def testSdfMCSAlignAtomMap(self):
"""Test case - match test with return of atom maps for foreign SDF with a CC definition"""
self.__lfh.write(
"\nStarting OeAlignDepictTests testSdfMCSAlignAtomMap\n")
try:
extPairTup = (os.path.join(self.__datadir, "ATP.sdf"),
os.path.join(self.__datadir, "ATP.cif"))
refPath = extPairTup[0]
fitId = extPairTup[1]
fitPath = extPairTup[1]
oed = OeDepictMCSAlign(verbose=self.__verbose, log=self.__lfh)
# oed.setSearchType(sType='exact')
oed.setSearchType(sType="exact")
#
oed.setRefPath(refPath, type="SDF")
# oed.setFitId(fitId,cachePath=self.__topCachePath)
oed.setFitPath(fitPath, title="ATP")
aML = oed.testAlign(suppressHydrogens=False,
unique=False,
minFrac=0.9)
if len(aML) > 0:
self.__lfh.write("Match suceeded for: %s %s\n" %
(refPath, fitId))
for ii, aM in enumerate(aML):
self.__lfh.write("Mapping: %4d %s\n" % (ii, aM))
else:
self.__lfh.write("Match failed for: %s %s\n" %
(refPath, fitId))
except: # noqa: E722 pylint: disable=bare-except
traceback.print_exc(file=self.__lfh)
self.fail()
def testMCSAlignPairListDepict(self):
"""Test case - List view of pairwise MCS alignment using pair id list input"""
self.__lfh.write(
"\nStarting OeAlignDepictTests testMCSAlignPairListDepict\n")
try:
oed = OeDepictMCSAlign(verbose=self.__verbose, log=self.__lfh)
oed.setPairIdList(self.__pairIdList, cachePath=self.__topCachePath)
imageFile = os.path.join(self.__testoutput,
"pair-list-example-mcs-alignment.pdf")
aML = oed.alignPairList(imagePath=imageFile)
if len(aML) > 0:
for (rCC, rAt, tCC, tAt) in aML:
self.__lfh.write("%5s %-5s %5s %-5s\n" %
(rCC, rAt, tCC, tAt))
except: # noqa: E722 pylint: disable=bare-except
traceback.print_exc(file=self.__lfh)
self.fail()
def testMCSAlignAtomMap(self):
"""Test case - match test with return of atom maps"""
self.__lfh.write("\nStarting OeAlignDepictTests testMCSAlignAtomMap\n")
try:
pairIdList = self.__readPairList(fn=self.__rnaPairFile)
oed = OeDepictMCSAlign(verbose=self.__verbose, log=self.__lfh)
for refId, fitId in pairIdList:
oed.setRefId(refId, cachePath=self.__topCachePath)
oed.setFitId(fitId, cachePath=self.__topCachePath)
aML = oed.testAlign()
if len(aML) > 0:
self.__lfh.write("Match suceeded for: %s %s\n" %
(refId, fitId))
else:
self.__lfh.write("Match failed for: %s %s\n" %
(refId, fitId))
except: # noqa: E722 pylint: disable=bare-except
traceback.print_exc(file=self.__lfh)
self.fail()
def testMCSAlignRnaPairListDepict(self):
"""Test case - Modified RNA nucleotide alignment with parent nucleotied using pair list input"""
self.__lfh.write(
"\nStarting OeAlignDepictTests testMCSAlignRnaPairListDepict\n")
try:
pairIdList = self.__readPairList(fn=self.__rnaPairFile)
oed = OeDepictMCSAlign(verbose=self.__verbose, log=self.__lfh)
oed.setPairIdList(pairIdList, cachePath=self.__topCachePath)
imageFile = os.path.join(self.__testoutput,
"rna-modified-pair-alignment.pdf")
aML = oed.alignPairList(imagePath=imageFile)
if len(aML) > 0:
for (rCC, rAt, tCC, tAt) in aML:
self.__lfh.write("%5s %-5s %5s %-5s\n" %
(rCC, rAt, tCC, tAt))
except: # noqa: E722 pylint: disable=bare-except
traceback.print_exc(file=self.__lfh)
self.fail()
def testMCSAlignPairDepict(self):
"""Test case - Simple pairwise MCSS alignment - Each aligned pair output to a separate image file"""
self.__lfh.write(
"\nStarting OeAlignDepictTests tstMCSalignPairDepict\n")
try:
oed = OeDepictMCSAlign(verbose=self.__verbose, log=self.__lfh)
oed.setRefId(self.__refId, cachePath=self.__topCachePath)
for fitId in self.__idList:
oed.setFitId(fitId, cachePath=self.__topCachePath)
fName = os.path.join(
self.__testoutput,
"ref-" + self.__refId + "-trg-" + fitId + ".png")
aML = oed.alignPair(imagePath=fName)
if len(aML) > 0:
for (rCC, rAt, tCC, tAt) in aML:
self.__lfh.write("%5s %-5s %5s %-5s\n" %
(rCC, rAt, tCC, tAt))
except: # noqa: E722 pylint: disable=bare-except
traceback.print_exc(file=self.__lfh)
self.fail()
def testMCSRelaxAlignPairDepict(self):
"""Test case - Relaxed pairwise MCSS alignment -"""
self.__lfh.write(
"\nStarting OeAlignDepictTests testMCSRelaceAlignPairDepict\n")
try:
oed = OeDepictMCSAlign(verbose=self.__verbose, log=self.__lfh)
oed.setSearchType(sType="relaxed")
oed.setRefPath(ccPath=os.path.join(self.__examples,
"PRDCC_000225.cif"),
title="PRD_000225",
suppressHydrogens=False)
oed.setFitPath(ccPath=os.path.join(self.__examples,
"L_LDI_990_.comp.cif"),
title="L_LDI_990",
suppressHydrogens=False)
fName = os.path.join(self.__testoutput, "relaxed-fit.png")
aML = oed.alignPair(imagePath=fName)
if len(aML) > 0:
for (rCC, rAt, tCC, tAt) in aML:
self.__lfh.write("%5s %-5s %5s %-5s\n" %
(rCC, rAt, tCC, tAt))
except Exception as e: # noqa: F841 pylint: disable=unused-variable
traceback.print_exc(file=self.__lfh)
self.fail()