Index

A

add_atom_to_non_polymer() (in module atomium.mmcif) (in module atomium.pdb) add_atom_to_polymer() (in module atomium.mmcif) (in module atomium.pdb) add_chain_to_model() (in module atomium.mmtf) add_het_to_dict() (in module atomium.mmtf) add_het_to_groups() (in module atomium.mmtf) add_secondary_structure_to_polymers() (in module atomium.mmcif) add_sequences_to_polymers() (in module atomium.mmcif) add_ss_to_chain() (in module atomium.mmtf) angle() (atomium.structures.Atom method) anisotropy (atomium.structures.Atom property) assemblies (atomium.data.File property) assembly_lines_to_assembly_dict() (in module atomium.pdb) assign_metrics_to_assembly() (in module atomium.mmcif) assign_transformations_to_assembly() (in module atomium.mmcif) Atom (class in atomium.structures) atom_dict_to_atom() (in module atomium.data) atom_dict_to_atom_dict() (in module atomium.mmcif) atom_line_to_dict() (in module atomium.pdb) atom_to_anisou_line() (in module atomium.pdb) atom_to_atom_line() (in module atomium.mmcif) (in module atomium.pdb) atomium.base module

atomium.data module atomium.mmcif module atomium.mmtf module atomium.pdb module atomium.structures module atomium.utilities module atoms() (atomium.structures.Het method) (atomium.structures.Ligand method) (atomium.structures.Residue method) atoms_in_sphere() (atomium.structures.AtomStructure method) (atomium.structures.Chain method) (atomium.structures.Het method) (atomium.structures.Ligand method) (atomium.structures.Model method) (atomium.structures.Molecule method) (atomium.structures.Residue method) AtomStructure (class in atomium.structures) attribute_matches_value() (in module atomium.base) authors (atomium.data.File property)

B

bond() (atomium.structures.Atom method)

bonded_atoms (atomium.structures.Atom property) bvalue (atomium.structures.Atom property)

C

center_of_mass (atomium.structures.AtomStructure property) (atomium.structures.Chain property) (atomium.structures.Het property) (atomium.structures.Ligand property) (atomium.structures.Model property) (atomium.structures.Molecule property) (atomium.structures.Residue property) chain (atomium.structures.Atom property) (atomium.structures.Het property) (atomium.structures.Ligand property) (atomium.structures.Residue property) Chain (class in atomium.structures) charge (atomium.structures.Atom property) (atomium.structures.AtomStructure property) (atomium.structures.Chain property) (atomium.structures.Het property) (atomium.structures.Ligand property) (atomium.structures.Model property) (atomium.structures.Molecule property) (atomium.structures.Residue property) check_ids() (atomium.structures.AtomStructure method) (atomium.structures.Chain method) (atomium.structures.Het method) (atomium.structures.Ligand method) (atomium.structures.Model method) (atomium.structures.Molecule method) (atomium.structures.Residue method)

classification (atomium.data.File property) code (atomium.data.File property) (atomium.structures.Residue property) consolidate_strings() (in module atomium.mmcif) copy() (atomium.structures.Atom method) (atomium.structures.Chain method) (atomium.structures.Ligand method) (atomium.structures.Residue method) covalent_radius (atomium.structures.Atom property) create_chains() (in module atomium.data) create_entities() (in module atomium.mmcif) create_grid() (atomium.structures.AtomStructure method) (atomium.structures.Chain method) (atomium.structures.Het method) (atomium.structures.Ligand method) (atomium.structures.Model method) (atomium.structures.Molecule method) (atomium.structures.Residue method) create_het() (in module atomium.data) create_ligands() (in module atomium.data)

D

data_dict_to_file() (in module atomium.data) decode_dict() (in module atomium.mmtf) dehydrate() (atomium.structures.Model method)

delta_decode() (in module atomium.mmtf) deposition_date (atomium.data.File property) distance_to() (atomium.structures.Atom method)

E

element (atomium.structures.Atom property) expression_system (atomium.data.File property) extract_assembly_remark() (in module atomium.pdb) extract_authors() (in module atomium.pdb) extract_crystallography() (in module atomium.pdb) extract_header() (in module atomium.pdb)

extract_keywords() (in module atomium.pdb) extract_missing_residues() (in module atomium.pdb) extract_resolution_remark() (in module atomium.pdb) extract_rvalue_remark() (in module atomium.pdb) extract_source() (in module atomium.pdb) extract_technique() (in module atomium.pdb) extract_title() (in module atomium.pdb)

F

fetch() (in module atomium.utilities) fetch_over_ssh() (in module atomium.utilities) file (atomium.structures.Model property) File (class in atomium.data) filetype (atomium.data.File property) filter_objects() (in module atomium.base) formula (atomium.structures.AtomStructure property) (atomium.structures.Chain property) (atomium.structures.Het property) (atomium.structures.Ligand property) (atomium.structures.Model property) (atomium.structures.Molecule property) (atomium.structures.Residue property)

full_name (atomium.structures.Het property) (atomium.structures.Ligand property) (atomium.structures.Residue property)

