From: Ben Soares <bsoares@dundee.ac.uk>
Date: Mon, 6 Jun 2022 13:03:50 +0000 (+0100)
Subject: JAL-4020 Added search for PyMOLWinWithConsole.bat (and PyMOLWin.exe) in likely places... 
X-Git-Tag: Release_2_11_2_6~52^2~6
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=483ecb5e4541537778844529cc93204f9124b68d

JAL-4020 Added search for PyMOLWinWithConsole.bat (and PyMOLWin.exe) in likely places starting with default install dir.  Added a new version (1.3) to ChimeraX
---

diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
index ad2a61b..0444895 100644
--- a/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
@@ -75,7 +75,7 @@ public class StructureManager
       "1.11.2", "1.11.1", "1.11" };
 
   // Missing 1.1 as this has known bug see JAL-2422
-  private static String[] CHIMERAX_VERSIONS = new String[] { "1.2.5", "1.0",
+  private static String[] CHIMERAX_VERSIONS = new String[] { "1.3", "1.2.5", "1.0",
       "0.93", "0.92", "0.91", "0.9" };
 
   static final String[] defaultStructureKeys = { "Structure", "pdb",
@@ -1017,7 +1017,7 @@ public class StructureManager
     {
       for (String root : new String[] { "\\Program Files",
           "C:\\Program Files", "\\Program Files (x86)",
-          "C:\\Program Files (x86)" })
+          "C:\\Program Files (x86)", String.format("%s\\AppData\\Local", System.getProperty("user.home"))})
       {
         String[] candidates = isChimeraX ? CHIMERAX_VERSIONS
                 : CHIMERA_VERSIONS;
diff --git a/src/jalview/ext/pymol/PymolManager.java b/src/jalview/ext/pymol/PymolManager.java
index 05d5bcc..1acce5e 100644
--- a/src/jalview/ext/pymol/PymolManager.java
+++ b/src/jalview/ext/pymol/PymolManager.java
@@ -101,6 +101,18 @@ public class PymolManager
     else if (os.startsWith("Windows"))
     {
       // todo Windows installation path(s)
+    	for (String root : new String[]
+      {
+        String.format("%s\\AppData\\Local", System.getProperty("user.home")),
+    		"\\Program Files", "C:\\Program Files", "\\Program Files (x86)",
+    		"C:\\Program Files (x86)" })
+    	{
+    	  for (String binary : new String [] {"PyMOLWinWithConsole.bat", "PyMOLWin.exe"})
+    	  {
+          pathList.add(String.format("%s\\Schrodinger\\PyMOL2\\%s", root, binary));
+    	  }
+    	}
+
     }
     else if (os.startsWith("Mac"))
     {