def testMCSAlignPairDepict(self):
"""Test case - Simple pairwise MCSS alignment - Each aligned pair output to a separate image file"""
try:
oed = OeDepictMCSAlignPage()
oed.setDisplayOptions(labelAtomName=True,
labelAtomCIPStereo=True,
labelAtomIndex=False,
labelBondIndex=False,
highlightStyleFit="ballAndStickInverse",
bondDisplayWidth=0.5)
oed.setRefMol(self.__oeMolD[self.__refId], self.__refId)
fitTupList = self.__getMolDepictList(self.__idList)
for fitTup in fitTupList:
oed.setFitMol(fitTup[0], fitTup[1])
imgPath = os.path.join(
self.__workPath,
"ref-" + self.__refId + "-trg-" + fitTup[1] + ".svg")
logger.info("Using image path %r", imgPath)
aML = oed.alignPair(imagePath=imgPath)
# self.assertGreater(len(aML), 2)
if aML:
for (rCC, rAt, tCC, tAt) in aML:
logger.debug("%5s %-5s %5s %-5s", rCC, rAt, tCC, tAt)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testMCSAlignListDepict(self):
"""Test case - List view of MCS alignment on single image -"""
try:
pairList = [(tup[0].upper(), self.__oeMolD[tup[0].upper()],
tup[1].upper(), self.__oeMolD[tup[1].upper()])
for tup in self.__pairIdList]
oed = OeDepictMCSAlignPage()
oed.setDisplayOptions(
imageSizeX=1500,
imageSizeY=1500,
labelAtomName=True,
labelAtomCIPStereo=True,
labelAtomIndex=False,
labelBondIndex=False,
highlightStyleFit="ballAndStickInverse",
gridRows=3,
gridCols=3,
bondDisplayWidth=1.0,
)
oed.setPairMolList(pairList)
imageFile = os.path.join(self.__workPath,
"mcs-align-with-list-single.svg")
aML = oed.alignOneWithList(imagePath=imageFile)
self.assertGreater(len(aML), 2)
if aML:
for (rCC, rAt, tCC, tAt) in aML:
logger.debug("%5s %-5s %5s %-5s", rCC, rAt, tCC, tAt)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def __pairDepictPage(self,
imagePath,
refId,
refTitle,
refMol,
fitId,
fitTitle,
fitMol,
matchOpts="strict"):
"""Depict pairwise alignment of the input reference and fit molecules.
Args:
imagePath (str): path to image (format by path extension)
refId (str): reference molecule identifier
refTitle (str): reference molecule title
refMol (obj): reference OE molecule object
fitId (str): fit molecule identifier
fitTitle (str): fit molecule title
fitMol (obj): fit OE molecule object
matchOpts (str, optional): alignment criteria (relaxed|relaxed-stereo|strict). Defaults to "strict".
Returns:
(list): atom mapping in all aligned figures
[(reference component Id, reference atom name, fit chemical component Id, fit atom name)
"""
aML = []
try:
oed = OeDepictMCSAlignPage()
oed.setSearchType(sType=matchOpts)
oed.setRefMol(refMol, refId, title=refTitle)
oed.setFitMol(fitMol, fitId, title=fitTitle)
oed.setDisplayOptions(
imageSizeX=2000,
imageSizeY=1000,
labelAtomName=True,
labelAtomCIPStereo=True,
labelAtomIndex=False,
labelBondIndex=False,
highlightStyleFit="ballAndStickInverse",
bondDisplayWidth=0.5,
highLightMatchColorRef="green",
highLightNotMatchColorRef="pink",
)
aML = oed.alignPair(imagePath=imagePath)
if aML:
for (rCC, rAt, tCC, tAt) in aML:
logger.debug("%5s %-5s %5s %-5s", rCC, rAt, tCC, tAt)
except Exception as e:
logger.exception("Failing with %s", str(e))
return aML
def __displayAlignedPair(self,
ccIdRef,
oeMolRef,
ccIdFit,
oeMolFit,
title=None):
oed = OeDepictMCSAlignPage()
