Package jSimMacs.gromacsrun

Examples of jSimMacs.gromacsrun.GromacsRun

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    List<String> command = GromacsCommandBuilder.getInstance()
        .createMakeNdxCommand(frame.getGTab().getFilePath(),
            frame.getGTab().getProjectLocation(), fileName);
    List<String> selectionCommand = GromacsCommandBuilder.getInstance()
        .createNdxSelectionCommand(atomSelection);
    GromacsRun gromacsRun = GromacsRunFactory.getGromacsRun(frame.getGTab()
        .getProjectLocation(), frame.getGTab().getRemoteProject());
    try {
      List<String> renameCommand = gromacsRun.make_ndx(command,
          selectionCommand, groupName);
      command = GromacsCommandBuilder.getInstance()
          .createMakeNdxRenameCommand(frame.getGTab().getFilePath(),
              frame.getGTab().getProjectLocation(), fileName);
      gromacsRun.renameNdxGroup(command, renameCommand);

    } catch (IOException e) {
      JOptionPane.showMessageDialog(frame, e.getMessage(), "Run error",
          JOptionPane.ERROR_MESSAGE);
      e.printStackTrace();
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      helperStream =  new TextAreaOutputStream(frame.getNewMessageBox(
          project.getName(), command.get(0)));
    }
    OutputStream outStream = getOutputStream(project.getName(), command.get(0), helperStream);

    GromacsRun gromacsRun = GromacsRunFactory.getGromacsRun(project
        .getLocation(), project);

    try {
      gromacsRun.startGromacsProgram(command, outStream, interactive, helperStream);
    } catch (IOException e) {
      JOptionPane.showMessageDialog(frame, e.getMessage(), "Run error",
          JOptionPane.ERROR_MESSAGE);
      e.printStackTrace();
    }
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      helperStream =  new TextAreaOutputStream(frame.getNewMessageBox(
          project.getName(), commandName));
    }
   
    OutputStream outStream = getOutputStream(project.getName(), commandName, helperStream);
    GromacsRun gromacsRun = GromacsRunFactory.getGromacsRun(project
        .getLocation(), project);

    try {
      gromacsRun.startGromacsProgram(command, outStream, interactive, helperStream);
    } catch (IOException e) {
      JOptionPane.showMessageDialog(frame, e.getMessage(), "Run error",
          JOptionPane.ERROR_MESSAGE);
      e.printStackTrace();
    }
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Related Classes of jSimMacs.gromacsrun.GromacsRun

  • jSimMacs.logic.JSimLogic
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