X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FPymolBindingModel.java;h=705102ad5c357a85cc3d036f36ea08244ac2c978;hb=747167089ecf8d6afc70d417f5a20352e029bd95;hp=538b101b22015f22a4099e08915eab15924fd132;hpb=2fb924ec0d110eb3ca6c3fb06efa27acd34b2750;p=jalview.git
diff --git a/src/jalview/gui/PymolBindingModel.java b/src/jalview/gui/PymolBindingModel.java
index 538b101..705102a 100644
--- a/src/jalview/gui/PymolBindingModel.java
+++ b/src/jalview/gui/PymolBindingModel.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.gui;
import java.util.ArrayList;
@@ -6,7 +26,7 @@ import java.util.List;
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;
@@ -70,16 +90,14 @@ public class PymolBindingModel extends AAStructureBindingModel
public void highlightAtoms(List 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();
@@ -87,18 +105,9 @@ public class PymolBindingModel extends AAStructureBindingModel
{
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;
}
@@ -131,7 +140,7 @@ public class PymolBindingModel extends AAStructureBindingModel
@Override
public boolean isViewerRunning()
{
- return pymolManager.isPymolLaunched();
+ return pymolManager != null && pymolManager.isPymolLaunched();
}
@Override
@@ -156,7 +165,7 @@ public class PymolBindingModel extends AAStructureBindingModel
}
else
{
- Cache.log.error("Failed to launch PyMOL!");
+ Console.error("Failed to launch PyMOL!");
}
return pymol != null;
}
@@ -171,6 +180,22 @@ public class PymolBindingModel extends AAStructureBindingModel
* 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);