molsysmt.form.parmed_Structure package

Submodules

molsysmt.form.parmed_Structure.add module

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

molsysmt.form.parmed_Structure.append_structures module

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

molsysmt.form.parmed_Structure.attributes module

molsysmt.form.parmed_Structure.copy module

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

molsysmt.form.parmed_Structure.extract module

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

molsysmt.form.parmed_Structure.get module

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

molsysmt.form.parmed_Structure.get.get_bond_order_from_bond(item, indices='all', skip_digestion=False)

molsysmt.form.parmed_Structure.get.get_bond_type_from_bond(item, indices='all', skip_digestion=False)

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

molsysmt.form.parmed_Structure.get.get_bonded_atoms_from_bond(item, indices='all', skip_digestion=False)

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

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

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

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

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

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

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

molsysmt.form.parmed_Structure.get.get_chain_id_from_chain(item, indices='all', skip_digestion=False)

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

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

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

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

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

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

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

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

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

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

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

molsysmt.form.parmed_Structure.get.get_chain_name_from_chain(item, indices='all', skip_digestion=False)

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

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

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

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

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

molsysmt.form.parmed_Structure.get.get_chain_type_from_chain(item, indices='all', skip_digestion=False)

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

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

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

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

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

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

molsysmt.form.parmed_Structure.get.get_component_id_from_component(item, indices='all', skip_digestion=False)

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

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

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

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

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

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

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

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

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

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

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

molsysmt.form.parmed_Structure.get.get_component_name_from_component(item, indices='all', skip_digestion=False)

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

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

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

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

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

molsysmt.form.parmed_Structure.get.get_component_type_from_component(item, indices='all', skip_digestion=False)

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

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

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

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

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

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

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

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

molsysmt.form.parmed_Structure.get.get_entity_id_from_entity(item, indices='all', skip_digestion=False)

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

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

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

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

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

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

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

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

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

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

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

molsysmt.form.parmed_Structure.get.get_entity_name_from_entity(item, indices='all', skip_digestion=False)

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

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

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

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

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

molsysmt.form.parmed_Structure.get.get_entity_type_from_entity(item, indices='all', skip_digestion=False)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

molsysmt.form.parmed_Structure.get.get_molecule_id_from_molecule(item, indices='all', skip_digestion=False)

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

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

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

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

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

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

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

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

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

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

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

molsysmt.form.parmed_Structure.get.get_molecule_name_from_molecule(item, indices='all', skip_digestion=False)

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

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

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

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

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

molsysmt.form.parmed_Structure.get.get_molecule_type_from_molecule(item, indices='all', skip_digestion=False)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

molsysmt.form.parmed_Structure.has_attribute module

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

molsysmt.form.parmed_Structure.is_form module

molsysmt.form.parmed_Structure.is_form.is_form(item)

molsysmt.form.parmed_Structure.iterators module

class molsysmt.form.parmed_Structure.iterators.StructuresIterator(molecular_system, atom_indices='all', start=0, interval=1, stop=None, chunk=1, structure_indices=None, skip_digestion=False)

Bases: object

class molsysmt.form.parmed_Structure.iterators.TopologyIterator(molecular_system)

Bases: object

molsysmt.form.parmed_Structure.merge module

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

molsysmt.form.parmed_Structure.set module

molsysmt.form.parmed_Structure.to_file_cif module

molsysmt.form.parmed_Structure.to_file_cif.to_file_cif(item, atom_indices='all', structure_indices='all', output_filename=None, skip_digestion=False)

molsysmt.form.parmed_Structure.to_file_mol2 module

molsysmt.form.parmed_Structure.to_file_mol2.to_file_mol2(item, atom_indices='all', structure_indices='all', output_filename=None, skip_digestion=False)

molsysmt.form.parmed_Structure.to_file_pdb module

molsysmt.form.parmed_Structure.to_file_pdb.to_file_pdb(item, atom_indices='all', structure_indices='all', output_filename=None, skip_digestion=False)

molsysmt.form.parmed_Structure.to_file_psf module

molsysmt.form.parmed_Structure.to_file_psf.to_file_psf(item, atom_indices='all', structure_indices='all', output_filename=None, skip_digestion=False)

molsysmt.form.parmed_Structure.to_mdtraj_Topology module

molsysmt.form.parmed_Structure.to_mdtraj_Topology.to_mdtraj_Topology(item, atom_indices='all', skip_digestion=False)

molsysmt.form.parmed_Structure.to_mdtraj_Trajectory module

molsysmt.form.parmed_Structure.to_mdtraj_Trajectory.to_mdtraj_Trajectory(item, atom_indices='all', structure_indices='all', skip_digestion=False)

molsysmt.form.parmed_Structure.to_molsysmt_MolSys module

molsysmt.form.parmed_Structure.to_molsysmt_MolSys.to_molsysmt_MolSys(item, atom_indices='all', structure_indices='all', skip_digestion=False)

molsysmt.form.parmed_Structure.to_molsysmt_Structures module

molsysmt.form.parmed_Structure.to_molsysmt_Structures.to_molsysmt_Structures(item, atom_indices='all', structure_indices='all', skip_digestion=False)

molsysmt.form.parmed_Structure.to_molsysmt_Topology module

molsysmt.form.parmed_Structure.to_molsysmt_Topology.to_molsysmt_Topology(item, atom_indices='all', skip_digestion=False)

molsysmt.form.parmed_Structure.to_nglview_NGLWidget module

molsysmt.form.parmed_Structure.to_nglview_NGLWidget.to_nglview_NGLWidget(item, atom_indices='all', structure_indices='all', skip_digestion=False)

molsysmt.form.parmed_Structure.to_openmm_Modeller module

molsysmt.form.parmed_Structure.to_openmm_Modeller.to_openmm_Modeller(item, atom_indices='all', structure_indices='all', skip_digestion=False)

molsysmt.form.parmed_Structure.to_openmm_Topology module

molsysmt.form.parmed_Structure.to_openmm_Topology.to_openmm_Topology(item, atom_indices='all', skip_digestion=False)

molsysmt.form.parmed_Structure.to_parmed_GromacsTopologyFile module

molsysmt.form.parmed_Structure.to_parmed_GromacsTopologyFile.to_parmed_GromacsTopologyFile(item, atom_indices='all', skip_digestion=False)

molsysmt.form.parmed_Structure.to_parmed_Structure module

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

Module contents