def writeOther(self, oeMol, filePath, title='None', constantMol=False):
try:
ofs = oemolostream()
ofs.open(filePath)
myMol = OEMol(oeMol)
myMol.SetTitle(title)
self.__lfh.write(
"+PdbxBuildChemComp.writeOther writing %s title %s\n" %
(filePath, myMol.GetTitle()))
if constantMol:
OEWriteConstMolecule(ofs, myMol)
else:
OEWriteMolecule(ofs, myMol)
return True
except Exception as e:
self.__lfh.write("+PdbxBuildChemComp.writeOther FAILING %s\n" %
str(e))
traceback.print_exc(file=self.__lfh)
return False
class OeBuildModelMol(object):
''' Utility methods for constructing OEMols from chemical component model instances.
'''
def __init__(self, verbose=True, log=sys.stderr):
self.__verbose = verbose
self.__debug = False
self.__lfh = log
#
# File system path to the chemical component dictionary definitions in (CVS checkout organization)
#
# Internal storage for current OE molecule
self.__oeMol = None
#
# Component identifier
#
self.__ccId = None
self.__modelId = None
#
# dictionary of element counts eD[atno]=count
self.__eD = {}
#
# Source data categories objects from chemical component definitions.
#
self.__ccAtomDL = None
self.__ccBondDL = None
self.__molXyzL = []
def setDebug(self, flag):
self.__debug = flag
def setChemCompModelPath(self, modelPath):
try:
ccm = PdbxChemCompModelIo(verbose=self.__verbose, log=self.__lfh)
ccm.setFilePath(modelPath)
ccDL = ccm.getAttribDictList(catName='pdbx_chem_comp_model')
cmp = PdbxChemCompModel(ccDL[0], self.__verbose, self.__lfh)
self.__modelId = cmp.getId()
self.__ccId = cmp.getCompId()
self.__ccAtomDL = ccm.getAttribDictList(
catName='pdbx_chem_comp_model_atom')
self.__ccBondDL = ccm.getAttribDictList(
catName='pdbx_chem_comp_model_bond')
return self.__modelId
except Exception as e:
self.__lfh.write(
"OeBuildModelMol(setChemCompModelPath) Fails for %s %s\n" %
(modelPath, str(e)))
traceback.print_exc(file=self.__lfh)
return None
def __clear(self):
self.__oeMol = None
self.__eD = {}
def serialize(self):
""" Create a string representing the content of the current OE molecule. This
serialization uses the OE internal binary format.
"""
oms = oemolostream()
oms.SetFormat(OEFormat_OEB)
oms.openstring()
OEWriteMolecule(oms, self.__oeMol)
if (self.__debug):
self.__lfh.write("OeBuildModelMol(Serialize) SMILES %s\n" %
OECreateCanSmiString(self.__oeMol))
self.__lfh.write("OeBuildModelMol(Serialize) atoms = %d\n" %
self.__oeMol.NumAtoms())
return oms.GetString()
def deserialize(self, oeS):
""" Reconstruct an OE molecule from the input string serialization (OE binary).
The deserialized molecule is used to initialize the internal OE molecule
within this object.
Returns True for success or False otherwise.
"""
self.__clear()
ims = oemolistream()
ims.SetFormat(OEFormat_OEB)
ims.openstring(oeS)
nmol = 0
mList = []
# for mol in ims.GetOEGraphMols():
for mol in ims.GetOEMols():
if (self.__debug):
self.__lfh.write("OeBuildModelMol(deserialize) SMILES %s\n" %
OECreateCanSmiString(mol))
self.__lfh.write("OeBuildModelMol(deserialize) title %s\n" %
mol.GetTitle())
self.__lfh.write("OeBuildModelMol(deserialize) atoms %d\n" %
mol.NumAtoms())
# mList.append(OEGraphMol(mol))
mList.append(OEMol(mol))
nmol += 1
#
if nmol >= 1:
self.__oeMol = mList[0]
self.__ccId = self.__oeMol.GetTitle()
#
if (self.__debug):
self.__lfh.write("OeBuildModelMol(deserialize) mols %d\n" %
nmol)
self.__lfh.write("OeBuildModelMol(deserialize) id %s\n" %
self.__ccId)
self.__lfh.write("OeBuildModelMol(deserialize) atoms %d\n" %
self.__oeMol.NumAtoms())
return True
else:
return False
def getElementCounts(self):
""" Get the dictionary of element counts (eg. eD[iAtNo]=iCount).
"""
if len(self.__eD) == 0:
# calculate from current oeMol
try:
self.__eD = {}
for atom in self.__oeMol.GetAtoms():
atNo = atom.GetAtomicNum()
if atNo not in self.__eD:
self.__eD[atNo] = 1
else:
self.__eD[atNo] += 1
except: # noqa: E722 pylint: disable=bare-except
pass
return self.__eD
def build3D(self):
try:
self.__build3D()
return True
except: # noqa: E722 pylint: disable=bare-except
return False
def __build3D(self):
""" Build OE molecule using model instance 3D coordinates and OE stereo perception.
