Revision: 21589
http://sourceforge.net/p/jmol/code/21589
Author: hansonr
Date: 2017-05-09 21:41:02 +0000 (Tue, 09 May 2017)
Log Message:
-----------
CIP JM3 fix
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 2017-05-09 20:03:13 UTC
(rev 21588)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-05-09 21:41:02 UTC
(rev 21589)
@@ -2387,6 +2387,7 @@
String subRS = "";
String s = (node1 == null ? "" : "~");
boolean isBranch = false;
+ boolean isrs = false;
if (atom != null) {
rule4List = new String[4]; // full list based on atoms[]
int[] mataList = new int[4]; //sequential pointers into rule4List
@@ -2426,8 +2427,10 @@
case 2:
if (node1 != null) {
// we want to now if these two are enantiomorphic, identical, or
diastereomorphic.
- switch (adj = (compareRule4aEnantiomers(rule4List[mataList[0]],
- rule4List[mataList[1]]))) {
+ if (root.atomIndex == 21)
+ System.out.println("testing21");
+ adj = (compareRule4aEnantiomers(rule4List[mataList[0]],
rule4List[mataList[1]]));
+ switch (adj) {
case DIASTEREOMERIC:
isBranch = true;
s = "";
@@ -2450,6 +2453,7 @@
case A_WINS:
case B_WINS:
isBranch = true;
+ isrs = subRS.indexOf("r") >= 0;
// enantiomers -- we have an r/s situation
// process to determine chirality, but then set ret[0] to be null
subRS = "";
@@ -2488,6 +2492,8 @@
System.out.println("for " + atoms[mataList[0]] +
atoms[mataList[1]] + " adj=" + adj + "S->rs=" + s);
break;
}
+ if (isrs)
+ s = s.toUpperCase(); // Rule 4c
subRS = "";
if (ret != null)
ret[0] = null;
@@ -2553,8 +2559,7 @@
* if diastereomeric
*/
private int compareRule4aEnantiomers(String rs1, String rs2) {
- if (rs1.indexOf("R") < 0 && rs1.indexOf("S") < 0
- || rs1.charAt(0) != rs2.charAt(0))
+ if (rs1.charAt(0) != rs2.charAt(0))
return NOT_RELEVANT;
int n = rs1.length();
if (n != rs2.length())
@@ -2561,8 +2566,9 @@
return NOT_RELEVANT; // TODO: ?? this may not be true -- paths with
and without O, N, C for example, that still have stereochemistry
if (rs1.equals(rs2))
return TIED;
+ String rs = (rs1.indexOf("R") < 0 && rs1.indexOf("S") < 0 ? "~rs" :
"~RS");
// System.out.println("testing ~RS here with " + rs1 + " and " + rs2);
- return checkEnantiomer(rs1, rs2, 1, n, "~RS");
+ return checkEnantiomer(rs1, rs2, 1, n, rs);
}
private int checkEnantiomer(String rs1, String rs2, int m, int n, String
rs) {
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