Hi guys, could someone who knows chemistry (I don't) tell me if I'm completely off the mark here?
Attached sdf is D-alanine downloaded from pubchem. Also from pubchem,
copied from the same "cid 71080" page is the inchi string:
InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m1/s1
(it's also in the file).
My understanding is that by CIP rules L-alanine is S-alanine and
D-alanine is R-alanine. So when I run (python)
mol = rdkit.Chem.SupplierFromFilename( "71080.sdf" ).next()
for atom in mol.GetAtoms() :
print ("%s%d" % (atom.GetSymbol(),(atom.GetIdx() + 1))),
if atom.GetChiralTag() ==\
rdkit.Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CW : print ": R"
elif atom.GetChiralTag() ==\
rdkit.Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CCW : print ": S"
elif atom.GetChiralTag() ==\
rdkit.Chem.rdchem.ChiralType.CHI_UNSPECIFIED : print ": N"
I should get a carbon with an "R". What I get is:
O1 : N
O2 : N
N3 : N
C4 : S
C5 : N
C6 : N
-- with or without calling rdkit.Chem.FindMolChiralCenters( mol )
Is this what's supposed to happen?
TIA
--
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
71080.sdf
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