Ok Greg. thank you for the sneak preview.
brian
________________________________
From: Greg Landrum <greg.land...@gmail.com>
Sent: Tuesday, July 14, 2020 11:36 PM
To: Bennion, Brian <benni...@llnl.gov>
Cc: Rafal Roszak <rmrmg.c...@gmail.com>; RDKit Discuss
<rdkit-discuss@lists.sourceforge.net>
Subject: Re: [Rdkit-discuss] changes in chirality in rdkit?
Hi Brian,
I think you're misinterpreting the drawings. Those two images look like they
correspond to the same molecule.
The easiest way to check things like this without having to interpret drawings
is to use Chem.FindMolChiralCenters, which will show you absolute stereo labels
for all stereoatoms:
In [2]: m1 =
Chem.MolFromSmiles('OC[C@@H]1O[C@H](Cn2c(N3CCCC3)nnc2[C@@H]2OCCC2)CC1')
In [3]: m2 =
Chem.MolFromSmiles('OC[C@H]1CC[C@@H](Cn2c([C@H]3CCCO3)nnc2N2CCCC2)O1')
In [4]: Chem.FindMolChiralCenters(m1)
Out[4]: [(2, 'R'), (4, 'S'), (16, 'R')]
In [5]: Chem.FindMolChiralCenters(m2)
Out[5]: [(2, 'R'), (5, 'S'), (9, 'R')]
Here's the substructure mapping between those molecules:
In [16]: match = m1.GetSubstructMatch(m2)
In [17]: match[2]
Out[17]: 2
In [18]: match[5]
Out[18]: 4
In [19]: match[9]
Out[19]: 16
The "R" and "S" labels that function produces are not necessarily correct
according to IUPAC rules (though in this case they are), but they are
consistently calculated.
As a preview: the 2020.09 RDKit release will include a new CIP calculator using
the algorithm described in this paper
https://pubs.acs.org/doi/10.1021/acs.jcim.8b00324. The new code, which I think
will be quite helpful for people who need CIP labels, was implemented by
Ricardo Rodriguez Schmidt at Schrodinger and derived from John Mayfield's java
implementation (https://github.com/SiMolecule/centres). Here's what it says
about your molecules:
In [6]: from rdkit.Chem import rdCIPLabeler
In [7]: rdCIPLabeler.AssignCIPLabels(m1)
In [8]: rdCIPLabeler.AssignCIPLabels(m2)
In [9]: [(i,x.GetProp("_CIPCode")) for i,x in enumerate(m1.GetAtoms()) if
x.HasProp('_CIPCode')]
Out[9]: [(2, 'R'), (4, 'S'), (16, 'R')]
In [10]: [(i,x.GetProp("_CIPCode")) for i,x in enumerate(m2.GetAtoms()) if
x.HasProp('_CIPCode')]
Out[10]: [(2, 'R'), (5, 'S'), (9, 'R')]
Best,
-greg
On Tue, Jul 14, 2020 at 6:36 PM Bennion, Brian via Rdkit-discuss
<rdkit-discuss@lists.sourceforge.net<mailto:rdkit-discuss@lists.sourceforge.net>>
wrote:
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:173510855394cff311]
The second string after RDKit processing is shown in the second image here.
[cid:173510855395b16b22]
-----Original Message-----
From: Rafal Roszak <rmrmg.c...@gmail.com<mailto:rmrmg.c...@gmail.com>>
Sent: Tuesday, July 14, 2020 1:25 AM
To: Bennion, Brian <benni...@llnl.gov<mailto:benni...@llnl.gov>>
Cc: Bennion, Brian via Rdkit-discuss
<rdkit-discuss@lists.sourceforge.net<mailto: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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