Hello Brain,
> The original smiles string
> "OC[C@@H]1O[C@H](Cn2c(N3CCCC3)nnc2[C@@H]2OCCC2)CC1"
>
> after conversion with rdkit
> "OC[C@H]1CC[C@@H](Cn2c([C@H]3CCCO3)nnc2N2CCCC2)O1"
After visualisation it seems to me that both smiles represent the same
structure (stereochemistry is the same, just molecule orientation is
diffrent). Canonical smiles from rdkit not allways is the same like
canonical smiles from other programs. If you want to prevent atom order
you can try use option canonical=False. See example below:
>>> mol1=Chem.MolFromSmiles('OC[C@@H]1O[C@H](Cn2c(N3CCCC3)nnc2[C@@H]2OCCC2)CC1')
>>> mol2=Chem.MolFromSmiles('OC[C@H]1CC[C@@H](Cn2c([C@H]3CCCO3)nnc2N2CCCC2)O1')
>>> Chem.MolToSmiles(mol1)
'OC[C@H]1CC[C@@H](Cn2c([C@H]3CCCO3)nnc2N2CCCC2)O1'
>>> Chem.MolToSmiles(mol2)
'OC[C@H]1CC[C@@H](Cn2c([C@H]3CCCO3)nnc2N2CCCC2)O1'
#canonical smiles for both smiles are the same (above) but without
canonicalisation you will get diffrent smiles:
>>> Chem.MolToSmiles(mol1, canonical=False)
'OC[C@@H]1O[C@H](Cn2c(N3CCCC3)nnc2[C@@H]2OCCC2)CC1'
>>> Chem.MolToSmiles(mol2, canonical=False)
'OC[C@H]1CC[C@@H](Cn2c([C@H]3CCCO3)nnc2N2CCCC2)O1'
Best,
Rafal
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