else:
can_dupes2[cas].append(data)
for cas in can_dupes2.keys():
groups = can_dupes2[cas]
if len(groups) > 1:
print 'compound with cas=%s is considered different by OB canonical smiles'%cas
for group in groups:
print group[0].write('can').strip()
print '-'*80
union = sorted([dupe[0] for dupe in cas_dupes.values()], key=lambda mol: mol.title)
save_mols(union, op.join(root, 'mutagenicity-all-cas-union.sdf'))
print '\t\tUnion size=%d' % len(union)
dest_sdf = op.join(root, 'mutagenicity-all-cas-union-prepared.sdf')
prepare_dataset(op.join(root, 'mutagenicity-all-cas-union.sdf'), rename=False, conformations=True)
#Depict the molecules
depict(dest_sdf)
#Molecular descriptors
print 'Computing fingerprints via JCompoundMapper' #TODO: Extract-method this
jcm_fingerprint(dest_sdf, ('ECFP', 'ECFPVariant', 'PHAP3POINT2D', 'SHED', 'DFS', 'RAD2D'))
jcm_fingerprint(dest_sdf, ('LSTAR', 'RAD3D', 'PHAP3POINT3D'))
print 'Computing descriptors via CDKDescUI'
cdkdescuiprops(dest_sdf, desc_types=('constitutional',))
print 'Computing spectrophores'
spectrophores(dest_sdf)
print 'Saving in several data analysis tools file formats'
prop4da(dest_sdf)
print '\tCreating \"master\" table: %s' % master_table
create_master_table(dest_sdf, master_table, fields=['Activity'])
print '\tCreating \"saliviewer\" table: %s' % sali_table
create_saliviewer_input(master_table, sali_table)
return dest_sdf, master_table
if __name__ == '__main__':
DEFAULT_AMESV2_DIR = op.join(op.expanduser('~'), 'Proyectos', 'bsc', 'data', 'filtering', 'mutagenicity')
root = DEFAULT_AMESV2_DIR
dataset = op.join(root, 'tox_benchmark_N6512.sdf') #TODO: check if it exists, otherwise download
dest_sdf, master_table = prepare_dataset(dataset)
#Depict the molecules
depict(dest_sdf)
#Molecular descriptors
print 'Computing descriptors via CDKDescUI'
cdkdescuiprops(dataset)
print 'Computing spectrophores'
spectrophores(dataset)
print 'Saving in several data analysis tools file formats'
prop4da(dataset)
print 'Computing fingerprints via JCompoundMapper' #TODO: Extract-method this
FINGERPRINTS = ('ECFP', 'CATS2D')
for fp in FINGERPRINTS:
print fp
output = op.join(root, 'tox_benchmark_N6512-jcm-' +fp +'.arff')
JCompoundMapperCLIDriver().fingerprint(dataset, output, label='Activity')
