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

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

The changes are now pushed (
https://github.com/rdkit/rdkit/commit/f0d4cf1ec63a4928a2a28fa62cf1d255099e72d0)
and are available on master.
The new functions are qmol_from_smiles() and qmol_from_ctab()

Best,
-greg


On Thu, Apr 2, 2015 at 10:51 AM, Greg Landrum <gre...@gm...>
wrote:

> 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...> 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
>>
>>