/* * 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 13, 2005 * Original author: Christopher Bruns */ package org.simtk.isimsu; import java.awt.*; import java.awt.event.*; import java.io.*; import java.net.MalformedURLException; import java.net.URL; import java.util.*; import java.util.regex.*; import java.text.DecimalFormat; import javax.jnlp.*; import javax.swing.*; import javax.swing.border.EmptyBorder; import org.jdom.*; import org.simtk.pdb.*; import org.simtk.molecularstructure.*; import org.simtk.mvc.SimpleObservable; import org.simtk.gui.*; import edu.stanford.ejalbert.BrowserLauncher; public class ISIMWrapper extends JFrame implements SaltSelectionListener { protected IonSelectionDialog ionDialog; protected IsimParameterDialog isimParameterDialog; public String programName = "SimTK ISIM"; public String interfaceName = programName + " Interface"; public String isimInterfaceVersion = "0.9.9"; public static final long serialVersionUID = 01L; LoadMoleculeAction loadMoleculeAction; // String pqrFileName; APBSParameters apbsParameters = null; ISIMParameters isimParameters = null; File parentWorkingDirectory; // parent directory of the next two File programDirectory; File workingDirectory; // if true, then results from previous run copied to working directory and // flag set; idea is to allow testing of program w/o waiting for // apbs/isim calculations to run int isTestRun; // File pqrStructureFile; SaltRangeSet availableIonConditionRanges = new SaltRangeSet(); // java.util.List availableIonConditions = new SaltRangeSet(); LogDialog logDialog; public Image isimIcon = new ImageIcon(getClass().getClassLoader().getResource("resources/images/isim_logo1_small.png")).getImage(); ISIMTask loadMacromoleculeTask, loadIonTask, adjustAPBSParametersTask, // computeMacromoleculePotentialTask, computeCombinedPotentialTask, setIsimParameterTask, apbsAndIsimTask, // inspectParametersTask, // computeGCMCPotentialTask, viewIonCountsTask ; ISIMStepRow chooseMoleculeRow; ISIMStepRow apbsSimulateRow = null; ISIMStepRow isimCombinedRow, viewIonCountsRow; ISIMStepRowWithProgressFile isimSimulateRow; ISIMWrapper() { // Constructor super(); setTitle(interfaceName); // Center of screen is better than the upper left corner setLocationRelativeTo(null); // Use a custom icon this.setIconImage(isimIcon); // Create a window for log messages logDialog = new LogDialog(this); logDialog.append("Progress log (" + programName + ")\n"); logDialog.append("Started " + new Date() + "\n"); logDialog.append("\n"); // loadIonConditions("resources/ion_conditions/test_ion_conditions2.xml"); // loadIonConditions("resources/ion_conditions/NaMgCl.xml"); // loadIonConditions("resources/ion_conditions/marke_NaMgCl.xml"); loadIonConditions("resources/ion_conditions/MgNaCl_basic_marke.xml"); // loadIonConditions("resources/ion_conditions/CaCl.xml"); // Create ionDialog after ion ranges are loaded, but before // ChooseIonsAction is created (in createStepRows()) ionDialog = new IonSelectionDialog(this, availableIonConditionRanges); ionDialog.addSaltSelectionListener(this); // Establish task dependencies createTasks(); // Use first ion condition to start with // SaltCondition initialSaltCondition = (SaltCondition) availableIonConditions.get(0); // apbsParameters = new APBSParameters(2.00, null, null, loadIonTask, initialSaltCondition); apbsParameters = new APBSParameters(); apbsParameters.setDependentTasks(loadIonTask, adjustAPBSParametersTask, loadMacromoleculeTask); apbsParameters.setMoleculePermittivity(2.0); apbsParameters.setIons(null); // dime options are 65, 97, 129, and 161 (for nlev = 4) apbsParameters.setDimension(97, 97, 97); // Isim Parameters isimParameters = new ISIMParameters(); isimParameterDialog = new IsimParameterDialog( apbsParameters, isimParameters, this, logDialog ); // Create one structure loading action object, for both button and menu activation loadMoleculeAction = new LoadMoleculeAction(this); isTestRun = 0; // Make close button well... close. // Revert to Frame behavior, w/ actionListener etc. // Disable JFrame handling of close event setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE); // Add old way of handling close event addWindowListener (new WindowAdapter() { public void windowClosing(WindowEvent e) { cleanUpAndExit(); } } ); createMenuBar(); createStepRows(); createDirectories(); apbsParameters.setMacroionPotentialFile(new File(workingDirectory, "macroionPotential.dx")); // SaltCondition noIonsCondition = new SaltCondition(); // noIonsCondition.setName("(no ions)"); // availableIonConditions.add(noIonsCondition); // apbsParameters.setIons(noIonsCondition); pack(); } /** * @param args */ public static void main(String[] args) { // Try to get Windows look and feel on Windows platform // Unless a non-Java look and feel is already selected if (UIManager.getLookAndFeel().getClass().getName().equals(UIManager.getCrossPlatformLookAndFeelClassName())) try { UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() ); } catch (Exception e) {} // Poorly documented new way to make sure that the GUI is created in the Event thread SwingUtilities.invokeLater(new Runnable() { public void run() { // // Build and start the GUI here. // ISIMWrapper isimFrame = new ISIMWrapper(); isimFrame.setVisible(true); // isimFrame.showLicenseDialog(); } }); } public void saltSelected(SaltSelectionEvent event) { SaltCondition condition = event.getSaltCondition(); // Use this as the simulation condition and declare step complete apbsParameters.setIons(condition); System.out.println("Salt selected"); } // set flag indicating test run is active and copy results from // results directory to working directory public void setIsTestRun( int inputIsTestRun, String resultsDirectory, String osName ) { isTestRun = inputIsTestRun; if( (isTestRun > 0) && (resultsDirectory != null) ){ // issue command to copy files from directory