def SetMolProp(self, value, pname, ptype='s', plen=6, floatPoint=3):
if not self._pmp:
logger.warning('SetAtomsProp: No PMP information!')
return
lines = self._pmp.splitlines()
plen = str(plen)
newpmp = ""
if ptype == 'str' or ptype == 'string' or ptype == 's':
ptype = 's'
elif ptype == 'float' or ptype == 'double' or ptype == 'f':
ptype = 'f'
elif ptype == 'int' or ptype == 'long' or ptype == 'i' or ptype == 'd':
ptype = 'd'
else:
ptype = 's'
## Formatting string format
if ptype != 'f':
sformat = "{:>" + plen + ptype + "}"
else:
sformat = "{:>" + plen + "." + str(floatPoint) + ptype + "}"
for line in lines:
if line[:17] == "REMARK 666 LABELS":
newpmp += "REMARK 111 MOLP: " + pname + ": " + ptype + ": " + sformat.format(
value) + "\n"
newpmp += line + '\n'
self.SetMolValue(value, pname, ptype)
else:
newpmp += line + '\n'
self._pmp = newpmp
def PMPfromPDBblock(self, PDBblock):
'''Convert PDB Block to PMP format.
PDB block can be generated from Chem.MolToPDBBlock(mol)
'''
lines = PDBblock.splitlines()
connectDict = {}
connectAtoms = []
for line in lines:
if line[:6] == 'CONECT':
tmp = line[6:].rstrip()
# Maybe some bug
if len(tmp) % 5 != 0:
logger.warning(
"PMPfromPDBblock(): Connect length maybe something wrong!"
)
if len(tmp) / 5 >= 2:
atomid = tmp[:5].strip()
connectAtoms.append(atomid)
connectDict[atomid] = [tmp[5:10].strip()]
for i in range(len(tmp) / 5 - 2):
connectDict[atomid].append(tmp[10 + 5 * i:15 +
5 * i].strip())
connectDict[atomid] = list(
OrderedDict.fromkeys(connectDict[atomid]))
else:
logger.warning(
"PMPfromPDBblock(): Connect length maybe too short!")
newblock = ""
firstline = False
for line in lines:
if line[:6] == "ATOM " or line[:6] == "HETATM":
if not firstline:
newblock += "REMARK 666 LABELS|PMP_INFO:80s\n"
firstline = True
atomid = line[6:11].strip()
if connectDict.has_key(atomid):
connects = connectDict[atomid]
bondnum = len(connects)
newblock += line[:55] + str(bondnum)
if bondnum > 4:
newblock += " " * 20
else:
for i in range(4):
if i <= bondnum - 1:
newblock += "%5s" % connects[i]
else:
newblock += " " * 5
newblock += line[76:] + "\n"
else:
newblock += line[:55] + "0" + " " * 20 + line[76:] + "\n"
else:
newblock += line + "\n"
return newblock
def MolMatchBondByMol2File(self, mol2file, mol=None):
'''Using ref mol2 file to modify the bond type of given molecule "mol".
If "mol" not given, using the inner molecule and update it!
'''
refmol = Chem.MolFromMol2File(mol2file, sanitize=True, removeHs=False)
if mol:
mdone = self.AssignBondOrdersFromTemplate(refmol, mol)
return mdone
elif self._mol:
mdone = self.AssignBondOrdersFromTemplate(refmol, self._mol)
pdbblock = Chem.MolToPDBBlock(mdone, flavor=4)
self._pmp = self.PMPfromPDBblock(pdbblock)
self._mol = mdone
return mdone
else:
logger.warning(
"MolMatchBondByMol2File: No input molecule was given!")
return None
def GetMolsFromSDFile(dataFilename, errFile, nameProp):
suppl = Chem.SDMolSupplier(dataFilename)
for idx, m in enumerate(suppl):
if not m:
if errFile:
if hasattr(suppl, 'GetItemText'):
d = suppl.GetItemText(idx)
errFile.write(d)
else:
logger.warning('full error file support not complete')
continue
smi = Chem.MolToSmiles(m, True)
if m.HasProp(nameProp):
nm = m.GetProp(nameProp)
if not nm:
logger.warning('molecule found with empty name property')
else:
nm = 'Mol_%d' % (idx + 1)
yield nm, smi, m
def GetMolsFromSDFile(dataFilename,errFile,nameProp):
suppl = Chem.SDMolSupplier(dataFilename)
for idx,m in enumerate(suppl):
if not m:
if errFile:
if hasattr(suppl,'GetItemText'):
d = suppl.GetItemText(idx)
errFile.write(d)
else:
logger.warning('full error file support not complete')
continue
smi = Chem.MolToSmiles(m,True)
if m.HasProp(nameProp):
nm = m.GetProp(nameProp)
if not nm:
logger.warning('molecule found with empty name property')
else:
nm = 'Mol_%d'%(idx+1)
yield nm,smi,m
def MolMatchBondBySmiles(self, smiles, mol=None):
'''Using ref smiles to modify the bond type of given molecule "mol".
