Neutralize using Standardiser affects subsequent MolSearch

Hi,

Just wondered if it was possible to get an explanation of the following Standardizer behaviour.  We are using JChem 5304.  Basically, we standardize a SMILES and use the standardized SMILES as a target in a MolSearch, which subsequently does not produce any hits.  We then take the standardized SMILES and reimport it, try the search again, and it produces a hit (which seems a bit odd):

 

final String smartsString = "[$(C(=O)[OH])]";

final Molecule smarts = MolImporter.importMol( smartsString, "smarts" );

final Molecule smiles = MolImporter.importMol( "c1ccccc1CC([O-])=O" );

final MolSearch search = new MolSearch();

final Standardizer standardizer = new Standardizer("neutralize");

standardizer.standardize(smiles);

search.setQuery(smarts);

search.setTarget(smiles);

System.out.println( "Match count after standardize: " + search.getMatchCount() );

final Molecule reimportedSmiles = MolImporter.importMol( smiles.toFormat("smiles"), "smiles" );

search.setTarget(reimportedSmiles);

System.out.println( "Match count after re-importing: " + search.getMatchCount() ); 

 

Apologies if this has been posted about before, I couldn't find anything talking about the same issue.

Thanks muchly. 

Since we are just travelling, you will get an answer early next week only. I am sorry for the delay.

Hi Derek,

 

It may be that the number of hydrogens are not updated during neutralize.

Could you check if adding a

smiles.valenceCheck();

call just after standardization would fix it? (It recalculates the number of implicit H-s for each atom.)

If it works ok, it will be a workaround for now, and we can add this directly into the neutralize action, too.

 

Thanks,

Szabolcs

Hi Derek,

Szabolcs's workaround works, please apply it until we fix this in Standardizer.
Sorry for the inconvenience.

Zsolt

Thanks guys, that seems to have done the trick.

D

Standardizer neutralize action fix will be available in next release.

Zsolt