Revision: 21632
http://sourceforge.net/p/jmol/code/21632
Author: hansonr
Date: 2017-06-07 03:02:12 +0000 (Wed, 07 Jun 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.18.1" // 2017.06.06
bug fix: CIP misses Rule 4b cases where a branching atom has R or S chirality.
-- see test_bt_P4.mol and test_bt_O3.mol (BH64.65 and BH64.66)
-- see AY236.179 (3D structure was diasteriomer, so I missed that)
bug fix: WRITE MOL should not generate > <JMOL_PARTIAL_CHARGES> because it is
not SDF format
bug fix: WRITE SDF should generate > <JMOL_PARTIAL_CHARGES> with a trailing
space
bug fix: (SMILES) targetString.find("SMILES",patternString) will fail for
.[C@H]2 (new group and attached to a connection number)
bug fix: SHOW CHEMICAL SMILES fails when logLevel is set > 4
new feature: WRITE SDF writes > <.... user data
-- can be set using MODEL PROPERTY "molData" x where x is an associative
array
-- can be read using _M.molData
new feature: associativeArray.pop() -- clears associativeArray
new feature: assArray1.push(assArray2) -- adds all key/value entries in
assArray2 to assArray1.
new feature: assArray1 + assArray2 -- adds all key/value entries into a new
associative array. (Complements a1 - a2)
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-06-05 03:54:30 UTC
(rev 21631)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-06-07 03:02:12 UTC
(rev 21632)
@@ -2615,9 +2615,8 @@
subRS = "";
break;
case NOT_RELEVANT:
- s = "";
+ // a and b are different priorities - we need to check to see if
we have a chiral branch node
isBranch = true;
- adj = TIED;
break;
case DIASTEREOMERIC_A_WINS:
case DIASTEREOMERIC_B_WINS:
@@ -2682,7 +2681,7 @@
if (ret != null)
ret[0] = this;
}
- if (!isBranch || adj == A_WINS || adj == B_WINS) {
+ if (!isBranch || adj == A_WINS || adj == B_WINS || adj ==
NOT_RELEVANT) {
if (isAlkene) {
if (!isBranch && alkeneChild != null) {
// must be alkeneParent
@@ -2731,7 +2730,7 @@
// if adj is 1 or -1, then we check for one fewer priorities
because
// it means we had two groups that were either enantiomers or
diasteriomers
- if (isBranch) {
+ if (isBranch && adj != NOT_RELEVANT) {
// if here, adj is A_WINS (-1), or B_WINS (1)
// we check based on A winning, but then reverse it if B
actually won
switch (checkPseudoHandedness(mataList, null)) {
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-06-05 03:54:30 UTC
(rev 21631)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-06-07 03:02:12 UTC
(rev 21632)
@@ -56,15 +56,21 @@
# TODO: fix UNDO
-Jmol.___JmolVersion="14.18.1"
+Jmol.___JmolVersion="14.18.1" // 2017.06.06
+bug fix: CIP misses Rule 4b cases where a branching atom has R or S chirality.
+ -- see test_bt_P4.mol and test_bt_O3.mol (BH64.65 and BH64.66)
+ -- see AY236.179 (3D structure was diasteriomer, so I missed that)
+
bug fix: WRITE MOL should not generate > <JMOL_PARTIAL_CHARGES> because it is
not SDF format
bug fix: WRITE SDF should generate > <JMOL_PARTIAL_CHARGES> with a trailing
space
+
bug fix: (SMILES) targetString.find("SMILES",patternString) will fail for
.[C@H]2 (new group and attached to a connection number)
bug fix: SHOW CHEMICAL SMILES fails when logLevel is set > 4
new feature: WRITE SDF writes > <.... user data
-- can be set using MODEL PROPERTY "molData" x where x is an associative
array
+ -- can be read using _M.molData
new feature: associativeArray.pop() -- clears associativeArray
new feature: assArray1.push(assArray2) -- adds all key/value entries in
assArray2 to assArray1.
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