[Jmol-commits] SF.net SVN: jmol:[20946] trunk/Jmol/src/org/jmol/smiles/SmilesGenerator. java

[<ha...@us...>]

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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