If "mol" not given, using the inner molecule and update it!
'''
# TODO: Some bug may be wrong even using
# "AllChem.RemoveHs(,updateExplicitCount=True)"
# to remove H. If smiles contain explicit H, can't match!!
#
refmol = Chem.MolFromSmiles(smiles, sanitize=True)
refmol = Chem.MolFromSmiles(Chem.MolToSmiles(refmol), sanitize=True)
if mol:
mdone = self.AssignBondOrdersFromTemplate(refmol, mol)
return mdone
elif self._mol:
mdone = self.AssignBondOrdersFromTemplate(refmol, self._mol)
pdbblock = Chem.MolToPDBBlock(mdone, flavor=4)
self._pmp = self.PMPfromPDBblock(pdbblock)
self._mol = mdone
return mdone
else:
logger.warning(
"MolMatchBondBySmiles: No input molecule was given!")
return None
def SetAtomsProp(self, values, pname, ptype='s', plen=6, floatPoint=3):
'''Set Atom property : values, property name, property type, string length'''
if len(values) != self._mol.GetNumAtoms():
logger.warning('SetAtomsProp: ' + self._mol.GetProp('Filename') +
'The length of values not equal to atom number!')
return
if not self._pmp:
logger.warning('SetAtomsProp: No PMP information!')
return
lines = self._pmp.splitlines()
newpmp = ""
findLabel = False
plen = str(plen)
if ptype == 'str' or ptype == 'string' or ptype == 's':
ptype = 's'
elif ptype == 'float' or ptype == 'double' or ptype == 'f':
ptype = 'f'
elif ptype == 'int' or ptype == 'long' or ptype == 'i' or ptype == 'd':
ptype = 'd'
else:
ptype = 's'
## Formatting string format
if ptype != 'f':
sformat = "{:>" + plen + ptype + "}"
else:
sformat = "{:>" + plen + "." + str(floatPoint) + ptype + "}"
atomcount = 0
for line in lines:
if not findLabel and line[:17] == "REMARK 666 LABELS":
newpmp += line + "|" + pname + ":" + plen + ptype + '\n'
elif line[:6] == "ATOM " or line[:6] == "HETATM":
newpmp += line + sformat.format(values[atomcount]) + '\n'
self.SetAtomValue(atomcount, values[atomcount], pname, ptype)
atomcount += 1
else:
newpmp += line + '\n'
self._pmp = newpmp
def AssignBondOrdersFromTemplate(refmol, mol):
""" assigns bond orders to a molecule based on the
bond orders in a template molecule
Arguments
- refmol: the template molecule
- mol: the molecule to assign bond orders to
An example, start by generating a template from a SMILES
and read in the PDB structure of the molecule
>>> import os
>>> from rdkit.Chem import AllChem
>>> template = AllChem.MolFromSmiles("CN1C(=NC(C1=O)(c2ccccc2)c3ccccc3)N")
>>> mol = AllChem.MolFromPDBFile(os.path.join(RDConfig.RDCodeDir, 'Chem', 'test_data', '4DJU_lig.pdb'))
>>> len([1 for b in template.GetBonds() if b.GetBondTypeAsDouble() == 1.0])
8
>>> len([1 for b in mol.GetBonds() if b.GetBondTypeAsDouble() == 1.0])
22
Now assign the bond orders based on the template molecule
>>> newMol = AllChem.AssignBondOrdersFromTemplate(template, mol)
>>> len([1 for b in newMol.GetBonds() if b.GetBondTypeAsDouble() == 1.0])
8
Note that the template molecule should have no explicit hydrogens
else the algorithm will fail.
