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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