def testCompareByBuildType(self):
"""Compare depictions constructed molecules with various builds from chemical defintions -
all build types 8769 (all)
connect - smiles 6743
model vs iso smiles 5937
ideal va iso smiles 7047
"""
doDepict = False
ccResultD = {}
genResultD = {}
smilesByBuildTypeD = {}
try:
ccMolD, ccIdxD = self.__getChemCompDefs()
#
limitPerceptions = True
# molBuildTypeL = ["model-xyz", "ideal-xyz", "connection-table", "oe-iso-smiles"]
molBuildTypeL = ["ideal-xyz", "oe-iso-smiles"]
#
startTime = time.time()
oefm = OeMoleculeFactory()
oefm.setQuiet()
for molBuildType in molBuildTypeL:
for ccId, idxD in ccIdxD.items():
ccObj = ccMolD[ccId]
# ----
ccIsoSmiles = idxD["oe-iso-smiles"]
ccSmiles = idxD["oe-smiles"]
# ----
tId = oefm.setChemCompDef(ccObj)
if not tId:
logger.info("Skipping bad component %r", ccId)
continue
self.assertEqual(tId, ccId)
ok = oefm.build(molBuildType=molBuildType,
limitPerceptions=limitPerceptions)
if not ok:
logger.info("Build using %r failed for %s",
molBuildType, ccId)
continue
# ------
oeMol = oefm.getGraphMol()
oeIsoSmiles = oefm.getIsoSMILES()
oeSmiles = oefm.getCanSMILES()
ccEq = oeIsoSmiles == ccIsoSmiles and oeSmiles == ccSmiles
#
oefmR = OeMoleculeFactory()
oefmR.setQuiet()
ccIdGen = ccId + "_gen"
oefmR.setDescriptor(oeIsoSmiles, "oe-iso-smiles", ccIdGen)
ok = oefmR.build(molBuildType="oe-iso-smiles",
limitPerceptions=limitPerceptions)
if not ok:
logger.info("Build using %r failed for %s",
molBuildType, ccIdGen)
continue
# ------
#
# oeMolGen = oefmR.getGraphMol()
oeIsoSmilesGen = oefmR.getIsoSMILES()
oeSmilesGen = oefmR.getCanSMILES()
genEq = oeIsoSmiles == oeIsoSmilesGen and oeSmiles == oeSmilesGen
smilesByBuildTypeD.setdefault(ccId, {}).setdefault(
molBuildType, []).append(oeIsoSmilesGen)
#
logger.debug("%s buildType %s ccEq %r genEq %r", ccId,
molBuildType, ccEq, genEq)
if not ccEq:
ccResultD.setdefault(molBuildType, []).append(ccId)
if not genEq:
genResultD.setdefault(molBuildType, []).append(ccId)
if doDepict:
pS = "-limited" if limitPerceptions else ""
imagePath = os.path.join(
self.__workPath,
ccId + "-%s%s.svg" % (molBuildType, pS))
oed = OeDepict()
title = ""
oed.setMolTitleList([(ccId, oeMol, title)])
oed.setDisplayOptions(labelAtomName=False,
labelAtomCIPStereo=True,
labelAtomIndex=False,
labelBondIndex=False,
cellBorders=False,
bondDisplayWidth=0.5)
oed.setGridOptions(rows=1, cols=1)
oed.prepare()
oed.write(imagePath)
logger.info(
"Completed comparing %d molecules in %d builds (%.4f seconds)",
len(ccIdxD), len(molBuildTypeL),
time.time() - startTime)
#
#
for molBuildType in molBuildTypeL:
if molBuildType in genResultD:
logger.info("GEN %s (%d) %r", molBuildType,
len(genResultD[molBuildType]),
genResultD[molBuildType])
numDiff = 0
for ccId, btD in smilesByBuildTypeD.items():
tS = set()
for molBuildType, sL in btD.items():
tS.add(sL[0])
if len(tS) > 1:
numDiff += 1
logger.debug("%s diff smiles (%d) %r", ccId, len(tS), tS)
logger.info("Components with inconsistent SMILES %d", numDiff)
#
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testDepictCCIdList(self):
"""Test case - single OE molecule depiction.
