Revision: 21652
http://sourceforge.net/p/jmol/code/21652
Author: hansonr
Date: 2017-07-06 12:37:34 +0000 (Thu, 06 Jul 2017)
Log Message:
-----------
* 7/6/17 Jmol 14.20.1 major rewrite to correct and simplify logic; full
validation
* for 433 structures (many duplicates) in AY236, BH64, MV64, MV116, JM, and L
(839 lines)
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 2017-07-06 07:19:40 UTC
(rev 21651)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-07-06 12:37:34 UTC
(rev 21652)
@@ -141,7 +141,7 @@
* code history:
*
* 7/4/17 Jmol 14.20.1 major rewrite to correct and simplify logic; full
validation
- * for 433 structures (many duplicates) in AY236, BH64, MV64, MV116, JM, and
L (840 lines)
+ * for 433 structures (many duplicates) in AY236, BH64, MV64, MV116, JM, and
L (839 lines)
*
* 6/30/17 Jmol 14.20.1 major rewrite of Rule 4b (999 lines)
*
@@ -1057,33 +1057,33 @@
* ignored if a is not null (just checking ene end top priority)
* @param cipAtom
* ignored if atom is not null
- * @param parent
+ * @param parentAtom
* null for tetrahedral, other alkene carbon for E/Z
*
- * @return if and E/Z test, [0:none, 1: atoms[0] is higher, 2: atoms[1] is
higher]
- * otherwise [0:none, 1:R, 2:S]
+ * @return if and E/Z test, [0:none, 1: atoms[0] is higher, 2: atoms[1] is
+ * higher] otherwise [0:none, 1:R, 2:S]
*/
private int getAtomChiralityLimited(SimpleNode atom, CIPAtom cipAtom,
- CIPAtom parent) {
+ SimpleNode parentAtom) {
int rs = NO_CHIRALITY;
- boolean isAlkeneEndCheck = (atom == null);
try {
+ boolean isAlkeneEndCheck = (atom == null);
if (isAlkeneEndCheck) {
- atom = cipAtom.atom;
+ // This is an alkene end determination.
+ atom = (root = cipAtom).atom;
+ cipAtom.htPathPoints = (cipAtom.parent = new CIPAtom().create(
+ parentAtom, null, true, false, false)).htPathPoints;
} else {
- // If this is a root-atom call (not an alkene end determination)
- // then this is a call to root; we do not know at this point if it
- // is an atom we can process or not
- cipAtom = new CIPAtom().create(atom, null, false, false, false);
+ // This is a root-atom call. We do not know at this point if it
+ // is an atom we can process or not.
+ root = cipAtom = new CIPAtom().create(atom, null, false, false, false);
int nSubs = atom.getCovalentBondCount(), elemNo = atom
.getElementNumber();
- boolean isSP2 = (nSubs == 3 && elemNo <= 10 &&
!cipAtom.isTrigonalPyramidal); // (IUPAC 2013.P-93.2.4)
- if (nSubs != (parent == null ? 4 : 3) - (nSubs == 3 && !isSP2 ? 1 : 0))
+ // P-93.2.4 no double bonds for S=X
+ if (nSubs != 4 - (nSubs != 3 || elemNo <= 10
+ && !cipAtom.isTrigonalPyramidal ? 0 : 1))
return NO_CHIRALITY;
}
- (root = cipAtom).parent = parent;
- if (parent != null)
- cipAtom.htPathPoints = parent.htPathPoints;
currentRule = RULE_1a;
if (cipAtom.setNode()) {
for (; currentRule <= RULE_5; currentRule++) {
@@ -1112,10 +1112,10 @@
}
// If this is an alkene end check, we just use STERE_S and
STEREO_R as markers
-
+
if (isAlkeneEndCheck)
return (cipAtom.atoms[0].isDuplicate ? 2 : 1);
-
+
rs = cipAtom.checkHandedness()
| (currentRule == RULE_5 && cipAtom.canBePseudo ?
JC.CIP_CHIRALITY_PSEUDO_FLAG
: 0);
@@ -1253,8 +1253,7 @@
*/
private int getAlkeneEndTopPriority(CIPAtom a, SimpleNode pa, boolean
isAxial) {
a.canBePseudo = isAxial;
- return getAtomChiralityLimited(null, a,
- new CIPAtom().create(pa, null, true, false, false)) - 1;
+ return getAtomChiralityLimited(null, a, pa) - 1;
}
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