# -*- coding: utf-8 -*-
"""This module defines classes for handling residues."""
from .subset import AtomSubset
from .atom import Atom
__all__ = ['Residue']
[docs]class Residue(AtomSubset):
"""Instances of this class point to atoms with same residue numbers (and
insertion codes) and are generated by :class:`.HierView` class.
Following built-in functions are customized for this class:
* :func:`len` returns the number of atoms in the instance.
* :func:`iter` yields :class:`.Atom` instances.
Indexing :class:`Residue` instances by *atom name* (:func:`str`), e.g.
``"CA"`` returns an :class:`.Atom` instance."""
__slots__ = ['_ag', '_indices', '_hv', '_acsi', '_selstr']
def __init__(self, ag, indices, hv, acsi=None, **kwargs):
AtomSubset.__init__(self, ag, indices, acsi, **kwargs)
self._hv = hv
def __repr__(self):
n_csets = self._ag.numCoordsets()
chain = self.getChid()
if chain is None:
chain = ''
else:
chain = ' from Chain {0}'.format(self.getChid())
if n_csets == 1:
return ('<Residue: {0} {1}{2}{3} from {4} ({5} atoms)>'
).format(self.getResname(), self.getResnum(),
self.getIcode() or '', chain, self._ag.getTitle(),
len(self))
elif n_csets > 1:
return ('<Residue: {0} {1}{2}{3} from {4} '
'({5} atoms; active #{6} of {7} coordsets)>').format(
self.getResname(), self.getResnum(), self.getIcode() or '',
chain, self._ag.getTitle(), len(self), self.getACSIndex(),
n_csets)
else:
return ('<Residue: {0} {1}{2}{3} from {4} ({5} atoms; '
'no coordinates)>').format(self.getResname(),
self.getResnum(), self.getIcode() or '', chain,
self._ag.getTitle(), len(self))
def __str__(self):
return '{0} {1}{2}'.format(self.getResname(), self.getResnum(),
self.getIcode() or '')
[docs] def getAtom(self, name):
"""Returns atom with given *name*, **None** if not found. Assumes that
atom names in the residue are unique. If more than one atoms with the
given *name* exists, the one with the smaller index will be returned.
"""
acsi = self.getACSIndex()
if isinstance(name, str):
nz = (self.getNames() == name).nonzero()[0]
if len(nz) > 0:
return Atom(self._ag, self._indices[nz[0]], acsi)
__getitem__ = getAtom
[docs] def getChain(self):
"""Returns the chain that the residue belongs to."""
chid = self.getChid()
segname = self.getSegname()
if chid is not None:
return self._hv.getChain(chid, segname)
[docs] def getResnum(self):
"""Returns residue number."""
return self._ag._getResnums()[self._indices[0]]
[docs] def setResnum(self, number):
"""Set residue number."""
self.setResnums(number)
[docs] def getResname(self):
"""Returns residue name."""
data = self._ag._getResnames()
if data is not None:
return data[self._indices[0]]
[docs] def setResname(self, name):
"""Set residue name."""
self.setResnames(name)
[docs] def getIcode(self):
"""Returns residue insertion code."""
data = self._ag._getIcodes()
if data is not None:
return data[self._indices[0]]
[docs] def setIcode(self, icode):
"""Set residue insertion code."""
self.setIcodes(icode)
[docs] def getResindex(self):
"""Returns residue index."""
return self._ag._getResindices()[self._indices[0]]
[docs] def getChid(self):
"""Returns chain identifier."""
chids = self._ag._getChids()
if chids is not None:
return chids[self._indices[0]]
[docs] def getSegname(self):
"""Returns segment name."""
segnames = self._ag._getSegnames()
if segnames is not None:
return segnames[self._indices[0]]
[docs] def getSegment(self):
"""Returns segment of the residue."""
segname = self.getSegname()
if segname is not None:
return self._hv.getSegment(segname)
[docs] def getSelstr(self):
"""Returns selection string that will select this residue."""
icode = self.getIcode() or ''
chain = self.getChain()
if chain is None:
if self._selstr:
return 'resnum {0}{1} and ({1})'.format(
self.getResnum(), icode, self._selstr)
else:
return 'resnum {0}{1}'.format(self.getResnum(), icode)
else:
return 'resnum {0}{1} and ({2})'.format(
self.getResnum(), icode, chain.getSelstr())
[docs] def getPrev(self):
"""Returns preceding residue in the atom group."""
nextIndex = self.getResindex()-1
if nextIndex < 0:
return None
return self._hv._getResidue(nextIndex)
[docs] def getNext(self):
"""Returns following residue in the atom group."""
return self._hv._getResidue(self.getResindex()+1)
