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.algebra # {#function_example_index_algebra}
11 <th>Function</th><th>Examples</th></tr>
14 <tr><td>@ref
IMP::algebra::Vector2D()</td><td>[domino/multiscale.py](domino_2multiscale_8py-example.html)</td></tr>
15 <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/nup84.py](kernel_2nup84_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), [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>
16 <tr><td>@ref
IMP::algebra::compose()</td><td>[em2d/optimize_em2d_with_montecarlo.py](em2d_2optimize_em2d_with_montecarlo_8py-example.html)</td></tr>
17 <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>
18 <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>
23 <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>
24 <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/nup84.py](kernel_2nup84_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>
25 <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>
26 <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>
27 <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)</td></tr>
32 # IMP.atom # {#function_example_index_atom}
34 <th>Function</th><th>Examples</th></tr>
35 <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>
37 <tr><td>@ref IMP::atom::Atom::get_is_setup()</td><td>[atom/assess_dope.py](atom_2assess_dope_8py-example.html)</td></tr>
42 <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>
43 <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>
44 <tr><td>@ref
IMP::atom::Hierarchy::setup_particle()</td><td>[atom/molecular_hierarchy.py](atom_2molecular_hierarchy_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), [kernel/nup84.py](kernel_2nup84_8py-example.html), [misc/decay.py](misc_2decay_8py-example.html), [multiresolution.py](multiresolution_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>
46 <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>
52 <tr><td>@ref
IMP::atom::add_bonds()</td><td>[atom/load_protein_restrain_bonds.py](atom_2load_protein_restrain_bonds_8py-example.html), [multiresolution.py](multiresolution_8py-example.html), [rmf/multiresolution.py](rmf_2multiresolution_8py-example.html)</td></tr>
53 <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>
55 <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/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>
61 <tr><td>@ref
IMP::atom::create_custom_bond()</td><td>[container/nonbonded_interactions.py](container_2nonbonded_interactions_8py-example.html)</td></tr>
62 <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), [kernel/nup84.py](kernel_2nup84_8py-example.html)</td></tr>
65 <tr><td>@ref
IMP::atom::create_protein()</td><td>[kernel/dependency_graph.py](kernel_2dependency_graph_8py-example.html), [kernel/nup84.py](kernel_2nup84_8py-example.html)</td></tr>
66 <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), [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), [kernel/nup84.py](kernel_2nup84_8py-example.html)</td></tr>
67 <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), [display/displaying_ensembles.py](display_2displaying_ensembles_8py-example.html), [kernel/dependency_graph.py](kernel_2dependency_graph_8py-example.html), [kernel/nup84.py](kernel_2nup84_8py-example.html)</td></tr>
68 <tr><td>@ref
IMP::atom::destroy()</td><td>[atom/cg_pdb.py](atom_2cg_pdb_8py-example.html), [atom/molecular_hierarchy.py](atom_2molecular_hierarchy_8py-example.html), [display/displaying_ensembles.py](display_2displaying_ensembles_8py-example.html), [kernel/dependency_graph.py](kernel_2dependency_graph_8py-example.html), [kernel/nup84.py](kernel_2nup84_8py-example.html)</td></tr>
70 <tr><td>@ref
IMP::atom::get_bounding_box()</td><td>[em/generate_density_map_of_fixed_dimension.py](em_2generate_density_map_of_fixed_dimension_8py-example.html)</td></tr>
71 <tr><td>@ref
