Merge pull request #24 from ncats/chirality_fix_cleanup

cleaned up JavaDoc comments.
ncats · May 10, 2024 · 6fe349b · 6fe349b
2 parents 26ef307 + 7735463
commit 6fe349b
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diff --git a/src/main/java/gov/nih/ncats/molwitch/cdk/CdkChemicalImpl.java b/src/main/java/gov/nih/ncats/molwitch/cdk/CdkChemicalImpl.java
@@ -253,7 +253,7 @@ public static void setMaxUndefinedStereoCenters(int maxUndefinedStereoCenters) {
 					CIPTool.label(cimp.getContainer());
 				} else {
 					Logger.getLogger(this.getClass().getName()).fine("This molecule is considered NOT complex");
-					CIPToolMod.label(cimp.getContainer(), cimp);
+					CIPToolMod.label(cimp.getContainer());
 				}
 
                for (int i = 0; i < container.getAtomCount(); i++) {

diff --git a/src/main/java/org/openscience/cdk/geometry/cip/CIPToolMod.java b/src/main/java/org/openscience/cdk/geometry/cip/CIPToolMod.java
@@ -75,28 +75,28 @@
  * the ligand ordering can go
  * <pre>
  * Possibility 1: both sub-ligands in right order
- *    3 vs 5 =>
- *    [2,3'] vs [6,5'] => 
- *    2 vs 6 => 2 is higher priority
+ *    3 vs 5 as follows
+ *    [2,3'] vs [6,5'] yields
+ *    2 vs 6 yields 2 is higher priority
  *    therefore 3 is higher priority (correct)
  * 
  * Possibility 2: 3 sub-ligands wrong order, 5 right order
- *    3 vs 5 =>
- *    [3',2] vs [6,5'] => 
- *    3' vs 6 => 6 is higher priority
+ *    3 vs 5 as follows
+ *    [3',2] vs [6,5'] results in
+ *    3' vs 6 yields 6 is higher priority
  *    therefore 5 is higher priority (incorrect)
  * 
  * Possibility 3: 3 sub-ligands RIGHT order, 5 wrong order
- *    3 vs 5 =>
- *    [2,3'] vs [5',6] => 
- *    2 vs 5' => 2 is higher priority
+ *    3 vs 5 as follows
+ *    [2,3'] vs [5',6] gives
+ *    2 vs 5' yields 2 is higher priority
  *    therefore 3 is higher priority (correct)
  * 
  * Possibility 4: both sub-ligands in WRONG order
- *    3 vs 5 =>
- *    [3',2] vs [5',6] => 
- *    3' vs 5' => TIE, go to next
- *    2 vs 6 => 2 is higher priority
+ *    3 vs 5 as follows:
+ *    [3',2] vs [5',6] yields
+ *    3' vs 5' gives a TIE, go to next
+ *    2 vs 6 results in 2 as higher priority
  *    therefore 3 is higher priority (correct)
  * </pre>
  * <p>
@@ -137,7 +137,7 @@ public static void setUseNewCentres(boolean centresRule) {
 	 *
      * @param container structure to label
      */
-    public static void label(IAtomContainer container, CdkChemicalImpl chemical) {
+    public static void label(IAtomContainer container) {
 
         //Experimental new labeller
         com.simolecule.centres.CdkLabeller.label(container);
@@ -161,6 +161,8 @@ public static void label(IAtomContainer container, CdkChemicalImpl chemical) {
 	 * GSRS-MODIFIED: Temporary bug fix for {@link CIPTool#getCIPChirality(IAtomContainer, ITetrahedralChirality)}
 	 * 
      * @param container structure to label
+     * @param stereoCenter one atom to identify
+     * @return type of chirality identified
      */
     public static CIP_CHIRALITY getCIPChirality(IAtomContainer container, ITetrahedralChirality stereoCenter) {
 
@@ -184,6 +186,8 @@ public static CIP_CHIRALITY getCIPChirality(IAtomContainer container, ITetrahedr
   	 * GSRS-MODIFIED: Temporary bug fix for {@link CIPTool#getCIPChirality(IAtomContainer, IDoubleBondStereochemistry)}
   	 * 
      * @param container structure to label
+     * @param stereoCenter one atom to process
+     * @return which type chirality was identified
      */    
     public static CIP_CHIRALITY getCIPChirality(IAtomContainer container, IDoubleBondStereochemistry stereoCenter) {
 

diff --git a/src/test/java/TestChiralRead.java b/src/test/java/TestChiralRead.java
@@ -1565,7 +1565,7 @@ public void testSlowChiralityFalse() throws Exception {
 		System.out.printf("total atoms: %d bonds: %d; rings: %d\n", c1.getAtomCount(), c1.getBondCount(), ringCount);
 		CdkChemicalImpl chem = (CdkChemicalImpl)c1.getImpl();
 
-		CIPToolMod.label(chem.getContainer(), chem);
+		CIPToolMod.label(chem.getContainer());
 		assertTrue(chem.getAtomCount()>0);
 		//List<TetrahedralChirality> chiralities= chem.getTetrahedrals();
 		/*List<Chirality> listChi=c1.atoms()
@@ -1795,7 +1795,7 @@ public void testSlowChiralityTrue() throws Exception {
 		CdkChemicalImpl chem = (CdkChemicalImpl)c1.getImpl();
 
 		long before = (new Date()).getTime();
-		CIPToolMod.label(chem.getContainer(), chem);
+		CIPToolMod.label(chem.getContainer());
 		long after =(new Date()).getTime();
 		System.out.printf("duration of 'label' call %d\n", (after-before));
 		assertTrue(chem.getAtomCount() >0);
@@ -1900,7 +1900,7 @@ public void testSlowChiralitySmall() throws Exception {
 		System.out.printf("total atoms: %d bonds: %d; rings: %d\n", c1.getAtomCount(), c1.getBondCount(), ringCount);
 		CdkChemicalImpl chem = (CdkChemicalImpl)c1.getImpl();
 
-		CIPToolMod.label(chem.getContainer(), chem);
+		CIPToolMod.label(chem.getContainer());
 		List<TetrahedralChirality> listChi= chem.getTetrahedrals();/*c1.atoms()
 				.filter(ca->ca.getChirality()!=Chirality.Non_Chiral)
 				.map(ca->ca.getChirality())