It also works if there are different formal charges (this was github issue 235):
>>> template=AllChem.MolFromSmiles('CN(C)C(=O)Cc1ccc2c(c1)NC(=O)c3ccc(cc3N2)c4ccc(c(c4)OC)[N+](=O)[O-]')
>>> mol = AllChem.MolFromMolFile(os.path.join(RDConfig.RDCodeDir, 'Chem', 'test_data', '4FTR_lig.mol'))
>>> AllChem.MolToSmiles(mol)
'COC1CC(C2CCC3C(O)NC4CC(CC(O)N(C)C)CCC4NC3C2)CCC1N(O)O'
>>> newMol = AllChem.AssignBondOrdersFromTemplate(template, mol)
>>> AllChem.MolToSmiles(newMol)
'COc1cc(-c2ccc3c(c2)Nc2ccc(CC(=O)N(C)C)cc2NC3=O)ccc1[N+](=O)[O-]'
"""
refmol2 = rdchem.Mol(refmol)
mol2 = rdchem.Mol(mol)
# do the molecules match already?
matching = mol2.GetSubstructMatch(refmol2)
if not matching: # no, they don't match
# check if bonds of mol are SINGLE
for b in mol2.GetBonds():
if b.GetBondType() != BondType.SINGLE:
b.SetBondType(BondType.SINGLE)
b.SetIsAromatic(False)
# set the bonds of mol to SINGLE
for b in refmol2.GetBonds():
b.SetBondType(BondType.SINGLE)
b.SetIsAromatic(False)
# set atom charges to zero;
for a in refmol2.GetAtoms():
a.SetFormalCharge(0)
for a in mol2.GetAtoms():
a.SetFormalCharge(0)
matching = mol2.GetSubstructMatches(refmol2, uniquify=False)
# do the molecules match now?
if matching:
if len(matching) > 1:
logger.warning(
"More than one matching pattern found - picking one")
matching = matching[0]
# apply matching: set bond properties
for b in refmol.GetBonds():
atom1 = matching[b.GetBeginAtomIdx()]
atom2 = matching[b.GetEndAtomIdx()]
b2 = mol2.GetBondBetweenAtoms(atom1, atom2)
b2.SetBondType(b.GetBondType())
b2.SetIsAromatic(b.GetIsAromatic())
# apply matching: set atom properties
for a in refmol.GetAtoms():
a2 = mol2.GetAtomWithIdx(matching[a.GetIdx()])
a2.SetHybridization(a.GetHybridization())
a2.SetIsAromatic(a.GetIsAromatic())
a2.SetNumExplicitHs(a.GetNumExplicitHs())
a2.SetFormalCharge(a.GetFormalCharge())
SanitizeMol(mol2)
if hasattr(mol2, '__sssAtoms'):
mol2.__sssAtoms = None # we don't want all bonds highlighted
else:
raise ValueError("No matching found")
return mol2
def AssignBondOrdersFromTemplate(refmol, mol):
""" assigns bond orders to a molecule based on the
bond orders in a template molecule
Arguments
- refmol: the template molecule
- mol: the molecule to assign bond orders to
An example, start by generating a template from a SMILES
and read in the PDB structure of the molecule
>>> from rdkit.Chem import AllChem
>>> template = AllChem.MolFromSmiles("CN1C(=NC(C1=O)(c2ccccc2)c3ccccc3)N")
>>> mol = AllChem.MolFromPDBFile(os.path.join(RDConfig.RDCodeDir, 'Chem', 'test_data', '4DJU_lig.pdb'))
>>> len([1 for b in template.GetBonds() if b.GetBondTypeAsDouble() == 1.0])
8
>>> len([1 for b in mol.GetBonds() if b.GetBondTypeAsDouble() == 1.0])
22
Now assign the bond orders based on the template molecule
>>> newMol = AllChem.AssignBondOrdersFromTemplate(template, mol)
>>> len([1 for b in newMol.GetBonds() if b.GetBondTypeAsDouble() == 1.0])
8
Note that the template molecule should have no explicit hydrogens
else the algorithm will fail.
