---------- Forwarded message ----------
From: Evgueni Kolossov <ekolos...@gmail.com>
Date: 2009/12/1
Subject: Re: [Rdkit-discuss] SubstructMatch
To: Greg Landrum <greg.land...@gmail.com>
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
> >
> >
> >
> > --
>
--
Dr. Evgueni Kolossov (PhD)
ekolos...@gmail.com
Tel. +44(0)1628 627168
Mob. +44(0)7812070446
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