From: Jim Procter <j.procter@dundee.ac.uk>
Date: Thu, 9 Jun 2022 13:07:04 +0000 (+0100)
Subject: Merge branch 'bug/JAL-4020_add_pymolwin_paths' into develop
X-Git-Tag: Release_2_11_2_6~52
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=efba321f20b819819c0b1cd9c9133d9d1a2ab314;hp=a9689ca54eaa10c839fafd5bb01c6ee6c17f5c9a

Merge branch 'bug/JAL-4020_add_pymolwin_paths' into develop
---

diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
index ad2a61b..f7dba79 100644
--- a/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
@@ -75,8 +75,8 @@ 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",
-      "0.93", "0.92", "0.91", "0.9" };
+  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",
       "pdbFileName", "PDB ID", "structure", "biopax.xref.PDB", "pdb_ids",
@@ -1017,7 +1017,8 @@ 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..7dfdb0c 100644
--- a/src/jalview/ext/pymol/PymolManager.java
+++ b/src/jalview/ext/pymol/PymolManager.java
@@ -32,12 +32,13 @@ import java.net.URL;
 import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Locale;
 
 import jalview.bin.Cache;
 import jalview.bin.Console;
 import jalview.gui.Preferences;
-import jalview.structure.StructureCommand;
 import jalview.structure.StructureCommandI;
+import jalview.util.Platform;
 
 public class PymolManager
 {
@@ -100,7 +101,24 @@ 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")), // default user path
+          "\\ProgramData", "C:\\ProgramData", // this is the default install
+                                              // path "for everyone"
+          System.getProperty("user.home"), "\\Program Files",
+          "C:\\Program Files", "\\Program Files (x86)",
+          "C:\\Program Files (x86)" })
+      {
+        for (String path : new String[] { "Schrodinger\\PyMOL2", "PyMOL" })
+        {
+          for (String binary : new String[] { "PyMOLWinWithConsole.bat",
+              "Scripts\\pymol.exe", "PyMOLWin.exe" })
+          {
+            pathList.add(String.format("%s\\%s\\%s", root, path, binary));
+          }
+        }
+      }
     }
     else if (os.startsWith("Mac"))
     {
@@ -254,8 +272,16 @@ public class PymolManager
         }
         List<String> args = new ArrayList<>();
         args.add(pymolPath);
+
+        // Windows PyMOLWin.exe needs an extra argument
+        if (Platform.isWin() && pymolPath.toLowerCase(Locale.ROOT)
+                .endsWith("\\pymolwin.exe"))
+        {
+          args.add("+2");
+        }
         args.add("-R"); // https://pymolwiki.org/index.php/RPC
         ProcessBuilder pb = new ProcessBuilder(args);
+        Console.debug("Running PyMOL as " + String.join(" ", pb.command()));
         pymolProcess = pb.start();
         error = "";
         break;
diff --git a/test/jalview/ext/pymol/PymolManagerTest.java b/test/jalview/ext/pymol/PymolManagerTest.java
index bfaeacf..daea0dc 100644
--- a/test/jalview/ext/pymol/PymolManagerTest.java
+++ b/test/jalview/ext/pymol/PymolManagerTest.java
@@ -74,7 +74,12 @@ public class PymolManagerTest
      * Windows
      */
     paths = PymolManager.getPymolPaths("Windows 10");
-    assertTrue(paths.isEmpty()); // TODO - Windows paths
+    assertTrue(paths.contains(System.getProperty("user.home")
+            + "\\AppData\\Local\\Schrodinger\\PyMOL2\\PyMOLWinWithConsole.bat"));
+    assertTrue(paths.contains(System.getProperty("user.home")
+            + "\\PyMOL\\PyMOLWinWithConsole.bat"));
+    assertTrue(paths
+            .contains("C:\\ProgramData\\PyMOL\\PyMOLWinWithConsole.bat"));
 
     /*
      * Other