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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