molsysmt.form.file_mmtf package#

Submodules#

molsysmt.form.file_mmtf.add module#

molsysmt.form.file_mmtf.add.add(to_item, item, atom_indices='all', structure_indices='all', skip_digestion=False)[source]#

molsysmt.form.file_mmtf.append_structures module#

molsysmt.form.file_mmtf.append_structures.append_structures(item, structure_id=None, time=None, coordinates=None, box=None, skip_digestion=False)[source]#

molsysmt.form.file_mmtf.attributes module#

molsysmt.form.file_mmtf.copy module#

molsysmt.form.file_mmtf.copy.copy(item, output_filename=None, skip_digestion=False)[source]#

molsysmt.form.file_mmtf.download module#

molsysmt.form.file_mmtf.download.download()[source]#

molsysmt.form.file_mmtf.extract module#

molsysmt.form.file_mmtf.extract.extract(item, atom_indices='all', structure_indices='all', output_filename=None, copy_if_all=True, skip_digestion=False)[source]#

molsysmt.form.file_mmtf.get module#

molsysmt.form.file_mmtf.get.get_alternate_location_from_atom(item, indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_alternate_location_from_system(item, structure_indices='all')#
molsysmt.form.file_mmtf.get.get_atom_id_from_atom(item, indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_atom_id_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_atom_id_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_atom_id_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_atom_id_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_atom_id_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_atom_index_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_atom_index_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_atom_index_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_atom_index_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_atom_index_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_atom_index_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_atom_name_from_atom(item, indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_atom_name_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_atom_name_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_atom_name_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_atom_name_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_atom_name_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_atom_type_from_atom(item, indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_atom_type_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_atom_type_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_atom_type_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_atom_type_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_atom_type_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_b_factor_from_atom(item, indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_b_factor_from_system(item, structure_indices='all')#
molsysmt.form.file_mmtf.get.get_bioassembly_from_system(item, skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_bond_index_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_bond_index_from_bond(item, indices='all')#
molsysmt.form.file_mmtf.get.get_bond_index_from_system(item)#
molsysmt.form.file_mmtf.get.get_bond_order_from_bond(item, indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_bond_type_from_bond(item, indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_bonded_atoms_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_bonded_atoms_from_bond(item, indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_bonded_atoms_from_system(item)#
molsysmt.form.file_mmtf.get.get_box_angles_from_system(item, structure_indices='all')#
molsysmt.form.file_mmtf.get.get_box_from_system(item, structure_indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_box_lengths_from_system(item, structure_indices='all')#
molsysmt.form.file_mmtf.get.get_box_shape_from_system(item, structure_indices='all')#
molsysmt.form.file_mmtf.get.get_box_volume_from_system(item, structure_indices='all')#
molsysmt.form.file_mmtf.get.get_chain_id_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_chain_id_from_chain(item, indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_chain_id_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_chain_id_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_chain_id_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_chain_id_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_chain_index_from_atom(item, indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_chain_index_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_chain_index_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_chain_index_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_chain_index_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_chain_index_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_chain_name_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_chain_name_from_chain(item, indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_chain_name_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_chain_name_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_chain_name_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_chain_name_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_chain_type_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_chain_type_from_chain(item, indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_chain_type_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_chain_type_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_chain_type_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_chain_type_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_component_id_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_component_id_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_component_id_from_component(item, indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_component_id_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_component_id_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_component_id_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_component_index_from_atom(item, indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_component_index_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_component_index_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_component_index_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_component_index_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_component_index_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_component_name_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_component_name_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_component_name_from_component(item, indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_component_name_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_component_name_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_component_name_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_component_type_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_component_type_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_component_type_from_component(item, indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_component_type_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_component_type_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_component_type_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_coordinates_from_atom(item, indices='all', structure_indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_coordinates_from_system(item, structure_indices='all')#
molsysmt.form.file_mmtf.get.get_entity_id_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_entity_id_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_entity_id_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_entity_id_from_entity(item, indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_entity_id_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_entity_id_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_entity_index_from_atom(item, indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_entity_index_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_entity_index_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_entity_index_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_entity_index_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_entity_index_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_entity_name_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_entity_name_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_entity_name_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_entity_name_from_entity(item, indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_entity_name_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_entity_name_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_entity_type_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_entity_type_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_entity_type_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_entity_type_from_entity(item, indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_entity_type_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_entity_type_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_formal_charge_from_atom(item, indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_formal_charge_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_formal_charge_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_formal_charge_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_formal_charge_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_formal_charge_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_formal_charge_from_system(item, indices='all')#
molsysmt.form.file_mmtf.get.get_group_id_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_group_id_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_group_id_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_group_id_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_group_id_from_group(item, indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_group_id_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_group_index_from_atom(item, indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_group_index_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_group_index_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_group_index_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_group_index_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_group_index_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_group_name_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_group_name_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_group_name_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_group_name_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_group_name_from_group(item, indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_group_name_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_group_type_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_group_type_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_group_type_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_group_type_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_group_type_from_group(item, indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_group_type_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_inner_bond_index_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_inner_bond_index_from_system(item)#
molsysmt.form.file_mmtf.get.get_inner_bonded_atoms_from_atom(item, indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_inner_bonded_atoms_from_system(item)#
