Revision: 20945
http://sourceforge.net/p/jmol/code/20945
Author: hansonr
Date: 2016-02-05 03:46:46 +0000 (Fri, 05 Feb 2016)
Log Message:
-----------
Jmol.___JmolVersion="14.4.2_2016.02.05"
bug fix: LOAD $benzene; SHOW smiles should give c1ccccc1 not c1=cc=cc=c1
bug fix: LOAD FILES "$caffeine" ":caffeine";print {1.1}.find("SMARTS",{2.1})
should give atoms, but it does not. Problem is with aromatic structure
to SMILES shows c=c instead of just cc. (SMARTS searching with c=c does
not match
Modified Paths:
--------------
branches/v14_4/Jmol/src/org/jmol/smiles/SmilesBond.java
branches/v14_4/Jmol/src/org/jmol/smiles/SmilesGenerator.java
branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/smiles/SmilesBond.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: branches/v14_4/Jmol/src/org/jmol/smiles/SmilesBond.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/smiles/SmilesBond.java 2016-02-04
15:01:39 UTC (rev 20944)
+++ branches/v14_4/Jmol/src/org/jmol/smiles/SmilesBond.java 2016-02-05
03:46:46 UTC (rev 20945)
@@ -52,8 +52,6 @@
static String getBondOrderString(int order) {
switch (order) {
- case 1:
- return "";
case 2:
return "=";
case 3:
Modified: branches/v14_4/Jmol/src/org/jmol/smiles/SmilesGenerator.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/smiles/SmilesGenerator.java
2016-02-04 15:01:39 UTC (rev 20944)
+++ branches/v14_4/Jmol/src/org/jmol/smiles/SmilesGenerator.java
2016-02-05 03:46:46 UTC (rev 20945)
@@ -567,7 +567,7 @@
if (sp2Atoms == null)
sp2Atoms = new Node[5];
if (bondPrev != null) {
- strBond = SmilesBond.getBondOrderString(bondPrev.getCovalentOrder());
+ strBond = (isAromatic && bsAromatic.get(prevIndex) ? "" :
SmilesBond.getBondOrderString(bondPrev.getCovalentOrder()));
if (prevSp2Atoms == null)
sp2Atoms[nSp2Atoms++] = prevAtom;
else
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-04
15:01:39 UTC (rev 20944)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-05
03:46:46 UTC (rev 20945)
@@ -7,8 +7,16 @@
# see also http://chemapps.stolaf.edu/jmol/zip for daily updates
-Jmol.___JmolVersion="14.4.2_2016.02.04"
+Jmol.___JmolVersion="14.4.2_2016.02.05"
+bug fix: LOAD $benzene; SHOW smiles should give c1ccccc1 not c1=cc=cc=c1
+bug fix: LOAD FILES "$caffeine" ":caffeine";print {1.1}.find("SMARTS",{2.1})
+ should give atoms, but it does not. Problem is with aromatic structure
+ to SMILES shows c=c instead of just cc. (SMARTS searching with c=c
does
+ not match
+
+JmolVersion="14.4.2_2016.02.04"
+
FEATURE NOTE: Prior to this version if the MO command was issued after use of
rotateSelected, the orbitals were calculated improperly, because
the
basis functions always must be applied for the original file
coordinate
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesBond.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesBond.java 2016-02-04 15:01:39 UTC
(rev 20944)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesBond.java 2016-02-05 03:46:46 UTC
(rev 20945)
@@ -52,8 +52,6 @@
static String getBondOrderString(int order) {
switch (order) {
- case 1:
- return "";
case 2:
return "=";
case 3:
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-04 15:01:39 UTC
(rev 20944)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-05 03:46:46 UTC
(rev 20945)
@@ -64,8 +64,12 @@
TODO: isosurface molecular has an issue with 2gb1
-Jmol.___JmolVersion="14.5.2_2016.02.04"
+Jmol.___JmolVersion="14.5.2_2016.02.05"
+bug fix: LOAD $benzene; SHOW smiles should give c1ccccc1 not c1=cc=cc=c1
+
+JmolVersion="14.5.2_2016.02.04"
+
FEATURE NOTE: Prior to this version if the MO command was issued after use of
rotateSelected, the orbitals were calculated improperly, because
the
basis functions always must be applied for the original file
coordinate
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