"""Align models in a PDB file or multiple structures in separate PDB files."""
from ..apptools import *
__all__ = ['prody_align']
[docs]def prody_align(*pdbs, **kwargs):
"""Align models in a PDB file or multiple structures in separate PDB files.
By default, protein chains will be matched based on selected atoms and
alignment will be performed based on matching residues. If non-protein
atoms are selected and selected atoms match in multiple structures,
they will be used for alignment.
:arg pdbs: PDB identifier(s) or filename(s)
:arg select: atom selection string, default is :term:`calpha`,
see :ref:`selections`
:arg model: for NMR files, reference model index, default is ``1``
:arg seqid: percent sequence identity, default is ``90``
:arg overlap: percent sequence overlap, default is ``90``
:arg prefix: prefix for output file, default is PDB filename
:arg suffix: output filename suffix, default is :file:`_aligned`"""
from numpy import all
from prody import LOGGER, writePDB, parsePDB
from prody import alignCoordsets, printRMSD, matchAlign, superpose
selstr = kwargs.get('select', 'calpha')
suffix = kwargs.get('suffix', '_aligned')
if len(pdbs) == 1:
pdb = pdbs[0]
LOGGER.info('Aligning multiple models in: ' + pdb)
prefix = kwargs.get('prefix')
model = kwargs.get('model')
pdb = parsePDB(pdb)
pdbselect = pdb.select(selstr)
if pdbselect is None:
subparser = kwargs.get('subparser')
if subparser:
subparser.error('Selection {0} do not match any atoms.'
.format(repr(selstr)))
else:
raise ValueError('select does not match any atoms')
LOGGER.info('{0} atoms will be used for alignment.'
.format(len(pdbselect)))
pdbselect.setACSIndex(model-1)
printRMSD(pdbselect, msg='Before alignment ')
alignCoordsets(pdbselect)
printRMSD(pdbselect, msg='After alignment ')
outfn = (prefix or pdb.getTitle()) + suffix + '.pdb'
LOGGER.info('Writing file: ' + outfn)
writePDB(outfn, pdb)
else:
pdbs = list(pdbs)
reffn = pdbs.pop(0)
seqid = kwargs.get('seqid')
overlap = kwargs.get('overlap')
LOGGER.info('Aligning structures onto: ' + reffn)
ref = parsePDB(reffn)
ref_sel = ref.select(selstr)
if ref_sel:
LOGGER.info('Selection {0} matched {1} atoms.'
.format(repr(selstr), len(ref_sel)))
else:
raise ValueError('selection {0} did not match any atoms'
.format(repr(selstr)))
match = True
if ref_sel.numAtoms('ca') < 2:
match = False
for arg in pdbs:
if arg == reffn:
continue
#if '_aligned.pdb' in arg:
# continue
LOGGER.info('Evaluating structure: ' + arg)
pdb = parsePDB(arg)
if match:
result = matchAlign(pdb, ref, seqid=seqid, overlap=overlap,
tarsel=selstr, allcsets=True,
cslabel='Model', csincr=1)
if result:
outfn = pdb.getTitle() + suffix + '.pdb'
LOGGER.info('Writing file: ' + outfn)
writePDB(outfn, pdb)
continue
pdb_sel = pdb.select(selstr)
LOGGER.info('Selection {0} matched {1} atoms.'
.format(repr(selstr), len(pdb_sel)))
if (len(pdb_sel) == len(ref_sel) and
all(pdb_sel.getNames() == ref_sel.getNames())):
printRMSD(ref_sel, pdb_sel, msg='Before alignment ')
superpose(pdb_sel, ref_sel)
printRMSD(ref_sel, pdb_sel, msg='After alignment ')
outfn = pdb.getTitle() + suffix + '.pdb'
LOGGER.info('Writing file: ' + outfn)
writePDB(outfn, pdb)
else:
LOGGER.warn('Failed to align structure ' + arg + '.')
def addCommand(commands):
subparser = commands.add_parser('align',
help='align models or structures')
subparser.add_argument('--quiet', help="suppress info messages to stderr",
action=Quiet, nargs=0)
subparser.add_argument('--examples', action=UsageExample, nargs=0,
help='show usage examples and exit')
subparser.set_defaults(usage_example=
"""Align models in a PDB structure or multiple PDB structures and save \
aligned coordinate sets. When multiple structures are aligned, ProDy will \
match chains based on sequence alignment and use best match for aligning the \
structures.
Fetch PDB structure 2k39 and align models (reference model is the first model):
$ prody align 2k39
Fetch PDB structure 2k39 and align models using backbone of residues with \
number less than 71:
$ prody align 2k39 --select "backbone and resnum < 71"
Align 1r39 and 1zz2 onto 1p38 using residues with number less than 300:
$ prody align --select "resnum < 300" 1p38 1r39 1zz2
Align all models of 2k39 onto 1aar using residues 1 to 70 (inclusive):
$ prody align --select "resnum 1 to 70" 1aar 2k39
Align 1fi7 onto 1hrc using heme atoms:
$ prody align --select "noh heme and chain A" 1hrc 1fi7""",
test_examples=[0, 1, 2, 3, 4,]
)
group = subparser.add_argument_group('atom/model selection')
group.add_argument('-s', '--select', dest='select', type=str,
default='calpha', metavar='SEL',
help='reference structure atom selection (default: %(default)s)')
group.add_argument('-m', '--model', dest='model', type=int,
default=1, metavar='INT',
help=('for NMR files, reference model index (default: %(default)s)'))
group = subparser.add_argument_group('chain matching options')
group.add_argument('-i', '--seqid', dest='seqid', type=int,
default=90, metavar='INT',
help=('percent sequence identity (default: %(default)s)'))
group.add_argument('-o', '--overlap', dest='overlap', type=int,
default=90, metavar='INT',
help=('percent sequence overlap (default: %(default)s)'))
group = subparser.add_argument_group('output options')
group.add_argument('-p', '--prefix', dest='prefix', type=str,
default='', metavar='STR',
help=('output filename prefix (default: PDB filename)'))
group.add_argument('-x', '--suffix', dest='suffix', type=str,
default='_aligned', metavar='STR',
help=('output filename suffix (default: %(default)s)'))
subparser.add_argument('pdb', nargs='+',
help='PDB identifier(s) or filename(s)')
subparser.set_defaults(func=lambda ns: prody_align(*ns.pdb,
**ns.__dict__))
subparser.set_defaults(subparser=subparser)