containing earliers results // to working directory String[] cpCommand = new String[4]; if( osName.compareTo( "Windows" ) == 0 ){ cpCommand[0] = "C:\\apps\\cygwin\\bin\\cp"; } else { cpCommand[0] = "/bin/cp"; } cpCommand[1] = "-R"; cpCommand[2] = resultsDirectory; cpCommand[3] = workingDirectory.toString(); logDialog.append( "Test run -- copying results from \n" + resultsDirectory + " to working directory \n" + workingDirectory + " using command=<" + cpCommand[0] + " " + cpCommand[1] + ">\n\n" ); ExternalProcessManager cpProcess = new ExternalProcessManager( cpCommand, workingDirectory, null ); cpProcess.start(); try { // wait for it to finish cpProcess.join(); if (cpProcess.exception == null) { logDialog.append("\n\nCopied results from " + cpCommand[2] + " to " + cpCommand[3] + "\n\n"); return; } else { // FAILURE - directory not copied logDialog.append("Results directory not copied: " + cpProcess.exception.toString() + "\n\n" ); } } catch (InterruptedException exc) { logDialog.append("InterruptedException -- Results directory not copied: " + exc.toString() + "\n\n" ); } // if this point is reached, the copy failed; if testRun set to 0, then // APBS and ISIM will be run -- on windows, just copy 'by hand' so want testRun flag // to be set to nonzero value (copy done before the view results button is activated) // isTestRun = 0; return; } } public int isTestRun( ) { return isTestRun; } // Load precomputed excess chemical potential data for ion conditions private void loadIonConditions(String resourceString) { logDialog.append("Loading ion conditions...\n"); ClassLoader classLoader = getClass().getClassLoader(); URL ionXMLURL = classLoader.getResource(resourceString); if (ionXMLURL == null) { JOptionPane.showMessageDialog(this, "Unable to load ion conditions resource XML file " + resourceString); return; } try { availableIonConditionRanges.addRanges(ionXMLURL); } catch (JDOMException exc) { exc.printStackTrace(); } catch (IOException exc) { exc.printStackTrace(); JOptionPane.showMessageDialog(this, "Problem loading ion conditions resource XML file " + resourceString); } logDialog.append("Ion conditions loaded.\n"); } // get logDialog LogDialog getLogDialog( ){ return logDialog; } /** * This method encodes the task dependencies of the kind that might * be specified in a makefile. * */ void createTasks() { loadMacromoleculeTask = new ISIMTask(); loadIonTask = new ISIMTask(); adjustAPBSParametersTask = new ISIMTask(); apbsAndIsimTask = new ISIMTask(); setIsimParameterTask = new ISIMTask(); computeCombinedPotentialTask = new ISIMTask(); viewIonCountsTask = new ISIMTask(); // We need a macromolecule before we compute the macromolecule potential apbsAndIsimTask.addPrerequisite(loadMacromoleculeTask); // computeMacromoleculePotentialTask.addPrerequisite(inspectParametersTask); // Since temperature and permittivity are now part of the ion dialog, APBS depends upon ion step apbsAndIsimTask.addPrerequisite(adjustAPBSParametersTask); // and upon the load Ion task apbsAndIsimTask.addPrerequisite(loadIonTask); // We need a macromolecule before we compute the macromolecule potential // computeMacromoleculePotentialTask.addPrerequisite(loadMacromoleculeTask); // computeMacromoleculePotentialTask.addPrerequisite(inspectParametersTask); // Since temperature and permittivity are now part of the ion dialog, APBS depends upon ion step // computeMacromoleculePotentialTask.addPrerequisite(adjustAPBSParametersTask); // and upon the load Ion task // computeMacromoleculePotentialTask.addPrerequisite(loadIonTask); // The second potential calculation requires both macromolecule and ions computeCombinedPotentialTask.addPrerequisite(loadMacromoleculeTask); computeCombinedPotentialTask.addPrerequisite(adjustAPBSParametersTask); computeCombinedPotentialTask.addPrerequisite(loadIonTask); // ISIM requires the ions, macromolecule, and the first macromolecule potential // computeGCMCPotentialTask.addPrerequisite(loadMacromoleculeTask); // computeGCMCPotentialTask.addPrerequisite(adjustAPBSParametersTask); // computeGCMCPotentialTask.addPrerequisite(loadIonTask); // computeGCMCPotentialTask.addPrerequisite(computeMacromoleculePotentialTask); // viewIonCountsTask.addPrerequisite(computeGCMCPotentialTask); viewIonCountsTask.addPrerequisite(apbsAndIsimTask); // Some tasks are good enough at the start, others need to be performed... loadIonTask.setStatus(DependentTask.READY_FOR_UPDATE, "(no ions)"); // Lack of ions is a reasonable state... adjustAPBSParametersTask.setStatus(DependentTask.CURRENT_AND_COMPLETE, ""); setIsimParameterTask.setStatus(DependentTask.CURRENT_AND_COMPLETE, "Optional"); loadMacromoleculeTask.setStatus(DependentTask.READY_FOR_UPDATE, "(no molecule loaded)"); // computeMacromoleculePotentialTask.setStatus(DependentTask.WAITING_FOR_PREREQUISITES, ""); computeCombinedPotentialTask.setStatus(DependentTask.WAITING_FOR_PREREQUISITES, ""); // computeGCMCPotentialTask.setStatus(DependentTask.WAITING_FOR_PREREQUISITES, ""); apbsAndIsimTask.setStatus(DependentTask.WAITING_FOR_PREREQUISITES, ""); viewIonCountsTask.setStatus(DependentTask.WAITING_FOR_PREREQUISITES, ""); } void createDirectories() { // Create a top level directory String topDirectoryName = "ISIM"; try { File tempDir = File.createTempFile(topDirectoryName, ""); // Turn the normal temp file into a directory if (!tempDir.delete()) throw new IOException("Unable to replace temporary file " + tempDir); if (!tempDir.mkdir()) throw new IOException("Unable to create temporary directory " + tempDir); parentWorkingDirectory = tempDir; workingDirectory = new File(tempDir, "working"); programDirectory = workingDirectory; if (! programDirectory.exists()) if (! programDirectory.mkdir()) throw new IOException("Unable to create program directory " + programDirectory); if (! workingDirectory.exists()) if (! workingDirectory.mkdir()) throw new IOException("Unable to