/* * 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 Sep 15, 2005 * Original author: Christopher Bruns */ package org.simtk.isimsu; import java.io.*; import java.util.*; import org.simtk.gui.*; import java.text.*; // DecimalFormat /** * * @author Christopher Bruns * * class to manage the running of the program APBS on a molecule */ public class RunAPBSThread extends JarDefinedExecutableThread implements MonitoredProcess { // ISIMTask apbsTask; ISIMWrapper isimWrapper; APBSParameters apbsParameters; ISIMStepParameters stepParameters; // Constructor RunAPBSThread(ISIMStepParameters s, APBSParameters p, ISIMWrapper isimWrapper) { stepParameters = s; apbsParameters = p; this.isimWrapper = isimWrapper; } public void run() { isimWrapper.appendToLog("Starting APBS 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; isimWrapper.appendToLog("Unpacking APBS executable...\n"); Vector initialArgs = new Vector(); try { initialArgs = unpackExecutable("dir_apbs", "apbs_executable_name", stepParameters.programDirectory); } catch (IOException exc) { reportFailure(exc, "error unpacking APBS executable"); return; } // // // See if apbs is already installed File apbsExecutableFile = new File(stepParameters.programDirectory, (String) initialArgs.elementAt(0)); // // If not, copy it from the jar file // if (! apbsExecutableFile.exists()) { // try { // // TODO get rid of all the APBSBinary stuff // // Use a mechanism like the file based mechanisim of pdb2pqr // OutputStream apbsOut = new FileOutputStream(apbsExecutableFile); // InputStream apbsIn = APBSBinary.getJarURL().openStream(); // StreamCopy.copy(apbsIn, apbsOut); // } // catch (IOException exc) { // exc.printStackTrace(); // System.exit(1); // } // } isimWrapper.appendToLog("Creating APBS input file...\n"); File workDir = stepParameters.workingDirectory; // 1 - create apbs input file File apbsInputFile = new File(workDir, "apbs_molecule.in"); // Create an APBS input file String apbsInputString = createAPBSInput(); isimWrapper.appendToLog("APBS input file:\n"); isimWrapper.appendToLog("\n\n********************\n\n"); isimWrapper.appendToLog(apbsInputString); isimWrapper.appendToLog("\n\n******************\n\n"); task.setStatus(DependentTask.ACTIVELY_UPDATING, "computing NLPB..."); try { BufferedWriter apbsInWriter = new BufferedWriter(new FileWriter(apbsInputFile)); apbsInWriter.write(apbsInputString); apbsInWriter.close(); } catch (IOException exc) { exc.printStackTrace(); task.setStatus(DependentTask.FAILED, "I/O error on APBS input file"); return; } // 2 - run apbs // Run the APBS command isimWrapper.appendToLog("Running APBS...\n"); String apbsCommand = apbsExecutableFile.getAbsolutePath(); String apbsArg1 = apbsInputFile.getName(); String[] apbsArgs = {apbsCommand, apbsArg1}; // Process apbsProcess = Runtime.getRuntime().exec(apbsArgs, null, tempDir); ExternalProcessManager apbsProcess = new ExternalProcessManager(apbsArgs, workDir); long startSeconds = new Date().getTime() / 1000; apbsProcess.start(); // Wait for process to end try { apbsProcess.join(); // Test whether the process worked if (apbsProcess.exception != null) reportFailure(apbsProcess.exception, ""); else { // This is the only point of success // Report the time taken long finishSeconds = new Date().getTime() / 1000; long elapsedSeconds = finishSeconds - startSeconds; long elapsedMinutes = elapsedSeconds / 60; elapsedSeconds = elapsedSeconds % 60; long elapsedHours = elapsedMinutes / 60; elapsedMinutes = elapsedMinutes % 60; NumberFormat twoDigits = new DecimalFormat(); twoDigits.setMinimumIntegerDigits(2); twoDigits.setMaximumIntegerDigits(2); twoDigits.setMaximumFractionDigits(0); String elapsedTime = "" + twoDigits.format(elapsedHours) + ":" + twoDigits.format(elapsedMinutes) + ":" + twoDigits.format(elapsedSeconds); task.setStatus(DependentTask.CURRENT_AND_COMPLETE, elapsedTime); logProcessOutput(apbsProcess); isimWrapper.appendToLog("APBS process completed successfully\n"); } return; } catch (InterruptedException exc) { logProcessOutput(apbsProcess); reportFailure(exc, "process interrupted"); return; } } private void logProcessOutput(ExternalProcessManager process) { isimWrapper.appendToLog("Standard error stream: \n\n"); isimWrapper.appendToLog("************************************ \n\n"); isimWrapper.appendToLog(process.getStdErr()); isimWrapper.appendToLog("\n\n************************************ \n\n"); isimWrapper.appendToLog("Standard output stream: \n\n"); isimWrapper.appendToLog("************************************ \n\n"); isimWrapper.appendToLog(process.getStdOut()); isimWrapper.appendToLog("\n\n************************************ \n\n"); } String createAPBSInput() { // String pqrFileName = apbsParameters.pqrInputFile.getAbsolutePath(); // danger - might contain spaces String pqrFileName = apbsParameters.getPqrInputFile().getName(); String moleculePotentialFileName = apbsParameters.getPotentialOutputFile().getName(); // Remove ".dx" suffix, apbs will add it automatically moleculePotentialFileName = moleculePotentialFileName.replaceAll("\\.dx$", ""); DecimalFormat threeDecimalPlaces = new DecimalFormat("#.###"); int dimeX = apbsParameters.getDimension()[0]; int dimeY = apbsParameters.getDimension()[1]; int dimeZ = apbsParameters.getDimension()[2]; String glenX = threeDecimalPlaces.format(apbsParameters.getGridLength()[0]); String glenY = threeDecimalPlaces.format(apbsParameters.getGridLength()[1]); String glenZ = threeDecimalPlaces.format(apbsParameters.getGridLength()[2]); return "read \n" + " mol pqr " + pqrFileName + "\n" + "end\n" + "\n" + "elec\n" + " mg-manual\n" + // dime options are 65, 97, 129, and 161 (for nlev = 4) " dime "+dimeX+" "+dimeY+" "+dimeZ+"\n" + " nlev 4\n" + " glen "+glenX+" "+glenY+" "+glenZ+"\n" + " gcent mol 1\n" + " mol 1\n" + " npbe\n" + " bcfl sdh\n" + " ion 1 0.000 2.0 # Zero ionic strength for initial run\n" + " ion -1 0.000 2.0\n" + " pdie " + threeDecimalPlaces.format(apbsParameters.getMoleculePermittivity()) + "\n" + " sdie " + threeDecimalPlaces.format(apbsParameters.getSolventPermittivity()) + "\n" + " srfm smol\n" + " chgm spl2\n" + " srad 1.4\n" + " swin 0.3\n" + " temp " + threeDecimalPlaces.format(apbsParameters.getTemperature()) + "\n" + " gamma 0.105\n" + " calcenergy no\n" + " calcforce no\n" + " write pot dx " + moleculePotentialFileName + "\n" + "end\n" + "\n" + "quit\n"; } void reportFailure(Exception exc, String msg) { exc.printStackTrace(); stepParameters.task.setStatus(DependentTask.FAILED, msg); isimWrapper.appendToLog("APBS process failed: " + msg + "\n");; return; } }