WITH substructures AS
(
SELECT *
FROM yourtable
WHERE mol @> 'NC(=O)C(=O)C'
)
SELECT *
FROM substructures
WHERE mol @> '[H]N([H])C(=O)C(=O)C'::qmol
On Fri, Mar 18, 2011 at 09:54, JP <jeanpaul.ebe...@inhibox.com> wrote:
> 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
>> > InhibOx Ltd
>> > Pembroke House
>> > 36-37 Pembroke Street
>> > Oxford
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>> > UK
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>
>
> --
>
> Jean-Paul Ebejer
> Early Stage Researcher
> InhibOx Ltd
> Pembroke House
> 36-37 Pembroke Street
> Oxford
> OX1 1BP
> UK
> (+44 / 0) 1865 262 034
>
>
> This email and any files transmitted with it are confidential and intended
> solely for the use of the individual or entity to whom they are addressed.
> Any unauthorised dissemination or copying of this email or its attachments,
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> Internet communications including emails and access and use of web sites
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> intercepted, corrupted, lost or arrive late. Furthermore, while we have
> taken steps to control the spread of viruses on our systems, we cannot
> guarantee that this email and any files transmitted with it are virus free.
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