Hi Dave,
This is a bug/feature (depends on how you look at it, I think it's a bug)
of the molecule-molecule equality function. That does not take
stereochemistry into account.
If you want a uniqueness constraint, I would suggest using a canonical
smiles column (i.e. by using mol_to_smiles() on the molecule column)
-greg
On Tue, Oct 7, 2014 at 2:51 PM, Dave Wood <davejw...@molplex.com> wrote:
> Dear All,
>
> A colleague and I have set up a structure database using the RDKit
> Postgres cartridge and we are getting a bit stuck on how to handle
> stereochemistry when adding new structures.
>
> Below is a test protocol to reproduce our problem.
>
> *Use case:*
>
> Each structure record should be unique taking into account any specified
> stereochemical information.
>
> Therefore, for the simple case of a compound with one stereocentre we
> should be able to create 3 records: both the R and S enantiomers, and the
> racemic/undefined case.
>
> *Problem:*
>
> Even when setting rdkit.do_chiral_sss=true it is only possible to create a
> record for the racemic/undefined structure if neither of the enantiomers is
> present.
>
> *Example to reproduce the behaviour:*
>
> Set up the emolecules db* as per this section of the RDKit tutorial (
> http://www.rdkit.org/docs/Cartridge.html#creating-a-database-from-a-file)
> and add a unique constraint in psql:
>
> ALTER TABLE mols ADD CONSTRAINT constraint_unique_m UNIQUE (m);
>
> Then try:
>
> SET rdkit.do_chiral_sss=true;
> INSERT INTO mols (m) VALUES ('CCC(C)O');
> INSERT INTO mols (m) VALUES ('CC[C@@H](C)O');
> INSERT INTO mols (m) VALUES ('CC[C@H](C)O');
>
> All 3 queries execute correctly, but:
>
> INSERT INTO mols (m) VALUES ('CCC[C@@H](C)O');
> INSERT INTO mols (m) VALUES ('CCC[C@H](C)O');
> INSERT INTO mols (m) VALUES ('CCCC(C)O'); -- this query fails
>
> ERROR: duplicate key value violates unique constraint
> "constraint_unique_m"
> DETAIL: Key (m)=(CCCC(C)O) already exists.
>
>
> So the question is whether this behaviour is by design (in order to fulfil
> some other requirement maybe), or whether it's an issue with the
> implementation?
>
>
> * the test db was created using the first 1000 entries from the latest
> emolecules smiles file.
> Many thanks in advance for your help with this.
>
> Dave
>
>
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