G

generate_assembly() (atomium.data.File method) get() (atomium.base.StructureSet method) get_atom_name() (in module atomium.mmcif) get_atoms_list() (in module atomium.mmtf) get_chain_ids_and_names() (in module atomium.mmtf) get_chains_list() (in module atomium.mmtf) get_entity_list() (in module atomium.mmtf) get_full_names() (in module atomium.pdb) get_group_definitions_list() (in module atomium.mmtf) get_groups() (in module atomium.mmtf)

get_groups_list() (in module atomium.mmtf) get_groups_per_chain() (in module atomium.mmtf) get_last_ter_line() (in module atomium.pdb) get_object_attribute_from_filter() (in module atomium.base) get_object_from_filter() (in module atomium.base) get_operation_id_groups() (in module atomium.mmcif) get_parse_functions() (in module atomium.utilities) get_structure_from_atom() (in module atomium.mmcif) get_structures() (in module atomium.mmtf) getone() (in module atomium.base)

H

helices (atomium.structures.Chain property) helix (atomium.structures.Residue property)

het (atomium.structures.Atom property) Het (class in atomium.structures)

I

id (atomium.structures.Atom property) (atomium.structures.AtomStructure property) (atomium.structures.Chain property) (atomium.structures.Het property) (atomium.structures.Ligand property) (atomium.structures.Model property) (atomium.structures.Molecule property) (atomium.structures.Residue property)

id_from_line() (in module atomium.pdb) ids (atomium.base.StructureSet property) internal_id (atomium.structures.Chain property) (atomium.structures.Ligand property) (atomium.structures.Molecule property) is_backbone (atomium.structures.Atom property) is_metal (atomium.structures.Atom property) is_side_chain (atomium.structures.Atom property) is_water (atomium.structures.Ligand property)

K

keywords (atomium.data.File property)

L

length (atomium.structures.Chain property) Ligand (class in atomium.structures)

location (atomium.structures.Atom property) loop_block_to_list() (in module atomium.mmcif)

M

make_aniso() (in module atomium.mmcif) (in module atomium.pdb) make_residue_id() (in module atomium.mmcif) make_secondary_structure() (in module atomium.mmcif) (in module atomium.pdb) make_sequences() (in module atomium.mmcif) (in module atomium.pdb) mass (atomium.structures.Atom property) (atomium.structures.AtomStructure property) (atomium.structures.Chain property) (atomium.structures.Het property) (atomium.structures.Ligand property) (atomium.structures.Model property) (atomium.structures.Molecule property) (atomium.structures.Residue property) merge_lines() (in module atomium.pdb) missing_residues (atomium.data.File property) mmcif_dict_to_data_dict() (in module atomium.mmcif) mmcif_lines_to_mmcif_blocks() (in module atomium.mmcif) mmcif_string_to_mmcif_dict() (in module atomium.mmcif) mmcif_to_data_transfer() (in module atomium.mmcif) mmtf_bytes_to_mmtf_dict() (in module atomium.mmtf)

mmtf_dict_to_data_dict() (in module atomium.mmtf) mmtf_to_data_transfer() (in module atomium.mmtf) model (atomium.data.File property) (atomium.structures.Atom property) (atomium.structures.Chain property) (atomium.structures.Ligand property) (atomium.structures.Molecule property) (atomium.structures.Residue property) Model (class in atomium.structures) model_dict_to_model() (in module atomium.data) models (atomium.data.File property) module atomium.base atomium.data atomium.mmcif atomium.mmtf atomium.pdb atomium.structures atomium.utilities Molecule (class in atomium.structures) move_to() (atomium.structures.Atom method) mro() (atomium.base.StructureClass method)

N

name (atomium.structures.Atom property) (atomium.structures.AtomStructure property) (atomium.structures.Chain property) (atomium.structures.Het property) (atomium.structures.Ligand property) (atomium.structures.Model property) (atomium.structures.Molecule property) (atomium.structures.Residue property) nearby_atoms() (atomium.structures.Atom method) (atomium.structures.AtomStructure method) (atomium.structures.Chain method) (atomium.structures.Het method) (atomium.structures.Ligand method) (atomium.structures.Model method) (atomium.structures.Molecule method) (atomium.structures.Residue method) nearby_chains() (atomium.structures.Atom method) (atomium.structures.AtomStructure method) (atomium.structures.Chain method) (atomium.structures.Het method) (atomium.structures.Ligand method) (atomium.structures.Model method) (atomium.structures.Molecule method) (atomium.structures.Residue method)

nearby_hets() (atomium.structures.Atom method) (atomium.structures.AtomStructure method) (atomium.structures.Chain method) (atomium.structures.Het method) (atomium.structures.Ligand method) (atomium.structures.Model method) (atomium.structures.Molecule method) (atomium.structures.Residue method) next (atomium.structures.Residue property) non_loop_block_to_list() (in module atomium.mmcif)

