SequenceStructureBinding, StructureSelectionManagerProvider
{
+
+ private static final boolean debug = false;
+
private static final String PHOSPHORUS = "P";
private static final String ALPHACARBON = "CA";
public void colourByChain()
{
colourBySequence = false;
- // this is not a valid Chimera command; is there one? Menu option hidden
- evalStateCommand("select *;color chain",false);
+ evalStateCommand("rainbow chain", false);
}
public void colourByCharge()
}
if (selectioncom.length() > 0)
{
- // TODO remove debug output
- System.out.println("Select regions:\n" + selectioncom.toString());
- System.out
- .println("Superimpose command(s):\n" + command.toString());
+ if (debug)
+ {
+ System.out.println("Select regions:\n" + selectioncom.toString());
+ System.out.println("Superimpose command(s):\n"
+ + command.toString());
+ }
allComs.append("~display all; chain @CA|P; ribbon "
+ selectioncom.toString() + ";"+command.toString());
// selcom.append("; ribbons; ");
{
selectioncom.setLength(selectioncom.length() - 1);
}
- System.out.println("Select regions:\n" + selectioncom.toString());
+ if (debug)
+ {
+ System.out.println("Select regions:\n" + selectioncom.toString());
+ }
allComs.append("; ~display all; chain @CA|P; ribbon "
+ selectioncom.toString() + "; focus");
// evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString());
private void waitForChimera()
{
- while (viewer.isBusy())
+ while (viewer != null && viewer.isBusy())
{
try {
Thread.sleep(15);
}
}
- boolean debug = true;
-
private void log(String message)
{
System.err.println("## Chimera log: " + message);
private void viewerCommandHistory(boolean enable)
{
- log("(Not yet implemented) History "
- + ((debug || enable) ? "on" : "off"));
+ // log("(Not yet implemented) History "
+ // + ((debug || enable) ? "on" : "off"));
}
public void loadInline(String string)