Hi everyone,
m = rdkit.Chem.SupplierFromFilename( filename, removeHs = False ).next()
sts = rdkit.Chem.FindMolChiralCenters( m, includeUnassigned = True )
for s in sts :
lbl = m.GetAtomWithIdx( s[0] ).GetSymbol() + str( s[0] + 1 )
print lbl, ":", s[1]For L-ALA 3D SDF the output is C4 : ? For D-ALA 3D SDF the output is also C4 : ? And for ALA 2D SDF the output is also C4 : ? If I change includeUnassigned to False, the list returned by FindMolChiralCenters() is empty. The SDFs have 1, 2, and 3 in the 7th column in the atom block. If I use m = rdkit.Chem.MolFromSmiles( 'C[C@@H](C(=O)O)N' ) instead, the output is C2 : S (this is L-ALA from the same PubChem record as the SDF). So it looks like MOL reader ignores chirality, is that the case? Thanks, -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
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