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, core/connectivity_restraint.py, display/displaying_ensembles.py, domino/restraint_cache.py, kernel/chain.py, kernel/dependency_graph.py, kernel/nup84.py, misc/decay.py, multiresolution.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::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, multiresolution.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, 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/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::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/score_protein_with_ligand.py, multistate.py |
IMP::atom::get_heavy_atom_CHARMM_parameters() | atom/charmm_forcefield.py, atom/charmm_forcefield_verbose.py |
IMP::atom::get_hierarchy_tree() | atom/edit_molecular_hierarchy.py, atom/molecular_hierarchy.py |
IMP::atom::get_leaves() | display/displaying_ensembles.py, em2d/clustering_of_pdb_models.py, em2d/collision_cross_section.py, kernel/dependency_graph.py, kernel/nup84.py, multiresolution.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/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, kernel/nup84.py, multiresolution.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() | multiresolution.py, 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 |