molsysmt.form.file_mmtf.get.get_molecule_id_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_molecule_id_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_molecule_id_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_molecule_id_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_molecule_id_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_molecule_id_from_molecule(item, indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_molecule_index_from_atom(item, indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_molecule_index_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_molecule_index_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_molecule_index_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_molecule_index_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_molecule_index_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_molecule_name_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_molecule_name_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_molecule_name_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_molecule_name_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_molecule_name_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_molecule_name_from_molecule(item, indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_molecule_type_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_molecule_type_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_molecule_type_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_molecule_type_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_molecule_type_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_molecule_type_from_molecule(item, indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_n_amino_acids_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_amino_acids_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_amino_acids_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_amino_acids_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_amino_acids_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_amino_acids_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_amino_acids_from_system(item)#
molsysmt.form.file_mmtf.get.get_n_atoms_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_atoms_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_atoms_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_atoms_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_atoms_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_atoms_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_atoms_from_system(item, skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_n_bioassemblies_from_system(item, skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_n_bonds_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_bonds_from_bond(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_bonds_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_bonds_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_bonds_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_bonds_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_bonds_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_bonds_from_system(item, skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_n_chains_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_chains_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_chains_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_chains_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_chains_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_chains_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_chains_from_system(item, skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_n_components_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_components_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_components_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_components_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_components_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_components_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_components_from_system(item, skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_n_dnas_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_dnas_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_dnas_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_dnas_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_dnas_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_dnas_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_dnas_from_system(item)#
molsysmt.form.file_mmtf.get.get_n_entities_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_entities_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_entities_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_entities_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_entities_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_entities_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_entities_from_system(item, skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_n_groups_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_groups_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_groups_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_groups_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_groups_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_groups_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_groups_from_system(item, skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_n_inner_bonds_from_atom(item, indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_n_inner_bonds_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_inner_bonds_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_inner_bonds_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_inner_bonds_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_inner_bonds_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_ions_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_ions_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_ions_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_ions_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_ions_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_ions_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_ions_from_system(item)#
molsysmt.form.file_mmtf.get.get_n_lipids_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_lipids_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_lipids_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_lipids_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_lipids_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_lipids_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_lipids_from_system(item)#
molsysmt.form.file_mmtf.get.get_n_molecules_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_molecules_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_molecules_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_molecules_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_molecules_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_molecules_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_molecules_from_system(item, skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_n_nucleotides_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_nucleotides_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_nucleotides_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_nucleotides_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_nucleotides_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_nucleotides_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_nucleotides_from_system(item)#
molsysmt.form.file_mmtf.get.get_n_peptides_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_peptides_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_peptides_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_peptides_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_peptides_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_peptides_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_peptides_from_system(item)#
molsysmt.form.file_mmtf.get.get_n_polysaccharides_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_polysaccharides_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_polysaccharides_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_polysaccharides_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_polysaccharides_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_polysaccharides_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_polysaccharides_from_system(item)#
molsysmt.form.file_mmtf.get.get_n_proteins_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_proteins_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_proteins_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_proteins_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_proteins_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_proteins_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_proteins_from_system(item)#
molsysmt.form.file_mmtf.get.get_n_rnas_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_rnas_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_rnas_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_rnas_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_rnas_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_rnas_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_rnas_from_system(item)#
molsysmt.form.file_mmtf.get.get_n_saccharides_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_saccharides_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_saccharides_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_saccharides_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_saccharides_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_saccharides_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_saccharides_from_system(item)#
molsysmt.form.file_mmtf.get.get_n_small_molecules_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_small_molecules_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_small_molecules_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_small_molecules_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_small_molecules_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_small_molecules_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_small_molecules_from_system(item)#
molsysmt.form.file_mmtf.get.get_n_structures_from_system(item, structure_indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_n_waters_from_atom(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_waters_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_waters_from_component(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_waters_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_waters_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_waters_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_n_waters_from_system(item)#
molsysmt.form.file_mmtf.get.get_occupancy_from_system(item, structure_indices='all')#
molsysmt.form.file_mmtf.get.get_partial_charge_from_atom(item, indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_partial_charge_from_chain(item, indices='all')#
molsysmt.form.file_mmtf.get.get_partial_charge_from_entity(item, indices='all')#
molsysmt.form.file_mmtf.get.get_partial_charge_from_group(item, indices='all')#
molsysmt.form.file_mmtf.get.get_partial_charge_from_molecule(item, indices='all')#
molsysmt.form.file_mmtf.get.get_partial_charge_from_system(item, indices='all')#
molsysmt.form.file_mmtf.get.get_structure_id_from_system(item, structure_indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_time_from_system(item, structure_indices='all', skip_digestion=False)[source]#
molsysmt.form.file_mmtf.get.get_velocities_from_system(item, structure_indices='all')#