create working directory " + workingDirectory); } catch (IOException exc) { exc.printStackTrace(); System.exit(1); } } void createMenuBar() { // Menus JMenuBar menuBar = new JMenuBar(); JMenu menu = new JMenu("File"); menuBar.add(menu); JMenuItem menuItem; // menuItem = new JMenuItem("Load PQR Structure File..."); // menuItem.addActionListener(loadMoleculeAction); // menu.add(menuItem); menuItem = new JMenuItem("About " + interfaceName + "..."); menuItem.addActionListener(new AboutAction(this)); menu.add(menuItem); menu.add(new JSeparator()); menuItem = new JMenuItem("Save Results"); // menuItem.addActionListener(new SaveAction(this)); menu.add(menuItem); menuItem = new JMenuItem("Quit"); menuItem.addActionListener(new QuitAction(this)); menu.add(menuItem); menu = new JMenu("View"); menuBar.add(menu); menuItem = new JMenuItem("View Log"); menuItem.addActionListener(new ViewLogAction(this)); menu.add(menuItem); menu = new JMenu("Help"); try { menuBar.setHelpMenu(menu); // Not yet implemented error!?!? } catch (java.lang.Error error) { // setHelpMenu seems to be "not yet implemented in java 1.4.2_06 menuBar.add(menu); } menuItem = new JMenuItem("About " + interfaceName + "..."); menuItem.addActionListener(new AboutAction(this)); menu.add(menuItem); menu.add(new JSeparator()); menuItem = new JMenuItem("Web Links:"); menuItem.setEnabled(false); menu.add(menuItem); menuItem = new JMenuItem(" Report a program problem (bug)..."); menuItem.addActionListener(new BrowserLaunchAction ("https://simtk.org/tracker/?func=add&atid=310&group_id=85")); menu.add(menuItem); menuItem = new JMenuItem(" Request a new program feature..."); menuItem.addActionListener(new BrowserLaunchAction ("https://simtk.org/tracker/?func=add&atid=311&group_id=85")); menu.add(menuItem); setJMenuBar(menuBar); } void createStepRows() { // One white container for all step rows JPanel stepsPanel = new JPanel(); stepsPanel.setBackground(Color.WHITE); GridBagLayout layout = new GridBagLayout(); stepsPanel.setLayout(layout); // Small border around outer edge for better white space feel stepsPanel.setBorder(new EmptyBorder(10,10,10,10)); // Put top row of header information ISIMStepRow headerRow = new ISIMStepRow(null, ""); headerRow.setLabels("", "", "Press buttons to perform tasks", "Status"); headerRow.insertButtonRow(stepsPanel, layout, ISIMStepRow.HEADER_ROW); // Create "choose molecule" row chooseMoleculeRow = new ISIMStepRow(loadMacromoleculeTask, "Choose Molecule..."); // chooseMoleculeRow.setLabels("", "(no molecule loaded)", "Choose Molecule...", "No"); chooseMoleculeRow.button.addActionListener(loadMoleculeAction); chooseMoleculeRow.button.setToolTipText("Click this button to begin choosing a macromolecule structure."); chooseMoleculeRow.insertButtonRow(stepsPanel, layout, ISIMStepRow.BUTTON_ROW); chooseMoleculeRow.updateRow(); // // Create "inspect parameters" row // ISIMStepRow paramsRow = new ISIMStepRow(inspectParametersTask, "Inspect parameters..."); // // paramsRow.setLabels("Temperature, Permittivity, etc. ", "", "Inspect parameters...", "Yes"); // // paramsRow.insertWithButton(stepsPanel, layout); // paramsRow.button.addActionListener(new InspectParametersAction(apbsParameters, this)); // paramsRow.updateRow(); // ClassLoader classLoader = getClass().getClassLoader(); Icon computerIcon = new ImageIcon(classLoader.getResource("resources/images/ComputerIcon.png")); // Create "choose ions" row ISIMStepRow ionsRow = new ISIMStepRow(loadIonTask, "Choose ion conditions..."); // ionsRow.setLabels("", "(no ions selected)", "Choose ion conditions...", "Yes"); ionsRow.insertButtonRow(stepsPanel, layout, ISIMStepRow.BUTTON_ROW); ionsRow.button.addActionListener(new ChooseIonsAction(ionDialog)); ionsRow.button.setToolTipText("Click this button to begin choosing dissolved ions."); ionsRow.updateRow(); // Create "Set simulation parameters" row ISIMStepRow simulationParameters = new ISIMStepRow( setIsimParameterTask, "Set Simulation Parameters"); // ionsRow.setLabels("", "(no ions selected)", "Choose ion conditions...", "Yes"); simulationParameters.insertButtonRow( stepsPanel, layout, ISIMStepRow.BUTTON_ROW ); simulationParameters.button.addActionListener(new SetParameterAction( isimParameterDialog) ); simulationParameters.button.setToolTipText("Set Simulation parameters."); simulationParameters.updateRow(); // Create "compute Poisson-Boltzman potential" row // apbsSimulateRow = new ISIMStepRow(apbsAndIsimTask, "Simulate Ions Apbs" ); // apbsSimulateRow.insertButtonRow(stepsPanel, layout, ISIMStepRow.BUTTON_ROW); // apbsSimulateRow.button.addActionListener(new SimulateIons(this)); // apbsSimulateRow.button.setIcon(computerIcon); // apbsSimulateRow.button.setToolTipText("Solve Poisson's Equation (APBS).\n WARNING: This might take several minutes."); // apbsSimulateRow.updateRow(); // Create "compute Poisson-Boltzman potential" row isimSimulateRow = new ISIMStepRowWithProgressFile(apbsAndIsimTask, "Simulate Ions Isim", this ); isimSimulateRow.insertButtonRow(stepsPanel, layout, ISIMStepRow.BUTTON_ROW); isimSimulateRow.button.addActionListener(new SimulateIons(this)); isimSimulateRow.button.setIcon(computerIcon); isimSimulateRow.button.setToolTipText("Perform GCMC simulation (ISIM).\n WARNING: This might take several minutes."); isimSimulateRow.updateRow(); // Create "compute Poisson-Boltzman potential" row // apbsRow = new ISIMStepRow(computeMacromoleculePotentialTask, "Compute macromolecule field (without ions)"); // apbsRow.insertButtonRow(stepsPanel, layout, ISIMStepRow.BUTTON_ROW); // apbsRow.button.addActionListener(new ComputeMoleculeAPBS(this)); // apbsRow.button.setIcon(computerIcon); // apbsRow.button.setToolTipText("Compute nonlinear Poisson-Boltzmann potential (APBS).