+/*
+ * 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;
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
{
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
*/
}
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"))
{
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;
int rc = conn.getResponseCode();
if (rc != HttpURLConnection.HTTP_OK)
{
- Cache.log.error(
+ Console.error(
String.format("Error status from %s: %d", rpcUrl, rc));
return result;
}
} catch (SocketException e)
{
// thrown when 'quit' command is sent to PyMol
- Cache.log.warn(String.format("Request to %s returned %s", rpcUrl,
+ Console.warn(String.format("Request to %s returned %s", rpcUrl,
e.toString()));
} catch (Exception e)
{
{
out.close();
}
+ if (Console.isTraceEnabled())
+ {
+ Console.trace("Sent: " + command.toString());
+ if (result != null)
+ {
+ Console.trace("Received: " + result);
+ }
+ }
}
return result;
}
}
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;
this.pymolXmlRpcPort = getPortNumber();
if (pymolXmlRpcPort > 0)
{
- Cache.log.info("PyMOL XMLRPC started on port " + pymolXmlRpcPort);
+ Console.info("PyMOL XMLRPC started on port " + pymolXmlRpcPort);
}
else
{
error += "Failed to read PyMOL XMLRPC port number";
- Cache.log.error(error);
+ Console.error(error);
pymolProcess.destroy();
pymolProcess = null;
}
}
} catch (Exception e)
{
- Cache.log.error("Failed to get REST port number from " + responses
+ Console.error("Failed to get REST port number from " + responses
+ ": " + e.getMessage());
// logger.error("Failed to get REST port number from " + responses + ": "
// + e.getMessage());
}
if (port == 0)
{
- Cache.log.error("Failed to start PyMOL with XMLRPC, response was: "
+ Console.error("Failed to start PyMOL with XMLRPC, response was: "
+ responses);
}
- Cache.log.error("PyMOL started with XMLRPC on port " + port);
+ Console.info("PyMOL started with XMLRPC on port " + port);
return port;
}