[Jmol-commits] SF.net SVN: jmol:[21084] trunk/Jmol/src/org/jmol/viewer/StateCreator.java

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

Revision: 21084
          http://sourceforge.net/p/jmol/code/21084
Author:   hansonr
Date:     2016-05-08 17:31:50 +0000 (Sun, 08 May 2016)
Log Message:
-----------
Jmol.___JmolVersion="14.5.5_2016.05.08"

new feature: Jmol now implemements a way of indicating atropisomer chirality. 
 -- measured dihedral angle is clockwise-positive front-to-back, as for Jmol dihedrals
 -- matching with {*}.find("SMILES","...a^nm-a...") where n and m are 1, 2, or 3  
    indicate first, second, or third, respectively, and indicate which bonds of 
    the biaryl bond, as written, are to the reference atoms.
 -- for example:
 
   $ load $biphenol
   $ connect @{@7|@8} @{@1|@2} atropisomer
   $ print {*}.find("SMARTS","c1(O)ccccc1^23-c2c(O)cccc2")
 
  ({0:13})
  
  Explained below.
  
 
  
new feature: CONNECT {pair1} {pair2} ATROPISOMER
 -- creates a new bond of type atropisomer (bond chirality in biaryl systems)
 -- each pair must include the bonded atom and its reference connected atom
 -- example:
 
   $ load $biphenol
   $ connect @{@7|@8} @{@1|@2} atropisomer
   $ getProperty bondinfo[7].type
   
   bondinfo[7].type	"atropisomer_23"
  
new feature: BONDORDER ATROPISOMER_nm
  -- not for general use; will be found in state file
  -- for example:
  
    select BONDS ({6});
    bondOrder atropisomer_23;

new feature: Jmol SMILES bond atropisomerism ^nm- and ^^nm-
 -- indicates atropisomerism (bond chirality in biaryl systems)
 -- ^ and ^^ for bonds similar to @ and and @@ for atoms
 -- n and m are single-digit bond selectors, generally one of 1, 2, or 3
 -- n = 1/2/3 means "reference atom is first/second/third bonded 
 -- ^- and ^^- same as ^22- and ^^22-, respectively
 -- example: 
   
   $ load $biphenol
   $ connect @{@7|@8} @{@1|@2} atropisomer
   $ print {*}.find("SMARTS","c1(O)cccc{c1^23-c2}c(O)cccc2")
   
   ({1 6})

  Here the "^23-" refers to the two carbons with connected oxygen atoms, because the second
  bond listed for the carbon on the left is to the c1(O) atom, and the third bond listed for
  the carbon on the right is to the other c(O) atom. Note that bond numbering includes the 
  implicit bond to the atom coming from the atom on its left, which for the second carbon, 
  starts with the atropisomeric bond itself, at least in this case. 

             1*23  1*23
     c1(O)ccccc1^23-c2c(O)cccc2
                                      

bug fix: Jmol SMILES directive /noaromatic/ should ignore ":" bond type 
bug fix: Jmol SMILES directive /aromaticDouble/ not implemented for SMILES
buf fix; Jmol SMARTS measurements should be required to come after branches
bug fix: Jmol SMILES parser should require connection numbers to be placed prior to branches
bug fix: Jmol SMILES should not allow (.t!50,60,70,80)
bug fix: Jmol SMILES should treat  search("[THR.*][THR.*]") should select all atoms in each group 
bug fix: Jmol SMILES should return ({}) not ERROR if no atoms are involved

code: StateCreator and Shape getStateInfo methods simplified and condensed

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/viewer/StateCreator.java

Modified: trunk/Jmol/src/org/jmol/viewer/StateCreator.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateCreator.java	2016-05-08 17:30:01 UTC (rev 21083)
+++ trunk/Jmol/src/org/jmol/viewer/StateCreator.java	2016-05-08 17:31:50 UTC (rev 21084)
@@ -1168,7 +1168,7 @@
       break;
     case JC.SHAPE_LABELS:
       Labels l = (Labels) shape;
-      if (l.isActive && l.bsSizeSet != null)
+      if (!l.isActive || l.bsSizeSet == null)
         return "";
       clearTemp();
       for (int i = l.bsSizeSet.nextSetBit(0); i >= 0; i = l.bsSizeSet

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