\nWARNING: This might take a few minutes."); // apbsRow.updateRow(); // Create "compute Poisson-Boltzman potential" row //ISIMStepRow apbsCombinedRow = new ISIMStepRow(computeCombinedPotentialTask, "Compute combined field"); // apbsCombinedRow.setLabels("Poisson-Boltzmann Potential (APBS)", "", "Compute combined field", "No"); // apbsCombinedRow.insertWithButton(stepsPanel, layout); // apbsCombinedRow.button.addActionListener(new ComputeMoleculeAPBS(this)); // apbsCombinedRow.button.setIcon(computerIcon); // apbsCombinedRow.updateRow(); // Create "compute GCMC potential" row // isimCombinedRow = new ISIMStepRow(computeGCMCPotentialTask, "Compute GCMC combined field"); // isimCombinedRow.setLabels("", "", "Compute GCMC combined field", "No"); // isimCombinedRow.insertButtonRow(stepsPanel, layout, ISIMStepRow.BUTTON_ROW); // isimCombinedRow.button.addActionListener(new ComputeISIM(this)); // isimCombinedRow.button.setIcon(computerIcon); // isimCombinedRow.button.setToolTipText("Compute Grand Canonical Monte Carlo ion distribution (ISIM).\nWARNING: This might take a few minutes."); // isimCombinedRow.updateRow(); // Create "view ion counts" row viewIonCountsRow = new ISIMStepRow(viewIonCountsTask, "View results"); viewIonCountsRow.insertButtonRow(stepsPanel, layout, ISIMStepRow.BUTTON_ROW); viewIonCountsRow.button.addActionListener(new ViewIonCountsAction(this)); viewIonCountsRow.button.setToolTipText("Click to see summary of ion simulation results."); viewIonCountsRow.updateRow(); getContentPane().add(stepsPanel); // Create help for all step rows chooseMoleculeRow.setHelpText( "" + programName + " Help: Load Molecule step" , "You must choose a molecule about which to compute the ionic\n" + "environment. Usually this molecule is RNA, DNA, or protein\n" + "\n"+ "Press the \"Choose Molecule\" Button to load a macromolecular\n" + "structure file. The file can be either in Protein Data Bank\n" + "(PDB) format, or in PQR format. PQR format contains partial\n" + "charge information for each atom, while PDB format does not.\n" , this ); ionsRow.setHelpText( "" + programName + " Help: Selected dissolved ions step" , "Select the set of dissolved ions in the solution. Concentrations\n" + "are specified in units of millimoles per liter (mM). Other parameters\n" + "include temperature, permittivity of the solvent, and permittivity of\n" + "the macroion. Excess chemical potentials for each ionic condition\n" + "are expensive to calculate, so they are precomputed.\n" , this ); if( apbsSimulateRow != null ){ apbsSimulateRow.setHelpText( "" + programName + " Help: Compute macromolecule field step" , "First, computes the macromolecule electrostatic field using\n" + "APBS; then simulates ion positions using ISIM.\n" , this ); } isimSimulateRow.setHelpText( "" + programName + " Help: Compute macromolecule field step" , "First, computes the macromolecule electrostatic field using\n" + "APBS; then simulates ion positions using ISIM.\n" , this ); // apbsRow.setHelpText( // "" + programName + " Help: Compute macromolecule field step" // , // "Computes the electrostatic field around the macromolecule using\n" + // "the Poisson Boltzmann equation. This step\n" + // "does not include the dissolved ions in the field calculation, but is\n" + // "required for the later GCMC calculation step. The field caculation is\n" + // "performed using the program APBS.\n" // , // this // ); // isimCombinedRow.setHelpText( // "" + programName + " Help: Compute complete field step" // , // "Computes the electrostatic field around the macromolecule using\n" + // "a Grand Canonical Monte Carlo (GCMC) method. This step\n" + // "includes both the macromolecule and the dissolved ions in the field\n"+ // "calculation. The calculation is performed using the program ISIM.\n" // , // this // ); viewIonCountsRow.setHelpText( "" + programName + " Help: View ion counts" , "'View ion counts' displays a table summarizing the average number\n" + "of ions in the simulation, compared to the number expected had the\n" + "macroion been absent. The difference counts can be thought of as\n" + "'salt ions associated with the macromolecule'\n" , this ); } String errorMessage; MoleculeAcquisitionMethodDialog moleculeAcquisitionMethodDialog = null; void askUserToChooseAMolecule() { if (moleculeAcquisitionMethodDialog == null) moleculeAcquisitionMethodDialog = new ISIMLoadMoleculeDialog(this, null); moleculeAcquisitionMethodDialog.setVisible(true); } void convertPDBToPQR(File pdbFile) { String convertMessage = "Converting PDB format structure file "+pdbFile+" to PQR format...\n"; appendToLog(convertMessage); // Run this outside of the event thread PDBToPQRThread thread = new PDBToPQRThread( new ISIMStepParameters(programDirectory, workingDirectory, loadMacromoleculeTask ), apbsParameters, pdbFile, this ); thread.start(); // Attach progress monitor to conversion thread ProgressDialog progressDialog = chooseMoleculeRow; loadMacromoleculeTask.setStatus(DependentTask.ACTIVELY_UPDATING, "Converting to PQR format"); ProgressManager progressManager; assert(progressDialog != null); if (progressDialog == null) progressManager = new ProgressManager( thread, this, convertMessage); else progressManager = new ProgressManager(thread, progressDialog); progressManager.start(); } void measureStructureSize (File pqrFile) { String convertMessage = "Measuring size of molecule in file "+pqrFile+"...\n"; appendToLog(convertMessage); // Run this outside of the event thread RunPsizeThread thread = new RunPsizeThread( new ISIMStepParameters(programDirectory, workingDirectory, loadMacromoleculeTask ), apbsParameters, pqrFile, this ); thread.start(); // Attach progress monitor to conversion thread ProgressDialog progressDialog = chooseMoleculeRow; loadMacromoleculeTask.setStatus(DependentTask.ACTIVELY_UPDATING, "Measuring molecule size"); ProgressManager progressManager; assert(progressDialog != null); if (progressDialog == null) progressManager = new ProgressManager( thread, this, convertMessage); else progressManager = new ProgressManager(thread, progressDialog); progressManager.start(); } public void setPqrFile(File pqrFile) { // ATOM 7948 H21 G 414 38.623 26.597 22.182 0.3200 0.2245 // X Y Z CHARGE RADIUS // 0000000001111111111222222222233333333334444444444555555555566666666667 // 1234567890123456789012345678901234567890123456789012345678901234567890 Pattern pqrAtomPattern = Pattern.compile("^(ATOM .