On Fri, Apr 27, 2012 at 5:11 PM, JP <[email protected]> wrote:
> Just installed RDKit 2012_03_1 on Debian 6.0.4, squeeze.
>
> RDKit works fine. I also built and installed the RDKit extension for
> postgresql in the following manner:
>
> % cd $RDBASE/Code/PgSQL/rdkit
> % make
> % sudo make install
>
> (I also did create extension rdkit in my database)
>
> Which also seemed to work well, until I ran
looks good so far.
>
> % make installcheck
>
> ============== running regression test queries ==============
> test rdkit-91 ... FAILED
<snip>
>
> SELECT count(*) FROM pgmol WHERE m @> mol_from_smarts('c1ccccc1');
> ! ERROR: function mol_from_smarts(unknown) does not exist
hmmm
> Which means that I do not have mol_from_smarts, which is a pain because that
> is exactly the reason I installed this version :) (to make use of the
> indices).
It's definitely in the release. Check line 75 here:
http://rdkit.svn.sourceforge.net/viewvc/rdkit/tags/Release_2012_03_1/Code/PgSQL/rdkit/rdkit.sql91.in?revision=2018&view=markup
I guess that the extension didn't get created correctly somehow.
Please look at wherever the extension is installed to and make sure
that mol_from_smarts() is in rdkit--3.1.sql and that the .so you
installed is in the right place. You might also try restarting the
postgresql server.
> Also, this method and its smiles counterpart is not mentioned
> in http://code.google.com/p/rdkit/wiki/DatabaseCartridgeReferenceDocumentation
that's an oversight... thanks for pointing it out.
-greg
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