molsysmt.form.file_pdb package#

Submodules#

molsysmt.form.file_pdb.add module#

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

molsysmt.form.file_pdb.append_structures module#

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

molsysmt.form.file_pdb.attributes module#

molsysmt.form.file_pdb.copy module#

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

molsysmt.form.file_pdb.download module#

molsysmt.form.file_pdb.download.download(pdb_id=None, output_filename=None, tempfile=False, wwPDB_Partner='RCSB PDB', skip_digestion=False)[source]#

molsysmt.form.file_pdb.extract module#

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

molsysmt.form.file_pdb.get module#

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

molsysmt.form.file_pdb.has_atoms_with_alternate_locations module#

molsysmt.form.file_pdb.has_atoms_with_alternate_locations.has_atoms_with_alternate_locations(filename)[source]#

molsysmt.form.file_pdb.has_attribute module#

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

molsysmt.form.file_pdb.is_form module#

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

molsysmt.form.file_pdb.iterators module#

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

Bases: object

class molsysmt.form.file_pdb.iterators.TopologyIterator(molecular_system)[source]#

Bases: object

molsysmt.form.file_pdb.merge module#

molsysmt.form.file_pdb.merge.merge(items, atom_indices='all', structure_indices='all', skip_digestion=False)[source]#

molsysmt.form.file_pdb.replace_HETATM_by_ATOM_in_terminal_cappings module#

molsysmt.form.file_pdb.replace_HETATM_by_ATOM_in_terminal_cappings.replace_HETATM_by_ATOM_in_terminal_cappings(molecular_system)[source]#

molsysmt.form.file_pdb.set module#

molsysmt.form.file_pdb.to_MDAnalysis_Topology module#

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

molsysmt.form.file_pdb.to_MDAnalysis_Universe module#

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

molsysmt.form.file_pdb.to_MDAnalysis_topology_PDBParser module#

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

molsysmt.form.file_pdb.to_file_mol2 module#

molsysmt.form.file_pdb.to_file_mol2.to_file_mol2(item, atom_indices='all', structure_indices='all', output_filename=None, skip_digestion=False)[source]#

molsysmt.form.file_pdb.to_file_pdb module#

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

molsysmt.form.file_pdb.to_mdtraj_PDBTrajectoryFile module#

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

molsysmt.form.file_pdb.to_mdtraj_Topology module#

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

molsysmt.form.file_pdb.to_mdtraj_Trajectory module#

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

molsysmt.form.file_pdb.to_molsysmt_MolSys module#

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

molsysmt.form.file_pdb.to_molsysmt_PDBFileHandler module#

molsysmt.form.file_pdb.to_molsysmt_PDBFileHandler.to_molsysmt_PDBFileHandler(item, skip_digestion=False)[source]#

molsysmt.form.file_pdb.to_molsysmt_Structures module#

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

molsysmt.form.file_pdb.to_molsysmt_Topology module#

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

molsysmt.form.file_pdb.to_nglview_NGLWidget module#

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

molsysmt.form.file_pdb.to_openmm_Modeller module#

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

molsysmt.form.file_pdb.to_openmm_PDBFile module#

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

molsysmt.form.file_pdb.to_openmm_Simulation module#

molsysmt.form.file_pdb.to_openmm_Simulation.to_openmm_Simulation(item, atom_indices='all', structure_indices='all', forcefield=None, non_bonded_method='no_cutoff', non_bonded_cutoff='1.0 nm', constraints=None, rigid_water=True, remove_cm_motion=True, hydrogen_mass=None, switch_distance=None, flexible_constraints=False, integrator='Langevin', temperature='300.0 K', collisions_rate='1.0 1/ps', integration_timestep='2.0 fs', platform='CUDA', skip_digestion=False)[source]#

molsysmt.form.file_pdb.to_openmm_System module#

molsysmt.form.file_pdb.to_openmm_System.to_openmm_System(item, atom_indices='all', structure_indices='all', forcefield=None, non_bonded_method='no_cutoff', non_bonded_cutoff='1.0 nm', constraints=None, rigid_water=True, remove_cm_motion=True, hydrogen_mass=None, switch_distance=None, flexible_constraints=False, skip_digestion=False)[source]#

molsysmt.form.file_pdb.to_openmm_Topology module#

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

molsysmt.form.file_pdb.to_parmed_Structure module#

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

molsysmt.form.file_pdb.to_pdbfixer_PDBFixer module#

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

molsysmt.form.file_pdb.to_pytraj_Topology module#

molsysmt.form.file_pdb.to_pytraj_Topology.to_pytraj_Topology(item, atom_indices='all', max_bond_length=None, skip_digestion=False)[source]#

molsysmt.form.file_pdb.to_pytraj_Trajectory module#

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

molsysmt.form.file_pdb.to_string_pdb_text module#

molsysmt.form.file_pdb.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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