Bio.PDB.Chain module

Chain class, used in Structure objects.

class Bio.PDB.Chain.Chain(id)

Bases: Entity[Model, Residue]

Define 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: int | None = None, fin: int | None = 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

__orig_bases__ = (Bio.PDB.Entity.Entity[ForwardRef('Model'), ForwardRef('Residue')],)

__parameters__ = ()