It also works if there are different formal charges (this was github issue 235):
>>> template=AllChem.MolFromSmiles('CN(C)C(=O)Cc1ccc2c(c1)NC(=O)c3ccc(cc3N2)c4ccc(c(c4)OC)[N+](=O)[O-]')
>>> mol = AllChem.MolFromMolFile(os.path.join(RDConfig.RDCodeDir, 'Chem', 'test_data', '4FTR_lig.mol'))
>>> AllChem.MolToSmiles(mol)
'COC1CC(C2CCC3C(O)NC4CC(CC(O)N(C)C)CCC4NC3C2)CCC1N(O)O'
>>> newMol = AllChem.AssignBondOrdersFromTemplate(template, mol)
>>> AllChem.MolToSmiles(newMol)
'COc1cc(-c2ccc3c(c2)Nc2ccc(CC(=O)N(C)C)cc2NC3=O)ccc1[N+](=O)[O-]'
"""
refmol2 = rdchem.Mol(refmol)
mol2 = rdchem.Mol(mol)
# do the molecules match already?
matching = mol2.GetSubstructMatch(refmol2)
if not matching: # no, they don't match
# check if bonds of mol are SINGLE
for b in mol2.GetBonds():
if b.GetBondType() != BondType.SINGLE:
b.SetBondType(BondType.SINGLE)
b.SetIsAromatic(False)
# set the bonds of mol to SINGLE
for b in refmol2.GetBonds():
b.SetBondType(BondType.SINGLE)
b.SetIsAromatic(False)
# set atom charges to zero;
for a in refmol2.GetAtoms():
a.SetFormalCharge(0)
for a in mol2.GetAtoms():
a.SetFormalCharge(0)
matching = mol2.GetSubstructMatches(refmol2, uniquify=False)
# do the molecules match now?
if matching:
if len(matching) > 1:
logger.warning("More than one matching pattern found - picking one")
matching = matching[0]
# apply matching: set bond properties
for b in refmol.GetBonds():
atom1 = matching[b.GetBeginAtomIdx()]
atom2 = matching[b.GetEndAtomIdx()]
b2 = mol2.GetBondBetweenAtoms(atom1, atom2)
b2.SetBondType(b.GetBondType())
b2.SetIsAromatic(b.GetIsAromatic())
# apply matching: set atom properties
for a in refmol.GetAtoms():
a2 = mol2.GetAtomWithIdx(matching[a.GetIdx()])
a2.SetHybridization(a.GetHybridization())
a2.SetIsAromatic(a.GetIsAromatic())
a2.SetNumExplicitHs(a.GetNumExplicitHs())
a2.SetFormalCharge(a.GetFormalCharge())
SanitizeMol(mol2)
if hasattr(mol2, '__sssAtoms'):
mol2.__sssAtoms = None # we don't want all bonds highlighted
else:
raise ValueError("No matching found")
return mol2
def Gen2DFingerprint(mol, sigFactory, perms=None, dMat=None):
""" generates a 2D fingerprint for a molecule using the
parameters in _sig_
**Arguments**
- mol: the molecule for which the signature should be generated
- sigFactory : the SigFactory object with signature parameters
NOTE: no preprocessing is carried out for _sigFactory_.
It *must* be pre-initialized.
- perms: (optional) a sequence of permutation indices limiting which
pharmacophore combinations are allowed
- dMat: (optional) the distance matrix to be used
"""
if not isinstance(sigFactory, SigFactory.SigFactory):
raise ValueError('bad factory')
featFamilies = sigFactory.GetFeatFamilies()
if _verbose:
print('* feat famillies:', featFamilies)
nFeats = len(featFamilies)
minCount = sigFactory.minPointCount
maxCount = sigFactory.maxPointCount
if maxCount > 3:
logger.warning(
' Pharmacophores with more than 3 points are not currently supported.\nSetting maxCount to 3.'
)
maxCount = 3
# generate the molecule's distance matrix, if required
if dMat is None:
from rdkit import Chem
useBO = sigFactory.includeBondOrder
dMat = Chem.GetDistanceMatrix(mol, useBO)
# generate the permutations, if required
if perms is None:
perms = []
for count in range(minCount, maxCount + 1):
perms += Utils.GetIndexCombinations(nFeats, count)
# generate the matches:
featMatches = sigFactory.GetMolFeats(mol)
if _verbose:
print(' featMatches:', featMatches)
sig = sigFactory.GetSignature()
for perm in perms:
# the permutation is a combination of feature indices
# defining the feature set for a proto-pharmacophore
featClasses = [0]
for i in range(1, len(perm)):
if perm[i] == perm[i - 1]:
featClasses.append(featClasses[-1])
else:
featClasses.append(featClasses[-1] + 1)
