From: Jim Procter <j.procter@dundee.ac.uk>
Date: Wed, 8 Dec 2021 15:45:51 +0000 (+0000)
Subject: JAL-3931 remove % and - from ids so Pymol doesn’t strip them out and truncate the... 
X-Git-Tag: Release_2_11_2_0~21^2~1^2~4
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9d80cca5113c0411aa06559d4bd3f86454459ce7;p=jalview.git

JAL-3931 remove % and - from ids so Pymol doesn’t strip them out and truncate the structure identifier that Jalview uses to refer to each file
---

diff --git a/src/jalview/gui/PymolBindingModel.java b/src/jalview/gui/PymolBindingModel.java
index 538b101..719ca53 100644
--- 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);