oed.setDisplayOptions(labelAtomName=True,
labelAtomCIPStereo=True,
labelAtomIndex=False,
labelBondIndex=False,
highlightStyleFit="ballAndStickInverse",
bondDisplayWidth=0.5)
oed.setRefMol(oeMolRef, ccIdRef)
oed.setFitMol(oeMolFit, ccIdFit)
myTitle = title if title else "compare"
imgPath = os.path.join(
self.__workPath, myTitle + "-" + ccIdRef + "-" + ccIdFit + ".svg")
# logger.info("Using image path %r", imgPath)
aML = oed.alignPair(imagePath=imgPath)
if aML:
for (rCC, rAt, tCC, tAt) in aML:
logger.debug("%5s %-5s %5s %-5s", rCC, rAt, tCC, tAt)
oed = OeDepictMCSAlignPage()
oed.setDisplayOptions(labelAtomName=True,
labelAtomCIPStereo=True,
labelAtomIndex=False,
labelBondIndex=False,
highlightStyleFit="ballAndStickInverse",
bondDisplayWidth=0.5)
def testRoundTrip(self):
"""Round trip smiles comparisons -"""
try:
ccMolD = self.__getChemCompDefs()
# useCache = True
# quietFlag = False
# molBuildTypeL = ["model-xyz", "ideal-xyz", None]
# molBuildTypeL = [None]
buildTypeRef = "oe-iso-smiles"
oemf1 = OeMoleculeFactory()
oemf2 = OeMoleculeFactory()
#
for ccId, ccObj in ccMolD.items():
# ----
ccIt = iter(PdbxChemCompIt(ccObj))
cc = next(ccIt)
formula = cc.getFormulaWithCharge()
# ccId = cc.getId()
ccName = cc.getName()
ifCharge = cc.getFormalChargeAsInt()
isAmbiguous = cc.getAmbiguousFlag() in ["Y", "y"]
isCurrent = cc.getReleaseStatus() in ["REL"]
logger.debug("%s name %r formula %r charge %d", ccId, ccName,
formula, ifCharge)
# ----
ccId = oemf1.setChemCompDef(ccObj)
ok = oemf1.build(molBuildType=buildTypeRef,
limitPerceptions=False)
if not ok:
logger.info(
"Build using %r failed for %s (ambiguous flag %r current %r)",
buildTypeRef, ccId, isAmbiguous, isCurrent)
#
isDiff = False
#
if isDiff:
genIsoSmi = oemf1.getCanSMILES()
oemf2 = OeMoleculeFactory()
oemf2.setDescriptor(genIsoSmi, "oe-iso-smiles", ccId)
oemf2.build(molBuildType="oe-iso-smiles",
limitPerceptions=False)
regenIsoSmi = oemf2.getIsoSMILES()
if genIsoSmi != regenIsoSmi:
logger.info(
"%s regenerated ISOSMILES differ \n -- INP: %s\n -- OUT: %s",
ccId, genIsoSmi, regenIsoSmi)
oed = OeDepictMCSAlignPage()
oed.setDisplayOptions(
labelAtomName=True,
labelAtomCIPStereo=True,
labelAtomIndex=False,
labelBondIndex=False,
labelBondCIPStereo=True,
highlightStyleFit="ballAndStickInverse",
highLightNotMatchColorRef="pink",
bondDisplayWidth=0.5,
)
oed.setRefMol(oemf1.getGraphMol(), ccId)
oed.setFitMol(oemf2.getGraphMol(), ccId)
imgPath = os.path.join(
self.__workPath,
"compare-assigned-" + ccId + "-calc-" + ccId + ".svg")
logger.info("Using image path %r", imgPath)
aML = oed.alignPair(imagePath=imgPath)
if aML:
for (rCC, rAt, tCC, tAt) in aML:
logger.info("%5s %-5s %5s %-5s", rCC, rAt, tCC,
tAt)
else:
logger.debug("%s matched all cases", ccId)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def __displayAlignedDescriptorPair(self,
ccId,
descrRef,
buildTypeRef,
descrFit,
buildTypeFit,
title=None,
limitPerceptions=True):
oeioU = OeIoUtils()
oeMolRef = oeioU.descriptorToMol(descrRef,
buildTypeRef,
limitPerceptions=limitPerceptions,
messageTag=ccId + ":" + buildTypeRef)
oeMolFit = oeioU.descriptorToMol(descrFit,
buildTypeFit,
limitPerceptions=limitPerceptions,
messageTag=ccId + ":" + buildTypeFit)
