I am not quite sure I got this - can you give me a practical example (with
WITH) ?
On 17 March 2011 20:05, Adrian Schreyer <adr...@cryst.bioc.cam.ac.uk> wrote:
> The easiest way would be to do a substructure search as a subquery or
> WITH statement first and then do a SMARTS search on the result. This
> way you can keep your hydrogens and the speed (most of it).
>
> Adrian
>
> On Thu, Mar 17, 2011 at 19:11, JP <jeanpaul.ebe...@inhibox.com> wrote:
> > Could the API possibly be altered to allow for H Removal (or not) ?
> >
> > On 17 March 2011 18:50, Greg Landrum <greg.land...@gmail.com> wrote:
> >>
> >> Hi JP,
> >>
> >> On Thu, Mar 17, 2011 at 2:55 PM, JP <jeanpaul.ebe...@inhibox.com>
> wrote:
> >> > I am using RDKit 2010_12_1, in particular the database cartridge - but
> I
> >> > am
> >> > quite positive this is an RDkit core problem.
> >>
> >> Well, problem... feature.. it's all a matter of perspective. :-S
> >>
> >> > Now - I am trying a substructure search (using '@>' operator on the
> >> > RDkit
> >> > molecule table) using smiles [H]N([H])C(=O)C(=O)C (so two explicit
> >> > hydrogens
> >> > on the N which is bound to a C with double bond to O) the following
> >> > molecule is returned:
> >> > I have the following smiles string:
> >> > O=C(C(=O)N1CC[NH2+]CC1)c1ccc(cc1C)C
> >> > Which RDKit::mol object
> >> > Cc1ccc(C(C(N2CC[NH2+]CC2)=O)=O)c(C)c1
> >> > But it shouldn't ! (No ?)
> >> > Any help will be as usual - much appreciated.
> >>
> >> Here's what happens: when you construct the query molecule from SMILES
> >> the Hs are removed, so the queries for [H]N([H])C(=O)C(=O)C and
> >> NC(=O)C(=O)C end up being identical.
> >>
> >> At the moment, if you want to include the Hs in the query you have to
> >> do a SMARTS query. This has the unfortunate side effect of making the
> >> query substantially slower.
> >>
> >> I agree that this behavior is "suboptimal". I'm going to have to think
> >> (and read) a bit to come up with a reasonable solution.
> >>
> >> -greg
> >
> >
> >
> > --
> >
> > Jean-Paul Ebejer
> > Early Stage Researcher
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Jean-Paul Ebejer
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InhibOx Ltd
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