Merge pull request #56 from mcneilco/bugfix/bingo-search-with-saltform

Fixes #55 Indigo structure search breaks when salt form structure mat…
mcneilco · May 4, 2018 · ba2e606 · ba2e606
2 parents e7f9e01 + 51bc7c6
commit ba2e606
Showing 1 changed file with 9 additions and 4 deletions.
diff --git a/src/main/java/com/labsynch/cmpdreg/chemclasses/indigo/ChemStructureServiceIndigoImpl.java b/src/main/java/com/labsynch/cmpdreg/chemclasses/indigo/ChemStructureServiceIndigoImpl.java
@@ -206,6 +206,11 @@ public int[] searchMolStructures(String molfile, String structureTable, String p
 		logger.debug("Search type is  " + searchType);		
 		logger.debug("Max number of results is  " + maxResults);		
 
+		logger.debug("Dissimilarity similarity is  " + simlarityPercent);		
+
+		float indSimilarity = 1.0f - simlarityPercent;
+		logger.debug("Indigo search similarity is  " + indSimilarity);		
+
 
 		if (searchType.equalsIgnoreCase("EXACT")){
 			searchType = exactSearchDef;
@@ -257,8 +262,8 @@ public int[] searchMolStructures(String molfile, String structureTable, String p
 			if (searchType.equalsIgnoreCase("SUBSTRUCTURE")) {
 				query.setParameter("parameters", "");
 			}else if (searchType.equalsIgnoreCase("SIMILARITY")) {
-				query.setParameter("minSimilarity", simlarityPercent);
-				query.setParameter("maxSimilarity", null);
+				query.setParameter("minSimilarity", indSimilarity);
+				query.setParameter("maxSimilarity", 1.0);
 				query.setParameter("metric", "Tanimoto");
 			}else {
 				String parameters = null;
@@ -440,8 +445,8 @@ public CmpdRegMolecule[] searchMols(String molfile, String structureTable, int[]
 			query.setParameter("queryMol", mol.molfile());
 			query.setMaxResults(maxResults);
 
-			if (inputCdIdHitList != null && inputCdIdHitList.length > 0) query.setParameter("filterCdIds", Arrays.asList(inputCdIdHitList));
-			
+			if (inputCdIdHitList != null && inputCdIdHitList.length > 0) query.setParameter("filterCdIds", Arrays.asList(ArrayUtils.toObject(inputCdIdHitList)));
+
 			//May need additional research / decisions around which options to use
 			//Basic Indigo search types corresponding to JChem search types
 			//CReg: "DUPLICATE" or "DUPLICATE_NO_TAUTOMER" :: JChem: "DUPLICATE", "TAUTOMER_SEARCH_OFF" :: Bingo.Exact, "ALL"