molsysmt.form.openmm_CharmmCrdFile package

Submodules

molsysmt.form.openmm_CharmmCrdFile.add module

molsysmt.form.openmm_CharmmCrdFile.add.add(to_item, item, atom_indices='all', structure_indices='all', skip_digestion=False)

molsysmt.form.openmm_CharmmCrdFile.append_structures module

molsysmt.form.openmm_CharmmCrdFile.append_structures.append_structures(item, structure_id=None, time=None, coordinates=None, box=None, skip_digestion=False)

molsysmt.form.openmm_CharmmCrdFile.attributes module

molsysmt.form.openmm_CharmmCrdFile.copy module

molsysmt.form.openmm_CharmmCrdFile.copy.copy(item, skip_digestion=False)

molsysmt.form.openmm_CharmmCrdFile.extract module

molsysmt.form.openmm_CharmmCrdFile.extract.extract(item, atom_indices='all', structure_indices='all', copy_if_all=True, skip_digestion=False)

molsysmt.form.openmm_CharmmCrdFile.get module

molsysmt.form.openmm_CharmmCrdFile.get.get_alternate_location_from_system(item, structure_indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_atom_id_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_CharmmCrdFile.get.get_atom_id_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_atom_id_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_atom_id_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_atom_id_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_atom_id_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_atom_index_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_atom_index_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_atom_index_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_atom_index_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_atom_index_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_atom_index_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_atom_name_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_CharmmCrdFile.get.get_atom_name_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_atom_name_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_atom_name_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_atom_name_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_atom_name_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_atom_type_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_CharmmCrdFile.get.get_atom_type_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_atom_type_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_atom_type_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_atom_type_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_atom_type_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_b_factor_from_system(item, structure_indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_bond_index_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_bond_index_from_bond(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_bond_index_from_system(item)

molsysmt.form.openmm_CharmmCrdFile.get.get_bonded_atoms_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_bonded_atoms_from_system(item)

molsysmt.form.openmm_CharmmCrdFile.get.get_box_angles_from_system(item, structure_indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_box_from_system(item, structure_indices='all', skip_digestion=False)

molsysmt.form.openmm_CharmmCrdFile.get.get_box_lengths_from_system(item, structure_indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_box_shape_from_system(item, structure_indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_box_volume_from_system(item, structure_indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_chain_id_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_chain_id_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_chain_id_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_chain_id_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_chain_id_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_chain_index_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_CharmmCrdFile.get.get_chain_index_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_chain_index_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_chain_index_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_chain_index_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_chain_index_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_chain_name_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_chain_name_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_chain_name_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_chain_name_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_chain_name_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_chain_type_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_chain_type_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_chain_type_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_chain_type_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_chain_type_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_component_id_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_component_id_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_component_id_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_component_id_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_component_id_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_component_index_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_CharmmCrdFile.get.get_component_index_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_component_index_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_component_index_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_component_index_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_component_index_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_component_name_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_component_name_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_component_name_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_component_name_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_component_name_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_component_type_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_component_type_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_component_type_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_component_type_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_component_type_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_coordinates_from_atom(item, indices='all', structure_indices='all', skip_digestion=False)

molsysmt.form.openmm_CharmmCrdFile.get.get_coordinates_from_system(item, structure_indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_entity_id_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_entity_id_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_entity_id_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_entity_id_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_entity_id_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_entity_index_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_CharmmCrdFile.get.get_entity_index_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_entity_index_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_entity_index_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_entity_index_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_entity_index_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_entity_name_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_entity_name_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_entity_name_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_entity_name_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_entity_name_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_entity_type_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_entity_type_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_entity_type_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_entity_type_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_entity_type_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_formal_charge_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_formal_charge_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_formal_charge_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_formal_charge_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_formal_charge_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_formal_charge_from_system(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_group_id_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_group_id_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_group_id_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_group_id_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_group_id_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_CharmmCrdFile.get.get_group_id_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_group_index_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_CharmmCrdFile.get.get_group_index_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_group_index_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_group_index_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_group_index_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_group_index_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_group_name_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_group_name_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_group_name_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_group_name_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_group_name_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_CharmmCrdFile.get.get_group_name_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_group_type_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_group_type_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_group_type_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_group_type_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_group_type_from_group(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_CharmmCrdFile.get.get_group_type_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_inner_bond_index_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_inner_bond_index_from_system(item)

molsysmt.form.openmm_CharmmCrdFile.get.get_inner_bonded_atoms_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_CharmmCrdFile.get.get_inner_bonded_atoms_from_system(item)

molsysmt.form.openmm_CharmmCrdFile.get.get_molecule_id_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_molecule_id_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_molecule_id_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_molecule_id_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_molecule_id_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_molecule_index_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_CharmmCrdFile.get.get_molecule_index_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_molecule_index_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_molecule_index_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_molecule_index_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_molecule_index_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_molecule_name_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_molecule_name_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_molecule_name_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_molecule_name_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_molecule_name_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_molecule_type_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_molecule_type_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_molecule_type_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_molecule_type_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_molecule_type_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_amino_acids_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_amino_acids_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_amino_acids_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_amino_acids_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_amino_acids_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_amino_acids_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_amino_acids_from_system(item)

molsysmt.form.openmm_CharmmCrdFile.get.get_n_atoms_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_atoms_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_atoms_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_atoms_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_atoms_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_atoms_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_atoms_from_system(item, skip_digestion=False)

molsysmt.form.openmm_CharmmCrdFile.get.get_n_bonds_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_bonds_from_bond(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_bonds_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_bonds_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_bonds_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_bonds_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_bonds_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_bonds_from_system(item, skip_digestion=False)

