[Jmol-developers] [ jmol-Patches-2760297 ] fix for autoBonds and $HOME/.jmol/properties

[SourceForge.net <no...@so...>]

Patches item #2760297, was opened at 2009-04-14 01:56
Message generated for change (Comment added) made by pimpimpim
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Category: None
Group: None
>Status: Closed
Priority: 5
Private: No
Submitted By: pim (pimpimpim)
Assigned to: Nobody/Anonymous (nobody)
Summary: fix for autoBonds and $HOME/.jmol/properties

Initial Comment:
autoBonds were not written away correctly to the jmol configuration file, nor did the autoBond=false show up correctly in the properties menu.

This simple fix corrects both of these issues.

Index: src/org/openscience/jmol/app/PreferencesDialog.java
===================================================================
--- src/org/openscience/jmol/app/PreferencesDialog.java (revision 10803)
+++ src/org/openscience/jmol/app/PreferencesDialog.java (working copy)
@@ -344,6 +344,7 @@
     c.weightx = 1.0;
     c.weighty = 1.0;
 
+    // Automatic calculation of bonds upon molecule load
     JPanel autobondPanel = new JPanel();
     autobondPanel.setLayout(new BoxLayout(autobondPanel, BoxLayout.Y_AXIS));
     autobondPanel.setBorder(new TitledBorder(GT._("Compute Bonds")));
@@ -359,14 +360,17 @@
     abYes.addActionListener(new ActionListener() {
 
       public void actionPerformed(ActionEvent e) {
-        viewer.setBooleanProperty("autoBond", true);
+        viewer.setBooleanProperty("autoBond", true);        
+        currentProperties.put("autoBond", "" + "true");
       }
     });
 
+    abNo.setSelected(!viewer.getAutoBond());
     abNo.addActionListener(new ActionListener() {
 
       public void actionPerformed(ActionEvent e) {
         viewer.setBooleanProperty("autoBond", false);
+        currentProperties.put("autoBond", "" + "false");     
       }
     });



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>Comment By: pim (pimpimpim)
Date: 2009-04-14 22:58

Message:
The above patch is commited to svn by myself.

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Comment By: Angel Herraez (aherraez)
Date: 2009-04-14 19:32

Message:
According to the doc, "connect" by itself will delete all bonds and
recalculate them using Jmol's algorithm (no bonds are retained from the
file). All new bonds are single.
To dump (delete) existing bonds, you can also use "connect" but with the
"delete" argument.


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Comment By: pim (pimpimpim)
Date: 2009-04-14 02:17

Message:
Note: changes in the autoBond parameter are currently (and in all versions
before) only in effect on the next molecule that is loaded, not on
currently loaded molecule. Is it at all possible to calculate bonds after
loading, or to dump existing bonds? And if so, would it be desired to add
that functionality.

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