Hi Toby,
On Wed, Aug 14, 2013 at 2:00 PM, Toby Wright <toby.wri...@inhibox.com>wrote:
> Hi,
>
> I think the following behaviour is a bug but feel free to correct me. I
> have an SD file (attached) with two stereoisomers of alanine (built by
> openbabel from the smiles). I want to read it and write it's contents as
> isomeric smiles. I execute the following:
>
> import rdkit
> from rdkit import Chem
>
> smiles_writer = Chem.SmilesWriter("ChiralTest.smi", includeHeader=False,
> isomericSmiles=True)
> suppl = Chem.SDMolSupplier("ChiralTest3D.sdf", sanitize=False)
> for mol in suppl:
> Chem.SanitizeMol(mol)
> smiles_writer.write(mol)
>
> smiles_writer.flush()
> smiles_writer.close()
>
> smiles_writer2 = Chem.SmilesWriter("ChiralTest2.smi", includeHeader=False,
> isomericSmiles=True)
> suppl2 = Chem.SDMolSupplier("ChiralTest3D.sdf", sanitize=True)
> for mol in suppl2:
> smiles_writer2.write(mol)
>
> smiles_writer2.flush()
> smiles_writer2.close()
>
> The file ChiralTest.smi now contains:
> [H]OC(=O)C([H])(N([H])[H])C([H])([H])[H] L-alanine
> [H]OC(=O)C([H])(N([H])[H])C([H])([H])[H] D-alanine
>
> and ChiralTest2.smi contains:
> C[C@H](N)C(=O)O L-alanine
> C[C@@H](N)C(=O)O D-alanine
>
>
> My question is why do I get different outputs depending on when
> sanitization was performed?
>
It's a bug, as you correctly assumed.
It's actually not the sanitization step per se. If that were the case, this
would work:
In [14]: s = Chem.SDMolSupplier('ChiralTest3D.sdf',sanitize=False)
In [15]: for m in s: Chem.SanitizeMol(m)
In [16]: for m in s: print Chem.MolToSmiles(m,True)
[H]OC(=O)C([H])(N([H])[H])C([H])([H])[H]
[H]OC(=O)C([H])(N([H])[H])C([H])([H])[H]
There is a step in the mol file parser that handles the stereochemistry
information from the CTAB. This step is only called if you do santization.
That is (probably) fixable; I'll definitely look into it.
In the meantime, if the only reason you are skipping the sanitization step
is to avoid having hydrogens removed, you can avoid that as follows:
In [18]: s = Chem.SDMolSupplier('ChiralTest3D.sdf',removeHs=False)
In [19]: for m in s: print Chem.MolToSmiles(m,True)
[H]OC(=O)[C@@]([H])(N([H])[H])C([H])([H])[H]
[H]OC(=O)[C@]([H])(N([H])[H])C([H])([H])[H]
-greg
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