def iterative_structural_align(aln, align_block=0):
"""Given an alignment of structures, iterate over parameter values
to obtain the best structural alignment."""
for seq in aln:
if seq.code == '_fix_pos':
raise modeller.ModellerError("This method does not work with fixed "
"alignment positions (_fix_pos)")
if not hasattr(seq, 'atoms'):
raise modeller.ModellerError("This method only works for an " + \
"alignment of structures.")
tmpdir = _TemporaryDirectory()
fil = tmpdir.get_path("inp.pir")
aln.write(file=fil)
opfile = tmpdir.get_path("salign_local_mid.ali")
opfile2 = tmpdir.get_path("salign_local.ali")
# -- Iterating over values of gap penalties and matrix offset
fw1=(1., 0., 0., 0., 1., 0.)
fw2=(0., 1., 0., 0., 0., 0.)
fw3=(0., 0., 0., 0., 1., 0.)
best = _BestAlignment(aln)
# -- Iterating over gap penalties 1D to get initial alignments
print("Iterate over 1D penalties to get initial alignments")
for ogp in _frange(-150, 1, 50):
for egp in _frange(-50, 1, 50):
for mo in _frange(-3.0, -0.05, 0.3):
best.try_seq_align(fil, opfile, fw1, ogp, egp, align_block, mo)
# -- Iterating over gap penalties 3D to get final alignments
print("Iterate over 3D penalties to get final alignments")
for ogp3d in _frange(0, 3, 1):
for egp3d in range(2, 5, 1):
best.try_struc_align(opfile, opfile2, fw2, ogp3d, egp3d,
align_block)
# try alternate initial alignments only if the qmax score is less than 70%
if best.qscore <= 70:
print("Trying alternate initial alignments")
for ogp in _frange(0.0, 2.2, 0.3):
for egp in _frange(0.1, 2.3, 0.3):
for mo in _frange(-3.0, -0.05, 0.3):
best.try_seq_align(fil, opfile, fw3, ogp, egp, align_block,
mo)
# -- Iterating over gap penalties 3D to get final alignments
print("Trying alternate final alignments")
for ogp3d in _frange(0, 3, 1):
for egp3d in range(2, 5, 1):
best.try_struc_align(opfile, opfile2, fw2, ogp3d, egp3d,
align_block)
print("final max quality = %g" % best.qscore)
if best.found_struc_align:
aln.clear()
aln.append(file=opfile2)
else:
raise modeller.ModellerError("Structure alignment failed")
def _assess(self, atmsel, schedule_scale=None, **vars):
self.count += 1
if self.count == 1:
return 10., ()
elif self.count == 2:
return 20., ()
elif self.count == 3:
raise modeller.ModellerError("SOAP error")
def iterative_structural_align(aln):
"""Given an alignment of structures, iterate over parameter values
to obtain the best structural alignment."""
for seq in aln:
if not hasattr(seq, 'atoms'):
raise modeller.ModellerError("This method only works for an " + \
"alignment of structures.")
tmpdir = _TemporaryDirectory()
fil = tmpdir.get_path("inp.pir")
aln.write(file=fil)
opfile = tmpdir.get_path("salign_local_mid.ali")
opfile2 = tmpdir.get_path("salign_local.ali")
# -- Iterating over values of gap penalties and matrix offset
qmax = 0.0
win_ogp3d = None
fw1=(1., 0., 0., 0., 1., 0.)
fw2=(0., 1., 0., 0., 0., 0.)
fw3=(0., 0., 0., 0., 1., 0.)
# -- Iterating over gap penalties 1D to get initial alignments
print "Iterate over 1D penalties to get initial alignments"
for ogp in _frange(-150, 1, 50):
for egp in _frange(-50, 1, 50):
for mo in _frange(-3.0, -0.05, 0.3):
aln.clear()
aln.append(file=fil)
try:
qwlty1 = _salign_fw_local_gaps1(aln,fw1,ogp,egp,mo)
if qwlty1.qscorepct >= qmax:
qmax = qwlty1.qscorepct
aln.write(file=opfile, alignment_format='PIR')
win_ogp = ogp
win_egp = egp
win_mo = mo
print "Qlty scrs", ogp,"\t",egp,"\t",qwlty1.qscorepct
except modeller.ModellerError, detail:
print "Set of parameters",fw1,ogp,egp,"resulted in the following error\t"+str(detail)
except modeller.ModellerError, detail:
print "Set of parameters",fw3,ogp,egp,"resulted in the following error\t"+str(detail)
# -- Iterating over gap penalties 3D to get final alignments
print "Trying alternate final alignments"
qmax3d = 0.
for ogp3d in _frange(0, 3, 1):
for egp3d in range(2, 5, 1):
aln.clear()
aln.append(file=opfile)
try:
qwlty2 = _salign_fw_gaps3(aln,fw2,ogp3d,egp3d)
if qwlty2.qscorepct >= qmax3d:
qmax3d = qwlty2.qscorepct
aln.write(file=opfile2, alignment_format='PIR')
win_ogp3d = ogp3d
win_egp3d = egp3d
print "Qlty scrs", ogp3d,"\t",egp3d,"\t",qwlty2.qscorepct
except modeller.ModellerError,detail:
print "Set of parameters",fw2,ogp3d,egp3d,"resulted in the following error\t"+str(detail)
qmax = max(qmax, qmax3d)
print "final max quality = ", qmax
if win_ogp3d is None:
raise modeller.ModellerError("Structure alignment failed")
else:
aln.clear()
aln.append(file=opfile2)