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 _get_adjacency_matrix(self, mol:oechem.OEMol) -> np.ndarray:
adj_mat = np.zeros((self.num_atoms, self.num_atoms))
for bond in mol.GetBonds():
bgn_idx = bond.GetBgnIdx()
end_idx = bond.GetEndIdx()
adj_mat[bgn_idx][end_idx] = 1
adj_mat[end_idx][bgn_idx] = 1
return adj_mat
def _add_charge_props(mol: oechem.OEMol, charged_copy: oechem.OEMol,
am1_results: oequacpac.OEAM1Results):
"""
Adds data from AM1 results to the given molecule. After this method is
called, the molecule will have a danceprops.DANCE_CHARGED_COPY_KEY
data storing the charged copy of the molecule. On that charged copy,
each bond will have a danceprops.DANCE_BOND_ORDER_KEY data telling its
Wiberg bond order.
"""
for bond in charged_copy.GetBonds():
bond.SetData(
danceprops.DANCE_BOND_ORDER_KEY,
am1_results.GetBondOrder(bond.GetBgnIdx(), bond.GetEndIdx()))
mol.SetData(danceprops.DANCE_CHARGED_COPY_KEY, charged_copy)
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