# -*- coding: utf-8 -*-
"""This module defines classes for handling polypeptide/nucleic acid chains."""
from numpy import arange, unique
from .subset import AtomSubset
from .atomic import AAMAP
__all__ = ['Chain']
def getSequence(resnames, **kwargs):
"""Returns polypeptide sequence from a list of *resnames* using one-letter residue
name abbreviations by default, or long (usually three letter) abbrevations
if *longSeq* is **True**."""
longSeq = kwargs.get('longSeq', False)
if longSeq:
return ' '.join(resnames)
get = AAMAP.get
return ''.join([get(rn, 'X') for rn in resnames])
[docs]
class Chain(AtomSubset):
"""Instances of this class point to atoms with same chain identifiers and
are generated by :class:`.HierView` class. Following built-in functions
are customized for this class:
* :func:`len` returns the number of residues in the chain
* :func:`iter` yields :class:`.Residue` instances
Indexing :class:`Chain` instances by:
- *residue number [, insertion code]* (:func:`tuple`),
e.g. ``10`` or ``10, "B"``, returns a :class:`.Residue`
- *slice* (:func:`slice`), e.g, ``10:20``, returns a list of
:class:`.Residue` instances"""
__slots__ = ['_ag', '_indices', '_hv', '_acsi', '_selstr', '_seq']
def __init__(self, ag, indices, hv, acsi=None, **kwargs):
AtomSubset.__init__(self, ag, indices, acsi, **kwargs)
self._hv = hv
self._seq = None
def __repr__(self):
n_csets = self._ag.numCoordsets()
segment = self.getSegment()
if segment is None:
segment = ''
else:
segment = ' from ' + str(segment)
if n_csets == 1:
return ('<Chain: {0}{1} from {2} ({3} residues, {4} atoms)>'
).format(self.getChid(), segment, self._ag.getTitle(),
self.numResidues(), self.numAtoms())
elif n_csets > 1:
return ('<Chain: {0}{1} from {2} ({3} residues, {4} '
'atoms; active #{5} of {6} coordsets)>'
).format(self.getChid(), segment, self._ag.getTitle(),
self.numResidues(), self.numAtoms(),
self.getACSIndex(), n_csets)
else:
return ('<Chain: {0}{1} from {2} ({3} residues, '
'{4} atoms; no coordinates)>'
).format(self.getChid(), segment, self._ag.getTitle(),
self.numResidues(), self.numAtoms())
def __str__(self):
return 'Chain ' + self.getChid()
def __getitem__(self, key):
if isinstance(key, tuple):
return self.getResidue(*key)
else:
return AtomSubset.__getitem__(self, key)
[docs]
def getSegment(self):
"""Returns segment of the chain."""
segname = self.getSegname()
if segname is not None:
return self._hv.getSegment(segname)
[docs]
def getSegname(self):
"""Returns segment name."""
segnames = self._ag._getSegnames()
if segnames is not None:
return segnames[self._indices[0]]
[docs]
def getResidue(self, resnum, icode=None):
"""Returns residue with number *resnum* and insertion code *icode*."""
return self._hv.getResidue(self.getChid(), resnum, icode,
self.getSegname())
[docs]
def iterResidues(self):
"""Yield residues."""
get = self._hv._getResidue
for index in unique(self._getResindices()):
yield get(index)
__iter__ = iterResidues
[docs]
def numResidues(self):
"""Returns number of residues."""
return len(set(self._getResindices()))
__len__ = numResidues
[docs]
def getChid(self):
"""Returns chain identifier."""
return self._ag._getChids()[self._indices[0]]
[docs]
def setChid(self, chid):
"""Set chain identifier."""
self.setChids(chid)
[docs]
def getChindex(self):
"""Returns chain index."""
return self._ag._getChindices()[self._indices[0]]
[docs]
def getSequence(self, **kwargs):
"""Returns one-letter sequence string for amino acids in the chain.
When *allres* keyword argument is **True**, sequence will include all
residues (e.g. water molecules) in the chain and **X** will be used for
non-standard residue names."""
if kwargs.get('allres', False):
get = AAMAP.get
if kwargs.get('longSeq', False):
seq = ' '.join([res.getResname() for res in self])
else:
seq = ''.join([get(res.getResname(), 'X') for res in self])
elif self._seq:
seq = self._seq
else:
calpha = self.calpha
if calpha:
seq = getSequence(calpha.getResnames(), **kwargs)
else:
seq = ''
self._seq = seq
return seq
[docs]
def getSelstr(self):
"""Returns selection string that selects atoms in this chain."""
segment = self.getSegment()
if segment is None:
if self._selstr:
return 'chain {0} and ({1})'.format(self.getChid(),
self._selstr)
else:
return 'chain {0}'.format(self.getChid())
else:
return 'chain {0} and ({1})'.format(self.getChid(),
segment.getSelstr())
[docs]
def getHierView(self, **kwargs):
"""Returns a hierarchical view of the this chain."""
return HierView(self, **kwargs)