Bio.PDB.Structure module

The structure class, representing a macromolecular structure.

class Bio.PDB.Structure.Structure(id)

Bases: Entity[None, Model]

The Structure class contains a collection of Model instances.

__init__(id)

Initialize the class.

level: str

__repr__()

Return the structure identifier.

get_models()

Return models.

get_chains()

Return chains from models.

get_residues()

Return residues from chains.

get_atoms()

Return atoms from residue.

atom_to_internal_coordinates(verbose: bool = False) → None

Create/update internal coordinates from Atom X,Y,Z coordinates.

Internal coordinates are bond length, angle and dihedral angles.

Parameters:

bool (verbose) – default False describe runtime problems

internal_to_atom_coordinates(verbose: bool = False) → None

Create/update atom coordinates from internal coordinates.

Parameters:

bool (verbose) – default False describe runtime problems

Raises:

Exception – if any chain does not have .internal_coord attribute

__orig_bases__ = (Bio.PDB.Entity.Entity[NoneType, ForwardRef('Model')],)

__parameters__ = ()

parent: _Parent | None

child_list: List[_Child]

child_dict: Dict[Any, _Child]