Revision: 21642
http://sourceforge.net/p/jmol/code/21642
Author: hansonr
Date: 2017-06-27 04:28:53 +0000 (Tue, 27 Jun 2017)
Log Message:
-----------
CIP Rule 4b fix; not generating chiral auxiliaries correctly (not sorting
through Rule 5).
Still an issue with Mata sequences, I think.
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 2017-06-25 23:19:27 UTC
(rev 21641)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-06-27 04:28:53 UTC
(rev 21642)
@@ -2286,6 +2286,7 @@
// resolved as "r" or "s"
// but generally we will want to process this as "R" and "S"
// note that this analysis cannot be done ahead of time
+
String aStr = rule4List[ia].substring(1), bStr = rule4List[ib]
.substring(1);
boolean haveRSOptions = false, isRule5 = (currentRule == RULE_5);
@@ -2292,11 +2293,17 @@
String sa = "", sb = "";
if (atoms[ia].nextChiralBranch != null) {
sa = atoms[ia].nextChiralBranch.getMataList(getFirstRef(aStr),
isRule5);
+ haveRSOptions = (sa.indexOf("|") >= 0);
}
if (atoms[ib].nextChiralBranch != null) {
sb = atoms[ib].nextChiralBranch.getMataList(getFirstRef(bStr),
isRule5);
+ if (haveRSOptions != (sb.indexOf("|") >= 0)) {
+ // P-92.5.2.1.i check -- one ref beats two refs
+ // this is a convenience check only, actually, as the
+ // ligand with two refs is guaranteed to lose to the one with one
ref.
+ return (haveRSOptions ? B_WINS : A_WINS);
+ }
}
- haveRSOptions = (sa.indexOf("|") >= 0 || sb.indexOf("|") >= 0);
if (haveRSOptions) {
aStr += "|" + sa;
bStr += "|" + sb;
@@ -2724,16 +2731,22 @@
//if (ret != null)
//ret[0] = null;
} else {
- // if here, adj is TIED (0) or
+ // if here, adj is TIED (0) or NOT_RELEVANT
CIPAtom atom1 = (CIPAtom) clone();
if (atom1.setNode()) {
atom1.addReturnPath(null, this);
- atom1.sortToRule(RULE_3);
- rs = atom1.checkHandedness();
- s = (rs == STEREO_R ? "R" : rs == STEREO_S ? "S" : "~");
- if (Logger.debugging)
- Logger.info("AUX " + s + " for " + atom1.myPath);
- parent.addMataRef(sphere, priority, rs);
+ int rule = atom1.sortToRule(RULE_5);
+ if (rule != TIED) {
+ rs = atom1.checkHandedness();
+ s = (rs == STEREO_R ? "R" : rs == STEREO_S ? "S" : "~");
+ if (atom1.isPseudo) {
+ s = s.toLowerCase();
+ } else {
+ parent.addMataRef(sphere, priority, rs);
+ }
+ if (Logger.debugging)
+ Logger.info("AUX " + s + " for " + atom1.myPath);
+ }
}
}
auxChirality = s;
@@ -2762,10 +2775,18 @@
return isChiral;
}
- private void sortToRule(int maxRule) {
+ /**
+ * Sort for auxiliary chirality determination
+ *
+ * @param maxRule
+ * @return TIED or deciding rule RULE_1a - RULE_5
+ */
+ private int sortToRule(int maxRule) {
for (int i = RULE_1a; i <= maxRule; i++)
- if (sortByRule(i))
- return;
+ if (sortByRule(i)) {
+ return (isPseudo ? RULE_5 : i);
+ }
+ return TIED;
}
private boolean isChiralSequence(String ssub) {
@@ -2802,7 +2823,7 @@
}
/**
- * Check for enantiomeric strings such as S;R; or SR
+ * Check for enantiomeric strings such as SSR/RRS
*
* @param i1
* @param i2
@@ -2817,18 +2838,25 @@
int n = rs1.length();
if (n != rs2.length())
return NOT_RELEVANT;
- if (rs1.equals(rs2))
+
+ if (atoms[i1].nextChiralBranch != null)
+ return NOT_RELEVANT;
+
+ if (rs1.equals(rs2)) {
+
+
+ // this is tricky, because we could have
+ // R S
+ // / /
+ // --~ and --~
+ // \ \
+ // R S
+
return TIED;
+ }
String rs = rs1 + rs2;
//System.out.println("compareRule4aIsomers:" + rs1 + " vs. " + rs2);
boolean haveRS = (rs.indexOf("R") >= 0 || rs.indexOf("S") >= 0);
- if ((rs.indexOf("r") >= 0 || rs.indexOf("s") >= 0)) {
- // consider Rule 4a here -- Sr beats R~ BH64_014
- if (rs1.endsWith("~"))
- return (DIASTEREOMERIC_B_WINS);
- if (rs2.endsWith("~"))
- return (DIASTEREOMERIC_A_WINS);
- }
rs = (haveRS ? "~RS" : "~rs");
if (haveRS) {
rs1 = PT.replaceAllCharacters(rs1, "rs", "~");
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