Bio.PDB.Chain module
Chain class, used in Structure objects.
- class Bio.PDB.Chain.Chain(id)
Bases:
Bio.PDB.Entity.EntityDefine Chain class.
Chain is an object of type Entity, stores residues and includes a method to access atoms from residues.
- __init__(id)
Initialize the class.
- __gt__(other)
Validate if id is greater than other.id.
- __ge__(other)
Validate if id is greater or equal than other.id.
- __lt__(other)
Validate if id is less than other.id.
- __le__(other)
Validate if id is less or equal than other id.
- __getitem__(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
- __contains__(id)
Check if a residue with given id is present in this chain.
- Arguments:
id - (string, int, string) or int
- __delitem__(id)
Delete item.
- Arguments:
id - (string, int, string) or int
- __repr__()
Return the chain identifier.
- get_unpacked_list()
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.
- has_id(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
- get_residues()
Return residues.
- get_atoms()
Return atoms from residues.
- 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, start: Optional[int] = None, fin: Optional[int] = None)
Create/update atom coordinates from internal coordinates.
- Parameters
bool (verbose) – default False describe runtime problems
- Param
start, fin integers optional sequence positions for begin, end of subregion to process. N.B. this activates serial residue assembly, <start> residue CA will be at origin
- Raises
Exception – if any chain does not have .internal_coord attribute