Bio.PDB.Residue module

Residue class, used by Structure objects.

class Bio.PDB.Residue.Residue(id, resname, segid)

Bases: Bio.PDB.Entity.Entity

Represents a residue. A Residue object stores atoms.

__init__(self, id, resname, segid)

Initialize the class.

__repr__(self)

Return the residue full id.

add(self, atom)

Add an Atom object.

Checks for adding duplicate atoms, and raises a PDBConstructionException if so.

sort(self)

Sort child atoms.

Atoms N, CA, C, O always come first, thereafter alphabetically by name, with any alternative location specifier for disordered atoms (altloc) as a tie-breaker.

flag_disordered(self)

Set the disordered flag.

is_disordered(self)

Return 1 if the residue contains disordered atoms.

get_resname(self)

Return the residue name.

get_unpacked_list(self)

Return the list of all atoms, unpack DisorderedAtoms.

get_segid(self)

Return the segment identifier.

get_atoms(self)

Return atoms.

get_atom(self)

Return atom.

class Bio.PDB.Residue.DisorderedResidue(id)

Bases: Bio.PDB.Entity.DisorderedEntityWrapper

DisorderedResidue is a wrapper around two or more Residue objects.

It is used to represent point mutations (e.g. there is a Ser 60 and a Cys 60 residue, each with 50 % occupancy).

__init__(self, id)

Initialize the class.

__repr__(self)

Return disordered residue full identifier.

add(self, atom)

Add atom to residue.

sort(self)

Sort the atoms in the child Residue objects.

disordered_add(self, residue)

Add a residue object and use its resname as key.

Arguments:

• residue - Residue object