IMP::atom::get_by_type()</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/molecular_hierarchy.py](atom_2molecular_hierarchy_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/optimize_em2d_with_montecarlo.py](em2d_2optimize_em2d_with_montecarlo_8py-example.html), [kernel/dependency_graph.py](kernel_2dependency_graph_8py-example.html), [kernel/nup84.py](kernel_2nup84_8py-example.html), [modeller/imp_restraints_in_modeller.py](modeller_2imp_restraints_in_modeller_8py-example.html), [modeller/modeller_restraints_in_imp.py](modeller_2modeller_restraints_in_imp_8py-example.html), [multiresolution.py](multiresolution_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), [saxs/profile.py](saxs_2profile_8py-example.html), [saxs/profile_fit.py](saxs_2profile_fit_8py-example.html)</td></tr>
72 <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/score_protein_with_ligand.py](atom_2score_protein_with_ligand_8py-example.html), [multistate.py](multistate_8py-example.html)</td></tr>
73 <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>
74 <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>
75 <tr><td>@ref
IMP::atom::get_internal_bonds()</td><td>[atom/load_protein_restrain_bonds.py](atom_2load_protein_restrain_bonds_8py-example.html)</td></tr>
76 <tr><td>@ref
IMP::atom::get_leaves()</td><td>[display/displaying_ensembles.py](display_2displaying_ensembles_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), [kernel/dependency_graph.py](kernel_2dependency_graph_8py-example.html), [kernel/nup84.py](kernel_2nup84_8py-example.html), [multiresolution.py](multiresolution_8py-example.html), [rmf/multiresolution.py](rmf_2multiresolution_8py-example.html), [rmf/pdb.py](rmf_2pdb_8py-example.html)</td></tr>
77 <tr><td>@ref
IMP::atom::get_residue()</td><td>[atom/molecular_hierarchy.py](atom_2molecular_hierarchy_8py-example.html)</td></tr>
78 <tr><td>@ref
IMP::atom::get_rmsd()</td><td>[em/local_fitting.py](em_2local_fitting_8py-example.html)</td></tr>
80 <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>
81 <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/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/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), [kernel/nup84.py](kernel_2nup84_8py-example.html), [multiresolution.py](multiresolution_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>
83 <tr><td>@ref
IMP::atom::setup_as_approximation()</td><td>[multiresolution.py](multiresolution_8py-example.html), [rmf/multiresolution.py](rmf_2multiresolution_8py-example.html)</td></tr>
84 <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>
85 <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>
86 <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>
88 # IMP.base # {#function_example_index_base}
90 <th>Function</th><th>Examples</th></tr>
91 <tr><td>@ref
IMP::base::add_bool_flag()</td><td>[example/range_restriction.py](example_2range_restriction_8py-example.html), [kernel/nup84.py](kernel_2nup84_8py-example.html)</td></tr>
94 <tr><td>@ref
IMP::base::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), [kernel/nup84.py](kernel_2nup84_8py-example.html), [misc/decay.py](misc_2decay_8py-example.html), [multiresolution.py](multiresolution_8py-example.html), [rmf/multiresolution.py](rmf_2multiresolution_8py-example.html), [rmf/simulation.py](rmf_2simulation_8py-example.html)</td></tr>
95 <tr><td>@ref
IMP::base::get_bool_flag()</td><td>[kernel/nup84.py](kernel_2nup84_8py-example.html), [misc/decay.py](misc_2decay_8py-example.html), [multiresolution.py](multiresolution_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>
97 <tr><td>@ref
IMP::base::get_relative_path()</td><td>[em2d/optimize_em2d_with_montecarlo.py](em2d_2optimize_em2d_with_montecarlo_8py-example.html)</td></tr>
99 <tr><td>@ref
IMP::base::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>
100 <tr><td>@ref
IMP::base::set_log_level()</td><td>[atom/rigid_brownian_dynamics.py](atom_2rigid_brownian_dynamics_8py-example.html), [base/log.py](base_2log_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), [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>
102 <tr><td>@ref
IMP::base::setup_from_argv()</td><td>[atom/dope_and_excluded_volume.cpp](atom_2dope_and_excluded_volume_8cpp-example.html), [base/flags.cpp](base_2flags_8cpp-example.html), [base/flags.py](base_2flags_8py-example.html), [core/incremental_mc.py](core_2incremental_mc_8py-example.html), [core/