# Get a set of matches at each index of
# the proto-pharmacophore.
matchPerms = [featMatches[x] for x in perm]
if _verbose:
print('\n->Perm: %s' % (str(perm)))
print(' matchPerms: %s' % (str(matchPerms)))
# Get all unique combinations of those possible matches:
matchesToMap = Utils.GetUniqueCombinations(matchPerms, featClasses)
for i, entry in enumerate(matchesToMap):
entry = [x[1] for x in entry]
matchesToMap[i] = entry
if _verbose:
print(' mtM:', matchesToMap)
for match in matchesToMap:
if sigFactory.shortestPathsOnly:
_ShortestPathsMatch(match, perm, sig, dMat, sigFactory)
return sig
def Gen2DFingerprint(mol, sigFactory, perms=None, dMat=None, bitInfo=None):
""" generates a 2D fingerprint for a molecule using the
parameters in _sig_
**Arguments**
- mol: the molecule for which the signature should be generated
- sigFactory : the SigFactory object with signature parameters
NOTE: no preprocessing is carried out for _sigFactory_.
It *must* be pre-initialized.
- perms: (optional) a sequence of permutation indices limiting which
pharmacophore combinations are allowed
- dMat: (optional) the distance matrix to be used
- bitInfo: (optional) used to return the atoms involved in the bits
"""
if not isinstance(sigFactory, SigFactory.SigFactory):
raise ValueError('bad factory')
featFamilies = sigFactory.GetFeatFamilies()
if _verbose:
print('* feat famillies:', featFamilies)
nFeats = len(featFamilies)
minCount = sigFactory.minPointCount
maxCount = sigFactory.maxPointCount
if maxCount > 3:
logger.warning(' Pharmacophores with more than 3 points are not currently supported.\n' +
'Setting maxCount to 3.')
maxCount = 3
# generate the molecule's distance matrix, if required
if dMat is None:
from rdkit import Chem
useBO = sigFactory.includeBondOrder
dMat = Chem.GetDistanceMatrix(mol, useBO)
# generate the permutations, if required
if perms is None:
perms = []
for count in range(minCount, maxCount + 1):
perms += Utils.GetIndexCombinations(nFeats, count)
# generate the matches:
featMatches = sigFactory.GetMolFeats(mol)
if _verbose:
print(' featMatches:', featMatches)
sig = sigFactory.GetSignature()
for perm in perms:
# the permutation is a combination of feature indices
# defining the feature set for a proto-pharmacophore
featClasses = [0]
for i in range(1, len(perm)):
if perm[i] == perm[i - 1]:
featClasses.append(featClasses[-1])
else:
featClasses.append(featClasses[-1] + 1)
# Get a set of matches at each index of
# the proto-pharmacophore.
matchPerms = [featMatches[x] for x in perm]
if _verbose:
print('\n->Perm: %s' % (str(perm)))
print(' matchPerms: %s' % (str(matchPerms)))
# Get all unique combinations of those possible matches:
matchesToMap = Utils.GetUniqueCombinations(matchPerms, featClasses)
for i, entry in enumerate(matchesToMap):
entry = [x[1] for x in entry]
matchesToMap[i] = entry
if _verbose:
print(' mtM:', matchesToMap)
for match in matchesToMap:
if sigFactory.shortestPathsOnly:
idx = _ShortestPathsMatch(match, perm, sig, dMat, sigFactory)
if idx is not None and bitInfo is not None:
l = bitInfo.get(idx, [])
l.append(match)
bitInfo[idx] = l
return sig
ts.append(t2 - t1)
if tests[16]:
logger.info('Generate topological fingerprints')
t1 = time.time()
for mol in mols:
Chem.RDKFingerprint(mol)
t2 = time.time()
logger.info('Results16: %.2f seconds' % (t2 - t1))
ts.append(t2 - t1)
if tests[17]:
logger.info('MMFF optimizing the molecules:')
t1 = time.time()
for i, mol in enumerate(mols):
mol = Chem.Mol(mol)
if not mol.GetNumConformers(): continue
if not AllChem.MMFFHasAllMoleculeParams(mol): continue
needMore = 1
while needMore:
try:
needMore = AllChem.MMFFOptimizeMolecule(mol, maxIters=200)
