#23 fix for autoBonds and $HOME/.jmol/properties


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");


  • pim

    pim - 2009-04-13

    patch fixing behavior of autoBonds and $HOME/.jmol/properties

  • pim

    pim - 2009-04-14

    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.

  • Angel Herraez

    Angel Herraez - 2009-04-14

    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.

  • pim

    pim - 2009-04-14

    The above patch is commited to svn by myself.

  • pim

    pim - 2009-04-14
    • status: open --> closed

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