Thank you for the workaround! It's working correctly now with the SMILES
solution. Also, I realized my predicted output from my original question
was incorrect; it should read:
2 0
2 1
1 1
Cheers,
-daniel
Daniel Hitchcock, PhD
www.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
On 9/14/2017 11:52 AM, Greg Landrum wrote:
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
<[email protected] <mailto:[email protected]>> 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),
CalcNumUnspecifiedAtomStereoCenters(mol))
Thanks in advance!
Cheers,
-daniel
--
Daniel Hitchcock, PhD
www.linkedin.com/pub/daniel-hitchcock/24/7b8/858/
<http://www.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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