2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.ext.pymol;
23 import java.io.BufferedReader;
25 import java.io.IOException;
26 import java.io.InputStream;
27 import java.io.InputStreamReader;
28 import java.io.PrintWriter;
29 import java.net.HttpURLConnection;
30 import java.net.SocketException;
32 import java.nio.file.Paths;
33 import java.util.ArrayList;
34 import java.util.List;
35 import java.util.Locale;
37 import jalview.bin.Cache;
38 import jalview.bin.Console;
39 import jalview.gui.Preferences;
40 import jalview.structure.StructureCommandI;
41 import jalview.util.Platform;
43 public class PymolManager
45 private static final int RPC_REPLY_TIMEOUT_MS = 15000;
47 private static final int CONNECTION_TIMEOUT_MS = 100;
49 private static final String POST1 = "<methodCall><methodName>";
51 private static final String POST2 = "</methodName><params>";
53 private static final String POST3 = "</params></methodCall>";
55 private Process pymolProcess;
57 private int pymolXmlRpcPort;
60 * Returns a list of paths to try for the PyMOL executable. Any user
61 * preference is placed first, otherwise 'standard' paths depending on the
66 public static List<String> getPymolPaths()
68 return getPymolPaths(System.getProperty("os.name"));
72 * Returns a list of paths to try for the PyMOL executable. Any user
73 * preference is placed first, otherwise 'standard' paths depending on the
77 * operating system as reported by environment variable
81 protected static List<String> getPymolPaths(String os)
83 List<String> pathList = new ArrayList<>();
85 String userPath = Cache.getDefault(Preferences.PYMOL_PATH, null);
88 pathList.add(userPath);
92 * add default installation paths
94 String pymol = "PyMOL";
95 if (os.startsWith("Linux"))
97 pathList.add("/usr/local/pymol/bin/" + pymol);
98 pathList.add("/usr/local/bin/" + pymol);
99 pathList.add("/usr/bin/" + pymol);
100 pathList.add(System.getProperty("user.home") + "/opt/bin/" + pymol);
102 else if (os.startsWith("Windows"))
104 for (String root : new String[] {
105 String.format("%s\\AppData\\Local",
106 System.getProperty("user.home")), // default user path
107 "\\ProgramData", "C:\\ProgramData", // this is the default install
108 // path "for everyone"
109 System.getProperty("user.home"), "\\Program Files",
110 "C:\\Program Files", "\\Program Files (x86)",
111 "C:\\Program Files (x86)" })
113 for (String path : new String[] { "Schrodinger\\PyMOL2", "PyMOL" })
115 for (String binary : new String [] {"PyMOLWinWithConsole.bat", "PyMOLWin.exe"})
117 pathList.add(String.format("%s\\%s\\%s", root, path, binary));
122 else if (os.startsWith("Mac"))
124 pathList.add("/Applications/PyMOL.app/Contents/MacOS/" + pymol);
129 public boolean isPymolLaunched()
131 // TODO pull up generic methods for external viewer processes
132 boolean launched = false;
133 if (pymolProcess != null)
137 pymolProcess.exitValue();
138 // if we get here, process has ended
139 } catch (IllegalThreadStateException e)
141 // ok - not yet terminated
149 * Sends the command to Pymol; if requested, tries to get and return any
150 * replies, else returns null
156 public List<String> sendCommand(StructureCommandI command,
159 String postBody = getPostRequest(command);
160 // System.out.println(postBody);// debug
161 String rpcUrl = "http://127.0.0.1:" + this.pymolXmlRpcPort;
162 PrintWriter out = null;
163 BufferedReader in = null;
164 List<String> result = getReply ? new ArrayList<>() : null;
168 URL realUrl = new URL(rpcUrl);
169 HttpURLConnection conn = (HttpURLConnection) realUrl.openConnection();
170 conn.setRequestProperty("accept", "*/*");
171 conn.setRequestProperty("content-type", "text/xml");
172 conn.setDoOutput(true);
173 conn.setDoInput(true);