optimize_balls.py](core_2optimize_balls_8py-example.html), [example/range_restriction.py](example_2range_restriction_8py-example.html), [kernel/chain.py](kernel_2chain_8py-example.html), [kernel/dependency_graph.py](kernel_2dependency_graph_8py-example.html), [kernel/nup84.py](kernel_2nup84_8py-example.html), [misc/decay.py](misc_2decay_8py-example.html), [multiresolution.py](multiresolution_8py-example.html), [rmf/multiresolution.py](rmf_2multiresolution_8py-example.html), [temperature_rem.py](temperature_rem_8py-example.html)</td></tr>
105 # IMP.core # {#function_example_index_core}
107 <th>Function</th><th>Examples</th></tr>
111 <tr><td>@ref IMP::core::RigidBody::get_is_setup()</td><td>[kernel/nup84.py](kernel_2nup84_8py-example.html)</td></tr>
112 <tr><td>@ref
IMP::core::RigidBody::setup_particle()</td><td>[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>
115 <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>
117 <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>
118 <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), [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>
119 <tr><td>@ref
IMP::core::get_centroid()</td><td>[em/local_fitting.py](em_2local_fitting_8py-example.html)</td></tr>
120 <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>
122 <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>
123 <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)</td></tr>
124 <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), [kernel/nup84.py](kernel_2nup84_8py-example.html)</td></tr>
126 # IMP.display # {#function_example_index_display}
128 <th>Function</th><th>Examples</th></tr>
129 <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>
130 <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>
137 # IMP.domino # {#function_example_index_domino}
139 <th>Function</th><th>Examples</th></tr>
140 <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>
141 <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>
142 <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>
143 <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>
144 <tr><td>@ref
IMP::domino::get_subsets()</td><td>[domino/domino_approach.py](domino_2domino_approach_8py-example.html)</td></tr>
147 <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>
149 # IMP.em # {#function_example_index_em}
151 <th>Function</th><th>Examples</th></tr>
154 <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>
157 <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/pdb2density.py](em_2pdb2density_8py-example.html)</td></tr>
160 <tr><td>@ref
IMP::em::read_map()</td><td>[em/fit_restraint.py](em_2fit_restraint_8py-example.html), [em/local_fitting.py](em_2local_fitting_8py-example.html)</td></tr>
161 <tr><td>@ref
IMP::em::write_map()</td><td>[em/analyze_convergence.py](em_2analyze_convergence_8py-example.html), [em/cube.py](em_2cube_8py-example.html), [em/generate_density_map_of_fixed_dimension.py](em_2generate_density_map_of_fixed_dimension_8py-example.html), [em/local_fitting.py](em_2local_fitting_8py-example.html), [em/pdb2density.py](em_2pdb2density_8py-example.html)</td></tr>
163 # IMP.em2d # {#function_example_index_em2d}
165 <th>Function</th><th>Examples</th></tr>
166 <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/optimize_em2d_with_montecarlo.py](em2d_2optimize_em2d_with_montecarlo_8py-example.html)</td></tr>
167 <tr><td>@ref
IMP::em2d::read_images()</td><td>[em2d/optimize_em2d_with_montecarlo.py](em2d_2optimize_em2d_with_montecarlo_8py-example.html)</td></tr>
169 # IMP.kernel # {#function_example_index_kernel}
171 <th>Function</th><th>Examples</th></tr>
172 <tr><td>@ref
IMP::kernel::Container()</td><td>[kernel/dependency_graph.py](kernel_2dependency_graph_8py-example.html)</td></tr>
176 <tr><td>@ref
IMP::kernel::Particle()</td><td>[kernel/dependency_graph.py](kernel_2dependency_graph_8py-example.html)</td></tr>
177 <tr><td>@ref
IMP::kernel::Restraint()</td><td>[kernel/dependency_graph.py](kernel_2dependency_graph_8py-example.html)</td></tr>
178 <tr><td>@ref
IMP::kernel::ScoreState()</td><td>[kernel/dependency_graph.py](kernel_2dependency_graph_8py-example.html)</td></tr>
179 <tr><td>@ref
