Hi Dimitri,
On Tue, Sep 30, 2014 at 1:48 AM, Dimitri Maziuk <dmaz...@bmrb.wisc.edu>
wrote:
> 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.
This is correct.
> 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?
>
Kind of, but what's happening isn't what you think.
The R/S (CIP) label on a molecule tells you about its absolute
stereochemistry.
The chiral tag, on the other hand, tells you about the relative positions
of the bonds *as* provided. There's no way to go directly from the chiral
tag to the CIP R/S assignment.
If you'd like to see the R/S tags, you can do something like this:
In [*2*]: m = Chem.MolFromMolFile('./71080.sdf')
In [*3*]: Chem.FindMolChiralCenters(m)
Out[*3*]: [(3, 'R')]
If you want more detail about the CW/CCW thing, let me know and I can do a
longer (but still brief) description.
-greg
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