Revision: 21656
http://sourceforge.net/p/jmol/code/21656
Author: hansonr
Date: 2017-07-07 14:47:49 +0000 (Fri, 07 Jul 2017)
Log Message:
-----------
* 7/7/17 Jmol 14.20.1 minor coding efficiencies (833 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 2017-07-07 14:36:40 UTC
(rev 21655)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-07-07 14:47:49 UTC
(rev 21656)
@@ -140,6 +140,8 @@
*
* code history:
*
+ * 7/7/17 Jmol 14.20.1 minor coding efficiencies (833 lines)
+ *
* 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 (836 lines)
*
@@ -1153,13 +1155,9 @@
atom = (root = cipAtom).atom;
cipAtom.htPathPoints = (cipAtom.parent = new CIPAtom().create(
parentAtom, null, true, false, false)).htPathPoints;
- } else {
- // 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();
- // P-93.2.4 no double bonds for S=X and P=X
- if (nSubs != 4 && !cipAtom.isTrigonalPyramidal)
+ } else if (!(root = cipAtom = new CIPAtom().create(atom, null, false,
false, false)).canBePseudo) {
+ // This is a root-atom call.
+ // Just checking here that center has 4 covalent bonds or is trigonal
pyramidal.
return NO_CHIRALITY;
}
if (cipAtom.setNode()) {
@@ -1583,7 +1581,8 @@
/**
* a flag set false in evaluation of Rule 5 to indicate that there was
more
- * than one R/S decision made, so this center cannot be r/s.
+ * than one R/S decision made, so this center cannot be r/s; initially just
+ * indicates that the atom has 4 covalent bonds or is trigonal pyriamidal
*/
boolean canBePseudo = true;
@@ -2943,7 +2942,7 @@
}
}
}
- } else if (isTrigonalPyramidal || bondCount == 4) {
+ } else if (canBePseudo) {
// if here, adj is TIED (0) or NOT_RELEVANT
CIPAtom atom1 = (CIPAtom) clone();
if (atom1.setNode()) {
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