"""
self.__clear()
self.__oeMol = OEMol()
#
self.__oeMol.SetTitle(self.__modelId)
aL = []
# Atom index dictionary
aD = {}
i = 1
for d in self.__ccAtomDL:
ccAt = PdbxChemCompModelAtom(d, self.__verbose, self.__lfh)
atName = ccAt.getName()
aD[atName] = i
i += 1
atNo = ccAt.getAtNo()
if atNo not in self.__eD:
self.__eD[atNo] = 1
else:
self.__eD[atNo] += 1
atType = ccAt.getType()
fc = ccAt.getFormalCharge()
# chFlag=ccAt.isChiral()
# arFlag=ccAt.isAromatic()
isotope = ccAt.getIsotope()
oeAt = self.__oeMol.NewAtom(atNo)
oeAt.SetName(atName)
oeAt.SetFormalCharge(fc)
# oeAt.SetChiral(chFlag)
oeAt.SetIsotope(isotope)
# oeAt.SetAromatic(arFlag)
# if chFlag:
# st=ccAt.getCIPStereo()
# if st == 'S' or st == 'R':
# oeAt.SetStringData("StereoInfo",st)
# if (self.__debug):
# self.__lfh.write("Atom - %s type %s atno %d isotope %d fc %d chFlag %r\n" % (atName,atType,atNo,isotope,fc,chFlag))
cTup = ccAt.getModelCoordinates()
# if (self.__verbose):
# self.__lfh.write("CC %s Atom - %s cTup %r\n" % (self.__ccId,atName,cTup))
self.__oeMol.SetCoords(oeAt, cTup)
if (self.__debug):
self.__lfh.write(
"Atom - %s type %s atno %d isotope %d fc %d (xyz) %r\n" %
(atName, atType, atNo, isotope, fc, cTup))
aL.append(oeAt)
for d in self.__ccBondDL:
ccBnd = PdbxChemCompModelBond(d, self.__verbose, self.__lfh)
(at1, at2) = ccBnd.getBond()
iat1 = aD[at1] - 1
iat2 = aD[at2] - 1
iType = ccBnd.getIntegerType()
#
# arFlag=ccBnd.isAromatic()
if (self.__debug):
self.__lfh.write(" %s %d -- %s %d (%d)\n" %
(at1, iat1, at2, iat2, iType))
oeBnd = self.__oeMol.NewBond(aL[iat1], aL[iat2], iType) # noqa: F841 pylint: disable=unused-variable
# oeBnd.SetAromatic(arFlag)
# if arFlag:
# oeBnd.SetIntType(5)
# st=ccBnd.getStereo()
# if st == 'E' or st =='Z':
# oeBnd.SetStringData("StereoInfo",st)
#
# run standard perceptions --
#
self.__oeMol.SetDimension(3)
OE3DToInternalStereo(self.__oeMol)
OEFindRingAtomsAndBonds(self.__oeMol)
# Other aromatic models: OEAroModelMDL or OEAroModelDaylight
OEAssignAromaticFlags(self.__oeMol, OEAroModelOpenEye)
self.updateCIPStereoOE()
def updateCIPStereoOE(self):
""" OE perception of CIP stereo -
"""
for atom in self.__oeMol.GetAtoms():
OEPerceiveCIPStereo(self.__oeMol, atom)
for bond in self.__oeMol.GetBonds():
if (bond.GetOrder() == 2):
OEPerceiveCIPStereo(self.__oeMol, bond)
def getGraphMolSuppressH(self):
""" Return the current constructed OE molecule with hydrogens suppressed.
"""
# OESuppressHydrogens(self.__oeMol, retainPolar=False,retainStereo=True,retainIsotope=True)
OESuppressHydrogens(self.__oeMol)
return self.__oeMol
def getMol(self):
""" Return the current constructed OE molecule.
"""
return self.__oeMol
def getCanSMILES(self):
""" Return the cannonical SMILES string derived from the current OD molecule.
"""
return OECreateCanSmiString(self.__oeMol)
def getIsoSMILES(self):
""" Return the cannonical stereo SMILES string derived from the current OE molecule.
"""
return OECreateIsoSmiString(self.__oeMol)
def getFormula(self):
""" Return the Hill order formulat derived from the current OE molecule.
"""
return OEMolecularFormula(self.__oeMol)
def getInChIKey(self):
""" Return the InChI key derived from the current OE molecule.
"""
return OECreateInChIKey(self.__oeMol)
def getInChI(self):
""" Return the InChI string derived from the current OE molecule.
"""
return OECreateInChI(self.__oeMol)
def getTitle(self):
""" Return the title assigned to the current OE molecule
"""
return self.__oeMol.GetTitle()
def getCoords(self):
""" Return coordinate list if a 3D molecule is built -- otherwise an empty list --
"""
return self.__molXyzL