Revision: 21491
http://sourceforge.net/p/jmol/code/21491
Author: hansonr
Date: 2017-04-07 02:55:42 +0000 (Fri, 07 Apr 2017)
Log Message:
-----------
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
Modified: trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-04-07 00:38:50 UTC
(rev 21490)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-04-07 02:55:42 UTC
(rev 21491)
@@ -14,6 +14,31 @@
/**
* A relatively simple implementation of Cohen-Ingold-Prelog rules for
assigning R/S chirality
*
+ * [1] getChirality(Node)
+ * new CIPAtom(Node)
+ * set()
+ * return getRorS();
+ *
+ * [2] CIPAtom.getRorS()
+ * sortSubstituents()
+ * return f(SmilesMatcher().getChirality())
+ *
+ *
+ * [3] sortSubstituents()
+ * if (necessary)
+ * breakTie(a,b)
+ *
+ * [4] breakTie(a,b)
+ * a.set(), b.set()
+ * for each substituent...
+ * compareAB(a.atoms[i], b.atoms[i])
+ * if (all are tied) ...
+ * sortSubstituents(a.atoms)
+ * sortSubstituents(b.atoms)
+ * for each substituent...
+ * breakTie(a.atoms[i], b.atoms[i])
+ *
+ *
* Introduced in Jmol 14.12.0
*
* @author Bob Hanson hans...@stolaf.edu
@@ -79,14 +104,15 @@
if (atom.getCovalentBondCount() != 4)
return "";
CIPAtom a = new CIPAtom(atom, null, false);
-
- String rs = (a.set() ? getRorS(a) : "");
+ if (!a.set())
+ return "";
+ String rs = getRorS(a);
if (Logger.debugging)
Logger.info(atom + " " + rs);
return rs;
}
- public String getRorS(CIPAtom a) {
+ private String getRorS(CIPAtom a) {
try {
CIPAtom[] atoms = sortSubstituents(a.atoms, false);
if (atoms == null)
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