JAL-3931 remove % and - from ids so Pymol doesn’t strip them out and truncate the...

diff --git a/src/jalview/gui/PymolBindingModel.java b/src/jalview/gui/PymolBindingModel.java
index 538b101..719ca53 100644 (file)
--- a/src/jalview/gui/PymolBindingModel.java
+++ b/src/jalview/gui/PymolBindingModel.java
@@ -171,6 +171,21 @@ 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)
+    {
+      Cache.log.error("Unxpected encoding exception for '"+pdbId+"'",x);
+    }
     cmd.addParameter(pdbId);
 
     executeCommand(cmd, false);