{57})([0-9 ][0-9]\\.[0-9]{4})\\s*$"); DecimalFormat radiusFormat = new DecimalFormat(" 0.0000"); // Expand radii by 1.4 Angstroms, to match method in Mark E.'s thesis File expandedDir = new File(workingDirectory, "expanded"); expandedDir.mkdir(); File expandedPqr = new File(expandedDir, pqrFile.getName()); double radiusIncrement = 1.40; try { // Copies src file to dst file. // If the dst file does not exist, it is created BufferedReader in = new BufferedReader(new InputStreamReader(new FileInputStream(pqrFile))); PrintStream out = new PrintStream(expandedPqr); String pqrLine; while ((pqrLine = in.readLine()) != null) { Matcher matcher = pqrAtomPattern.matcher(pqrLine); if (matcher.matches()) { out.print(matcher.group(1)); // TODO modify radius double radius = new Double(matcher.group(2)); radius += radiusIncrement; out.println(radiusFormat.format(radius)); } else { // Not an atom line? -- send through unmolested out.println(pqrLine); } } in.close(); out.close(); } catch (IOException exc) { appendToLog("!!!ERROR creating PQR file with solvent expanded radii"); appendToLog(" Using unexpanded file instead."); expandedPqr = pqrFile; } // Run psize.py on the molecule to get the molecule dimensions measureStructureSize(expandedPqr); // moleculeFile should already be in PQR format apbsParameters.setPqrInputFile(expandedPqr); // loadMacromoleculeTask.dataDescription = pqrFile.getName(); // loadMacromoleculeTask.setStatus(DependentTask.CURRENT_AND_COMPLETE, pqrFile.getName()); appendToLog("Using molecule structure file " + expandedPqr + "\n"); } /** * Routine to recursively delete a directory and its contents. * Adapted from http://joust.kano.net/weblog/archives/000071.html * Note that this routine could be very dangerous. * * @param dir * @return Returns "true" on success, "false" otherwise */ private static boolean recursiveDeleteDir(File dir) { if (dir == null) return false; // to see if this directory is actually a symbolic link to a directory, // we want to get its canonical path - that is, we follow the link to // the file it's actually linked to File candir; try { candir = dir.getCanonicalFile(); } catch (IOException e) { return false; } // TODO - but this does not work on Windows // (distinguishing between symbolic links and real files) // getAbsoluteFile() returns a File with shortened names, e.g. "C:\DOCUME~1\CHRIST~1\LOCALS~1\Temp\ISIM58047" // getCanonicalFile() returns expanded names, e.g. "C:\Documents and Settings\Christopher Bruns\Local Settings\Temp\ISIM58047" // The File.equals(File) method returns *false* between these two cases // (It should return *true*) // File absdir = dir.getAbsoluteFile(); // a symbolic link has a different canonical path than its actual path, // unless it's a link to itself // if (! (candir.equals(absdir)) ) { // this file is a symbolic link, and there's no reason for us to // follow it, because then we might be deleting something outside of // the directory we were told to delete // return false; // } // Warning: there is a possible race condition here, if the file becomes // a symbolic link after the above check, but before the delete. // now we go through all of the files and subdirectories in the // directory and delete them one by one File[] files = candir.listFiles(); if (files != null) { for (int i = 0; i < files.length; i++) { File file = files[i]; // in case this directory is actually a symbolic link, or it's // empty, we want to try to delete the link before we try // anything boolean deleted = file.delete(); if (!deleted) { // deleting the file failed, so maybe it's a non-empty // directory if (file.isDirectory()) recursiveDeleteDir(file); // otherwise, there's nothing else we can do } } } // now that we tried to clear the directory out, we can try to delete it // again return dir.delete(); } /** * Routine to delete a directory and its contents. * Adapted from http://joust.kano.net/weblog/archives/000071.html * This is meant to be safer than the recursiveDeleteDir() method, because * It does not recursively follow subdirectories. * It is intended to remove symbolic links in the dirctory, but not the * targets of those links. * This method will fail (and return false) if the argument directory * returns false. In this case the contents of the directory may only * be partially removed. * * @param dir * @return Returns "true" on success, "false" otherwise */ private static boolean deleteDir(File dir) { if (dir == null) return false; File absdir = dir.getAbsoluteFile(); // now we go through all of the files and subdirectories in the // directory and delete them one by one File[] files = absdir.listFiles(); if (files != null) { for (int i = 0; i < files.length; i++) { File file = files[i]; // in case this directory is actually a symbolic link, or it's // empty, we want to try to delete the link before we try // anything // boolean deleted = file.delete(); file.delete(); // Note: non-empty directories do not get deleted. This is the price // of relative safety compared to recursiveDeleteDir } } // now that we tried to clear the directory out, we can try to delete it // again return dir.delete(); } /** * Delete working area and all files therein * */ private void destroyAllOfMyBeautifulWork() { boolean deleteSucceeded = true; // Start optimistic // First remove inner working directory logDialog.append("Deleting " + workingDirectory + "...\n"); if (! deleteDir(workingDirectory)) deleteSucceeded = false; // Then remove top level working directory, i.e. the resulte of createTempFile() logDialog.append("Deleting " + parentWorkingDirectory + "...