#
oed = OeDepictMCSAlignPage()
oed.setSearchType(sType="graph-relaxed", minAtomMatchFraction=0.50)
oed.setDisplayOptions(labelAtomName=True,
labelAtomCIPStereo=True,
labelAtomIndex=False,
labelBondIndex=False,
highlightStyleFit="ballAndStickInverse",
bondDisplayWidth=0.5)
oed.setRefMol(oeMolRef, ccId)
oed.setFitMol(oeMolFit, ccId)
myTitle = title if title else buildTypeRef + "-" + buildTypeFit
imgPath = os.path.join(self.__workPath, myTitle + "-" + ccId + ".svg")
logger.info("Using image path %r", imgPath)
aML = oed.alignPair(imagePath=imgPath)
if aML:
logger.info("%s aligned image path %r", ccId, imgPath)
for (rCC, rAt, tCC, tAt) in aML:
logger.debug("%5s %-5s %5s %-5s", rCC, rAt, tCC, tAt)
def __depictAlignedPair(self, oeMolRef, displayIdRef, oeMolFit,
displayIdFit, imagePath, **kwargs):
"""Depict pairwise MCSS alignment"""
try:
#
oed = OeDepictMCSAlignPage()
oed.setSearchType(sType="relaxed")
#
oed.setRefMol(oeMolRef, displayIdRef)
oed.setFitMol(oeMolFit, displayIdFit)
#
# imagePath = self.__makeImagePath()
# ---
bondDisplayWidth = 10.0
numAtomsRef = oeMolRef.NumAtoms()
if numAtomsRef > 100 and numAtomsRef <= 200:
bondDisplayWidth = 6.0
elif numAtomsRef > 200:
bondDisplayWidth = 4.0
# ---
oed.setDisplayOptions(
imageSizeX=kwargs.get("imageSizeX", 2500),
imageSizeY=kwargs.get("imageSizeX", 2500),
labelAtomName=kwargs.get("labelAtomName", False),
labelAtomCIPStereo=kwargs.get("labelAtomCIPStereo", True),
labelAtomIndex=kwargs.get("labelAtomIndex", False),
labelBondIndex=kwargs.get("labelBondIndex", False),
labelBondCIPStereo=kwargs.get("labelBondCIPStereo", True),
cellBorders=kwargs.get("cellBorders", True),
bondDisplayWidth=bondDisplayWidth,
highlightStyleFit=kwargs.get("highlightStyleFit",
"ballAndStickInverse"),
)
#
aML = oed.alignPair(imagePath=imagePath)
logger.info("Aligned atom count %d", len(aML))
#
# self.assertGreater(len(aML), 1)
# if aML:
# for (rCC, rAt, tCC, tAt) in aML:
# logger.debug("%5s %-5s %5s %-5s", rCC, rAt, tCC, tAt)
return True
except Exception as e:
logger.exception("Failing with %s", str(e))
return False
def testMCSRelaxAlignPairDepict(self):
"""Test case - Relaxed pairwise MCSS alignment"""
try:
oed = OeDepictMCSAlignPage()
oed.setSearchType(sType="relaxed")
# oed.setDisplayOptions(
# labelAtomName=True, labelAtomCIPStereo=True, labelAtomIndex=False, labelBondIndex=False, highlightStyleFit="ballAndStickInverse", bondDisplayWidth=0.5
# )
oed.setRefMol(self.__oeMolD[self.__refId], self.__refId)
fitTupList = self.__getMolDepictList(self.__idList)
for fitTup in fitTupList:
oed.setFitMol(fitTup[0], fitTup[1])
fName = os.path.join(
self.__workPath, "relaxed-ref-" + self.__refId + "-trg-" +
fitTup[1] + ".svg")
oed.setDisplayOptions(
imageSizeX=2000,
imageSizeY=1000,
labelAtomName=True,
labelAtomCIPStereo=True,
labelAtomIndex=False,
labelBondIndex=False,
highlightStyleFit="ballAndStickInverse",
bondDisplayWidth=1.0,
)
aML = oed.alignPair(imagePath=fName)
logger.debug("refId %r fitId %r aML %r", self.__refId,
fitTup[1], len(aML))
self.assertGreater(len(aML), 1)
if aML:
for (rCC, rAt, tCC, tAt) in aML:
logger.debug("%5s %-5s %5s %-5s", rCC, rAt, tCC, tAt)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()