def matchAlign(mobile, target, **kwargs):
"""Superpose *mobile* onto *target* based on best matching pair of chains.
This function uses :func:`matchChains` for matching chains and returns a
tuple that contains the following items:
* *mobile* after it is superposed,
* matching chain from *mobile* as a :class:`.AtomMap` instance,
* matching chain from *target* as a :class:`.AtomMap` instance,
* percent sequence identity of the match,
* percent sequence overlap of the match.
:arg mobile: atoms that contain a protein chain
:type mobile: :class:`.Chain`, :class:`.AtomGroup`, :class:`.Selection`
:arg target: atoms that contain a protein chain
:type target: :class:`.Chain`, :class:`.AtomGroup`, :class:`.Selection`
:arg tarsel: *target* atoms that will be used for alignment,
default is ``'calpha'``
:type tarsel: str
:arg allcsets: align all coordinate sets of *mobile*, default is **True**
:type allcsets: bool
:keyword seqid: percent sequence identity, default is 90
:type seqid: float
:keyword overlap: percent overlap, default is 90
:type overlap: float
:keyword pwalign: perform pairwise sequence alignment
:type pwalign: bool"""
selstr = kwargs.pop('tarsel', 'calpha')
if selstr == 'calpha':
selstr = None
subset = 'calpha'
if selstr:
if selstr in _SUBSETS:
subset = selstr
else:
subset = 'all'
sel = target.select(selstr)
if sel is None:
raise ValueError('selection {0} did not match any atoms'.format(
repr(selstr)))
chid = set(sel.getChids())
if len(chid) == 1:
chid = chid.pop()
target = target.select('chain ' + chid)
match = matchChains(mobile, target, subset=subset, **kwargs)
if not match:
return
match = match[0]
mob = match[0]
tar = match[1]
if selstr:
which = SELECT.getIndices(tar, selstr)
n_atoms = len(which)
else:
which = slice(None)
n_atoms = len(tar)
selstr = 'calpha'
if kwargs.get('allcets', True):
csets = list(range(mobile.numCoordsets())) # PY3K: OK
else:
csets = [mobile.getACSIndex()]
LOGGER.info('Alignment is based on {0} atoms matching {1}.'.format(
n_atoms, repr(selstr)))
printRMSD(tar._getCoords()[which],
mob._getCoordsets()[:, which],
msg='Before alignment ')
for acsi in csets:
mob.setACSIndex(acsi)
mobile.setACSIndex(acsi)
calcTransformation(mob._getCoords()[which],
tar._getCoords()[which]).apply(mobile)
printRMSD(tar._getCoords()[which],
mob._getCoordsets()[:, which],
msg='After alignment ')
return (mobile, ) + match
def testGetBoolArray(self):
self.assertEqual(len(AM), len(SELECT.getBoolArray(AM, 'name CA')))
def matchAlign(mobile, target, **kwargs):
"""Superpose *mobile* onto *target* based on best matching pair of chains.
This function uses :func:`matchChains` for matching chains and returns a
tuple that contains the following items:
* *mobile* after it is superposed,
* matching chain from *mobile* as a :class:`.AtomMap` instance,
* matching chain from *target* as a :class:`.AtomMap` instance,
* percent sequence identity of the match,
* percent sequence overlap of the match.
:arg mobile: atoms that contain a protein chain
:type mobile: :class:`.Chain`, :class:`.AtomGroup`, :class:`.Selection`
:arg target: atoms that contain a protein chain
:type target: :class:`.Chain`, :class:`.AtomGroup`, :class:`.Selection`
:arg tarsel: *target* atoms that will be used for alignment,
default is ``'calpha'``
:type tarsel: str
:arg allcsets: align all coordinate sets of *mobile*, default is **True**
:type allcsets: bool
:keyword seqid: percent sequence identity, default is 90
:type seqid: float
:keyword overlap: percent overlap, default is 90
:type overlap: float
:keyword pwalign: perform pairwise sequence alignment
:type pwalign: bool"""
selstr = kwargs.pop('tarsel', 'calpha')
if selstr == 'calpha':
selstr = None
subset = 'calpha'
if selstr:
if selstr in _SUBSETS:
subset = selstr
else:
subset = 'all'
sel = target.select(selstr)
if sel is None:
raise ValueError('selection {0} did not match any atoms'
.format(repr(selstr)))
chid = set(sel.getChids())
if len(chid) == 1:
chid = chid.pop()
target = target.select('chain ' + chid)
match = matchChains(mobile, target, subset=subset, **kwargs)
if not match:
return
match = match[0]
mob = match[0]
tar = match[1]
if selstr:
which = SELECT.getIndices(tar, selstr)
n_atoms = len(which)
else:
which = slice(None)
n_atoms = len(tar)
selstr = 'calpha'
if kwargs.get('allcets', True):
csets = range(mobile.numCoordsets()) # PY3K: OK
else:
csets = [mobile.getACSIndex()]
LOGGER.info('Alignment is based on {0} atoms matching {1}.'
.format(n_atoms, repr(selstr)))
printRMSD(tar._getCoords()[which], mob._getCoordsets()[:, which],
msg='Before alignment ')
for acsi in csets:
mob.setACSIndex(acsi)
mobile.setACSIndex(acsi)
calcTransformation(mob._getCoords()[which],
tar._getCoords()[which]).apply(mobile)
printRMSD(tar._getCoords()[which], mob._getCoordsets()[:, which],
msg='After alignment ')
return (mobile,) + match
def testGetBoolArray(self):
self.assertEqual(len(AM), len(SELECT.getBoolArray(AM, 'name CA')))
