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

[Greg L. <gre...@gm...>]

Hi Michal,

Glad to hear this matches what you are looking for. I have already added
the feature to the cartridge and will check it in later today/tomorrow
morning.

-greg

On Thursday, April 2, 2015, Michal Krompiec <mic...@gm...>
wrote:

> Hi Greg,
> Thank you, this is exactly what I needed.
>
> On 2 April 2015 at 05:22, Greg Landrum <gre...@gm...
> <javascript:_e(%7B%7D,'cvml','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
>
>