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import gzip
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem.PyMol import MolViewer
try:
v = MolViewer()
v.DeleteAll()
except Exception:
v = None
outf = open('chembl_20_chiral.problems.smi', 'w+')
noconff = open('chembl_20_chiral.noconfs.smi', 'w+')
for i, line in enumerate(gzip.open('../Data/chembl_20_chiral.smi.gz')):
line = line.strip().decode().split(' ')
mol = Chem.MolFromSmiles(line[0])
if not mol:
continue
cents = Chem.FindMolChiralCenters(mol, includeUnassigned=True)
if len([y for x, y in cents if y == '?']):
continue
nm = line[1]
csmi = Chem.MolToSmiles(mol, True)
for j in range(100):
mh = Chem.AddHs(mol)
ok = AllChem.EmbedMolecule(mh, randomSeed=j + 1)
if ok >= 0:
Chem.AssignAtomChiralTagsFromStructure(mh)
newm = Chem.RemoveHs(mh)
smi = Chem.MolToSmiles(newm, True)
if smi != csmi:
print('%d %d %s:\n%s\n%s' % (i, j, nm, csmi, smi))
print('%s %s %d' % (line[0], line[1], j + 1), file=outf)
if v is not None:
v.ShowMol(mh, name='%s-%d' % (nm, j), showOnly=False)
break # move immediately onto the next molecule
else:
print('noconf %d %d %s: %s' % (i, j, nm, line[0]))
print('%s %s %d' % (line[0], line[1], j + 1), file=noconff)
print('Done with mol %d' % i)
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