Evgueni,
Please provide specific maps that don't make sense.
-greg
On Tue, Dec 1, 2009 at 11:50 AM, Evgueni Kolossov <ekolos...@gmail.com> wrote:
> Fragment: *CCCC
> Structure: S=C(CC1CCCCC1)N1CCC(c2nc[nH]c2)CC1
>
> Code
> //////////////////////////////////////////////////////////////////
> void CFragmentation::ReplaceDummies(RDKit::RWMol * frag)
> {
> RDKit::QueryAtom *qat = new RDKit::QueryAtom();
> qat->setQuery(RDKit::makeAtomNullQuery());
>
> for(unsigned int i=0; i<frag->getNumAtoms(); i++)
> {
> if(frag->getAtomWithIdx(i)->getAtomicNum()==0)
> frag->replaceAtom(i,qat);
> }
> delete qat;
> }
> //////////////////////////////////////////////////////////////////
> std;:string strSmilesFrag = "*CCCC", strSmilesStruct =
> "S=C(CC1CCCCC1)N1CCC(c2nc[nH]c2)CC1";
> std::vector< RDKit::MatchVectType > vMatches;
>
> RDKit::RWMol *frag = new RDKit::RWMol();
> frag = RDKit::SmilesToMol(iter->strSmilesFrag);
> SciDB::CFragmentation::ReplaceDummies(frag);
>
> RDKit::ROMol *mol = new RDKit::ROMol();
> mol = RDKit::SmilesToMol(strSmilesStruct);
>
> int nMap = RDKit::SubstructMatch(*mol, *frag,vMatches);
>
> I believe nMap = 17 does not make sense!
>
> Regards,
> Evgueni
>
> 2009/12/1 Greg Landrum <greg.land...@gmail.com>
>>
>> If you've looked at the matches and found specific ones that don't
>> make sense, please post them, the exact query and molecule you used
>> (including the atom numbering), and the code you are using to do the
>> matching and I will take a look.
>>
>> -greg
>>
>>
>> On Tue, Dec 1, 2009 at 10:52 AM, Evgueni Kolossov <ekolos...@gmail.com>
>> wrote:
>> > Yes, Greg,
>> >
>> > I believe that result 17 matches for this fragment does not make any
>> > sense
>> >
>> > 2009/12/1 Greg Landrum <greg.land...@gmail.com>
>> >>
>> >> Dear Evgueni,
>> >>
>> >> On Tue, Dec 1, 2009 at 10:21 AM, Evgueni Kolossov <ekolos...@gmail.com>
>> >> wrote:
>> >> >
>> >> > I have enclosed 2 files - images for structure and fragment. When
>> >> > using
>> >> > unsigned int SubstructMatch() I am getting value = 17!!! Looking like
>> >> > function is not taking in account atom types and flag uniquify is not
>> >> > working at all - or may be I am missing something? Can you please
>> >> > comment on
>> >> > this behaviour?
>> >>
>> >> I guess I don't really see anything particularly unusual. Have you
>> >> tried looking at the values you get for the matches? Is there a
>> >> particular result you see that doesn't make sense?
>> >>
>> >> -greg
>> >
>> >
>> >
>> > --
>
>
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