Hi all, since the new release I'm experiencing problems with exact structure search in the cartridge. If an index is defined on the mol column exact structure search ( @= ) doesn't work (i.e. yields no results). I tried it with rdkit compiled from source under CentOS 6.5 and with the RPMs from Gianluca Sforna for Fedora 20. In both cases postgres 9.3 was used. Can anyone confirm this or am I missing something?
Here's what I've done (based on the emolecules example from the docs): RDKit 2014.09 (not working): ##################### [moe@localhost db]$ createdb emolecules [moe@localhost db]$ psql -c 'create extension rdkit' emolecules CREATE EXTENSION [moe@localhost db]$ psql -c 'SELECT rdkit_version()' emolecules rdkit_version --------------- 0.73.0 (1 row) [moe@localhost db]$ wget http://downloads.emolecules.com/free/2014-10-01/version.smi.gz [...] 2014-10-31 10:52:29 (1,08 MB/s) - 'version.smi.gz' saved [88871202/88871202] [moe@localhost db]$ psql -c 'create table raw_data (id SERIAL, smiles text, emol_id integer, parent_id integer)' emolecules CREATE TABLE [moe@localhost db]$ zcat version.smi.gz | sed '1d; s/\\/\\\\/g' | psql -c "copy raw_data (smiles,emol_id,parent_id) from stdin with delimiter ' '" emolecules [moe@localhost db]$ psql emolecules psql (9.3.5) Type "help" for help. emolecules=# SELECT * INTO mols FROM (SELECT id,mol_from_smiles(smiles::cstring) m FROM raw_data) tmp WHERE m IS NOT null LIMIT 1000; SELECT 1000 emolecules=# SELECT * FROM mols WHERE m @= Mol_From_Smiles('CCOC(=N)CC'); id | m -----+------------ 383 | CCOC(=N)CC (1 row) emolecules=# CREATE INDEX molidx ON mols USING gist(m); CREATE INDEX emolecules=# SELECT * FROM mols WHERE m @= Mol_From_Smiles('CCOC(=N)CC'); id | m ----+--- (0 rows) emolecules=# DROP INDEX molidx; DROP TABLE mols; SELECT * INTO mols FROM (SELECT id,mol_from_smiles(smiles::cstring) m FROM raw_data) tmp WHERE m IS NOT null LIMIT 1000; SELECT * FROM mols WHERE m @= Mol_From_Smiles('CCOC(=N)CC'); DROP INDEX DROP TABLE SELECT 1000 id | m -----+------------ 383 | CCOC(=N)CC (1 row) ##################### RDKit 2014.03 (working): ##################### -bash-4.1$ createdb emolecules_test -bash-4.1$ psql -c 'SELECT rdkit_version()' emolecules_test rdkit_version --------------- 0.72.0 (1 row) -bash-4.1$ psql -c 'create table raw_data (id SERIAL, smiles text, emol_id integer, parent_id integer)' emolecules_test CREATE TABLE -bash-4.1$ zcat version.smi.gz | sed '1d; s/\\/\\\\/g' | psql -c "copy raw_data (smiles,emol_id,parent_id) from stdin with delimiter ' '" emolecules_test -bash-4.1$ psql emolecules_test psql (9.3.4) Type "help" for help. emolecules_test=# SELECT * INTO mols FROM (SELECT id,mol_from_smiles(smiles::cstring) m FROM raw_data) tmp WHERE m IS NOT null LIMIT 1000; SELECT 1000 emolecules_test=# SELECT * FROM mols WHERE m @= Mol_From_Smiles('CCOC(=N)CC'); id | m -----+------------ 383 | CCOC(=N)CC (1 row) emolecules_test=# CREATE INDEX molidx ON mols USING gist(m); CREATE INDEX emolecules_test=# SELECT * FROM mols WHERE m @= Mol_From_Smiles('CCOC(=N)CC'); id | m -----+------------ 383 | CCOC(=N)CC (1 row) emolecules_test=# DROP INDEX molidx; DROP TABLE mols; SELECT * INTO mols FROM (SELECT id,mol_from_smiles(smiles::cstring) m FROM raw_data) tmp WHERE m IS NOT null LIMIT 1000; SELECT * FROM mols WHERE m @= Mol_From_Smiles('CCOC(=N)CC'); DROP INDEX DROP TABLE SELECT 1000 id | m -----+------------ 383 | CCOC(=N)CC (1 row) ##################### Best, Daniel
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