fixes mcneilco/acas#728 empty mol files should be considered the same…

src/main/java/com/labsynch/labseer/chemclasses/indigo/ChemStructureServiceIndigoImpl.java

@@ -635,6 +635,16 @@ public String toSmiles(String molStructure) {
 		}
 	}
 
+	@Override
+	public boolean isEmpty(String molStructure) throws CmpdRegMolFormatException {
+		// Return empty if no atoms bonds or SGroups
+		CmpdRegMoleculeIndigoImpl mol = new CmpdRegMoleculeIndigoImpl(molStructure);
+		Boolean hasAtoms =  mol.countAtoms() == 0.0;
+		Boolean hasBonds =  mol.countBonds() == 0.0;
+		Boolean hasSGroups = mol.countGenericSGroups() == 0.0 && mol.countDataSGroups() == 0.0;
+		return !hasAtoms && !hasBonds && !hasSGroups;
+	}
+
 	@Override
 	public double getMolWeight(String molStructure) throws CmpdRegMolFormatException {
 		CmpdRegMoleculeIndigoImpl mol = new CmpdRegMoleculeIndigoImpl(molStructure);

src/main/java/com/labsynch/labseer/chemclasses/jchem/ChemStructureServiceJChemImpl.java

@@ -1717,10 +1717,30 @@ public boolean deleteStructure(String structureTable, int cdId){
 		return deleteSuccessful;
 	}
 
+	@Override
+	public boolean isEmpty(String molStructure) {
+		MolHandler mh = null;
+		boolean badStructureFlag = false;
+		Molecule mol = null;
+		try {
+			mh = new MolHandler(molStructure);
+			mol = mh.getMolecule();			
+		} catch (MolFormatException e) {
+			badStructureFlag = true;
+		}
+
+		if (!badStructureFlag){
+			return mol.isEmpty();
+		} else {
+			return true;
+		}
+	}
 
 	@Override
 	public boolean standardizedMolCompare(String queryMol, String targetMol) throws CmpdRegMolFormatException{
 		try{
+			// If both mols are empty then they are equal
+			if(isEmpty(queryMol) && isEmpty(targetMol)) return true;
 			CmpdRegMoleculeJChemImpl queryMolWrapper = new CmpdRegMoleculeJChemImpl(queryMol);
 			CmpdRegMoleculeJChemImpl targetMolWrapper = new CmpdRegMoleculeJChemImpl(queryMol);
 			StandardizedMolSearch molSearch = new StandardizedMolSearch();

src/main/java/com/labsynch/labseer/service/BulkLoadServiceImpl.java

@@ -571,9 +571,9 @@ public Parent validateParent(Parent parent, Collection<BulkLoadPropertyMappingDT
 			throw new MissingPropertyException("Stereo category is See Comments, but no stereo comment provided");
 		}
 		int[] dupeParentList = {};
-		if(mainConfig.getServerSettings().getRegisterNoStructureCompoundsAsUniqueParents() && chemStructureService.getMolWeight(parent.getMolStructure()) == 0.0) {
+		if(mainConfig.getServerSettings().getRegisterNoStructureCompoundsAsUniqueParents() && chemStructureService.isEmpty(parent.getMolStructure()) ) {
 			//if true then we are no checking this one for hits
-			logger.warn("mol weight is 0 and registerNoStructureCompoundsAsUniqueParents so not checking for dupe parents by structure but other dupe checking will be done");
+			logger.warn("mol is empty and registerNoStructureCompoundsAsUniqueParents so not checking for dupe parents by structure but other dupe checking will be done");
 		} else {
 			dupeParentList = chemStructureService.checkDupeMol(parent.getMolStructure(), "Parent_Structure", "Parent");
 		}

src/main/java/com/labsynch/labseer/service/ChemStructureService.java

@@ -92,5 +92,7 @@ public int[] searchMolStructures(String molfile, String structureTable,
 	public boolean compareStructures(String preMolStruct, String postMolStruct, String string);
 
 	public boolean standardizedMolCompare(String queryMol, String targetMol) throws CmpdRegMolFormatException;
+
+	public boolean isEmpty(String molFile) throws CmpdRegMolFormatException;
 
 }

src/main/java/com/labsynch/labseer/service/ParentServiceImpl.java

@@ -95,8 +95,8 @@ public ParentValidationDTO validateUniqueParent(Parent queryParent) throws CmpdR
 		}
 		Collection<ParentDTO> dupeParents = new HashSet<ParentDTO>();
 		int[] dupeParentList = {};
-		if (mainConfig.getServerSettings().getRegisterNoStructureCompoundsAsUniqueParents() && chemStructureService.getMolWeight(queryParent.getMolStructure()) == 0) {
-			logger.warn("mol weight is 0 and registerNoStructureCompoundsAsUniqueParents so not checking for dupe parents by structure but other dupe checking will be done");
+		if (mainConfig.getServerSettings().getRegisterNoStructureCompoundsAsUniqueParents() && chemStructureService.isEmpty(queryParent.getMolStructure()) ) {
+			logger.warn("mol is empty and registerNoStructureCompoundsAsUniqueParents so not checking for dupe parents by structure but other dupe checking will be done");
 		} {
 			dupeParentList = chemStructureService.checkDupeMol(queryParent.getMolStructure(), "Parent_Structure", "Parent");
 		}
@@ -237,9 +237,9 @@ public int findPotentialDupeParentStructures(String dupeCheckFile){
 			CmpdRegSDFWriter dupeMolExporter = cmpdRegSDFWriterFactory.getCmpdRegSDFWriter(dupeCheckFile);
 			for  (Long parentId : parentIds){
 				parent = Parent.findParent(parentId);
-				if(registerNoStructureCompoundsAsUniqueParents && chemStructureService.getMolWeight(parent.getMolStructure()) == 0) {
+				if(registerNoStructureCompoundsAsUniqueParents && chemStructureService.isEmpty(parent.getMolStructure())) {
 					//if true then we are no checking this one for hits
-					logger.warn("mol weight is 0 and registerNoStructureCompoundsAsUniqueParents is true so not checking for dupe parent");
+					logger.warn("mol is empty and registerNoStructureCompoundsAsUniqueParents is true so not checking for dupe parent");
 					hits = new int[0];
 				} else {
 					hits = chemStructureService.searchMolStructures(parent.getMolStructure(), "Parent_Structure", "DUPLICATE_TAUTOMER");