def clashing_atoms(molecule1: oechem.OEGraphMol,
molecule2: oechem.OEGraphMol) -> bool:
"""
Evaluates if the atoms of two molecules are clashing.
Parameters
----------
molecule1: oechem.OEGraphMol
An OpenEye molecule.
molecule2: oechem.OEGraphMol
An OpenEye molecule.
Returns
-------
: bool
If any atoms of two molecules are clashing
"""
import math
oechem.OEAssignCovalentRadii(molecule1)
oechem.OEAssignCovalentRadii(molecule2)
coordinates1_list = [
molecule1.GetCoords()[x] for x in sorted(molecule1.GetCoords().keys())
]
coordinates2_list = [
molecule2.GetCoords()[x] for x in sorted(molecule2.GetCoords().keys())
]
for atom1, coordinates1 in zip(molecule1.GetAtoms(), coordinates1_list):
for atom2, coordinates2 in zip(molecule2.GetAtoms(),
coordinates2_list):
clash_threshold = atom1.GetRadius() + atom2.GetRadius()
distance = math.sqrt(
sum((coordinate1 - coordinate2)**2.0
for coordinate1, coordinate2 in zip(
coordinates1, coordinates2)))
if distance <= clash_threshold:
return True
return False
class OeBuildMol(object):
''' Utility methods for constructing OEGraphMols from chemical component definition objects.
'''
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
#
# dictionary of element counts eD[atno]=count
self.__eD = {}
#
# Source data categories objects from chemical component definitions.
self.__dcChemCompAtom = None
self.__dcChemCompBond = None
#
self.__molXyzL = []
def setDebug(self, flag):
self.__debug = flag
def setChemCompPath(self, ccPath):
try:
myReader = IoAdapter(self.__verbose, self.__lfh)
cL = myReader.readFile(ccPath)
self.__ccId = cL[0].getName()
self.__dcChemCompAtom = cL[0].getObj("chem_comp_atom")
self.__dcChemCompBond = cL[0].getObj("chem_comp_bond")
return self.__ccId
except Exception as e:
self.__lfh.write("OeBuildMol(setChemCompPath) Fails for %s %s\n" %
(ccPath, str(e)))
traceback.print_exc(file=self.__lfh)
return None
def setOeMol(self, inpOeMol, ccId):
""" Load this object with an existing oeMOL()
"""
self.__clear()
self.__oeMol = OEMol(inpOeMol)
self.__ccId = ccId
self.getElementCounts()
def set(self, ccId, dcChemCompAtom=None, dcChemCompBond=None):
""" Assign source data categories -
"""
self.__ccId = ccId
self.__dcChemCompAtom = dcChemCompAtom
self.__dcChemCompBond = dcChemCompBond
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("OeBuildMol(Serialize) SMILES %s\n" %
OECreateCanSmiString(self.__oeMol))
self.__lfh.write("OeBuildMol(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("OeBuildMol(deserialize) SMILES %s\n" %
OECreateCanSmiString(mol))
self.__lfh.write("OeBuildMol(deserialize) title %s\n" %
mol.GetTitle())
self.__lfh.write("OeBuildMol(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("OeBuildMol(deserialize) mols %d\n" % nmol)
self.__lfh.write("OeBuildMol(deserialize) id %s\n" %
self.__ccId)
self.__lfh.write("OeBuildMol(deserialize) atoms %d\n" %
self.__oeMol.NumAtoms())
return True
else:
return False
def simpleAtomNames(self):
"""
"""
for atom in self.__oeMol.GetAtoms():
atom.SetIntType(atom.GetAtomicNum())
atom.SetType(OEGetAtomicSymbol(atom.GetAtomicNum()))
OETriposAtomNames(self.__oeMol)
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, coordType="model", setTitle=True):
try:
self.__build3D(coordType=coordType, setTitle=setTitle)
return True
except Exception as e:
self.__lfh.write("OeBuildMol(build3D) Failing %s\n" % str(e))
traceback.print_exc(file=self.__lfh)
return False
def __build3D(self, coordType="model", setTitle=True):
""" Build OE molecule using 3D coordinates and OE stereo perception.
"""
self.__clear()
# self.__oeMol=OEGraphMol()
self.__oeMol = OEMol()
#
if setTitle:
self.__oeMol.SetTitle(self.__ccId)
aL = []
# Atom index dictionary
aD = {}
i = 1
atomIt = PdbxChemCompAtomIt(self.__dcChemCompAtom, self.__verbose,
self.__lfh)
for ccAt in atomIt:
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()
leavingAtom = ccAt.getLeavingAtomFlag()
oeAt = self.__oeMol.NewAtom(atNo)
oeAt.SetName(atName)
oeAt.SetFormalCharge(fc)
oeAt.SetStringData("pdbx_leaving_atom_flag", leavingAtom)
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))
if ((coordType == 'model') and ccAt.hasModelCoordinates()):
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)
elif ((coordType == 'ideal') and ccAt.hasIdealCoordinates()):
cTup = ccAt.getIdealCoordinates()
self.__oeMol.SetCoords(oeAt, cTup)
else:
pass
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)
bondIt = PdbxChemCompBondIt(self.__dcChemCompBond, self.__verbose,
self.__lfh)
for ccBnd in bondIt:
(at1, at2) = ccBnd.getBond()
iat1 = aD[at1] - 1
iat2 = aD[at2] - 1
iType = ccBnd.getIntegerType()
#
arFlag = ccBnd.isAromatic() # noqa: F841 pylint: disable=unused-variable
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 updatePerceptions3D(self):
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 build2D(self, setTitle=True): # pylint: disable=unused-argument
try:
self.__build2D(setTitle=True)
return True
except: # noqa: E722 pylint: disable=bare-except
return False
def __build2D(self, setTitle=True):
""" Build molecule using existing assignments of chemical information in the CC definition.