labelAtomName=True, labelAtomCIPStereo=True, labelAtomIndex=False, labelBondIndex=False, abelBondCIPStereo=True, cellBorders=False, bondDisplayWidth=3.0
"""
try:
oeMolTitleList = self.__getMolDepictList(self.__ccIdList)
for ccId, mol, title in oeMolTitleList:
imagePath = os.path.join(self.__workPath, ccId + ".svg")
oed = OeDepict()
title = ""
oed.setMolTitleList([(ccId, mol, title)])
oed.setDisplayOptions(labelAtomName=False,
labelAtomCIPStereo=True,
labelAtomIndex=False,
labelBondIndex=False,
labelBondCIPStereo=True,
cellBorders=False,
bondDisplayWidth=8.0)
oed.setGridOptions(rows=1, cols=1, cellBorders=False)
oed.prepare()
oed.write(imagePath)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testDepictByBuildType(self):
"""Compare depictions constructed molecules with various builds from chemical defintions -"""
try:
ccIdList = self.__ccIdList
ccMolD = self.__getChemCompDefs()
#
limitPerceptions = True
molBuildTypeL = ["model-xyz", "ideal-xyz", "connection-table", "oe-iso-smiles"]
#
startTime = time.time()
oefm = OeMoleculeFactory()
for molBuildType in molBuildTypeL:
for ccId in ccIdList:
ccObj = ccMolD[ccId]
# ----
tId = oefm.setChemCompDef(ccObj)
self.assertEqual(tId, ccId)
ok = oefm.build(molBuildType=molBuildType, limitPerceptions=limitPerceptions)
if not ok:
logger.info("Build using %r failed for %s", molBuildType, ccId)
continue
#
oeMol = oefm.getGraphMol()
pS = "-limited" if limitPerceptions else ""
imagePath = os.path.join(self.__workPath, ccId + "-%s%s.svg" % (molBuildType, pS))
oed = OeDepict()
title = ""
oed.setMolTitleList([(ccId, oeMol, title)])
oed.setDisplayOptions(labelAtomName=False, labelAtomCIPStereo=True, labelAtomIndex=False, labelBondIndex=False, cellBorders=False, bondDisplayWidth=0.5)
oed.setGridOptions(rows=1, cols=1)
oed.prepare()
oed.write(imagePath)
logger.info("Completed depictions on %d molecules (%.4f seconds)", len(ccIdList) * len(molBuildTypeL), time.time() - startTime)
#
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testDepictOneSDF(self):
"""Test case - get, read, build OE molecule from SDF file, and depict the molecule."""
try:
imagePath = os.path.join(self.__workPath, "benzene-from-smi.svg")
sdfPath = os.path.join(self.__dataPath, "ATP.sdf")
oeio = OeIoUtils()
oeMolL = oeio.fileToMols(sdfPath)
#
oed = OeDepict()
oed.setMolTitleList([("ATP", oeMolL[0], "Title for ATP")])
oed.setDisplayOptions(labelAtomName=True,
labelAtomCIPStereo=True,
labelBondCIPStereo=True,
labelAtomIndex=False,
labelBondIndex=False,
bondDisplayWidth=0.5)
oed.setGridOptions(rows=1, cols=1)
oed.prepare()
oed.write(imagePath)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testDepictSMILES(self):
"""Test case - create depiction from SMILES descriptor."""
try:
imagePath = os.path.join(self.__workPath, "benzene-from-smi.svg")
oeio = OeIoUtils()
oeMol = oeio.smilesToMol("c1ccccc1")
oed = OeDepict()
oed.setMolTitleList([("benzene", oeMol, "Title for benzene")])
oed.setDisplayOptions(labelAtomName=False,
labelAtomCIPStereo=True,
labelBondCIPStereo=True,
labelAtomIndex=False,
labelBondIndex=False,
bondDisplayWidth=1.0)
oed.setGridOptions(rows=1, cols=1)
oed.prepare()
oed.write(imagePath)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testDepictGrid(self):
"""Test case - depict molecule list grid."""
try:
oeMolTitleList = self.__getMolDepictList(self.__ccIdList)
oed = OeDepict()
oed.setMolTitleList(oeMolTitleList)
oed.setDisplayOptions(imageX=1000,
imageY=1000,
labelAtomName=True,
labelAtomCIPStereo=True,
labelBondCIPStereo=True,
labelAtomIndex=False,
labelBondIndex=False,
bondDisplayWidth=0.5)
oed.setGridOptions(rows=2, cols=2)
oed.prepare()
oed.write(os.path.join(self.__workPath, "myIdListtest.png"))
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testDepictCCIdListLabeled(self):
"""Test case - single OE molecule depiction."""
