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