X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fext%2Fpymol%2FPymolManager.java;h=ddc8d84e859cc46bcff1613b3117df1cfed0b4b2;hb=8a2a0cda7067530f8481c2aec203e18d555f2dfd;hp=db712699d24b2ae204559d85fea075f681c58eba;hpb=cb8e52fbbc5f725e3f7f48c672cdddb0690bd978;p=jalview.git

diff --git a/src/jalview/ext/pymol/PymolManager.java b/src/jalview/ext/pymol/PymolManager.java
index db71269..ddc8d84 100644
--- a/src/jalview/ext/pymol/PymolManager.java
+++ b/src/jalview/ext/pymol/PymolManager.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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.pymol;
 
 import java.io.BufferedReader;
@@ -12,12 +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
 {
@@ -60,14 +81,13 @@ public class PymolManager
   protected static List<String> getPymolPaths(String os)
   {
     List<String> pathList = new ArrayList<>();
-  
-    String userPath = Cache
-            .getDefault(Preferences.PYMOL_PATH, null);
+
+    String userPath = Cache.getDefault(Preferences.PYMOL_PATH, null);
     if (userPath != null)
     {
       pathList.add(userPath);
     }
-  
+
     /*
      * add default installation paths
      */
@@ -81,7 +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"))
     {
@@ -121,7 +158,7 @@ public class PymolManager
           boolean getReply)
   {
     String postBody = getPostRequest(command);
-    // System.out.println(postBody);// debug
+    // jalview.bin.Console.outPrintln(postBody);// debug
     String rpcUrl = "http://127.0.0.1:" + this.pymolXmlRpcPort;
     PrintWriter out = null;
     BufferedReader in = null;
@@ -235,8 +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;
@@ -319,7 +364,7 @@ public class PymolManager
       Console.error("Failed to start PyMOL with XMLRPC, response was: "
               + responses);
     }
-    Console.error("PyMOL started with XMLRPC on port " + port);
+    Console.info("PyMOL started with XMLRPC on port " + port);
     return port;
   }