O

open() (in module atomium.utilities)

operation_id_groups_to_operations() (in module atomium.mmcif) optimise_distances() (atomium.structures.Model method)

P

pack_sequences() (in module atomium.pdb) pairing_with() (atomium.structures.AtomStructure method) (atomium.structures.Chain method) (atomium.structures.Het method) (atomium.structures.Ligand method) (atomium.structures.Model method) (atomium.structures.Molecule method) (atomium.structures.Residue method) pairwise_atoms() (atomium.structures.AtomStructure method) (atomium.structures.Chain method) (atomium.structures.Het method) (atomium.structures.Ligand method) (atomium.structures.Model method) (atomium.structures.Molecule method) (atomium.structures.Residue method)

parse_binary_field() (in module atomium.mmtf) parse_string() (in module atomium.utilities) pdb_dict_to_data_dict() (in module atomium.pdb) pdb_string_to_pdb_dict() (in module atomium.pdb) present_sequence (atomium.structures.Chain property) previous (atomium.structures.Residue property)

Q

query() (in module atomium.base)

R

radius_of_gyration (atomium.structures.AtomStructure property) (atomium.structures.Chain property) (atomium.structures.Het property) (atomium.structures.Ligand property) (atomium.structures.Model property) (atomium.structures.Molecule property) (atomium.structures.Residue property) recursive_decode() (in module atomium.mmtf) Residue (class in atomium.structures) resolution (atomium.data.File property) rfree (atomium.data.File property) rmsd_with() (atomium.structures.AtomStructure method) (atomium.structures.Chain method) (atomium.structures.Het method) (atomium.structures.Ligand method) (atomium.structures.Model method) (atomium.structures.Molecule method) (atomium.structures.Residue method)

rotate() (atomium.structures.Atom method) (atomium.structures.AtomStructure method) (atomium.structures.Chain method) (atomium.structures.Het method) (atomium.structures.Ligand method) (atomium.structures.Model method) (atomium.structures.Molecule method) (atomium.structures.Residue method) rotate_atoms() (atomium.structures.Atom static method) run_length_decode() (in module atomium.mmtf) rvalue (atomium.data.File property)

S

save() (atomium.structures.AtomStructure method) (atomium.structures.Chain method) (atomium.structures.Het method) (atomium.structures.Ligand method) (atomium.structures.Model method) (atomium.structures.Molecule method) (atomium.structures.Residue method) (in module atomium.utilities) sequence (atomium.structures.Chain property) source_organism (atomium.data.File property)

split_residue_id() (in module atomium.mmcif) split_values() (in module atomium.mmcif) strand (atomium.structures.Residue property) strands (atomium.structures.Chain property) strip_quotes() (in module atomium.mmcif) structure_to_mmcif_string() (in module atomium.mmcif) structure_to_mmtf_string() (in module atomium.mmtf) structure_to_pdb_string() (in module atomium.pdb) StructureClass (class in atomium.base) structures (atomium.base.StructureSet property) StructureSet (class in atomium.base)

T

technique (atomium.data.File property) title (atomium.data.File property) transform() (atomium.structures.Atom method) (atomium.structures.AtomStructure method) (atomium.structures.Chain method) (atomium.structures.Het method) (atomium.structures.Ligand method) (atomium.structures.Model method) (atomium.structures.Molecule method) (atomium.structures.Residue method) transform_atoms() (atomium.structures.Atom static method) translate() (atomium.structures.Atom method) (atomium.structures.AtomStructure method) (atomium.structures.Chain method) (atomium.structures.Het method) (atomium.structures.Ligand method) (atomium.structures.Model method) (atomium.structures.Molecule method) (atomium.structures.Residue method)

translate_atoms() (atomium.structures.Atom static method) trim() (atomium.structures.Atom method) (atomium.structures.AtomStructure method) (atomium.structures.Chain method) (atomium.structures.Het method) (atomium.structures.Ligand method) (atomium.structures.Model method) (atomium.structures.Molecule method) (atomium.structures.Residue method)

U

update_crystallography_dict() (in module atomium.mmcif) update_description_dict() (in module atomium.mmcif) (in module atomium.pdb) update_dict() (in module atomium.pdb) update_experiment_dict() (in module atomium.mmcif) (in module atomium.pdb) update_geometry_dict() (in module atomium.mmcif) (in module atomium.pdb)

update_lines_with_entities() (in module atomium.mmcif) update_lines_with_structures() (in module atomium.mmcif) update_models_list() (in module atomium.mmcif) (in module atomium.mmtf) (in module atomium.pdb) update_quality_dict() (in module atomium.mmcif) (in module atomium.pdb)