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
% make installcheck
============== running regression test queries ==============
test rdkit-91 ... FAILED
test props ... ok
test btree ... ok
test molgist ... ok
test bfpgist-91 ... ok
test sfpgist ... ok
test slfpgist ... ok
test fps ... ok
Opening "/opt/RDKit_2012_03_1/Code/PgSQL/rdkit/regression.diffs" I can see
*** /opt/RDKit_2012_03_1/Code/PgSQL/rdkit/expected/rdkit-91.out 2012-03-04
16:24:44.000000000 +0000
--- /opt/RDKit_2012_03_1/Code/PgSQL/rdkit/results/rdkit-91.out 2012-04-27
16:19:12.000000000 +0100
***************
*** 63,97 ****
(1 row)
SELECT count(*) FROM pgmol WHERE m @> mol_from_smarts('c1ccccc1');
! count
! -------
! 901
! (1 row)
!
SELECT count(*) FROM pgmol WHERE m @> mol_from_smarts('c1cccnc1');
! count
! -------
! 245
! (1 row)
!
SELECT count(*) FROM pgmol WHERE m @> mol_from_smarts('c1ccc[n,c]c1');
! count
! -------
! 939
! (1 row)
!
SELECT count(*) FROM pgmol WHERE mol_from_smarts('c1ccccc1') <@ m;
! count
! -------
! 901
! (1 row)
!
SELECT count(*) FROM pgmol WHERE mol_from_smarts('c1ccc[n,c]c1') <@ m;
! count
! -------
! 939
! (1 row)
!
SELECT id, rdkit_fp(m) AS f INTO pgbfp FROM pgmol;
CREATE UNIQUE INDEX bfp_ididx ON pgbfp (id);
SELECT id, morgan_fp(m,1) AS f INTO pgsfp FROM pgmol;
--- 63,92 ----
(1 row)
SELECT count(*) FROM pgmol WHERE m @> mol_from_smarts('c1ccccc1');
! ERROR: function mol_from_smarts(unknown) does not exist
! LINE 1: SELECT count(*) FROM pgmol WHERE m @> mol_from_smarts('c1ccc...
! ^
! HINT: No function matches the given name and argument types. You might
need to add explicit type casts.
SELECT count(*) FROM pgmol WHERE m @> mol_from_smarts('c1cccnc1');
! ERROR: function mol_from_smarts(unknown) does not exist
! LINE 1: SELECT count(*) FROM pgmol WHERE m @> mol_from_smarts('c1ccc...
! ^
! HINT: No function matches the given name and argument types. You might
need to add explicit type casts.
SELECT count(*) FROM pgmol WHERE m @> mol_from_smarts('c1ccc[n,c]c1');
! ERROR: function mol_from_smarts(unknown) does not exist
! LINE 1: SELECT count(*) FROM pgmol WHERE m @> mol_from_smarts('c1ccc...
! ^
! HINT: No function matches the given name and argument types. You might
need to add explicit type casts.
SELECT count(*) FROM pgmol WHERE mol_from_smarts('c1ccccc1') <@ m;
! ERROR: function mol_from_smarts(unknown) does not exist
! LINE 1: SELECT count(*) FROM pgmol WHERE mol_from_smarts('c1ccccc1')...
! ^
! HINT: No function matches the given name and argument types. You might
need to add explicit type casts.
SELECT count(*) FROM pgmol WHERE mol_from_smarts('c1ccc[n,c]c1') <@ m;
! ERROR: function mol_from_smarts(unknown) does not exist
! LINE 1: SELECT count(*) FROM pgmol WHERE mol_from_smarts('c1ccc[n,c]...
! ^
! HINT: No function matches the given name and argument types. You might
need to add explicit type casts.
SELECT id, rdkit_fp(m) AS f INTO pgbfp FROM pgmol;
CREATE UNIQUE INDEX bfp_ididx ON pgbfp (id);
SELECT id, morgan_fp(m,1) AS f INTO pgsfp FROM pgmol;
======================================================================
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).
Also, this method and its smiles counterpart is not mentioned in
http://code.google.com/p/rdkit/wiki/DatabaseCartridgeReferenceDocumentation
Any help is really appreciated.
-
Jean-Paul Ebejer
Early Stage Researcher
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