MolSearch not recognizing generic atoms

Hi

I'm having a problem getting MolSearch to use generic atoms in the query, specifically X=F,Cl,Br.

Attached at the target and query mols.

Molecule targetMol = // target molecule
Molecule queryMol = // query molecule with generic atoms
MolSearch molsearch = new MolSearch();

MolSearchOptions opts = new MolSearchOptions(SearchConstants.SUBSTRUCTURE);

opts.setChargeMatching(SearchConstants.CHARGE_MATCHING_EXACT);

molsearch.setSearchOptions(opts);

molsearch.setTarget(targetMol);

molsearch.setQuery(queryMol);
boolean result = molsearch.isMatching()

// result is false

Hi Daniel,

Because of the aromatic ring in query and target molecules use

MolSearch molsearch = new StandardizedMolSearch();

See API documentation here: https://www.chemaxon.com/jchem/doc/dev/java/api/chemaxon/sss/search/StandardizedMolSearch.html

Best regards,

Krisztina