Hello Rafal,
Nice to see you on this forum. I completely expect reordering of smiles
strings from program to program. This is why I like to convert them to images
The tetrahydrofuran with the methoxy group has inverted stereochemistry of its
substituents.
The original string is shown in the first image.
[cid:image001.png@01D659C1.FD411770]
The second string after RDKit processing is shown in the second image here.
[cid:image002.png@01D659C1.FD411770]
-----Original Message-----
From: Rafal Roszak <rmrmg.c...@gmail.com>
Sent: Tuesday, July 14, 2020 1:25 AM
To: Bennion, Brian <benni...@llnl.gov>
Cc: Bennion, Brian via Rdkit-discuss <rdkit-discuss@lists.sourceforge.net>
Subject: Re: [Rdkit-discuss] changes in chirality in rdkit?
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]2OCC
>>> C2)CC1')
>>> mol2=Chem.MolFromSmiles('OC[C@H]1CC[C@@H](Cn2c([C@H]3CCCO3)nnc2N2CCC
>>> C2)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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