Hi Daniel,
this is some oddity that happens with molecules constructed from InChIs.
CalcNumAtomStereoCenters() returns sensible results if you call it on the
molecules constructed from SMILES:
In [24]: mol_list2 = [Chem.MolFromSmiles(Chem.MolToSmiles(mol,True)) for
mol in mol_list]
In [25]: [CalcNumUnspecifiedAtomStereoCenters(mol) for mol in mol_list2]
Out[25]: [0, 1, 1]
In [26]: [CalcNumAtomStereoCenters(mol) for mol in mol_list2]
Out[26]: [2, 2, 1]
I will try to track this down.
-greg
On Thu, Sep 14, 2017 at 4:47 PM, Daniel Hitchcock <dhi...@broadinstitute.org
> wrote:
> Hi All,
>
> I have a list of compounds (InChi strings) that I need to filter.
> Basically I need to identify which molecules are missing stereo information.
>
> I came across the "CalcNumUnspecifiedAtomStereoCenters" which sounded
> exactly like what I needed, but unfortunately all it does it return 0s, as
> well as the "CalcNumAtomStereoCenters" function. I've viewed the molecules
> using MolToImage(mol).show() to verify the stereo information is accurate,
> and it's all there.
>
> Here is the code I used. It's in python 3.5.2, and
> rdkit.Chem.rdMolDescriptors._CalcNumUnspecifiedAtomStereoCenters_version
> is 1.0.0
>
> """
> Three molecules with stereochemistry.
> stereo_inchi - 2 stereocenters specified
> am_inchi - 1 sterecenter sepcified, the other ambiguous
> unspec_inchi - 1 stereocenter, unmentioned in the InChi string
>
> Program should output:
> 2 0
> 1 1
> 0 1
> """
> from rdkit.Chem import MolFromInchi, MolToInchi
> from rdkit.Chem.AllChem import CalcNumAtomStereoCenters,
> CalcNumUnspecifiedAtomStereoCenters
> stereo_inchi = 'InChI=1S/C10H10O6/c1-5(9(12)13)16-8-4-6(10(14)15)2-3-7(8)
> 11/h2-4,7-8,11H,1H2,(H,12,13)(H,14,15)/t7-,8-/m1/s1'
> am_inchi = 'InChI=1S/C11H21NO5/c1-8(13)5-11(16)17-9(6-10(14)15)7-12(2,
> 3)4/h8-9,13H,5-7H2,1-4H3/t8?,9-/m1/s1'
> unspec_inchi = 'InChI=1S/C14H27NO4/c1-5-6-7-8-9-14(18)19-12(10-13(16)17)
> 11-15(2,3)4/h12H,5-11H2,1-4H3'
> mol_list = [stereo_inchi, am_inchi, unspec_inchi]
> mol_list = [MolFromInchi(mol) for mol in mol_list]
> for mol in mol_list:
> print(CalcNumAtomStereoCenters(mol), CalcNumUnspecifiedAtomStereoCe
> nters(mol))
>
>
> Thanks in advance!
>
> Cheers,
>
> -daniel
>
> --
> Daniel Hitchcock, PhDwww.linkedin.com/pub/daniel-hitchcock/24/7b8/858/
> Research Scientist I
> Metabolomics Platform
> The Broad Institute of MIT and Harvard
> 415 Main St, Cambridge, 02142
>
>
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