/* * 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 . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.ext.pymol; import java.io.BufferedReader; import java.io.File; import java.io.IOException; import java.io.InputStream; import java.io.InputStreamReader; import java.io.PrintWriter; import java.net.HttpURLConnection; import java.net.SocketException; 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.StructureCommandI; import jalview.util.Platform; public class PymolManager { private static final int RPC_REPLY_TIMEOUT_MS = 15000; private static final int CONNECTION_TIMEOUT_MS = 100; private static final String POST1 = ""; private static final String POST2 = ""; private static final String POST3 = ""; private Process pymolProcess; private int pymolXmlRpcPort; /** * Returns a list of paths to try for the PyMOL executable. Any user * preference is placed first, otherwise 'standard' paths depending on the * operating system. * * @return */ public static List getPymolPaths() { return getPymolPaths(System.getProperty("os.name")); } /** * Returns a list of paths to try for the PyMOL executable. Any user * preference is placed first, otherwise 'standard' paths depending on the * operating system. * * @param os * operating system as reported by environment variable * {@code os.name} * @return */ protected static List getPymolPaths(String os) { List pathList = new ArrayList<>(); String userPath = Cache.getDefault(Preferences.PYMOL_PATH, null); if (userPath != null) { pathList.add(userPath); } /* * add default installation paths */ String pymol = "PyMOL"; if (os.startsWith("Linux")) { pathList.add("/usr/local/pymol/bin/" + pymol); pathList.add("/usr/local/bin/" + pymol); pathList.add("/usr/bin/" + pymol); pathList.add(System.getProperty("user.home") + "/opt/bin/" + pymol); } else if (os.startsWith("Windows")) { 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")) { pathList.add("/Applications/PyMOL.app/Contents/MacOS/" + pymol); } return pathList; } public boolean isPymolLaunched() { // TODO pull up generic methods for external viewer processes boolean launched = false; if (pymolProcess != null) { try { pymolProcess.exitValue(); // if we get here, process has ended } catch (IllegalThreadStateException e) { // ok - not yet terminated launched = true; } } return launched; } /** * Sends the command to Pymol; if requested, tries to get and return any * replies, else returns null * * @param command * @param getReply * @return */ public List sendCommand(StructureCommandI command, boolean getReply) { String postBody = getPostRequest(command); // jalview.bin.Console.outPrintln(postBody);// debug String rpcUrl = "http://127.0.0.1:" + this.pymolXmlRpcPort; PrintWriter out = null; BufferedReader in = null; List result = getReply ? new ArrayList<>() : null; try { URL realUrl = new URL(rpcUrl); HttpURLConnection conn = (HttpURLConnection) realUrl.openConnection(); conn.setRequestProperty("accept", "*/*"); conn.setRequestProperty("content-type", "text/xml"); conn.setDoOutput(true); conn.setDoInput(true); out = new PrintWriter(conn.getOutputStream()); out.print(postBody); out.flush(); int rc = conn.getResponseCode(); if (rc != HttpURLConnection.HTTP_OK) { Console.error( String.format("Error status from %s: %d", rpcUrl, rc)); return result; } InputStream inputStream = conn.getInputStream(); if (getReply) { in = new BufferedReader(new InputStreamReader(inputStream)); String line; while ((line = in.readLine()) != null) { result.add(line); } } } catch (SocketException e) { // thrown when 'quit' command is sent to PyMol Console.warn(String.format("Request to %s returned %s", rpcUrl, e.toString())); } catch (Exception e) { e.printStackTrace(); } finally { if (out != null) { out.close(); } if (Console.isTraceEnabled()) { Console.trace("Sent: " + command.toString()); if (result != null) { Console.trace("Received: " + result); } } } return result; } /** * Builds the body of the XML-RPC format POST request to execute the command * * @param command * @return */ static String getPostRequest(StructureCommandI command) { StringBuilder sb = new StringBuilder(64); sb.append(POST1).append(command.getCommand()).append(POST2); if (command.hasParameters()) { for (String p : command.getParameters()) { /* * for now assuming all are string - element is optional * refactor in future if other data types needed * https://www.tutorialspoint.com/xml-rpc/xml_rpc_data_model.htm */ sb.append("").append(p) .append(""); } } sb.append(POST3); return sb.toString(); } public Process launchPymol() { // todo pull up much of this // Do nothing if already launched if (isPymolLaunched()) { return pymolProcess; } String error = "Error message: "; for (String pymolPath : getPymolPaths()) { try { // ensure symbolic links are resolved pymolPath = Paths.get(pymolPath).toRealPath().toString(); File path = new File(pymolPath); // uncomment the next line to simulate Pymol not installed // path = new File(pymolPath + "x"); if (!path.canExecute()) { error += "File '" + path + "' does not exist.\n"; continue; } List 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; } catch (Exception e) { // Pymol could not be started using this path error += e.getMessage(); } } if (pymolProcess != null) { this.pymolXmlRpcPort = getPortNumber(); if (pymolXmlRpcPort > 0) { Console.info("PyMOL XMLRPC started on port " + pymolXmlRpcPort); } else { error += "Failed to read PyMOL XMLRPC port number"; Console.error(error); pymolProcess.destroy(); pymolProcess = null; } } return pymolProcess; } private int getPortNumber() { // TODO pull up most of this! int port = 0; InputStream readChan = pymolProcess.getInputStream(); BufferedReader lineReader = new BufferedReader( new InputStreamReader(readChan)); StringBuilder responses = new StringBuilder(); try { String response = lineReader.readLine(); while (response != null) { responses.append("\n" + response); // expect: xml-rpc server running on host localhost, port 9123 if (response.contains("xml-rpc")) { String[] tokens = response.split(" "); for (int i = 0; i < tokens.length - 1; i++) { if ("port".equals(tokens[i])) { port = Integer.parseInt(tokens[i + 1]); break; } } } if (port > 0) { break; // hack for hanging readLine() } response = lineReader.readLine(); } } catch (Exception e) { Console.error("Failed to get REST port number from " + responses + ": " + e.getMessage()); // logger.error("Failed to get REST port number from " + responses + ": " // + e.getMessage()); } finally { try { lineReader.close(); } catch (IOException e2) { } } if (port == 0) { Console.error("Failed to start PyMOL with XMLRPC, response was: " + responses); } Console.info("PyMOL started with XMLRPC on port " + port); return port; } }