molsysmt.form.file_mmtf.has_attribute module#

molsysmt.form.file_mmtf.has_attribute.has_attribute(molecular_system, attribute, include_none=False, skip_digestion=False)[source]#

molsysmt.form.file_mmtf.is_form module#

molsysmt.form.file_mmtf.is_form.is_form(item)[source]#

molsysmt.form.file_mmtf.iterators module#

class molsysmt.form.file_mmtf.iterators.StructuresIterator(molecular_system, atom_indices='all', start=0, step=1, stop=None, chunk=1, structure_indices=None, output_type='values', skip_digestion=False, **kwargs)[source]#

Bases: StructuresIterator

class molsysmt.form.file_mmtf.iterators.TopologyIterator(molecular_system, element='atom', indices='all', start=0, step=1, stop=None, chunk=1, output_type='values', skip_digestion=False, **kwargs)[source]#

Bases: TopologyIterator

molsysmt.form.file_mmtf.merge module#

molsysmt.form.file_mmtf.merge.merge(to_item, item, atom_indices='all', structure_indices='all', skip_digestion=False)[source]#

molsysmt.form.file_mmtf.set module#

molsysmt.form.file_mmtf.to_MDAnalysis_Universe module#

molsysmt.form.file_mmtf.to_MDAnalysis_Universe.to_MDAnalysis_Universe(item, atom_indices='all', structure_indices='all', skip_digestion=False)[source]#

molsysmt.form.file_mmtf.to_file_mmtf module#

molsysmt.form.file_mmtf.to_file_mmtf.to_file_mmtf(item, atom_indices='all', structure_indices='all', output_name=None, copy_if_all=True, skip_digestion=False)[source]#

molsysmt.form.file_mmtf.to_file_pdb module#

molsysmt.form.file_mmtf.to_file_pdb.to_file_pdb(item, atom_indices='all', structure_indices='all', output_filename=None, skip_digestion=False)[source]#

molsysmt.form.file_mmtf.to_mdtraj module#

mmtf.py: Used for loading mmtf files.

class molsysmt.form.file_mmtf.to_mdtraj.MMTFTrajectoryFile(filename, mode='r', force_overwrite=True, standard_names=True)[source]#

Bases: object

Interface for reading and writing to MMTF files.

Parameters:

  • filename (str) – The filename to open. A path to a file on disk.

  • mode ({'r', 'w'}) – The mode in which to open the file, either ‘r’ for read or ‘w’ for write.

  • force_overwrite (bool) – If opened in write mode, and a file by the name of filename already exists on disk, should we overwrite it?

