Bio.PDB.Model module¶
Model class, used in Structure objects.
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class
Bio.PDB.Model.
Model
(id, serial_num=None)¶ Bases:
Bio.PDB.Entity.Entity
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.
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__init__
(self, id, serial_num=None)¶ Initialize.
- Arguments:
id - int
serial_num - int
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__repr__
(self)¶ Return model identifier.
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get_chains
(self)¶ Return chains.
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get_residues
(self)¶ Return residues.
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get_atoms
(self)¶ Return atoms.
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atom_to_internal_coordinates
(self, 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
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internal_to_atom_coordinates
(self, 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
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