\n"); if (! deleteDir(parentWorkingDirectory)) deleteSucceeded = false; if (deleteSucceeded) logDialog.append("Delete succeeded.\n"); else logDialog.append("Delete failed.\n"); } void cleanUpAndExit() { destroyAllOfMyBeautifulWork(); System.exit(0); } public void appendToLog(String logMessage) { logDialog.append(logMessage); } public void showLicenseDialog() { // TODO - put actual licenses in help menu final String licenseText = "" +interfaceName + " version " + isimInterfaceVersion + "\n" +"\n" +interfaceName + " is a Java graphical user interface that runs \n" +"the programs ABPS and ISIM.\n" +"\n" +"The " + interfaceName + " Java application is distributed under an \n" +"MIT open source license (see Documentation).\n" +"\n" +"APBS (Adaptive Poisson Boltzmann Solver) is available from \n" +"http://apbs.sourceforge.net/\n" +"\n" +"ISIM (Ion Simulator) is available from \n" +"http://mccammon.ucsd.edu/isim/" ; JOptionPane.showMessageDialog(this, licenseText, interfaceName + " Licence", JOptionPane.INFORMATION_MESSAGE); } class BrowserLaunchAction implements ActionListener { String urlString; BrowserLaunchAction(String u) {urlString = u;} public void actionPerformed(ActionEvent e) { URL url; try {url = new URL(urlString);} catch (MalformedURLException exc) { // Show information dialog, so the savvy user will be able to // go to the url manually, in case the browser open fails. JOptionPane.showConfirmDialog( ISIMWrapper.this, "Problem opening browser to page " + urlString + "\n" + exc, "!!! Error opening web browser !!!", JOptionPane.DEFAULT_OPTION, JOptionPane.ERROR_MESSAGE ); return; } try { // This only works when started in a web start application BasicService bs = (BasicService)ServiceManager.lookup("javax.jnlp.BasicService"); bs.showDocument(url); } catch (UnavailableServiceException exc) { // launchErrorConfirmDialog("Problem opening browser to page " + urlString + "\n" + exc, // "JNLP Error!"); try {BrowserLauncher.openURL(urlString);} catch (IOException exc2) { JOptionPane.showConfirmDialog( ISIMWrapper.this, "Problem opening browser to page " + urlString + "\n" + exc, "!!! Error opening web browser !!!", JOptionPane.DEFAULT_OPTION, JOptionPane.ERROR_MESSAGE ); } } } } // accessor for apbs parameters class public APBSParameters getApbsParameters( ){ return apbsParameters; } // accessor for isim parameters class public ISIMParameters getIsimParameters( ){ return isimParameters; } } class ViewLogAction implements ActionListener { ISIMWrapper parentFrame; public ViewLogAction(ISIMWrapper parentFrame) { this.parentFrame = parentFrame; } public void actionPerformed(ActionEvent e) { parentFrame.logDialog.setLocationRelativeTo(parentFrame); parentFrame.logDialog.setVisible(true); } } class AboutAction implements ActionListener { ISIMWrapper parentFrame; public AboutAction(ISIMWrapper parentFrame) { this.parentFrame = parentFrame; } public void actionPerformed(ActionEvent e) { JOptionPane.showMessageDialog( parentFrame, "" + parentFrame.interfaceName + " version " + parentFrame.isimInterfaceVersion + "\n" + "created by Christopher Bruns at SimTK.org\n" + "Includes binary executables for APBS and ISIM (see documentation).", "About " + parentFrame.interfaceName, JOptionPane.PLAIN_MESSAGE); } } //class ComputeISIM implements ActionListener { // ISIMWrapper parentFrame; // // public ComputeISIM(ISIMWrapper parent) { // this.parentFrame = parent; // } // // public void actionPerformed(ActionEvent e) { // RunISIMThread thread = // new RunISIMThread( // new ISIMStepParameters(parentFrame.programDirectory, // parentFrame.workingDirectory, // parentFrame.computeGCMCPotentialTask), // parentFrame.apbsParameters, // parentFrame // ); // thread.start(); // // // And another process to monitor the download process // ProgressDialog progressDialog = parentFrame.isimCombinedRow; // ProgressManager progressManager = new ProgressManager(thread, progressDialog); // progressManager.start(); // } //} /** * * @author Christopher Bruns * * SimulateIons combines functions of ComputeMoleculeAPBS and ComputeISIM */ class SimulateIons implements ActionListener { ISIMWrapper parentFrame; public SimulateIons(ISIMWrapper parent) { parentFrame = parent; } public void actionPerformed(ActionEvent e) { SimulateIonsThread thread = new SimulateIonsThread( new ISIMStepParameters(parentFrame.programDirectory, parentFrame.workingDirectory, parentFrame.apbsAndIsimTask), parentFrame.apbsParameters, parentFrame); thread.start(); // And another process to monitor the download process ProgressDialog progressDialog = parentFrame.isimSimulateRow; ProgressManager progressManager = new ProgressManager(thread, progressDialog); progressManager.start(); } } //class ComputeMoleculeAPBS implements ActionListener { // ISIMWrapper parentFrame; // // public ComputeMoleculeAPBS(ISIMWrapper parent) { // parentFrame = parent; // } // // public void actionPerformed(ActionEvent e) { // // RunAPBSThread thread = // new RunAPBSThread( // new ISIMStepParameters(parentFrame.programDirectory, // parentFrame.workingDirectory, // parentFrame.computeMacromoleculePotentialTask), // parentFrame.apbsParameters, // parentFrame); // thread.start(); // // // And another process to monitor the download process // ProgressDialog progressDialog = parentFrame.apbsRow; // ProgressManager progressManager = new ProgressManager(thread, progressDialog); // progressManager.start(); // // } //} class ViewIonCountsAction implements ActionListener { ISIMWrapper parentFrame; IonCountDialog ionCountDialog; ViewIonCountsAction(ISIMWrapper parentFrame) { this.parentFrame = parentFrame; ionCountDialog = new IonCountDialog(parentFrame); } public void actionPerformed(ActionEvent e) { // Show the user the ion table try { // Set start time of view counts action