__enter__()[source]#

Support the context manager protocol

__exit__(*exc_info)[source]#

Support the context manager protocol

close()[source]#

Close the file

property closed#

Whether the file is closed.

distance_unit = 'angstroms'#
static parse_residue_atoms(residue, dictionary)[source]#
property positions#

Returns the cartesian coordinates of the atoms if mode=’r’. If mode=’w’ returns none.

property topology#

Returns the topology of the mmtf file if mode=’r’. If mode=’w’ returns none.

property unit_cell_angles#

Returns the unit cell angles of the mmtf file if mode=’r’. If mode=’w’ returns none.

property unit_cell_lengths#

Returns the unit cell lengths of the mmtf file if mode=’r’. If mode=’w’ returns none.

write(positions, topology, unit_cell_lengths=None, unit_cell_angles=None, b_factors=None)[source]#

Write a mmtf file to disk

Parameters:

  • positions (array_like) – The list of atomic positions to write.

  • topology (mdtraj.Topology) – The Topology defining the model to write.

  • unit_cell_lengths ({tuple, None}) – Lengths of the three unit cell vectors, or None for a non-periodic system

  • unit_cell_angles ({tuple, None}) – Angles between the three unit cell vectors, or None for a non-periodic system

  • b_factors (array_like, default=None, shape=(n_atoms,)) – Save bfactors. Should contain a single number for each atom in the topology

class molsysmt.form.file_mmtf.to_mdtraj.TrajMMTFEncoder[source]#

Bases: MMTFEncoder

An MMTF encoder with a custom finalize structure method, and a method to write temporary files.

finalize_structure()[source]#

Cleanup the structure

write_temp_file()[source]#

Writes a temporary file.

molsysmt.form.file_mmtf.to_mdtraj.load_mmtf(filename, stride=None, atom_indices=None, frame=None)[source]#

Load an MMTF file.

Parameters:

  • filename (str) – Path to the MMTF file on disk.

  • stride (int, default=None) – Only read every stride-th model from the file

  • atom_indices (array_like, optional) – If not none, then read only a subset of the atoms coordinates from the file. These indices are zero-based.

  • frame (int, optional) – Use this option to load only a single model from a MMTF file on disk. If frame is None, the default, all models in file will be loaded. If supplied, stride will be ignored.

molsysmt.form.file_mmtf.to_mmtf_MMTFDecoder module#

molsysmt.form.file_mmtf.to_mmtf_MMTFDecoder.to_mmtf_MMTFDecoder(item, atom_indices='all', structure_indices='all', skip_digestion=False)[source]#

molsysmt.form.file_mmtf.to_molsysmt_MolSys module#

molsysmt.form.file_mmtf.to_molsysmt_MolSys.to_molsysmt_MolSys(item, atom_indices='all', structure_indices='all', skip_digestion=False)[source]#

molsysmt.form.file_mmtf.to_molsysmt_Structures module#

molsysmt.form.file_mmtf.to_molsysmt_Structures.to_molsysmt_Structures(item, atom_indices='all', structure_indices='all', skip_digestion=False)[source]#

molsysmt.form.file_mmtf.to_molsysmt_Topology module#

molsysmt.form.file_mmtf.to_molsysmt_Topology.to_molsysmt_Topology(item, atom_indices='all', skip_digestion=False)[source]#

molsysmt.form.file_mmtf.to_openmm_Topology module#

molsysmt.form.file_mmtf.to_openmm_Topology.to_openmm_Topology(item, atom_indices='all', structure_indices='all', skip_digestion=False)[source]#

molsysmt.form.file_mmtf.to_string_amino_acids_1 module#

molsysmt.form.file_mmtf.to_string_amino_acids_1.to_string_amino_acids_1(item, group_indices='all', skip_digestion=False)[source]#

molsysmt.form.file_mmtf.to_string_amino_acids_3 module#

molsysmt.form.file_mmtf.to_string_amino_acids_3.to_string_amino_acids_3(item, group_indices='all', skip_digestion=False)[source]#

molsysmt.form.file_mmtf.to_string_pdb_text module#

molsysmt.form.file_mmtf.to_string_pdb_text.to_string_pdb_text(item, atom_indices='all', structure_indices='all', skip_digestion=False)[source]#

Module contents#

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