I didn't expect it to be so easy !! I took me no effort at all :p
Anyway -- thanks for this really gentle introduction to the code. I guess I
will just familiarize myself with checking out, editing and rebuilding the
code other than the actual development. Till next time I need something...
The only thing left for me to offer is that if you give me rights I will
include it in the documentation
http://code.google.com/p/rdkit/wiki/DatabaseCartridgeReferenceDocumentation
Of course I will make a note that it will be released in the next version...
(2011_02?)
Cheers
JP
On 10 March 2011 05:24, Greg Landrum <greg.land...@gmail.com> wrote:
> Hi JP,
>
> On Wed, Mar 9, 2011 at 3:27 PM, JP <jeanpaul.ebe...@inhibox.com> wrote:
> > Following the documentation on:
> >
> http://code.google.com/p/rdkit/wiki/DatabaseCartridgeReferenceDocumentation
> > I can see no obvious way how to calculate rotatable bonds per molecule
> > through the database cartridge.
>
> Yeah, that's not exposed yet.
>
> > If there isn't a way: how difficult would it be to add this myself? (I
> need
> > this info through sql so I can just use it in my queries).
> > Presumably RDkit already does this: and it is just missing on the DB API.
> > Correct?
>
> yep.
>
> > Where do I start?
>
> I was torn here between explaining how to do it and just doing it,
> which probably is quicker. :-)
>
> Then I realized I could just do it and point you to how it was done,
> so here we go.
>
> At the moment the rotatable bonds count is done purely in Python using
> the code in
> $RDBASE/rdkit/Chem/Lipinski.py
> It counts the number of times the SMARTS pattern
> [!$(*#*)&!D1]-&!@[!$(*#*)&!D1] matches the molecule. This should
> ideally be added as a function in the C++ interface, and I will do
> that at some point, but for this example I did the simpler thing and
> added the computation to the cartridge code directly.
>
> I checked this in with rev1659:
> http://rdkit.svn.sourceforge.net/viewvc/rdkit?view=revision&revision=1659
>
> The first thing I did was add the computation function in C++ in
> adapter.cpp:
>
> http://rdkit.svn.sourceforge.net/viewvc/rdkit/trunk/Code/PgSQL/rdkit/adapter.cpp?r1=1659&r2=1658&pathrev=1659
> It's pretty simple: count the number of times the substructure appears.
>
> This is also added to the rdkit.h header:
>
> http://rdkit.svn.sourceforge.net/viewvc/rdkit/trunk/Code/PgSQL/rdkit/rdkit.h?r1=1659&r2=1658&pathrev=1659
>
> Then I needed to make this available in C so that postgresql can call
> it. That's here:
>
> http://rdkit.svn.sourceforge.net/viewvc/rdkit/trunk/Code/PgSQL/rdkit/mol_op.c?r1=1659&r2=1658&pathrev=1659
>
> Add the function definition for postgresql:
>
> http://rdkit.svn.sourceforge.net/viewvc/rdkit/trunk/Code/PgSQL/rdkit/rdkit.sql.in?r1=1659&r2=1658&pathrev=1659
>
> and then add a test:
>
> http://rdkit.svn.sourceforge.net/viewvc/rdkit/trunk/Code/PgSQL/rdkit/sql/props.sql?r1=1659&r2=1658&pathrev=1659
> and the expected result:
>
> http://rdkit.svn.sourceforge.net/viewvc/rdkit/trunk/Code/PgSQL/rdkit/expected/props.out?r1=1659&r2=1658&pathrev=1659
>
> after that, I ran "make", "make install", and "make installcheck" and
> it was done.
>
> Hope that helps,
> -greg
>
--
Jean-Paul Ebejer
Early Stage Researcher
InhibOx Ltd
Pembroke House
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Oxford
OX1 1BP
UK
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