def compute_properties(args):
if args.oformat == 'sdf':
outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True)
else:
outfile = open(args.output, 'w')
if args.header:
mol = next(pybel.readfile(args.iformat, args.input))
metadata = cheminfolib.get_properties_ext(mol)
outfile.write(
'%s\n' %
'\t'.join([cheminfolib.ColumnNames[key] for key in metadata]))
for mol in pybel.readfile(args.iformat, args.input):
if mol.OBMol.NumHvyAtoms() > 5:
metadata = cheminfolib.get_properties_ext(mol)
if args.oformat == 'sdf':
[
mol.data.update(
{cheminfolib.ColumnNames[key]: metadata[key]})
for key in metadata
]
outfile.write(mol)
else:
outfile.write(
'%s\n' %
('\t'.join([str(metadata[key]) for key in metadata])))
outfile.close()
def __init__(self, molecule):
prop = cheminfolib.get_properties_ext(molecule)
self.mol = molecule.write("mol")
self.set_bits = len(molecule.calcfp().bits)
"""
maccs = ['0']*166
for i in molecule.calcfp('MACCS').bits:
maccs[i-1] = '1'
self.maccs = ''.join(maccs)
fp3 = ['0']*1024
for i in molecule.calcfp('FP3').bits:
fp3[i-1] = '1'
self.fp3 = ''.join(fp3)
fp4 = ['0']*1024
for i in molecule.calcfp('FP4').bits:
fp4[i-1] = '1'
self.fp4 = ''.join(fp4)
"""
self.inchi = prop["inchi"]
self.inchi_key_first = prop["inchi_key"][:14]
self.inchi_key_last = prop["inchi_key"][15:]
self.can_smiles = prop["can"]
self.spectrophore = prop["spectrophore"]
self.molwt = prop["molwt"]
self.logp = prop["logp"]
self.mr = prop["mr"]
self.hbd = prop["donors"]
self.hba = prop["acceptors"]
self.psa = prop["psa"]
self.rotbonds = prop["rotbonds"]
self.rings = prop["rings"]
self.atoms = prop["atoms"]
def __init__(self, molecule):
prop = cheminfolib.get_properties_ext(molecule)
self.mol = molecule.write("mol")
self.set_bits = len(molecule.calcfp().bits)
"""
maccs = ['0']*166
for i in molecule.calcfp('MACCS').bits:
maccs[i-1] = '1'
self.maccs = ''.join(maccs)
fp3 = ['0']*1024
for i in molecule.calcfp('FP3').bits:
fp3[i-1] = '1'
self.fp3 = ''.join(fp3)
fp4 = ['0']*1024
for i in molecule.calcfp('FP4').bits:
fp4[i-1] = '1'
self.fp4 = ''.join(fp4)
"""
self.inchi = prop["inchi"]
self.inchi_key_first = prop["inchi_key"][:14]
self.inchi_key_last = prop["inchi_key"][15:]
self.can_smiles = prop["can"]
self.spectrophore = prop["spectrophore"]
self.molwt = prop["molwt"]
self.logp = prop["logp"]
self.mr = prop["mr"]
self.hbd = prop["donors"]
self.hba = prop["acceptors"]
self.psa = prop["psa"]
self.rotbonds = prop["rotbonds"]
self.rings = prop["rings"]
self.atoms = prop["atoms"]
def compute_properties(args):
if args.oformat == 'sdf':
outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True)
else:
outfile = open(args.output, 'w')
if args.header:
mol = pybel.readfile(args.iformat, args.input).next()
metadata = cheminfolib.get_properties_ext(mol)
outfile.write( '%s\n' % '\t'.join( [ cheminfolib.ColumnNames[key] for key in metadata ] ) )
for mol in pybel.readfile(args.iformat, args.input):
if mol.OBMol.NumHvyAtoms() > 5:
metadata = cheminfolib.get_properties_ext(mol)
if args.oformat == 'sdf':
[ mol.data.update( { cheminfolib.ColumnNames[key] : metadata[key] } ) for key in metadata ]
outfile.write(mol)
else:
outfile.write( '%s\n' % ('\t'.join( [ str(metadata[key]) for key in metadata ] ) ) )
outfile.close()