IMP::kernel::Restraints()</td><td>[modeller/imp_restraints_in_modeller.py](modeller_2imp_restraints_in_modeller_8py-example.html)</td></tr>
184 # IMP.rmf # {#function_example_index_rmf}
186 <th>Function</th><th>Examples</th></tr>
188 <tr><td>@ref
IMP::rmf::add_hierarchies()</td><td>[misc/decay.py](misc_2decay_8py-example.html), [multiresolution.py](multiresolution_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>
189 <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), [kernel/nup84.py](kernel_2nup84_8py-example.html), [rmf/simulation.py](rmf_2simulation_8py-example.html)</td></tr>
190 <tr><td>@ref
IMP::rmf::add_restraints()</td><td>[domino/restraint_cache.py](domino_2restraint_cache_8py-example.html), [kernel/nup84.py](kernel_2nup84_8py-example.html), [misc/decay.py](misc_2decay_8py-example.html), [rmf/simulation.py](rmf_2simulation_8py-example.html)</td></tr>
193 <tr><td>@ref
IMP::rmf::get_example_path()</td><td>[multiresolution.py](multiresolution_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>
195 <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>
196 <tr><td>@ref
IMP::rmf::save_frame()</td><td>[domino/restraint_cache.py](domino_2restraint_cache_8py-example.html), [kernel/chain.py](kernel_2chain_8py-example.html), [kernel/nup84.py](kernel_2nup84_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>
198 # IMP.saxs # {#function_example_index_saxs}
200 <th>Function</th><th>Examples</th></tr>
202 <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>
204 # IMP.statistics # {#function_example_index_statistics}
206 <th>Function</th><th>Examples</th></tr>
208 <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>
static Residue setup_particle(kernel::Model *m, ParticleIndex pi, ResidueType t, int index, int insertion_code)
display::Geometries create_geometries(RMF::FileConstHandle parent)
AtomType add_atom_type(std::string name, Element e)
Create a new AtomType.
PartitionalClusteringWithCenter * create_lloyds_kmeans(Embedding *embedding, unsigned int k, unsigned int iterations)
Hierarchies get_leaves(Hierarchy h)
static State setup_particle(kernel::Model *m, ParticleIndex pi, unsigned int index)
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.
boost::graph DependencyGraph
A directed graph on the interactions between the various objects in the model.
atom::Hierarchies create_hierarchies(RMF::FileConstHandle fh, kernel::Model *m)
void write_pdb(const Selection &mhd, base::TextOutput out, unsigned int model=1)
static FloatKey get_mass_key()
void show_molecular_hierarchy(Hierarchy h)
Print out the molecular hierarchy.
static RigidBody setup_particle(kernel::Model *m, ParticleIndex pi, kernel::ParticleIndexesAdaptor ps)
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)
RMF::FrameID save_frame(RMF::FileHandle file, std::string name="")
void setup_as_approximation(kernel::Particle *h, const kernel::ParticlesTemp &other)
IMP::kernel::PairScore PairScore
void set_log_timer(bool tb)
Set whether log messages are tagged with the current log time.
static FloatKey get_radius_key()
Get the key for the radius.
SampledDensityMap * particles2density(const kernel::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.
static Atom setup_particle(kernel::Model *m, ParticleIndex pi, Atom other)
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.
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)
void set_log_level(LogLevel l)
Set the current global log level.
SubsetGraph get_junction_tree(const InteractionGraph &ig)
void add_restraints(RMF::FileHandle fh, const kernel::Restraints &hs)
void add_radii(Hierarchy d, const ForceFieldParameters *ffp=get_all_atom_CHARMM_parameters(), FloatKey radius_key=FloatKey("radius"))
void set_pair_score(PairScore *ps, Int atype, Int btype)
Set the PairScore to delegate to for a given pair of particle types.
std::string get_example_path(std::string file_name)
Return the path to installed example data for this module.
bool get_bool_flag(std::string name)
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
std::string create_temporary_file_name(std::string prefix="imp_temp", std::string suffix="")
Create a temporary file.
