Jan, Thanks for the confirmation. Since this is almost certainly a bug in RDKit is there any chance for a quick bug fix release?
Kind regards, Michał Nowotka On Thu, Jun 18, 2015 at 7:06 PM, Jan Holst Jensen <[email protected]> wrote: > Hi Michael, > > I don't know what's wrong, but I can confirm the behavior on an RDKit > build based on 2013_09_2: > > select id, molecule > from parents$calc_props > where molecule operator(rdkit.@>) 'CC[C@H](C)C(=O)O[C@H]1C[C@ > @H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H]3C[C@@H](O)CC(=O)O3)[C@H]21' > limit 10 > > id molecule 56 CC[C@H](C)C(=O)O[C@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@H > ](CC[C@@H]3C[C@@H](O)CC(=O)O3)[C@H]21 > select id, molecule > from parents$calc_props > where molecule operator(rdkit.<@) 'CC[C@H](C)C(=O)O[C@H]1C[C@ > @H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H]3C[C@@H](O)CC(=O)O3)[C@H]21' > limit 10 > > <same result as above - record with ID = 56> > > select id, molecule > from parents$calc_props > where molecule operator(rdkit.@=) 'CC[C@H](C)C(=O)O[C@H]1C[C@ > @H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H]3C[C@@H](O)CC(=O)O3)[C@H]21' > limit 10 > > <no results> > > The operator should work according to docs > > http://www.rdkit.org/docs/Cartridge.html > > Substructure and exact structure search > > - @> : substructure search operator. Returns whether or not the mol or > qmol on the right is a substructure of the mol on the left. > - <@ : substructure search operator. Returns whether or not the mol or > qmol on the left is a substructure of the mol on the right. > - @= : returns whether or not two molecules are the same. > > > A workaround is this: > > select id, molecule > from parents$calc_props > where molecule operator(rdkit.<@) 'CC[C@H](C)C(=O)O[C@H]1C[C@ > @H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H]3C[C@@H](O)CC(=O)O3)[C@H]21' > and molecule operator(rdkit.@>) 'CC[C@H](C)C(=O)O[C@H]1C[C@ > @H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H]3C[C@@H](O)CC(=O)O3)[C@H]21' > limit 10 > > which returns the molecule as intended. It was suggested by Greg in an > ancient post from 2010: > > http://sourceforge.net/p/rdkit/mailman/message/26662092/ > > Cheers > -- Jan > > > On 2015-06-18 18:01, Michał Nowotka wrote: > > Hi, > > I'm working on mychembl_20 and I have latest stable RDKit version > ("Release_2015_03_1") installed and compiled as postgres cartridge. > > Some facts: > > 1. All tests went fine, including tests for postgres extension. > 2. Substructure (@>) and similarity (tanimoto_sml) searches are working fine. > > Now I'm trying to execute this SQL statement: > > SELECT COUNT(*) > FROM "mols_rdkit" > WHERE (m@='C'); > > This runs without errors but returns 0. It returns 0 for any SMILES > string, even if I know that the structure exists in the database. > > Table "mold_rdkit" exists, is not empty and has column "m" (as I said, > substructure and similarity are working fine). > > Am I doing something wrong? Is there anything I can do to verify if > the problem is related to RDKit or something else? > > Kind regards, > > Michał Nowotka > > >
------------------------------------------------------------------------------
_______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
