I believe none of them if take in account cyclic and non-cyclic atoms
2009/12/1 Greg Landrum <greg.land...@gmail.com>
> 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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