def alignPDBEnsemble(ensemble, suffix='_aligned', outdir='.', gzip=False):
"""Align PDB files using transformations from *ensemble*, which may be
a :class:`.PDBEnsemble` or a :class:`.PDBConformation` instance. Label of
the conformation (see :meth:`~.PDBConformation.getLabel`) will be used to
determine the PDB structure and model number. First four characters of
the label is expected to be the PDB identifier and ending numbers to be the
model number. For example, the :class:`.Transformation` from conformation
with label *2k39_ca_selection_'resnum_<_71'_m116* will be applied to 116th
model of structure **2k39**. After applicable transformations are made,
structure will be written into *outputdir* as :file:`2k39_aligned.pdb`.
If *gzip* is **True**, output files will be compressed. Return value is
the output filename or list of filenames, in the order files are processed.
Note that if multiple models from a file are aligned, that filename will
appear in the list multiple times."""
if not isinstance(ensemble, (PDBEnsemble, PDBConformation)):
raise TypeError('ensemble must be a PDBEnsemble or PDBConformation')
if isinstance(ensemble, PDBConformation):
ensemble = [ensemble]
if gzip:
gzip = '.gz'
else:
gzip = ''
output = []
pdbdict = {}
for conf in ensemble:
trans = conf.getTransformation()
if trans is None:
raise ValueError('transformations are not calculated, call '
'`superpose` or `iterpose`')
label = conf.getLabel()
pdb = label[:4]
filename = pdbdict.get(pdb, fetchPDB(pdb))
if filename is None:
LOGGER.warning('PDB file for conformation {0} is not found.'
.format(label))
output.append(None)
continue
LOGGER.info('Parsing PDB file {0} for conformation {1}.'
.format(pdb, label))
acsi = None
model = label.rfind('m')
if model > 3:
model = label[model+1:]
if model.isdigit():
acsi = int(model) - 1
LOGGER.info('Applying transformation to model {0}.'
.format(model))
if isinstance(filename, str):
ag = parsePDB(filename)
else:
ag = filename
if acsi is not None:
if acsi >= ag.numCoordsets():
LOGGER.warn('Model number {0} for {1} is out of range.'
.format(model, pdb))
output.append(None)
continue
ag.setACSIndex(acsi)
trans.apply(ag)
outfn = os.path.join(outdir, pdb + suffix + '.pdb' + gzip)
if ag.numCoordsets() > 1:
pdbdict[pdb] = ag
else:
writePDB(outfn, ag)
output.append(os.path.normpath(outfn))
for pdb, ag in pdbdict.items(): # PY3K: OK
writePDB(os.path.join(outdir, pdb + suffix + '.pdb' + gzip), ag)
if len(output) == 1:
return output[0]
else:
return output
def alignPDBEnsemble(ensemble, suffix='_aligned', outdir='.', gzip=False):
"""Align PDB files using transformations from *ensemble*, which may be
a :class:`.PDBEnsemble` or a :class:`.PDBConformation` instance. Label of
the conformation (see :meth:`~.PDBConformation.getLabel`) will be used to
determine the PDB structure and model number. First four characters of
the label is expected to be the PDB identifier and ending numbers to be the
model number. For example, the :class:`.Transformation` from conformation
with label *2k39_ca_selection_'resnum_<_71'_m116* will be applied to 116th
model of structure **2k39**. After applicable transformations are made,
structure will be written into *outputdir* as :file:`2k39_aligned.pdb`.
If ``gzip=True``, output files will be compressed. Return value is
the output filename or list of filenames, in the order files are processed.
Note that if multiple models from a file are aligned, that filename will
appear in the list multiple times."""
if not isinstance(ensemble, (PDBEnsemble, PDBConformation)):
raise TypeError('ensemble must be a PDBEnsemble or PDBConformation')
if isinstance(ensemble, PDBConformation):
ensemble = [ensemble]
if gzip:
gzip = '.gz'
else:
gzip = ''
output = []
pdbdict = {}
for conf in ensemble:
trans = conf.getTransformation()
if trans is None:
raise ValueError('transformations are not calculated, call '
'`superpose` or `iterpose`')
label = conf.getLabel()
pdb = label[:4]
filename = pdbdict.get(pdb, fetchPDB(pdb))
if filename is None:
LOGGER.warning(
'PDB file for conformation {0} is not found.'.format(label))
output.append(None)
continue
LOGGER.info('Parsing PDB file {0} for conformation {1}.'.format(
pdb, label))
acsi = None
model = label.rfind('m')
if model > 3:
model = label[model + 1:]
if model.isdigit():
acsi = int(model) - 1
LOGGER.info('Applying transformation to model {0}.'.format(model))
if isinstance(filename, str):
ag = parsePDB(filename)
else:
ag = filename
if acsi is not None:
if acsi >= ag.numCoordsets():
LOGGER.warn('Model number {0} for {1} is out of range.'.format(
model, pdb))
output.append(None)
continue
ag.setACSIndex(acsi)
trans.apply(ag)
outfn = os.path.join(outdir, pdb + suffix + '.pdb' + gzip)
if ag.numCoordsets() > 1:
pdbdict[pdb] = ag
else:
writePDB(outfn, ag)
output.append(os.path.normpath(outfn))
for pdb, ag in pdbdict.items(): # PY3K: OK
writePDB(os.path.join(outdir, pdb + suffix + '.pdb' + gzip), ag)
if len(output) == 1:
return output[0]
else:
return output