Bonds get_internal_bonds(Hierarchy mhd)
Get the bonds internal to this tree.
algebra::BoundingBoxD< 3 > get_bounding_box(const Hierarchy &h)
Get a bounding box for the Hierarchy.
static XYZ setup_particle(kernel::Model *m, ParticleIndex pi)
DependencyGraph get_pruned_dependency_graph(kernel::Model *m)
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 path to installed example data for this module.
void optimize_balls(const kernel::ParticlesTemp &ps, const kernel::RestraintsTemp &rs=kernel::RestraintsTemp(), const PairPredicates &excluded=PairPredicates(), const OptimizerStates &opt_states=OptimizerStates(), base::LogLevel ll=base::DEFAULT)
algebra::Vector3D get_centroid(const XYZs &ps)
Get the centroid.
HierarchyTree get_hierarchy_tree(Hierarchy h)
Get a graph for the passed Hierarchy.
kernel::Restraint * create_distance_restraint(const Selection &n0, const Selection &n1, double x0, double k, std::string name="Distance%1%")
FormFactorTable * get_default_form_factor_table()
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.
ScoreStates maintain invariants in the Model.
std::string get_example_path(std::string file_name)
Return the path to installed example data for this module.
DensityMap * read_map(std::string filename, MapReaderWriter *reader)
Read a density map from a file and return it.
InteractionGraph get_interaction_graph(ScoringFunctionAdaptor rs, const ParticleStatesTable *pst)
DependencyGraph get_dependency_graph(kernel::Model *m)
kernel::Restraint * create_connectivity_restraint(const Selections &s, double k, std::string name="Connectivity%1%")
Create a restraint connecting the selections.
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 add_to_log(LogLevel level, std::string to_write)
Write a string to the log, for Python.
static Reference setup_particle(kernel::Model *m, ParticleIndex pi, kernel::ParticleIndexAdaptor reference)
std::string get_example_path(std::string file_name)
Return the path to installed example data for this module.
Hierarchy read_pdb(base::TextInput input, kernel::Model *model, PDBSelector *selector=get_default_pdb_selector(), bool select_first_model=true)
MergeTree get_merge_tree(ScoringFunctionAdaptor input, const ParticleStatesTable *pst)
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)
Generates a Transformation2D object from a rotation around a point.
IMP::kernel::Container Container
std::string get_relative_path(std::string base, std::string relative)
Return a path to a file relative to another file.
static XYZR setup_particle(kernel::Model *m, ParticleIndex pi)
Rotation3D get_random_rotation_3d()
Pick a rotation at random from all possible rotations.
std::string get_string_flag(std::string name)
void add_hierarchy(RMF::FileHandle fh, atom::Hierarchy hs)
double get_distance(const Plane3D &pln, const Vector3D &p)
Return the distance between a plane and a point in 3D.
void add_bool_flag(std::string name, std::string description)
static Bonded setup_particle(kernel::Model *m, ParticleIndex pi)
void transform(Hierarchy h, const algebra::Transformation3D &tr)
Transform a hierarchy. This is aware of rigid bodies.
static Hierarchy setup_particle(kernel::Model *m, ParticleIndex pi, DecoratorTraits tr=get_default_decorator_traits())
static Molecule setup_particle(kernel::Model *m, ParticleIndex pi)
core::XYZR create_cover(const Selection &s, std::string name=std::string())
static double cross_correlation_coefficient(const DensityMap *grid1, const DensityMap *grid2, float grid2_voxel_data_threshold, bool allow_padding=false, FloatPair norm_factors=FloatPair(0., 0.))
Calculates the cross correlation coefficient between two maps.
static Hierarchy setup_particle(kernel::Model *m, kernel::ParticleIndex pi, kernel::ParticleIndexesAdaptor children=kernel::ParticleIndexesAdaptor())
static Cover setup_particle(kernel::Model *m, ParticleIndex pi, ParticleIndexesAdaptor members)
void add_string_flag(std::string name, std::string default_value, std::string description)
void write_map(DensityMap *m, std::string filename, MapReaderWriter *writer)
Write a density map to a file.
double get_distance(XYZ a, XYZ b)
Compute the distance between a pair of particles.
