Revision: 20946
http://sourceforge.net/p/jmol/code/20946
Author: hansonr
Date: 2016-02-05 05:56:01 +0000 (Fri, 05 Feb 2016)
Log Message:
-----------
Jmol.___JmolVersion="14.4.2_2016.02.05"
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
frame, not the rotated frame. In addition, if MOs were calculated
prior to
use of rotateSelected or translateSelected, then they would not
"track"
with the modified atom positions. So MOs and
rotate/translateSelected
were completely incompatible. Jmol 14.4.2 fixes this issue. It
should be
possible now to produce correct MOs before or after use of
rotateSelected.
Note that ALL atoms in a specified model must be moved in order
for this
tracking of MOs to take place. This functionality was introduced
in
14.4.1_2016.01.28, but that version (never released) does not
properly
check to see that ALL the atoms in a model have been involved in
the rotation.
FEATURE NOTE: If rotateSelected or translateSelected is used to move all atoms
in a
model, and after that the state is saved, then Jmol 14.4.2
will save a state that is not readable in 14.4.1. This is
necessary
because of the added FRAME ORIENTATION command, which is used in
the states
to indicate the relationship of a model to its file coordinates.
The MO
reader requires this so that it can rotate the coordinates back
to their
original position prior to doing its calculation.
new feature: variable _versionDate
$ show _versionDate
_versionDate = "14.4.1_2016.01.16 2016-01-15 17:25"
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
bug fix: JVXL files saved from models that involve full model
rotate/translateSelected
do not get restored properly.
bug fix: molecular orbitals do not move with atoms
when full molecule is moved using rotateSelected or translateSelected
bug fix: IboView/Molpro XML reader validated for multi-molecule XML files
-- to concatenate Molpro XML files, you must supply a new root tag as well as
remove all <?...?> directives.
-- DOS CMD file example:
catxml.bat ibo*.xml test.xml
where catxml.bat is:
copy /b %1 _temp
echo ^<OUTER^> > %2
type _temp | find /V "<?" >> %2
echo ^</OUTER^> >> %2
bug fix: IboView/Molpro XML Reader validated for reading orbitals
bug fix: MOs need to move with atoms and be restored from state properly
after use of ROTATESELECTED.
-- note that fix for 14.4 does not include state saving, as that would break
previous subversions
bug fix: Spartan file reader not working properly after MacSpartan ->
Spartan14 upgrade
bug fix: mol, xyz readers not reporting model name like other readers
bug fix: d = [start:1,end:10] fails due to reserved word "end" (also "select",
"case", "default", "if", "for", etc.)
bug fix: color "chain" (with quotes) should work, allowing for x="chain"; color
@x
bug fix: inappropriate use of REGEX in ["a","b"].find("x")
bug fix: ".xxx" should be allowed as a math continuation:
print script("show spacegroup all")
.split()
.find("Hall symbol:")
bug fix: labels, echos, and measurements improperly shaded when z-shaded with
nonblack background
bug fix: rendering error when set zshade followed by set antialiasdisplay
bug fix: labels, echos, and measurements disappear when z-shaded
code: better loading of surfaces -- no longer requires javajs.util.XmlUtil
code: removal of unnecessary api interfaces MinimizerInterface,
VolumeDataInterface, QuantumPlaneCalculationInterface, MOCalculationInterface,
MepCalculationInterface
code: new abstract reader XmlMOReader
code: JmolZipUtilities interface removed
code: JmolBinary reduced to just all Spartan-related methods
code: polyhedra, pointgroup, load =ams/, load "xxxx#_DOCACHE_" features from
14.5 added to 14.4
code: (JavaScript) refactoring to allow faster, cleaner load for biomodels
code: (JavaScript) refactoring to reduce extraneous file download
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java 2016-02-05 03:46:46 UTC
(rev 20945)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java 2016-02-05 05:56:01 UTC
(rev 20946)
@@ -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
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