimension.py
  • em/local_fitting.py
  • em/pdb2density.py
• IMP::example::optimize_balls():
  • misc/decay.py
• IMP::restrainer::create_simple_connectivity_on_rigid_bodies():
  • restrainer/simple_connectivity_on_rigid_bodies.py
• IMP::restrainer::get_example_path():
  • restrainer/basic_display.py
  • restrainer/basic_setup.py
  • restrainer/em_restraint.py
  • restrainer/nup84_complex_in_bead_representation.py
  • restrainer/rigid_body_and_excluded_volume_restraint.py
  • restrainer/saxs_restraint.py
  • restrainer/simple_connectivity_on_rigid_bodies.py
  • restrainer/simple_em_fit.py
  • restrainer/simple_excluded_volume.py
• IMP::restrainer::set_rigid_bodies():
  • restrainer/simple_connectivity_on_rigid_bodies.py
  • restrainer/simple_excluded_volume.py
• IMP::rmf::add_geometries():
  • misc/decay.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/nup84.py
  • rmf/simulation.py
• IMP::rmf::add_restraints():
  • domino/restraint_cache.py
  • kernel/nup84.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():
  • domino/restraint_cache.py
  • kernel/nup84.py
  • rmf/geometry.py
  • rmf/link.py
  • rmf/pdb.py
• IMP::saxs::default_form_factor_table():
  • saxs/profile_fit.py
• IMP::saxs::get_example_path():
  • saxs/profile.py
  • saxs/profile_fit.py
• IMP::statistics::create_centrality_clustering():
  • statistics/write_a_metric.py
• IMP::statistics::create_lloyds_kmeans():
  • kernel/basic_optimization.py
  • statistics/kmeans.py