Hierarchies get_by_type(Hierarchy mhd, GetByType t)
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 Colored setup_particle(kernel::Model *m, ParticleIndex pi, Color color)
Images read_images(const Strings &names, const ImageReaderWriter *rw)
double get_rmsd(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2)
A restraint is a term in an IMP ScoringFunction.
Float compute_fitting_score(const kernel::ParticlesTemp &ps, DensityMap *em_map, FloatKey wei_key=atom::Mass::get_mass_key())
Compute fitting scores for a given set of rigid transformations.
XYZRs create_xyzr_particles(kernel::Model *m, unsigned int num, Float radius, Float box_side=10)
Create a set of particles with random coordinates.
VectorD< D > get_random_vector_in(const BoundingBoxD< D > &bb)
Generate a random vector in a box with uniform density.
std::string get_example_path(std::string file_name)
Return the path to installed example data for this module.
Color get_display_color(unsigned int i)
Hierarchy read_mol2(base::TextInput mol2_file, kernel::Model *model, Mol2Selector *mol2sel=nullptr)
Create a hierarchy from a Mol2 file.
void load_frame(RMF::FileConstHandle file, RMF::FrameID frame)
static Chain setup_particle(kernel::Model *m, ParticleIndex pi, std::string id)
DensityMap * create_density_map(const DensityMap *other)
create a copy of another map
int get_state_index(Hierarchy h)
Walk up the hierarchy to find the current state.
void write_help(std::ostream &out=std::cerr)
static const IMP::core::HierarchyTraits & get_traits()
Get the molecular hierarchy HierarchyTraits.
std::string get_example_path(std::string file_name)
Return the path to installed example data for this module.
void destroy(Hierarchy d)
Delete the Hierarchy.
void add_protein_ligand_score_data(Hierarchy h)
static Mass setup_particle(kernel::Model *m, ParticleIndex pi, Float mass)
base::Vector< VectorD< D > > get_grid_interior_cover_by_spacing(const BoundingBoxD< D > &bb, double s)
std::string get_example_path(std::string file_name)
Return the path to installed example data for this module.
algebra::Sphere3D get_enclosing_sphere(const XYZs &v)
Get a sphere enclosing the set of XYZRs.
Value get_linearly_interpolated(const GridD< D, Storage, Value, Embedding > &g, const VectorD< D > &pt)
double get_rmsd(const core::XYZs &s0, const core::XYZs &s1)
IMP::kernel::Particle Particle
std::string get_example_path(std::string file_name)
Return the path to installed example data for this module.
Residue get_residue(Atom d, bool nothrow=false)
Return the Residue containing this atom.
kernel::Restraint * create_excluded_volume_restraint(const Hierarchies &hs, double resolution=-1)
Rotation3D get_identity_rotation_3d()
Return a rotation that does not do anything.
Hierarchy create_protein(kernel::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.
Color get_gray_color(double f)
Return the a grayscale value for f.
void link_hierarchies(RMF::FileConstHandle fh, const atom::Hierarchies &hs)
static Diffusion setup_particle(kernel::Model *m, ParticleIndex pi, Float D)
void add_dope_score_data(atom::Hierarchy h)
base::Vector< VectorD< D > > get_vertices(const BoundingBoxD< D > &bb)
Return a list of the 8 bounding points for the bounding box.
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.
static Fragment setup_particle(kernel::Model *m, ParticleIndex pi)
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)
void load_particle_states(const Subset &s, const Assignment &ss, const ParticleStatesTable *pst)
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.
CHARMMParameters * get_all_atom_CHARMM_parameters()
PartitionalClustering * create_centrality_clustering(Metric *d, double far, int k)
FittingSolutions local_rigid_fitting(kernel::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.
void add_bonds(Hierarchy d, const ForceFieldParameters *ffp=get_all_atom_CHARMM_parameters())
static RigidBodyDiffusion setup_particle(kernel::Model *m, ParticleIndex pi)
std::string get_example_path(std::string file_name)
Return the path to installed example data for this module.