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/
Research Scientist I
Metabolomics Platform
The Broad Institute of MIT and Harvard
415 Main St, Cambridge, 02142
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
