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;
36 import jalview.bin.Cache;
37 import jalview.bin.Console;
38 import jalview.gui.Preferences;
39 import jalview.structure.StructureCommandI;
41 public class PymolManager
43 private static final int RPC_REPLY_TIMEOUT_MS = 15000;
45 private static final int CONNECTION_TIMEOUT_MS = 100;
47 private static final String POST1 = "<methodCall><methodName>";
49 private static final String POST2 = "</methodName><params>";
51 private static final String POST3 = "</params></methodCall>";
53 private Process pymolProcess;
55 private int pymolXmlRpcPort;
58 * Returns a list of paths to try for the PyMOL executable. Any user
59 * preference is placed first, otherwise 'standard' paths depending on the
64 public static List<String> getPymolPaths()
66 return getPymolPaths(System.getProperty("os.name"));
70 * Returns a list of paths to try for the PyMOL executable. Any user
71 * preference is placed first, otherwise 'standard' paths depending on the
75 * operating system as reported by environment variable
79 protected static List<String> getPymolPaths(String os)
81 List<String> pathList = new ArrayList<>();
83 String userPath = Cache.getDefault(Preferences.PYMOL_PATH, null);
86 pathList.add(userPath);
90 * add default installation paths
92 String pymol = "PyMOL";
93 if (os.startsWith("Linux"))
95 pathList.add("/usr/local/pymol/bin/" + pymol);
96 pathList.add("/usr/local/bin/" + pymol);
97 pathList.add("/usr/bin/" + pymol);
98 pathList.add(System.getProperty("user.home") + "/opt/bin/" + pymol);
100 else if (os.startsWith("Windows"))
102 for (String root : new String[] {
103 String.format("%s\\AppData\\Local",
104 System.getProperty("user.home")), // default user path
105 "\\ProgramData", "C:\\ProgramData", // this is the default install
106 // path "for everyone"
107 System.getProperty("user.home"), "\\Program Files",
108 "C:\\Program Files", "\\Program Files (x86)",
109 "C:\\Program Files (x86)" })
111 for (String path : new String[] { "Schrodinger\\PyMOL2", "PyMOL" })
113 for (String binary : new String[] { "PyMOLWinWithConsole.bat" })
115 pathList.add(String.format("%s\\%s\\%s", root, path, binary));
120 else if (os.startsWith("Mac"))
122 pathList.add("/Applications/PyMOL.app/Contents/MacOS/" + pymol);
127 public boolean isPymolLaunched()
129 // TODO pull up generic methods for external viewer processes
130 boolean launched = false;
131 if (pymolProcess != null)
135 pymolProcess.exitValue();
136 // if we get here, process has ended
137 } catch (IllegalThreadStateException e)
139 // ok - not yet terminated
147 * Sends the command to Pymol; if requested, tries to get and return any
148 * replies, else returns null
154 public List<String> sendCommand(StructureCommandI command,
157 String postBody = getPostRequest(command);
158 // System.out.println(postBody);// debug
159 String rpcUrl = "http://127.0.0.1:" + this.pymolXmlRpcPort;
160 PrintWriter out = null;
161 BufferedReader in = null;
162 List<String> result = getReply ? new ArrayList<>() : null;
166 URL realUrl = new URL(rpcUrl);
167 HttpURLConnection conn = (HttpURLConnection) realUrl.openConnection();
168 conn.setRequestProperty("accept", "*/*");
169 conn.setRequestProperty("content-type", "text/xml");
170 conn.setDoOutput(true);
171 conn.setDoInput(true);
172 out = new PrintWriter(conn.getOutputStream());
175 int rc = conn.getResponseCode();
176 if (rc != HttpURLConnection.HTTP_OK)
179 String.format("Error status from %s: %d", rpcUrl, rc));
183 InputStream inputStream = conn.getInputStream();
186 in = new BufferedReader(new InputStreamReader(inputStream));
188 while ((line = in.readLine()) != null)
193 } catch (SocketException e)
195 // thrown when 'quit' command is sent to PyMol
196 Console.warn(String.format("Request to %s returned %s", rpcUrl,
198 } catch (Exception e)
207 if (Console.isTraceEnabled())
209 Console.trace("Sent: " + command.toString());
212 Console.trace("Received: " + result);
220 * Builds the body of the XML-RPC format POST request to execute the command
225 static String getPostRequest(StructureCommandI command)
227 StringBuilder sb = new StringBuilder(64);
228 sb.append(POST1).append(command.getCommand()).append(POST2);
229 if (command.hasParameters())
231 for (String p : command.getParameters())
234 * for now assuming all are string - <string> element is optional
235 * refactor in future if other data types needed
236 * https://www.tutorialspoint.com/xml-rpc/xml_rpc_data_model.htm
238 sb.append("<parameter><value>").append(p)
239 .append("</value></parameter>");
243 return sb.toString();
246 public Process launchPymol()
248 // todo pull up much of this
249 // Do nothing if already launched
250 if (isPymolLaunched())
255 String error = "Error message: ";
256 for (String pymolPath : getPymolPaths())
260 // ensure symbolic links are resolved
261 pymolPath = Paths.get(pymolPath).toRealPath().toString();
262 File path = new File(pymolPath);
263 // uncomment the next line to simulate Pymol not installed
264 // path = new File(pymolPath + "x");
265 if (!path.canExecute())
267 error += "File '" + path + "' does not exist.\n";
270 List<String> args = new ArrayList<>();
272 args.add("-R"); // https://pymolwiki.org/index.php/RPC
273 ProcessBuilder pb = new ProcessBuilder(args);
274 pymolProcess = pb.start();
277 } catch (Exception e)
279 // Pymol could not be started using this path
280 error += e.getMessage();
284 if (pymolProcess != null)
286 this.pymolXmlRpcPort = getPortNumber();
287 if (pymolXmlRpcPort > 0)
289 Console.info("PyMOL XMLRPC started on port " + pymolXmlRpcPort);
293 error += "Failed to read PyMOL XMLRPC port number";
294 Console.error(error);
295 pymolProcess.destroy();
303 private int getPortNumber()
305 // TODO pull up most of this!
307 InputStream readChan = pymolProcess.getInputStream();
308 BufferedReader lineReader = new BufferedReader(
309 new InputStreamReader(readChan));
310 StringBuilder responses = new StringBuilder();
313 String response = lineReader.readLine();
314 while (response != null)
316 responses.append("\n" + response);
317 // expect: xml-rpc server running on host localhost, port 9123
318 if (response.contains("xml-rpc"))
320 String[] tokens = response.split(" ");
321 for (int i = 0; i < tokens.length - 1; i++)
323 if ("port".equals(tokens[i]))
325 port = Integer.parseInt(tokens[i + 1]);
332 break; // hack for hanging readLine()
334 response = lineReader.readLine();
336 } catch (Exception e)
338 Console.error("Failed to get REST port number from " + responses
339 + ": " + e.getMessage());
340 // logger.error("Failed to get REST port number from " + responses + ": "
341 // + e.getMessage());
347 } catch (IOException e2)
353 Console.error("Failed to start PyMOL with XMLRPC, response was: "
356 Console.info("PyMOL started with XMLRPC on port " + port);