def main():
args = parse_arguments()
print('Read from {}'.format(args.infile))
print('Write to {}'.format(args.outfile))
suppl = create_mol_supplier(args.infile)
if not suppl:
print('ERROR - unrecognised file format for {}'.format(infile))
exit(1)
with open(args.outfile, 'w') as of:
for mol in suppl:
if args.fptype == 'Morgan':
fp = GetMorganFingerprintAsBitVect(mol, args.size, nBits=args.numbits)
elif args.fptype == 'Path':
fp = RDKFingerprint(mol, fpSize=args.numbits, maxPath=args.size)
of.write('{} {}\n'.format(mol.GetProp('_Name'), DataStructs.BitVectToText(fp)))
def get_maccs_fingerprint_from_mol(m):
if m is None: return None
k = MACCSkeys.GenMACCSKeys(m)
textk = DataStructs.BitVectToText(k)
binaryvec = np.array(list(map(int, textk)))
return binaryvec
def get_fingerprint(self) : #### Current supported fingerprint is MACCS
self.fingerprint_collector['MACCS']=DataStructs.BitVectToText(MACCSkeys.GenMACCSKeys(self.mol))
## minPath=1,maxPath=7,fpSize=2048,nBitsPerHash=4,useHs=True,
## tgtDensity=0.0,minSize=128
## returns ExplicitBitVect
##
## GenMACCSKeys (no args)
## returns SparseBitVect
##
smiA = 'NCCc1cc(O)c(O)cc1'
smiB = 'CNC(C)Cc1cc(O)c(O)cc1'
molA = Chem.MolFromSmiles(smiA)
molB = Chem.MolFromSmiles(smiB)
for fper in fpers:
fpA = fper(molA)
fptxtA = DataStructs.BitVectToText(fpA)
print(fptxtA)
size = fpA.GetNumBits()
count = 0
for i in range(fpA.GetNumBits()):
if fpA.GetBit(i): count += 1
print(count, size)
if fper == GenMACCSKeys:
onbits = tuple(fpA.GetOnBits())
print(str(onbits))
for i in onbits:
print(Chem.MACCSkeys.smartsPatts[i][0])
fpB = fper(molB)
fptxtB = DataStructs.BitVectToText(fpB)
print(fptxtB)
