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