def _generateFPs(mol, fragmentMethod='Morgan'):
aBits = {}
fp = None
# circular Morgan fingerprint fragmentation, we use a simple invariant than ususal here
if fragmentMethod == 'Morgan':
tmp = {}
fp = AllChem.GetMorganFingerprint(
mol,
radius=2,
invariants=utilsFP.generateAtomInvariant(mol),
bitInfo=tmp)
aBits = utilsFP.getMorganEnvironment(mol, tmp, fp=fp, minRad=2)
fp = fp.GetNonzeroElements()
# path-based RDKit fingerprint fragmentation
elif fragmentMethod == 'RDK':
fp = AllChem.UnfoldedRDKFingerprintCountBased(mol,
maxPath=5,
minPath=3,
bitInfo=aBits)
fp = fp.GetNonzeroElements()
# get the final BRICS fragmentation (= smallest possible BRICS fragments of a molecule)
elif fragmentMethod == 'Brics':
fragMol = BRICS.BreakBRICSBonds(mol)
propSmi = _prepBRICSSmiles(fragMol)
fp = Counter(propSmi.split('.'))
else:
print("Unknown fragment method")
return fp, aBits
def getBits(mol):
'''
Parameters
----------
mol : rdkit mol object to be broken up into fragments by breaking
rotable bonds
Returns
-------
mols : A list of rdkit mol objects
'''
# find the rotatable bonds
bonds = mol.GetSubstructMatches(RotatableBondSmarts)
bonds = [((x, y), (0, 0)) for x, y in bonds]
p = BRICS.BreakBRICSBonds(mol, bonds=bonds)
mols = [mol for mol in Chem.GetMolFrags(p, asMols=True)]
return mols
if tests[9]:
logger.info('Writing: Mol blocks')
t1 = time.time()
for mol in mols:
mb = Chem.MolToMolBlock(mol)
t2 = time.time()
logger.info('Results10: %.2f seconds' % (t2 - t1))
ts.append(t2 - t1)
if tests[10]:
from rdkit.Chem import BRICS
logger.info('BRICS decomposition')
t1 = time.time()
for mol in mols:
d = BRICS.BreakBRICSBonds(mol)
t2 = time.time()
logger.info('Results11: %.2f seconds' % (t2 - t1))
ts.append(t2 - t1)
if tests[11]:
logger.info('Generate 2D coords')
t1 = time.time()
for mol in mols:
AllChem.Compute2DCoords(mol)
t2 = time.time()
logger.info('Results12: %.2f seconds' % (t2 - t1))
ts.append(t2 - t1)
if tests[12]:
logger.info('Generate topological fingerprints')
tempValue = FindDoubleBonds(inputFrags[i])
if tempValue >= 0:
# Find C.2 = C.2 bond
dbFragList.append(fragmentMolblocks[i])
else:
newFragmentMolBlocks.append(fragmentMolblocks[i])
reconnectedDBFrags = ProcessDoubleBonds(parentMolblock, dbFragList)
newFragmentMolBlocks = newFragmentMolBlocks + reconnectedDBFrags
newFragmentMol = []
for i in range(len(newFragmentMolBlocks)):
tempFragMol = Chem.MolFromMolBlock(newFragmentMolBlocks[i],sanitize=False)
newFragmentMol.append(tempFragMol)
# return tuple mol-objects
return tuple(newFragmentMol)
suppl2 = rdmolops.RemoveHs(suppl)
new2 = BRICS.BreakBRICSBonds(suppl2)
mfl2 = Chem.GetMolFrags(new2, asMols=True, sanitizeFrags=False)
mfl3 = ReconnectDoubleBond(suppl2,mfl2)
for i in range(len(mfl3)):
print(Chem.MolToMolBlock(mfl3[i]))
pass
#FindDoubleBonds(mfl2[i])