try:
oeMolTitleList = self.__getMolDepictList(self.__ccIdList)
for ccId, mol, title in oeMolTitleList:
imagePath = os.path.join(self.__workPath,
ccId + "-labeled.svg")
oed = OeDepict()
title = ""
oed.setMolTitleList([(ccId, mol, title)])
bondDisplayWidth = 10.0
numAtoms = mol.NumAtoms()
if numAtoms > 100 and numAtoms <= 200:
bondDisplayWidth = 6.0
elif mol.NumAtoms() > 200:
bondDisplayWidth = 4.0
oed.setDisplayOptions(
labelAtomName=True,
labelAtomCIPStereo=True,
labelAtomIndex=False,
labelBondIndex=False,
labelBondCIPStereo=True,
cellBorders=False,
bondDisplayWidth=bondDisplayWidth,
)
oed.setGridOptions(rows=1, cols=1, cellBorders=False)
oed.prepare()
oed.write(imagePath)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def __depictOne(self, oeMol, imagePath, **kwargs):
"""Single
Args:
oeMol (object): instance of an OE graph molecule
imagePath (string): file path for image
Returns:
bool: True for success or False otherwise
"""
try:
title = kwargs.get("title", None)
oed = OeDepict()
oed.setMolTitleList([("Target", oeMol, title)])
# ---
bondDisplayWidth = 10.0
numAtoms = oeMol.NumAtoms()
if numAtoms > 100 and numAtoms <= 200:
bondDisplayWidth = 6.0
elif numAtoms > 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,
)
oed.setGridOptions(rows=1, cols=1, cellBorders=False)
oed.prepare()
oed.write(imagePath)
self.__imageCount += 1
return True
except Exception as e:
logger.exception("Failing with %s", str(e))
return False
def makeImages(self):
""" Create images for all public chemical components with and without atom labels.
"""
try:
if not self.__setLicense(self.__licensePath):
logger.error("Invalid license details - exiting")
return False
for ccId, oeMol in self.__oeMolD.items():
imagePath = os.path.join(self.__imagePath, "image", ccId[0],
ccId + ".svg")
oed = OeDepict()
title = ""
oed.setMolTitleList([(ccId, oeMol, title)])
# ---
bondDisplayWidth = 10.0
numAtoms = oeMol.NumAtoms()
if numAtoms > 100 and numAtoms <= 200:
bondDisplayWidth = 6.0
elif numAtoms > 200:
bondDisplayWidth = 4.0
# ---
oed.setDisplayOptions(
labelAtomName=False,
labelAtomCIPStereo=True,
labelAtomIndex=False,
labelBondIndex=False,
labelBondCIPStereo=True,
cellBorders=False,
bondDisplayWidth=bondDisplayWidth,
)
oed.setGridOptions(rows=1, cols=1, cellBorders=False)
oed.prepare()
oed.write(imagePath)
for ccId, oeMol in self.__oeMolD.items():
imagePath = os.path.join(self.__imagePath, "image_labeled",
ccId[0], ccId + ".svg")
oed = OeDepict()
title = ""
oed.setMolTitleList([(ccId, oeMol, title)])
# ---
bondDisplayWidth = 10.0
numAtoms = oeMol.NumAtoms()
if numAtoms > 100 and numAtoms <= 200:
bondDisplayWidth = 6.0
elif numAtoms > 200:
bondDisplayWidth = 4.0
# ---
oed.setDisplayOptions(
labelAtomName=True,
labelAtomCIPStereo=True,
labelAtomIndex=False,
labelBondIndex=False,
labelBondCIPStereo=True,
cellBorders=False,
bondDisplayWidth=bondDisplayWidth,
)
oed.setGridOptions(rows=1, cols=1, cellBorders=False)
oed.prepare()
oed.write(imagePath)
return True
except Exception as e:
logger.exception("Failing with %s", str(e))
return False
def testDepictAll(self):
"""Test case - single OE molecule depiction."""
try:
for ccId, oeMol in self.__oeMolD.items():
imagePath = os.path.join(self.__workPath, "image", ccId[0],
ccId + ".svg")
oed = OeDepict()
title = ""
oed.setMolTitleList([(ccId, oeMol, title)])
oed.setDisplayOptions(labelAtomName=False,
labelAtomCIPStereo=True,
labelAtomIndex=False,
labelBondIndex=False,
labelBondCIPStereo=True,
cellBorders=False,
bondDisplayWidth=0.5)
oed.setGridOptions(rows=1, cols=1)
oed.prepare()
oed.write(imagePath)
for ccId, oeMol in self.__oeMolD.items():
imagePath = os.path.join(self.__workPath, "image_labeled",
ccId[0], ccId + ".svg")
oed = OeDepict()
title = ""
oed.setMolTitleList([(ccId, oeMol, title)])
oed.setDisplayOptions(labelAtomName=True,
labelAtomCIPStereo=True,
labelAtomIndex=False,
labelBondIndex=False,
abelBondCIPStereo=True,
cellBorders=False,
bondDisplayWidth=0.5)
oed.setGridOptions(rows=1, cols=1)
oed.prepare()
oed.write(imagePath)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()