molsysmt.form.openmm_CharmmCrdFile.get.get_n_chains_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_chains_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_chains_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_chains_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_chains_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_chains_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_chains_from_system(item, skip_digestion=False)

molsysmt.form.openmm_CharmmCrdFile.get.get_n_components_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_components_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_components_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_components_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_components_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_components_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_components_from_system(item, skip_digestion=False)

molsysmt.form.openmm_CharmmCrdFile.get.get_n_dnas_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_dnas_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_dnas_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_dnas_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_dnas_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_dnas_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_dnas_from_system(item)

molsysmt.form.openmm_CharmmCrdFile.get.get_n_entities_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_entities_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_entities_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_entities_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_entities_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_entities_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_entities_from_system(item, skip_digestion=False)

molsysmt.form.openmm_CharmmCrdFile.get.get_n_groups_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_groups_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_groups_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_groups_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_groups_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_groups_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_groups_from_system(item, skip_digestion=False)

molsysmt.form.openmm_CharmmCrdFile.get.get_n_inner_bonds_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.openmm_CharmmCrdFile.get.get_n_inner_bonds_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_inner_bonds_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_inner_bonds_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_inner_bonds_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_inner_bonds_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_ions_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_ions_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_ions_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_ions_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_ions_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_ions_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_ions_from_system(item)

molsysmt.form.openmm_CharmmCrdFile.get.get_n_lipids_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_lipids_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_lipids_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_lipids_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_lipids_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_lipids_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_lipids_from_system(item)

molsysmt.form.openmm_CharmmCrdFile.get.get_n_molecules_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_molecules_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_molecules_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_molecules_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_molecules_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_molecules_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_molecules_from_system(item, skip_digestion=False)

molsysmt.form.openmm_CharmmCrdFile.get.get_n_nucleotides_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_nucleotides_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_nucleotides_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_nucleotides_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_nucleotides_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_nucleotides_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_nucleotides_from_system(item)

molsysmt.form.openmm_CharmmCrdFile.get.get_n_peptides_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_peptides_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_peptides_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_peptides_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_peptides_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_peptides_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_peptides_from_system(item)

molsysmt.form.openmm_CharmmCrdFile.get.get_n_polysaccharides_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_polysaccharides_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_polysaccharides_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_polysaccharides_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_polysaccharides_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_polysaccharides_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_polysaccharides_from_system(item)

molsysmt.form.openmm_CharmmCrdFile.get.get_n_proteins_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_proteins_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_proteins_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_proteins_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_proteins_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_proteins_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_proteins_from_system(item)

molsysmt.form.openmm_CharmmCrdFile.get.get_n_rnas_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_rnas_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_rnas_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_rnas_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_rnas_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_rnas_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_rnas_from_system(item)

molsysmt.form.openmm_CharmmCrdFile.get.get_n_saccharides_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_saccharides_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_saccharides_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_saccharides_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_saccharides_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_saccharides_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_saccharides_from_system(item)

molsysmt.form.openmm_CharmmCrdFile.get.get_n_small_molecules_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_small_molecules_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_small_molecules_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_small_molecules_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_small_molecules_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_small_molecules_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_small_molecules_from_system(item)

molsysmt.form.openmm_CharmmCrdFile.get.get_n_structures_from_system(item, structure_indices='all', skip_digestion=False)

molsysmt.form.openmm_CharmmCrdFile.get.get_n_waters_from_atom(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_waters_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_waters_from_component(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_waters_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_waters_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_waters_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_n_waters_from_system(item)

molsysmt.form.openmm_CharmmCrdFile.get.get_occupancy_from_system(item, structure_indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_partial_charge_from_chain(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_partial_charge_from_entity(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_partial_charge_from_group(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_partial_charge_from_molecule(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_partial_charge_from_system(item, indices='all')

molsysmt.form.openmm_CharmmCrdFile.get.get_structure_id_from_system(item, structure_indices='all', skip_digestion=False)

molsysmt.form.openmm_CharmmCrdFile.get.get_time_from_system(item, structure_indices='all', skip_digestion=False)

molsysmt.form.openmm_CharmmCrdFile.get.get_velocities_from_system(item, structure_indices='all')

molsysmt.form.openmm_CharmmCrdFile.has_attribute module

molsysmt.form.openmm_CharmmCrdFile.has_attribute.has_attribute(molecular_system, attribute, include_none=False, skip_digestion=False)

molsysmt.form.openmm_CharmmCrdFile.is_form module

molsysmt.form.openmm_CharmmCrdFile.is_form.is_form(item)

molsysmt.form.openmm_CharmmCrdFile.iterators module

class molsysmt.form.openmm_CharmmCrdFile.iterators.StructuresIterator(molecular_system, atom_indices='all', start=0, step=1, stop=None, chunk=1, structure_indices=None, output_type='values', skip_digestion=False)

Bases: object

class molsysmt.form.openmm_CharmmCrdFile.iterators.TopologyIterator(molecular_system, element='atom', indices='all', start=0, step=1, stop=None, chunk=1, output_type='values', skip_digestion=False)

Bases: object

molsysmt.form.openmm_CharmmCrdFile.merge module

molsysmt.form.openmm_CharmmCrdFile.merge.merge(items, atom_indices='all', structure_indices='all', skip_digestion=False)

molsysmt.form.openmm_CharmmCrdFile.set module

molsysmt.form.openmm_CharmmCrdFile.to_openmm_CharmmCrdFile module

molsysmt.form.openmm_CharmmCrdFile.to_openmm_CharmmCrdFile.to_openmm_CharmmCrdFile(item, atom_indices='all', structure_indices='all', copy_if_all=True, skip_digestion=False)

Module contents