def depict_smiles(smiles): """ OEChem and OEDepict image generation """ # Image to draw on image = OEImage(400, 400) # Process SMILES mol = OEGraphMol() parsed = OESmilesToMol(mol, str(unquote(smiles))) if parsed: # Create image of molecule newtitle = [] for c in mol.GetTitle(): newtitle.append(choice(ALL_EMOJI)) mol.SetTitle(("".join(newtitle)).encode("UTF-8")) OEPrepareDepiction(mol) disp = OE2DMolDisplay(mol) for adisp in disp.GetAtomDisplays(): adisp.SetLabel(choice(ALL_EMOJI).encode("UTF-8")) OERenderMolecule(image, disp) else: # Create error image font = OEFont(OEFontFamily_Helvetica, OEFontStyle_Default, 20, OEAlignment_Center, OERed) image.DrawText(OE2DPoint(image.GetWidth()/2.0, image.GetHeight()/2.0), 'Your SMILES is not valid', font) img_content = OEWriteImageToString('svg', image) return Response(img_content, mimetype='image/svg+xml')
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