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 <[email protected]>
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 <[email protected]>
> wrote:
>
>> Hi Greg,
>> Thank you, this is exactly what I needed.
>>
>> On 2 April 2015 at 05:22, Greg Landrum <[email protected]> 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
>>
>>
------------------------------------------------------------------------------
Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
_______________________________________________
Rdkit-discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
