diff --git a/src/main/java/gov/nih/ncats/molwitch/cdk/CdkChemicalImpl.java b/src/main/java/gov/nih/ncats/molwitch/cdk/CdkChemicalImpl.java index 7814c6e..6cfd813 100644 --- 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 index dcd17ca..fd45e38 100644 --- 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 *
* 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) **
@@ -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
index b3425dd..219f410 100644
--- 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