/* * Copyright (c) 2005, Stanford University. All rights reserved. * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions * are met: * - Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * - Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the distribution. * - Neither the name of the Stanford University nor the names of its * contributors may be used to endorse or promote products derived * from this software without specific prior written permission. * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS * FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE * COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, * BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE * POSSIBILITY OF SUCH DAMAGE. */ /* * Created on June 12, 2006 -- modified version of RunPymolThread.java * Original author: Christopher Bruns, Mark Friedrichs */ package org.simtk.isimsu; import java.io.*; import java.util.*; import org.simtk.gui.*; /** * * @author Christopher Bruns * * class to manage the running of the program Pymol on a molecule */ public class RunPymolThread extends JarDefinedExecutableThread implements MonitoredProcess { // ISIMTask pymolTask; ISIMWrapper isimWrapper; APBSParameters pymolParameters; ISIMStepParameters stepParameters; int displayFileType; // Constructor RunPymolThread(ISIMStepParameters s, APBSParameters p, ISIMWrapper isimWrapper) { stepParameters = s; pymolParameters = p; this.isimWrapper = isimWrapper; } public void run() { String methodName = "RunPymolThread "; isimWrapper.appendToLog( methodName + "Starting Pymol task...\n"); ISIMTask task = stepParameters.task; // Don't do anything if it appears that someone else is already doing this task if (task.isRunning()) return; String pymolDirectory = "dir_pymol"; String pymolExecutableName = "pymol_arguments"; isimWrapper.appendToLog( methodName + "Unpacking Pymol executable from \n <" + pymolDirectory + "/" + pymolExecutableName + "> to\n <" + stepParameters.programDirectory + ">\n"); Vector initialArgs = new Vector(); try { initialArgs = unpackExecutable( pymolDirectory, pymolExecutableName, stepParameters.programDirectory); } catch (IOException exc) { reportFailure(exc, "error unpacking Pymol executable"); return; } isimWrapper.appendToLog( methodName + " Unpacked Pymol executable." ); // get OS (Windows, Linux, Mac ) String osName = ExternalProcessManager.getOsType(); isimWrapper.appendToLog( methodName + " Osname=" + osName + "\n" ); // get location of Pymol (from muffin, generic locations on machine or as a // last resort from the user // if not found, then bail out after loggin message GetPymolLocation getPymolLocation = new GetPymolLocation( isimWrapper, isimWrapper.getLogDialog() ); String pymolLocation = getPymolLocation.getPathToPymolExecutable( osName ); if( pymolLocation == null ){ isimWrapper.appendToLog( methodName + "Pymol path unavailable." ); return; } String pymolEnvironmentPath = getPymolLocation.getPymolEnvironmentPath( pymolLocation, osName ); String pythonEnvironmentPath = getPymolLocation.getPythonEnvironmentPath( pymolLocation, osName ); isimWrapper.appendToLog( methodName + "Pymol executable path=<" + pymolLocation + ">\n" ); isimWrapper.appendToLog( methodName + "Pymol environment path=<" + pymolEnvironmentPath + ">\n" ); isimWrapper.appendToLog( methodName + "Python environment path=<" + pythonEnvironmentPath + ">\n" ); // Generate the full command line for the system call Vector cmdArgs = new Vector(); cmdArgs.addElement( pymolLocation ); // -x Disable external GUI -- causes problems on Mac (maybe other platforms too) // Warren recommended -x, but problems // -i Disable the internal OpenGL GUI (object list, menus, etc.) // -q Quiet launch. Suppress splash screen & other chatter. // -F command line at bottom of display screen absent // -m force Pymol to launch w/ X11; -m causes problems when not using // MacBundle (can't find Python sys module if( osName.compareToIgnoreCase( "Mac" ) == 0 && java.util.regex.Pattern.matches( ".*MacPyMOL$", pymolLocation ) ){ cmdArgs.addElement( "-iFmq" ); } else { cmdArgs.addElement( "-iFq" ); } File workDir = stepParameters.workingDirectory; // Put later arguments from executable name into command path for( int ii = 1; ii < initialArgs.size(); ii++) { cmdArgs.addElement((String) initialArgs.elementAt(ii)); } isimWrapper.appendToLog( methodName + "No. arguments=" + cmdArgs.size() + "\n" ); // Convert to a string array for use by ExternalProcessManager String[] pymolCommand = new String[cmdArgs.size()]; pymolCommand = (String[]) cmdArgs.toArray(pymolCommand); pymolCommand[2] = workDir.getAbsolutePath() + File.separator + pymolCommand[2]; // diagnostics String message = "\nIssuing Pymol command=<"; for( int ii = 0; ii < pymolCommand.length; ii++ ){ message += " " + pymolCommand[ii]; } message += ">\n"; isimWrapper.appendToLog( message ); // set the PYMOL_PATH and PYTHONHOME environment variables Map environmentMap = new HashMap(); message = ""; if( osName.compareToIgnoreCase( "Mac" ) == 0 && java.util.regex.Pattern.matches( ".*MacPyMOL$", pymolLocation ) ){ // not sure why these environment variables are needed message += "Setting environment variables CWD and PWD"; environmentMap.put( "CWD", workDir.getAbsolutePath() ); environmentMap.put( "PWD", workDir.getAbsolutePath() ); } else { // Note: if the PYTHONPATH is set then the /System/Framework/.../python2.x // is not searched and the program (Pymol) fails; the ext/lib/python2.x // directory is not supplied w/ the download (it is provided w/ the Windows and // Linux) environmentMap.put( "DISPLAY", ":0.0" ); environmentMap.put( "PYMOL_PATH", pymolEnvironmentPath ); environmentMap.put( "PYTHONHOME", pythonEnvironmentPath ); message += "Setting environment variables DISPLAY, PYMOL_PATH, PYTHONHOME"; } isimWrapper.appendToLog( message ); // start process, but don't wait for it to complete ExternalProcessManager pymolProcess = new ExternalProcessManager(pymolCommand, workDir, environmentMap ); pymolProcess.setLogDialog( isimWrapper.getLogDialog() ); pymolProcess.setWaitForCompletion( 0 ); pymolProcess.start(); return; } void reportFailure(Exception exc, String msg) { exc.printStackTrace(); stepParameters.task.setStatus(DependentTask.FAILED, msg); isimWrapper.appendToLog("Pymol process failed: " + msg + "\n");; return; } }