parentFrame.viewIonCountsTask.setStatus(DependentTask.ACTIVELY_UPDATING, ""); ionCountDialog.loadAllIonCounts(); ionCountDialog.setLocationRelativeTo(parentFrame); ionCountDialog.setVisible(true); // Mark view action complete parentFrame.viewIonCountsTask.setStatus(DependentTask.CURRENT_AND_COMPLETE, ""); } catch (IOException exc) { exc.printStackTrace(); // TODO problem reading ion information files } } } class LoadMoleculeAction implements ActionListener { ISIMWrapper parentFrame; LoadMoleculeAction(ISIMWrapper parent) { parentFrame = parent; } public void actionPerformed(ActionEvent e) { parentFrame.askUserToChooseAMolecule(); } } class QuitAction implements ActionListener { ISIMWrapper isimWrapper; QuitAction(ISIMWrapper isimWrapper) { this.isimWrapper = isimWrapper; } public void actionPerformed(ActionEvent e) { isimWrapper.cleanUpAndExit(); } } //class InspectParametersAction implements ActionListener { // APBSParameters parameters; // ParameterDialog dialog; // JFrame parentFrame; // // InspectParametersAction(APBSParameters p, JFrame parent) { // parameters = p; // parentFrame = parent; // } // // public void actionPerformed(ActionEvent e) { // if (dialog == null) { // dialog = new ParameterDialog(parameters, parentFrame); // } // dialog.setVisible(true); // } //} class ChooseIonsAction implements ActionListener { IonSelectionDialog ionDialog; ChooseIonsAction(IonSelectionDialog ionDialog) { this.ionDialog = ionDialog; } public void actionPerformed(ActionEvent e) { ionDialog.setVisible(true); } } class SetParameterAction implements ActionListener { IsimParameterDialog isimParameterDialog; SetParameterAction( IsimParameterDialog ionDialog) { this.isimParameterDialog = ionDialog; } public void actionPerformed(ActionEvent e) { isimParameterDialog.setVisible(true); } } class IsimTextField extends JTextField { static int fixedLabelLength = 50; static int fixedTextLength = 10; /** * */ private static final long serialVersionUID = 1L; private JLabel label = null; GridBagConstraints constraints = new GridBagConstraints(); IsimTextField( String labelString, String initialValue, Container jPanel, int rowIndex, GridBagLayout gridBagLayout ){ constraints.anchor = GridBagConstraints.EAST; constraints.gridwidth = GridBagConstraints.RELATIVE; //next-to-last constraints.fill = GridBagConstraints.NONE; constraints.gridy = rowIndex; constraints.weightx = 0.0; //reset to default JPanel rowPanel = new JPanel(); jPanel.add( rowPanel ); // rowPanel.setLayout( new BoxLayout( rowPanel, BoxLayout.X_AXIS) ); gridBagLayout.setConstraints( rowPanel, constraints ); if( labelString != null ){ /* if( labelString.length() < fixedLabelLength ){ StringBuffer newLabel = new StringBuffer( labelString ); while( newLabel.length() < fixedLabelLength ){ newLabel.append( " " ); } labelString = newLabel.toString(); } */ label = new JLabel( labelString, RIGHT ); System.out.println( "Label: " + labelString + " " + labelString.length() ); if( rowPanel != null ){ rowPanel.add( label, constraints ); } label.setLabelFor( this ); } if( initialValue != null ){ setText( initialValue ); } if( rowPanel != null ){ constraints.gridwidth = GridBagConstraints.REMAINDER; //end row constraints.fill = GridBagConstraints.HORIZONTAL; constraints.weightx = 1.0; rowPanel.add( this, constraints ); } setColumns( fixedTextLength ); } } class IntegerTextField extends IsimTextField { private static final long serialVersionUID = 1L; final static String badchars = "`~!@#$%^&*()_+=\\|\"':;?/>.<, "; IntegerTextField( String labelString, int initialValue, Container jPanel, int rowIndex, GridBagLayout gridBagLayout ){ super( labelString, Integer.toString( initialValue ), jPanel, rowIndex, gridBagLayout ); } public void processKeyEvent(KeyEvent keyEvent ) { char c = keyEvent.getKeyChar(); if( (Character.isLetter(c) && !keyEvent.isAltDown()) || badchars.indexOf(c) > -1 ){ keyEvent.consume(); return; } if( c == '-' && getDocument().getLength() > 0 ){ keyEvent.consume(); } else { super.processKeyEvent(keyEvent); } } } class DoubleTextField extends IsimTextField { private static final long serialVersionUID = 1L; final static String badchars = "`~!@#$%^&*()_+=\\|\"':;?/><, "; DoubleTextField( String labelString, double initialValue, Container jPanel, int rowIndex, GridBagLayout gridBagLayout ){ super( labelString, Double.toString( initialValue ), jPanel, rowIndex, gridBagLayout ); } public void processKeyEvent(KeyEvent keyEvent ) { char c = keyEvent.getKeyChar(); if( ( (Character.isLetter(c) && c != 'e' && c != 'E') && !keyEvent.isAltDown()) || badchars.indexOf(c) > -1 ){ keyEvent.consume(); return; } super.processKeyEvent(keyEvent); } } // Interface in which to view and control the parameters class IsimParameterDialog extends JDialog implements ActionListener { public static final long serialVersionUID = 01L; APBSParameters apbsParameters; ISIMParameters isimParameters; LogDialog logDialog; JButton doneButton = new JButton("Done"); DoubleTextField temperatureTextFieldD, solventPermittivityTextFieldD, moleculePermittivityTextFieldD; IntegerTextField randomSeedTextFieldI, totalMonteCarloStepsI; IsimParameterDialog( APBSParameters inputApbsParameters, ISIMParameters inputIsimParameters, JFrame parentFrame, LogDialog inputLogDialog ) { super( parentFrame, "Simulation Parameters" ); setLocationRelativeTo(parentFrame); logDialog = inputLogDialog; apbsParameters = inputApbsParameters; isimParameters = inputIsimParameters; GridBagLayout layout = new GridBagLayout(); getContentPane().setLayout( layout ); // Text at the top of the dialog // JPanel headerPanel = new JPanel(); // headerPanel.add(new JLabel("Simulation parameters")); // getContentPane().add(headerPanel); int rowIndex = 0; //temperatureTextFieldD = new DoubleTextField( " Temperature(\u00B0K) ", // apbsParameters.getTemperature(), getContentPane(), rowIndex++, layout ); // solventPermittivityTextFieldD = new DoubleTextField( " Relative