def _set_aromatic(cls, ring_matches: List[Dict[int, int]], oe_molecule: oechem.OEMol): """Flag all specified ring atoms and all ring bonds between those atoms as being aromatic. Parameters ---------- ring_matches The indices of the atoms in each of the rings to flag as aromatic. oe_molecule The molecule to assign the aromatic flags to. """ atoms = {atom.GetIdx(): atom for atom in oe_molecule.GetAtoms()} bonds = { tuple(sorted((bond.GetBgnIdx(), bond.GetEndIdx()))): bond for bond in oe_molecule.GetBonds() } for ring_match in ring_matches: ring_atom_indices = {match for match in ring_match.values()} for matched_atom_index in ring_atom_indices: atoms[matched_atom_index].SetAromatic(True) for (index_a, index_b), bond in bonds.items(): if index_a not in ring_atom_indices or index_b not in ring_atom_indices: continue if not bond.IsInRing(): continue bond.SetAromatic(True)
def num_nitrogens_in_molecule(mol: oechem.OEMol): """ Counts the number of trivalent nitrogens in the given molecule. """ checker = oechem.OEIsInvertibleNitrogen() num_trivalent_nitrogens = 0 for atom in mol.GetAtoms(): if checker(atom): num_trivalent_nitrogens += 1 return num_trivalent_nitrogens
def _get_node_features(self, mol: oechem.OEMol) -> np.ndarray: node_feat = [self._featurize_atom(a) for a in mol.GetAtoms()] node_feat = np.array(node_feat) return node_feat
def add_h(mol: oechem.OEMol): """Add explicit hydrogens to a molecule""" for atom in mol.GetAtoms(): oechem.OEAddExplicitHydrogens(mol, atom)
def _relevant_if_contains_nitrogen(mol: oechem.OEMol) -> bool: return any(atom.GetAtomicNum() == _NITROGEN for atom in mol.GetAtoms())
def add_h(mol: oechem.OEMol): """Add explicit hydrogens for test cases""" for atom in mol.GetAtoms(): oechem.OEAddExplicitHydrogens(mol, atom)
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