"""
self.__clear()
self.__oeMol = OEGraphMol()
if setTitle:
self.__oeMol.SetTitle(self.__ccId)
aL = []
i = 1
# Atom index dictionary
aD = {}
atomIt = PdbxChemCompAtomIt(self.__dcChemCompAtom, self.__verbose,
self.__lfh)
for ccAt in atomIt:
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()
leavingAtom = ccAt.getLeavingAtomFlag()
oeAt = self.__oeMol.NewAtom(atNo)
oeAt.SetName(atName)
oeAt.SetFormalCharge(fc)
oeAt.SetStringData("pdbx_leaving_atom_flag", leavingAtom)
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))
aL.append(oeAt)
bondIt = PdbxChemCompBondIt(self.__dcChemCompBond, self.__verbose,
self.__lfh)
for ccBnd in bondIt:
(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)
oeBnd.SetAromatic(arFlag)
if arFlag:
oeBnd.SetIntType(5)
st = ccBnd.getStereo()
if st == 'E' or st == 'Z':
oeBnd.SetStringData("StereoInfo", st)
#
# run standard perceptions --
OEFindRingAtomsAndBonds(self.__oeMol)
OEPerceiveChiral(self.__oeMol)
for oeAt in self.__oeMol.GetAtoms():
st = oeAt.GetStringData("StereoInfo")
if st == 'R':
OESetCIPStereo(self.__oeMol, oeAt, OECIPAtomStereo_R)
elif st == 'S':
OESetCIPStereo(self.__oeMol, oeAt, OECIPAtomStereo_S)
for oeBnd in self.__oeMol.GetBonds():
st = oeBnd.GetStringData("StereoInfo")
if st == 'E':
OESetCIPStereo(self.__oeMol, oeBnd, OECIPBondStereo_E)
elif st == 'Z':
OESetCIPStereo(self.__oeMol, oeBnd, OECIPBondStereo_Z)
if (self.__debug):
for ii, atm in enumerate(self.__oeMol.GetAtoms()):
self.__lfh.write("OeBuildMol.build2d - atom %d %s\n" %
(ii, atm.GetName()))
def importFile(self, filePath, type='2D'): # pylint: disable=redefined-builtin
""" Contruct a OEGraphMol using the content of the input file. The input
file must have a file extension recognized by the OE toolkit (e.g. .sdf)
"""
ifs = oemolistream()
if not ifs.open(filePath):
return False
#
# self.__oeMol = OEGraphMol()
self.__oeMol = OEMol()
OEReadMolecule(ifs, self.__oeMol)
# OETriposAtomNames(self.__oeMol)
if type == '2D':
# run standard perceptions --
OEFindRingAtomsAndBonds(self.__oeMol)
OEPerceiveChiral(self.__oeMol)
for oeAt in self.__oeMol.GetAtoms():
st = oeAt.GetStringData("StereoInfo")
if st == 'R':
OESetCIPStereo(self.__oeMol, oeAt, OECIPAtomStereo_R)
elif st == 'S':
OESetCIPStereo(self.__oeMol, oeAt, OECIPAtomStereo_S)
for oeBnd in self.__oeMol.GetBonds():
st = oeBnd.GetStringData("StereoInfo")
if st == 'E':
OESetCIPStereo(self.__oeMol, oeBnd, OECIPBondStereo_E)
elif st == 'Z':
OESetCIPStereo(self.__oeMol, oeBnd, OECIPBondStereo_Z)
elif type == '3D':
# 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()
OEAddExplicitHydrogens(self.__oeMol)
self.__molXyzL = []
aC = {}
for ii, atm in enumerate(self.__oeMol.GetAtoms()):
iAtNum = atm.GetAtomicNum()
if iAtNum in aC:
aC[iAtNum] += 1
else:
aC[iAtNum] = 1
# Less than idea - should have an API
atName = PdbxChemCompConstants._periodicTable[iAtNum - 1] + str(
aC[iAtNum]) # pylint: disable=protected-access
atm.SetName(atName)
#
xyzL = OEFloatArray(3)
self.__oeMol.GetCoords(atm, xyzL)
self.__molXyzL.append(
(ii, atm.GetIdx(), atm.GetAtomicNum(), atm.GetName(),
atm.GetType(), xyzL[0], xyzL[1], xyzL[2]))
return True
def importSmiles(self, smiles):
""" Contruct a OEGraphMol using the input descriptor.
"""
self.__oeMol = OEGraphMol()
if OEParseSmiles(self.__oeMol, smiles):
OEFindRingAtomsAndBonds(self.__oeMol)
OEPerceiveChiral(self.__oeMol)
return True
#
return False
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 OEMol(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 getCcId(self):
""" Return the CC id of this object -
"""
return self.__ccId
def getCoords(self):
""" Return coordinate list if a 3D molecule is built -- otherwise an empty list --
"""
return self.__molXyzL