174 out = new PrintWriter(conn.getOutputStream());
177 int rc = conn.getResponseCode();
178 if (rc != HttpURLConnection.HTTP_OK)
181 String.format("Error status from %s: %d", rpcUrl, rc));
185 InputStream inputStream = conn.getInputStream();
188 in = new BufferedReader(new InputStreamReader(inputStream));
190 while ((line = in.readLine()) != null)
195 } catch (SocketException e)
197 // thrown when 'quit' command is sent to PyMol
198 Console.warn(String.format("Request to %s returned %s", rpcUrl,
200 } catch (Exception e)
209 if (Console.isTraceEnabled())
211 Console.trace("Sent: " + command.toString());
214 Console.trace("Received: " + result);
222 * Builds the body of the XML-RPC format POST request to execute the command
227 static String getPostRequest(StructureCommandI command)
229 StringBuilder sb = new StringBuilder(64);
230 sb.append(POST1).append(command.getCommand()).append(POST2);
231 if (command.hasParameters())
233 for (String p : command.getParameters())
236 * for now assuming all are string - <string> element is optional
237 * refactor in future if other data types needed
238 * https://www.tutorialspoint.com/xml-rpc/xml_rpc_data_model.htm
240 sb.append("<parameter><value>").append(p)
241 .append("</value></parameter>");
245 return sb.toString();
248 public Process launchPymol()
250 // todo pull up much of this
251 // Do nothing if already launched
252 if (isPymolLaunched())
257 String error = "Error message: ";
258 for (String pymolPath : getPymolPaths())
262 // ensure symbolic links are resolved
263 pymolPath = Paths.get(pymolPath).toRealPath().toString();
264 File path = new File(pymolPath);
265 // uncomment the next line to simulate Pymol not installed
266 // path = new File(pymolPath + "x");
267 if (!path.canExecute())
269 error += "File '" + path + "' does not exist.\n";
272 List<String> args = new ArrayList<>();
275 // Windows PyMOLWin.exe needs an extra argument
276 if (Platform.isWin() && pymolPath.toLowerCase(Locale.ROOT).endsWith("\\pymolwin.exe"))
280 args.add("-R"); // https://pymolwiki.org/index.php/RPC
281 ProcessBuilder pb = new ProcessBuilder(args);
282 Console.debug("Running PyMOL as "+String.join(" ", pb.command()));
283 pymolProcess = pb.start();
286 } catch (Exception e)
288 // Pymol could not be started using this path
289 error += e.getMessage();
293 if (pymolProcess != null)
295 this.pymolXmlRpcPort = getPortNumber();
296 if (pymolXmlRpcPort > 0)
298 Console.info("PyMOL XMLRPC started on port " + pymolXmlRpcPort);
302 error += "Failed to read PyMOL XMLRPC port number";
303 Console.error(error);
304 pymolProcess.destroy();
312 private int getPortNumber()
314 // TODO pull up most of this!
316 InputStream readChan = pymolProcess.getInputStream();
317 BufferedReader lineReader = new BufferedReader(
318 new InputStreamReader(readChan));
319 StringBuilder responses = new StringBuilder();
322 String response = lineReader.readLine();
323 while (response != null)
325 responses.append("\n" + response);
326 // expect: xml-rpc server running on host localhost, port 9123
327 if (response.contains("xml-rpc"))
329 String[] tokens = response.split(" ");
330 for (int i = 0; i < tokens.length - 1; i++)
332 if ("port".equals(tokens[i]))
334 port = Integer.parseInt(tokens[i + 1]);
341 break; // hack for hanging readLine()
343 response = lineReader.readLine();
345 } catch (Exception e)
347 Console.error("Failed to get REST port number from " + responses
348 + ": " + e.getMessage());
349 // logger.error("Failed to get REST port number from " + responses + ": "
350 // + e.getMessage());
356 } catch (IOException e2)
362 Console.error("Failed to start PyMOL with XMLRPC, response was: "
365 Console.info("PyMOL started with XMLRPC on port " + port);