Greg,
I think you should distinguish between dummy atoms and connection points -
for fragments it is connection points we are talking about. So, it suppose
to ignore this atom (but not bond!) during matching process. May be just add
another bool flag to allow user select different behavior?
Regards,
Evgueni
2009/11/6 Evgueni Kolossov <ekolos...@gmail.com>
> Hi Greg,
>
> Yes, this is solution I been thinking about as well but there is 2
> problems:
> 1. It will slow dawn mapping process which is slow already
> 2. What atom to use for replacement?
>
> What if I will just remove this atom(s)?
>
> Regards,
> Evgueni
>
> 2009/11/6 Greg Landrum <greg.land...@gmail.com>
>
> On Wed, Nov 4, 2009 at 7:54 PM, Greg Landrum <greg.land...@gmail.com>
>> wrote:
>> >
>> > On Wed, Nov 4, 2009 at 3:26 PM, Evgueni Kolossov <ekolos...@gmail.com>
>> wrote:
>> >>
>> >> I found that SubstructMatch would not work if query is a fragment (with
>> *
>> >> atoms).
>> >> Can you suggest solution for this problem?
>> >
>> > That's a bug. Dummy atoms (things with atomic number zero) that do not
>> > have an isotope specification should match anything. If you have a
>> > sourceforge account, please enter the bug, otherwise let me know and I
>> > will enter it.
>>
>> After going back through the code and thinking about this for a while
>> I'm going to change my original answer: it's not a bug that standard
>> dummy atoms only match other dummy atoms. When I saw the "*" in the
>> original message I started thinking about the QueryAtoms produced by a
>> "*" in SMARTS, which definitely should (and do) match other dummies.
>> The behavior with standard Atoms is useful for things like flagging
>> attachment points of R groups on a scaffold. Here's an example:
>>
>> [5] >>> f= Chem.MolFromSmiles('c1cccnc1*')
>>
>> [6] >>> p = Chem.MolFromSmarts('c1cccnc1*')
>>
>> [9] >>> m = Chem.MolFromSmiles('c1ccc(C)nc1*')
>>
>> Matching using f, which has dummy Atoms only gives one match:
>> [10] >>> m.GetSubstructMatches(f)
>> Out[10]: ((0, 1, 2, 3, 5, 6, 7),)
>>
>> But matching using p, which has a QueryAtom built from "*" matches twice:
>> [11] >>> m.GetSubstructMatches(p)
>> Out[11]: ((0, 1, 2, 3, 5, 6, 7), (2, 1, 0, 6, 5, 3, 4))
>>
>> For your use case, I'd suggest replacing the dummies in your fragments
>> with QueryAtoms that have the appropriate query, something like this
>> (not tested):
>>
>> //---------------------------------------------
>> #include <GraphMol/RDKitQueries.h>
>>
>> void replaceDummies(RWMol *frag){
>> QueryAtom *qat = new QueryAtom();
>> qat->setQuery(makeAtomNullQuery());
>> for(unsigned int i=0;i<frag->getNumAtoms();++i){
>> if(frag->getAtomWithIdx(i)->getAtomicNum()==0){
>> frag->replaceAtom(i,qat);
>> }
>> }
>> delete qat;
>> }
>> //---------------------------------------------
>>
>> I hope this helps,
>> -greg
>>
>
>
>
>
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