Bio.PDB.Chain module¶
Chain class, used in Structure objects.
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class
Bio.PDB.Chain.
Chain
(id)¶ Bases:
Bio.PDB.Entity.Entity
Define Chain class.
Chain is an object of type Entity, stores residues and includes a method to access atoms from residues.
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__init__
(self, id)¶ Initialize the class.
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__gt__
(self, other)¶ Validate if id is greater than other.id.
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__ge__
(self, other)¶ Validate if id is greater or equal than other.id.
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__lt__
(self, other)¶ Validate if id is less than other.id.
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__le__
(self, other)¶ Validate if id is less or equal than other id.
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__getitem__
(self, id)¶ Return the residue with given id.
The id of a residue is (hetero flag, sequence identifier, insertion code). If id is an int, it is translated to (” “, id, ” “) by the _translate_id method.
- Arguments:
id - (string, int, string) or int
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__contains__
(self, id)¶ Check if a residue with given id is present in this chain.
- Arguments:
id - (string, int, string) or int
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__delitem__
(self, id)¶ Delete item.
- Arguments:
id - (string, int, string) or int
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__repr__
(self)¶ Return the chain identifier.
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get_unpacked_list
(self)¶ Return a list of undisordered residues.
Some Residue objects hide several disordered residues (DisorderedResidue objects). This method unpacks them, ie. it returns a list of simple Residue objects.
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has_id
(self, id)¶ Return 1 if a residue with given id is present.
The id of a residue is (hetero flag, sequence identifier, insertion code).
If id is an int, it is translated to (” “, id, ” “) by the _translate_id method.
- Arguments:
id - (string, int, string) or int
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get_residues
(self)¶ Return residues.
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get_atoms
(self)¶ Return atoms from residues.
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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, start: Union[int, NoneType] = None, fin: Union[int, NoneType] = None)¶ Create/update atom coordinates from internal coordinates.
- Parameters
bool (verbose) – default False describe runtime problems
- Param
start, fin lists sequence position, insert code for begin, end of subregion to process
- Raises
Exception – if any chain does not have .pic attribute
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