Revision: 21666
http://sourceforge.net/p/jmol/code/21666
Author: hansonr
Date: 2017-07-20 13:40:04 +0000 (Thu, 20 Jul 2017)
Log Message:
-----------
CIP Rule 2 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 2017-07-20 11:42:01 UTC
(rev 21665)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-07-20 13:40:04 UTC
(rev 21666)
@@ -55,6 +55,8 @@
*
* - deeply validated
*
+ * - included revised Rules 1b, and 2.
+ *
* - implemented in Java (Jmol) and JavaScript (JSmol)
*
* - only two Java classes; roughly 1000 lines
@@ -209,6 +211,28 @@
* simple models. By moving that distance to be the sphere of the parent atom
of
* the duplicate, the problem is resolved.
*
+ * Added clarification to Rule 2:
+ *
+ * Rule 2: Higher mass precedes lower mass, where mass is defined in the
+ * case of nonduplicate atoms with identified isotopes for elements as
+ * their exact isotopic mass and, in all other cases, as their
+ * element's atomic weight.
+ *
+ * Rationale: BB is not self-consistent, including both "mass number" (in the
rule)
+ * and "atomic mass" in the description, where "79Br < Br < 81Br". And again
we have the
+ * same Kekule-ambiguous issue as in Rule 1b. The added clarification fixes
the Kekule
+ * issue (not using isotope mass number for duplicate atoms), solves the
problem
+ * that F < 19F (though 100% nat. abundance), and is easily programmable.
+ *
+ * In Jmol the logic is very simple, actually using the isotope mass number,
actually,
+ * but doing two checks:
+ *
+ * a) if one of five specific isotopes, reverse the test, and
+ * b) if on the list of 100% natural isotopes or one of the non-natural
elements,
+ * use the average atomic mass.
+ *
+ * See CIPAtom.getMass();
+ *
* @author Bob Hanson hans...@stolaf.edu
*/
public class CIPChirality {
@@ -1781,7 +1805,7 @@
private boolean isType(String rule2Type) {
return PT.isOneOf(
- ";" + (int) mass + Elements.elementSymbolFromNumber((int) elemNo),
+ (int) mass + Elements.elementSymbolFromNumber((int) elemNo),
rule2Type);
}
@@ -2016,10 +2040,6 @@
Logger.info("---");
}
- // if this is Rule 4b or 5, then we do a check of the forward-based
stereochemical path
-
- boolean checkRule4List = (rule4List != null && (currentRule == RULE_4b
|| currentRule == RULE_5));
-
int loser, score;
for (int i = 0; i < 4; i++) {
CIPAtom a = atoms[i];
@@ -2092,9 +2112,9 @@
if (currentRule == RULE_5 && nPriorities == 4 && nPrioritiesPrev == 2)
{
// Rule 5 has decided the issue, but how many decisions did we make?
- // If priorities [0 0 2 2] went to [1 2 3 4] then
+ // If priorities [0 0 2 2] went to [0 1 2 3] then
// we have two Rule-5 decisions -- R,S,R',S'.
- // In that case, Rule 5 resuls in R/S, not r/s.
+ // In that case, Rule 5 results in R/S, not r/s.
//
// S
// -
@@ -2520,7 +2540,11 @@
* @return 0 (TIED), -1 (A_WINS), or 1 (B_WINS)
*/
private int checkRule2(CIPAtom b) {
- return (b.getMass() == getMass() ? TIED : reverseRule2 == (b.mass >
mass) ? A_WINS : B_WINS);
+ System.out.println(getMass() + " vs " + b.getMass() + " " + (b.getMass()
== getMass() ? TIED :
+ (reverseRule2 || b.reverseRule2) == (b.mass > mass) ? A_WINS :
B_WINS));
+
+ return (b.getMass() == getMass() ? TIED :
+ (reverseRule2 || b.reverseRule2) == (b.mass > mass) ? A_WINS : B_WINS);
}
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