Bio.PDB.Model module

Model class, used in Structure objects.

class Bio.PDB.Model.Model(id, serial_num=None)

Bases: Entity[Structure, Chain]

The object representing a model in a structure.

In a structure derived from an X-ray crystallography experiment, only a single model will be present (with some exceptions). NMR structures normally contain many different models.

__init__(id, serial_num=None)

Initialize.

Arguments:

• id - int

• serial_num - int

__repr__()

Return model identifier.

get_chains()

Return chains.

get_residues()

Return residues.

get_atoms()

Return atoms.

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

__orig_bases__ = (Bio.PDB.Entity.Entity[ForwardRef('Structure'), ForwardRef('Chain')],)

__parameters__ = ()

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 .pic attribute