Solvent Permittivity ", // apbsParameters.getSolventPermittivity(), getContentPane(), rowIndex++, layout ); randomSeedTextFieldI = new IntegerTextField( " Random Number Generator Seed ", isimParameters.getRandomSeed(), getContentPane(), rowIndex++, layout ); totalMonteCarloStepsI = new IntegerTextField( " Monte Carlo Steps ", isimParameters.getTotalMonteCarloSteps(), getContentPane(), rowIndex++, layout ); moleculePermittivityTextFieldD = new DoubleTextField( " Macromolecule Permittivity ", apbsParameters.getMoleculePermittivity(), getContentPane(), rowIndex++, layout ); GridBagConstraints constraints = new GridBagConstraints(); constraints.gridwidth = 1; constraints.ipadx = 50; constraints.gridx = 0; constraints.gridy = rowIndex++; // Buttons JPanel buttonPanel = new JPanel(); buttonPanel.add( doneButton); doneButton.addActionListener(this); getContentPane().add( buttonPanel, constraints ); this.pack(); } // Capture button events and parameter change events here boolean automaticDisplayUpdating = false; public void actionPerformed(ActionEvent event) { if (event.getSource() == doneButton) { setVisible(false); // apbsParameters.setTemperature( (new Double((String) temperatureTextFieldD.getText())).doubleValue() ); // apbsParameters.setSolventPermittivity((new Double((String) solventPermittivityTextFieldD.getText())).doubleValue() ); apbsParameters.setMoleculePermittivity( (new Double((String) moleculePermittivityTextFieldD.getText())).doubleValue() ); isimParameters.setRandomSeed( (new Integer((String) randomSeedTextFieldI.getText())).intValue() ); isimParameters.setTotalMonteCarloSteps( (new Integer((String) totalMonteCarloStepsI.getText())).intValue() ); // logDialog.append( "T=" + temperatureTextFieldD.getText() + "\n" ); // logDialog.append( "solventPerm=" + solventPermittivityTextFieldD.getText() + "\n" ); logDialog.append( " molPerm=" + moleculePermittivityTextFieldD.getText() + "\n" ); logDialog.append( " MC steps=" + totalMonteCarloStepsI.getText() + "\n" ); logDialog.append( "randomSeed=" + randomSeedTextFieldI.getText() + "\n" ); } } } class ISIMLoadMoleculeDialog extends MoleculeAcquisitionMethodDialog { ISIMWrapper parentFrame; ISIMLoadMoleculeDialog(ISIMWrapper frame, ProgressDialog progressDialog) { super(frame, progressDialog); this.parentFrame = frame; setTitle("Choose Molecule (" + parentFrame.programName + ")"); setLocationRelativeTo(parentFrame); this.setDefaultPdbId("1GRZ"); // Default to an RNA structure } static final long serialVersionUID = 01L; public void readStructureFromMoleculeCollection(MoleculeCollection molecules) { // Do nothing, we want files, not molecules, for this wrapper // This function should never even be called, if we override handleMoleculeURL properly } // Override handleMoleculeURL to manipulate files instead of loading molecules protected void handleMoleculeUrl(URL url) throws IOException { parentFrame.loadMacromoleculeTask.setStatus(DependentTask.ACTIVELY_UPDATING, "Loading molecule..."); String loadingMessage = "Loading structure from " + url + "..."; parentFrame.appendToLog("\n" + loadingMessage + "\n"); CopyPdbFileProcess copyFileProcess = new CopyPdbFileProcess(url, fileLoadObservable); copyFileProcess.start(); // And another process to monitor the download process ProgressDialog progressDialog = parentFrame.chooseMoleculeRow; ProgressManager progressManager; if (progressDialog == null) progressManager = new ProgressManager( copyFileProcess, parentFrame, loadingMessage); else progressManager = new ProgressManager(copyFileProcess, progressDialog); progressManager.start(); } boolean isPDBFile(String fileName) { // Determine file type from the name if (fileName == null) return false; String name = fileName.toLowerCase(); if ( name.endsWith(".pdb") ) return true; if ( name.endsWith(".pdb1") ) return true; if ( name.endsWith(".pdb2") ) return true; if ( name.endsWith(".ent") ) return true; if ( name.endsWith(".brk") ) return true; if ( name.toLowerCase().endsWith(".pqr") ) return false; if ( name.toLowerCase().indexOf(".pqr") >= 0 ) return false; if ( name.toLowerCase().indexOf(".pdb") >= 0 ) return true; return false; } class CopyPdbFileProcess extends LoadPdbUrlProcess { CopyPdbFileProcess(URL url, SimpleObservable loadMoleculeObservable) { super(url, loadMoleculeObservable); } // Override loadMolecules to create a file instead of loading a molecule protected void loadMolecules() throws IOException, InterruptedException { InputStream inStream = getInputStream(); // Determine file name String fileName = this.url.getFile(); // strip off all but the file name (no path) int pathEnd = fileName.lastIndexOf("/"); if (pathEnd >= 0) fileName = fileName.substring(pathEnd + 1); // Remove compression suffixes from file name fileName = fileName.replaceAll("\\.Z$", ""); fileName = fileName.replaceAll("\\.gz$", ""); // Create local file of molecular structure File outputFile = new File(parentFrame.workingDirectory, fileName); OutputStream outStream = new FileOutputStream(outputFile); // StreamCopy.copy(inStream, outStream); BufferedReader reader = new BufferedReader(new InputStreamReader(inStream)); BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(outStream)); String line; while ( (line = reader.readLine()) != null) { // Skip empty lines if (line.length() < 20) continue; // Remove water molecules if (line.substring(17,20).equals("HOH")) continue; if (line.substring(17,20).equals("WAT")) continue; if (line.substring(17,20).equals("H2O")) continue; // Remove records that confuse PDB2PQR if (line.substring(0,5).equals("LINK ")) continue; if (line.substring(0,5).equals("SITE ")) continue; writer.write(line); writer.write("\n"); } writer.flush(); inStream.close(); outStream.close(); // 2 - if PDB format, convert to PQR if (isPDBFile(fileName)) { parentFrame.convertPDBToPQR(outputFile); } else { parentFrame.setPqrFile(outputFile); } reactivate(); } } }