Thanks Greg,
I have calculated it will slow down on about 30% using this replacement
which is significant for big datasets.
>The substructure matching uses atoms and bonds, and returns the
>results as lists of atom indices; how (and why) would you propose to
>ignore an atom but not a bond?
I mean take bond in account as it is but use "match any" for dummy atom
Regards,
Evgueni
2009/11/7 Greg Landrum <greg.land...@gmail.com>
> Combining two answers into one:
>
> On Fri, Nov 6, 2009 at 7:59 AM, Evgueni Kolossov <ekolos...@gmail.com>
> wrote:
> > 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?
>
> I'm not sure I understand what you mean about slowing down the mapping
> process. If you replace the dummies in your fragments with query
> atoms, as I proposed in the sample code in my earlier message, the
> substructure search should not be substantially slower. The
> replacement itself also won't take that long, unless you really have a
> *lot* of fragments.
>
>
> On Fri, Nov 6, 2009 at 9:03 AM, Evgueni Kolossov <ekolos...@gmail.com>
> wrote:
> >
> > I think you should distinguish between dummy atoms and connection points
> -
> > for fragments it is connection points we are talking about.
>
> The code doesn't understand anything about connection points... it
> just has atoms. Dummy atoms are atoms with atomic number zero. The
> substructure matching code applied to normal Atoms (i.e. not
> QueryAtoms) compares two atoms by checking to see if their atomic
> numbers match, so dummies match dummies. Additionally, when isotopes
> are specified, it checks that the specified isotopes match.
> QueryAtoms, on the other had, allow client code to specify the
> function that's used for matching. The example I provided showed how
> to use a function that matches any atom; which I think is what you are
> looking for.
>
> > 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?
>
> The substructure matching uses atoms and bonds, and returns the
> results as lists of atom indices; how (and why) would you propose to
> ignore an atom but not a bond?
>
> -greg
>
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