Ah right. No - we don't do R and S assignment. But I don't see how a
sensible QSAR model could possibly relate the count of R and S centers to a
physical property. What does that even mean?
OBAtom.IsChiral() does not do what you think it's doing. In fact, in the
development version it has been removed.
I'm afraid you'll have to figure out the floodfill yourself unless someone
wants to help out. It's a standard graph algorithm that can be done with a
breadth first or depth first search using a stack. If you google it up, or
read Sedgewick's Algorithms you should be able to figure it out.
Regards,
- Noel
On Tue, 14 May 2019 at 03:59, Spencer Trinh <trinh.kc...@gmail.com> wrote:
> Hi Noel,
>
>
> Thanks for response. The paper didn't really mention the R/S configuration
> but their supplemental had it. Here is the first two rows of their
> supplemental dataset.
>
> CID SMILES MW N O XLogP HBD HBA RotB tPSA nStereo R S
> Lipitor 60823 CC(C)C1=C(C(=C(N1CC[C@H](C[C@H
> ](CC(=O)O)O)O)C2=CC=C(C=C2)F)C3=CC=CC=C3)C(=O)NC4=CC=CC=C4 558,64 2 5 5,7
> 4 7 12 112,0 2 2 0
> Nexium 4594 CC1=CN=C(C(=C1OC)C)CS(=O)C2=NC3=C(N2)C=C(C=C3)OC 345,42 3 3
> 0,6 1 6 5 77,1 1 1 0
>
>
> For the stereocenters I wrote:
>
> nStereo=0
> for atom in mol:
> if atom.OBAtom.IsChiral() and atom.OBAtom.GetAtomicNum() == 6:
> nStereo+=1
>
> Would that work just like OBStereoFacade? I'm not familiar with using that
> class.
>
> I'm not sure how to conduct a floodfill search of a molecule. Are there
> examples that you can point me to? I simply wrote this but I lack the
> knowledge to carry on:
>
> mol =
> pybel.readstring('smi','CC(=O)SC1CC2=CC(=O)CCC2(C3C1C4CCC5(C4(CC3)C)CCC(=O)O5)C')
> for a in mol:
> if a.OBAtom.IsInRing():
> print(f'{a.idx}, {a.atomicnum}, {a.cidx}')
>
> Can you provide further assistance? Thanks.
>
>
> Best regards,
>
>
> Spencer
>
>
> Vào Th 2, 13 thg 5, 2019 vào lúc 09:45 Noel O'Boyle <
> baoille...@gmail.com> đã viết:
>
>> Hi Spencer,
>>
>> To count the number of ring systems, simply find a ring atom that you
>> have not yet visited (OBAtom.IsInRing()) and floodfill through all of the
>> adjacent ring atoms via bonds that are in a ring. That's ring system 1.
>> Repeat to find additional ring systems.
>>
>> In the reference you point to, they don't count the number of R
>> stereocenters and S stereocenters. They use "chiralCenterCount()", defined
>> as " Calculates the number of tetrahedral stereogenic centers" (
>> https://forum.chemaxon.com/ftopic2417.html). If you use the
>> OBStereoFacade, you should be able to count up the stereo centers.
>> Hopefully this number is the same as you are expecting.
>>
>> Regards,
>> Noel
>>
>>
>>
>> On Mon, 13 May 2019 at 02:03, Spencer Trinh <trinh.kc...@gmail.com>
>> wrote:
>>
>>> Hi Openbabel developers,
>>>
>>> I am trying to reproduce the data from this paper:
>>> https://www.ncbi.nlm.nih.gov/pubmed/25618349
>>>
>>> They listed 20 chemical descriptors used for a pca analysis. I am having
>>> trouble figuring out how they calculated the ring system count. Is there a
>>> way to count the number of ring systems as opposed to standard rings? For
>>> example, spiro rings are considered one instead of two, etc. I simply know
>>> how to get ring count through: mol.OBMol.GetSSSR(). Also, I don't know how
>>> to count the number of R stereocenters and S stereocenters. Is this
>>> possible with Openbabel? I would assume so since it can do a lot of things.
>>> Thank you.
>>>
>>>
>>>
>>> Best regards,
>>>
>>>
>>> Spencer
>>> _______________________________________________
>>> OpenBabel-discuss mailing list
>>> OpenBabel-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>>
>>
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