Re: [Rdkit-discuss] sanitization removes Hs - is this expected?

[Michal K. <mic...@gm...>]

Hi Greg,
Thank you, this is exactly what I needed.

On 2 April 2015 at 05:22, Greg Landrum <gre...@gm...> wrote:

>
> Skipping sanitization, as you propose, isn't going to help here: the
> kekulized form of the ring will not be converted to aromatic and you won't
> get the matches you are looking for.
>
Indeed. Previously I stored my dataset as smiles with explicit hydrogens,
and created the query mols by adding Hs and then deleting hydrogens at
substitution sites and finally converting to SMARTS - a messy workaround,
but producing the right result.


> Here's an approach to this that works in Python :
>


And this is exactly what I wanted. To illustrate it more precisely: your
pattern (2-H-pyrimidine) matches pyrimidine, 5-methylpyrimidine but does
not match 2-pyrimidine:

>>> m =Chem.MolFromSmiles('c1ccnc([H])n1',sanitize=False);
>>> nm=Chem.MergeQueryHs(m)
>>> Chem.SanitizeMol(nm)
rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE
>>> Chem.MolFromSmiles('c1ccncn1').HasSubstructMatch(nm)
True
>>> Chem.MolFromSmiles('c1c(C)cncn1').HasSubstructMatch(nm)
True
>>> Chem.MolFromSmiles('c1ccnc(C)n1').HasSubstructMatch(nm)
False
>>>



>
> Being able to do something equivalent in the cartridge would certainly be
> useful. What I'd suggest is the addition of two functions:
> "query_mol_from_smiles()" and "query_mol_from_ctab()" that do this.
>

I'll do it.


Then you could do queries like:
> select * from mols where m @> query_mol_from_smiles('c1ccnc([H])n1');
> and have it do the right thing.
>
> Sound reasonable?
>
> -greg
>
>
Best wishes,
Michal