renamed maxUndefined to maxUndefinedStereoCenters

cleaned up atom deletion in getSizeOfLargestRingSystem
prevent double calls to getSizeOfLargestRingSystem
use real logging instead of println

src/main/java/gov/nih/ncats/molwitch/cdk/CdkChemical2FactoryImpl.java

@@ -31,6 +31,7 @@
 import java.io.StringReader;
 import java.util.Map;
 import java.util.function.Consumer;
+import java.util.logging.Logger;
 import java.util.stream.Stream;
 
 import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
@@ -532,14 +533,16 @@ public boolean isDefault() {
 
 	@Override
 	public void applyParameters(Map<String, Object> params){
-		System.out.println("in CdkChemical2FactoryImpl.applyParameters");
+		Logger.getLogger(this.getClass().getName()).fine("in CdkChemical2FactoryImpl.applyParameters");
 		if( params.get("complexityCutoff") != null) {
 			CdkChemicalImpl.setComplexityCutoff((Integer) params.get("complexityCutoff"));
-			System.out.printf("complexityCutoff: %s\n", params.get("complexityCutoff"));
+			Logger.getLogger(this.getClass().getName()).fine(
+					String.format("complexityCutoff: %s\n", params.get("complexityCutoff")));
 		}
-		if( params.get("maxUndefined") != null ) {
-			CdkChemicalImpl.setMaxUndefinedStereoCenters((Integer)params.get("maxUndefined"));
-			System.out.printf("maxUndefined: %s\n", params.get("maxUndefined"));
+		if( params.get("maxUndefinedStereoCenters") != null ) {
+			CdkChemicalImpl.setMaxUndefinedStereoCenters((Integer)params.get("maxUndefinedStereoCenters"));
+			Logger.getLogger(this.getClass().getName()).fine(
+					String.format("maxUndefinedStereoCenters: %s\n", params.get("maxUndefinedStereoCenters")));
 		}
 	}
 }

src/main/java/gov/nih/ncats/molwitch/cdk/CdkChemicalImpl.java

@@ -156,7 +156,9 @@ public static void setMaxUndefinedStereoCenters(int maxUndefinedStereoCenters) {
 		CdkChemicalImpl.maxUndefinedStereoCenters = maxUndefinedStereoCenters;
 	}
 
-	private static int maxUndefinedStereoCenters = 20;
+	//This parameter allows us to prevent a long calculation that enumerates all possibilities of undefined stereocenters.
+	//  this should typically be set to values < 10
+	private static int maxUndefinedStereoCenters = 5;
 
 //	CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(SilentChemObjectBuilder.getInstance());
 
@@ -215,8 +217,9 @@ public static void setMaxUndefinedStereoCenters(int maxUndefinedStereoCenters) {
     }
 
 	CachedSupplier<Boolean> complexitySupplier =CachedSupplier.of(()->{
-		Logger.getLogger(this.getClass().getName()).info("getSizeOfLargestRingSystem(this): " + getSizeOfLargestRingSystem(this));
-		return getSizeOfLargestRingSystem(this)> complexityCutoff;
+		int sizeOfLargestRingSystem = getSizeOfLargestRingSystem(this);
+		Logger.getLogger(this.getClass().getName()).info("getSizeOfLargestRingSystem(this): " + sizeOfLargestRingSystem);
+		return sizeOfLargestRingSystem > complexityCutoff;
 	});
 
 	CachedSupplier<Integer> perceiveAtomTypesOfNonQueryAtoms = CachedSupplier.of(()->{

src/main/java/org/openscience/cdk/geometry/cip/CIPToolMod.java

@@ -306,15 +306,16 @@ public static int getSizeOfLargestRingSystem(CdkChemicalImpl chemical) {
             return 0;
         }
 
+        List<Atom> atomsToRemove = new ArrayList<>();
         for(int i = copy.getAtomCount()-1; i >=0; i--) {
             Atom atom = copy.getAtom(i);
             if(atom.getBondCount() == 0) {
                 //System.out.printf("atom %d of symbol %s has no bonds and will be deleted\n", i, atom.getSymbol());
-                copy.removeAtom(i);
+                //copy.removeAtom(i);
+                atomsToRemove.add(atom);
             }
         }
-
-        ChemObject chemObject = new ChemObject();
+        atomsToRemove.forEach(a->copy.removeAtom(a));
 
         Iterator<CdkChemicalImpl> iterator = copy.connectedComponents();
         int fragmentCount=0;