import java.util.Map;
import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.pymol.PymolCommands;
public void highlightAtoms(List<AtomSpec> atoms)
{
/*
- * https://pymolwiki.org/index.php/Label#examples
+ * https://pymolwiki.org/index.php/indicate#examples
*/
StringBuilder sb = new StringBuilder();
for (AtomSpec atom : atoms)
{
// todo promote to StructureCommandsI.showLabel()
- // todo handle CA|P correctly
String modelId = getModelIdForFile(atom.getPdbFile());
- sb.append(String.format(" %s//%s/%d/CA", modelId,
- atom.getChain(),
+ sb.append(String.format(" %s//%s/%d/*", modelId, atom.getChain(),
atom.getPdbResNum()));
}
String labelSpec = sb.toString();
{
return;
}
- StructureCommandI command = new StructureCommand("label", labelSpec, LABEL_FORMAT);
+ StructureCommandI command = new StructureCommand("indicate", labelSpec);
executeCommand(command, false);
- /*
- * and remove the label(s) previously shown
- */
- if (lastLabelSpec != null)
- {
- command = new StructureCommand("label", lastLabelSpec, "");
- executeCommand(command, false);
- }
-
lastLabelSpec = labelSpec;
}
@Override
public boolean isViewerRunning()
{
- return pymolManager.isPymolLaunched();
+ return pymolManager != null && pymolManager.isPymolLaunched();
}
@Override
}
else
{
- Cache.log.error("Failed to launch PyMOL!");
+ Console.error("Failed to launch PyMOL!");
}
return pymol != null;
}
* a second parameter sets the pdbid as the loaded PyMOL object name
*/
String pdbId = pe.getId();
+ try
+ {
+ String safePDBId = java.net.URLEncoder.encode(pdbId, "UTF-8");
+ pdbId = safePDBId.replace('%', '_');
+ pdbId = pdbId.replace("-", "__");
+ char fc = pdbId.charAt(0);
+ // put an 's' before any numerics
+ if (fc >= '0' && fc <= '9')
+ {
+ pdbId = 's' + pdbId;
+ }
+ // pdbId.replace('-', 0)
+ } catch (Exception x)
+ {
+ Console.error("Unxpected encoding exception for '" + pdbId + "'", x);
+ }
cmd.addParameter(pdbId);
executeCommand(cmd, false);