except ValueError:
logger.warning('Problems with MMFF and mol %d' % i)
break
t2 = time.time()
logger.info('Results17: %.2f seconds' % (t2 - t1))
ts.append(t2 - t1)
print('times: ', ' || '.join(['%.1f' % x for x in ts]))
logger.info('Generate topological fingerprints')
t1=time.time()
for mol in mols:
Chem.RDKFingerprint(mol)
t2 = time.time()
logger.info('Results16: %.2f seconds'%(t2-t1))
ts.append(t2-t1)
if tests[17]:
logger.info('MMFF optimizing the molecules:')
t1=time.time()
for i,mol in enumerate(mols):
mol = Chem.Mol(mol)
if not mol.GetNumConformers(): continue
if not AllChem.MMFFHasAllMoleculeParams(mol): continue
needMore=1
while needMore:
try:
needMore=AllChem.MMFFOptimizeMolecule(mol,maxIters=200)
except ValueError:
logger.warning('Problems with MMFF and mol %d'%i)
break
t2 = time.time()
logger.info('Results17: %.2f seconds'%(t2-t1))
ts.append(t2-t1)
print('times: ',' || '.join(['%.1f'%x for x in ts]))
def AssignBondOrdersFromTemplate(self, refmol, mol):
""" assigns bond orders to a molecule based on the
bond orders in a template molecule
Revised from AllChem.AssignBondOrderFromTemplate(refmol, mol)
"""
AllChem.AssignBondOrdersFromTemplate
refmol2 = Chem.rdchem.Mol(refmol)
mol2 = Chem.rdchem.Mol(mol)
# do the molecules match already?
matching = mol2.GetSubstructMatch(refmol2)
if not matching: # no, they don't match
# check if bonds of mol are SINGLE
for b in mol2.GetBonds():
if b.GetBondType() != Chem.BondType.SINGLE:
b.SetBondType(Chem.BondType.SINGLE)
b.SetIsAromatic(False)
# set the bonds of mol to SINGLE
for b in refmol2.GetBonds():
b.SetBondType(Chem.BondType.SINGLE)
b.SetIsAromatic(False)
# set atom charges to zero;
for a in refmol2.GetAtoms():
a.SetFormalCharge(0)
for a in mol2.GetAtoms():
a.SetFormalCharge(0)
matching = mol2.GetSubstructMatches(refmol2, uniquify=False)
# do the molecules match now?
if matching:
if len(matching) > 1:
#logger.warning("More than one matching pattern found - picking one")
pass
matchings = matching[:]
for matching in matchings:
#matching = matching[0] ## use each matching
# apply matching: set bond properties
for b in refmol.GetBonds():
atom1 = matching[b.GetBeginAtomIdx()]
atom2 = matching[b.GetEndAtomIdx()]
b2 = mol2.GetBondBetweenAtoms(atom1, atom2)
b2.SetBondType(b.GetBondType())
b2.SetIsAromatic(b.GetIsAromatic())
# apply matching: set atom properties
for a in refmol.GetAtoms():
a2 = mol2.GetAtomWithIdx(matching[a.GetIdx()])
a2.SetHybridization(a.GetHybridization())
a2.SetIsAromatic(a.GetIsAromatic())
a2.SetNumExplicitHs(a.GetNumExplicitHs())
a2.SetFormalCharge(a.GetFormalCharge())
try:
Chem.SanitizeMol(mol2)
if hasattr(mol2, '__sssAtoms'):
mol2.__sssAtoms = None # we don't want all bonds highlighted
break
except ValueError:
logger.warning(
"More than one matching pattern, Fail at this matching. Try next."
)
else:
raise ValueError("No matching found")
return mol2
if tests[16]:
logger.info("Generate topological fingerprints")
t1 = time.time()
for mol in mols:
Chem.RDKFingerprint(mol)
t2 = time.time()
logger.info("Results16: %.2f seconds" % (t2 - t1))
ts.append(t2 - t1)
if tests[17]:
logger.info("MMFF optimizing the molecules:")
t1 = time.time()
for i, mol in enumerate(mols):
mol = Chem.Mol(mol)
if not mol.GetNumConformers():
continue
if not AllChem.MMFFHasAllMoleculeParams(mol):
continue
needMore = 1
while needMore:
try:
needMore = AllChem.MMFFOptimizeMolecule(mol, maxIters=200)
except ValueError:
logger.warning("Problems with MMFF and mol %d" % i)
break
t2 = time.time()
logger.info("Results17: %.2f seconds" % (t2 - t1))
ts.append(t2 - t1)
print("times: ", " || ".join(["%.1f" % x for x in ts]))