It looks like this discussion is still unresolved. Greg's going to have a pile
of things on his desk (eDesk?) when he gets back from holidays. :)
On Jan 30, 2012, at 1:26 PM, JP wrote:
> But then I will have to add the "if not clean_mol.GetNumAtoms():"
> before/after replacing/editing molecule parts, after reading molecules,
> before writing them etc. i.e. I'd need this statement in a lot of places.
> This is why I asked if it should be considered a valid molecule - because if
> these moves in SanitizeMol I wouldn't need any of that e.g. I can assume that
> the molecule I have in hand, is valid and if I still wanted these molecules
> (for some not so clear reason) I could just switch of sanitization off, on
> the methods that allow it.
I just ran into this myself. I used SaltRemover on CHEMBL1644029, which is
potassium nitrate. The SaltRemover removed both ions, leaving me with an empty
structure.
I blithely wrote the de-salted structures to a file. It wasn't until I had
RDKit read the structures later, when trying to figure out the message
"Problems encountered parsing data fields", that I realized that I had
de-salted a salt, leaving nothing.
>>> from rdkit import Chem
>>> from rdkit.Chem import SaltRemover
>>> remover = SaltRemover.SaltRemover()
>>> mol = Chem.MolFromSmiles("[K+].[O-]N(=O)=O")
>>> mol2 = remover.StripMol(mol)
>>> Chem.SDWriter("/dev/stdout").write(mol2)
RDKit
0 0 0 0 0 0 0 0 0 0999 V2000
M END
$$$$
>>> writer = Chem.SDWriter("empty.sdf")
>>> writer.write(mol2)
>>> writer.close()
>>> for mol in Chem.ForwardSDMolSupplier("empty.sdf"):
... print "I have", repr(mol)
...
[00:02:16] ERROR: on line 5 Problems encountered parsing data fields
[00:02:16] ERROR: moving to the begining of the next molecule
I have <rdkit.Chem.rdchem.Mol object at 0x101e00b40>
>>>
I agree with JP. Either:
1) this is an ERROR, in which case a) the reader should yield a None rather
than a molecule object, and b) the writer should refused to write it, or
2) this is not an ERROR, and the reader should be fixed so it doesn't log an
error message for this case. Since it's either valid syntax or it isn't, it
probably shouldn't generate any message.
Of these, I prefer #2.
Cheers,
Andrew
da...@dalkescientific.com
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