Hmm, can't be driving users mad... that's no good!
You just need to tell the cartridge build that it should use InChI:
% USE_INCHI=1 USE_POPCOUNT=1 make
This will get easier when we have the cartridge build integrated into
cmake, but for now that's the solution...
-greg
p.s. the USE_POPCOUNT=1 is something that's worth setting on modern compute
hardware; it will make similarity calculations significantly faster.
On Thu, Feb 12, 2015 at 3:37 PM, JP <[email protected]> wrote:
> Hi there RDKitters,
>
> I am trying to install inchi functionality from the database, and all I
> keep getting is:
>
> testdb=# select mol_inchi('CCC'::mol);
> mol_inchi
> ---------------------
> InChI not available
> (1 row)
>
> SO what I have done till now...
>
> From external/INCHI-API - I execute ./download-inchi.sh
> This downloads all the correct inchi library file... Then following the
> instructions on https://code.google.com/p/rdkit/wiki/BuildingTheCartridge
> (but of course, turning inchi support on):
>
> cmake -DRDK_BUILD_INCHI_SUPPORT=ON ..
> make clean
> make
> make install
>
> And now if I go in python:
>
> Python 2.6.6 (r266:84292, Dec 26 2010, 22:31:48)
> [GCC 4.4.5] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import rdkit
> >>> from rdkit import Chem
> >>> from rdkit.Chem import AllChem
> >>> AllChem.INCHI_AVAILABLE
> True
> >>>
>
> Brilliant. Here I stop my running postgresql installation.
>
> cd $RDBASE/Code/PgSQL/rdkit
> sudo rm /opt/postgresql-9.3.4/lib/rdkit.so
>
> cd $RDBASE/Code/PgSQL/rdkit
> make clean
> make
> sudo make install # in order to get this to work I had to change the this
> line in the Makefile PG_CONFIG = /opt/postgresql-9.3.4/bin/pg_config
> make installcheck # before this I restart postgresql
>
> All final 9 tests pass. And I can see a new rdkit.so in the postgresql
> lib directory.
>
> I login a database
> createdb testdb
> testdb=#create extension rdkit;
> testdb=# load 'rdkit.so' # just to be sure latest is loaded...
> testdb=# select mol_inchi('CCC'::mol);
> mol_inchi
> ---------------------
> InChI not available
> (1 row)
>
> This also looks good:
> echo $LD_LIBRARY_PATH
> /opt/postgresql-9.3.4/lib:/opt/RDKit_2014_09_2/lib:
>
>
>
> I am going crazy trying iterations and permutations of the above. Can
> anyone tell me what I am doing wrong? One added combination is perhaps
> that I have other databases which have the rdkit extension installed (from
> a previous version).
>
> This is using RDKit 2014_09_2
>
>
>
>
>
> -
> Jean-Paul Ebejer
> Early Stage Researcher
>
>
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sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
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