/*
 ----------------------------------------------------------------------------
 "THE BEER-WARE LICENSE" (Revision 42):
 <dkratzert@gmx.de> wrote this file. As long as you retain
 this notice you can do whatever you want with this stuff. If we meet some day,
 and you think this stuff is worth it, you can buy me a beer in return.
 Daniel Kratzert
 ----------------------------------------------------------------------------
*/

//#include "bits/stdc++.h"
#include <QtGui>
#include <QDir>
#include <QNetworkAccessManager>
#include "dsrgui.h"
#include "window.h"
#include "dsrglwindow.h"
#include "dsreditwindow.h"
#include "deprecation.h"
#include "itsme.h"

#if defined(Q_OS_WIN) || defined(Q_WS_WIN32)
   static const QString mysystem = "win";
#else
   static const QString mysystem = "unix";
#endif

/*
Explanations

- This GUI is for DSR https://dkratzert.de/dsr.html
- DSR stores the information for pre-defined molecular fragments and their
  restraints in a text database in $DSR_DB_DIR.
- This GUI uses that information to provide a convenient interface for DSR.
- DSR is controlled by a special command in the SHELXL res file starting with REM DSR ...
  and by commandline options.
- A special command line option -ah tells DSR to print the information about a
  fragment in a special format for this GUI.
  It is a list of html-like tags <tag> data </tag> with ;; separated values containing for
  example the unit cell information and coordinates of the fragment. The first line
  contains the version number of DSR.
- The GUI first runs dsr with -lc to get a list of all fragment names in the database.
  A mouse click on a fragment in the list invokes "dsr -ah name" to get the details of
  the selected fragment (and stores it in struct DSRMol). This details are also used to
  edit the fragment ("edit fragment" button).
- The text widget below the search field displays some status output from DSR,
  especially the text output from DSR during the fragment transfer/fit to the target structure.

- merging: go into shelxle-kratzert and svn merge -r 165:HEAD /Users/daniel/Downloads/shelxle-trunk
       "-r (latest own commit):HEAD"    svn merge -r 165:HEAD d:\downloads\shelxle-svn\trunk
*/


/*
 * TODO:
*/


DSRGui::DSRGui(Molecule *mole, QString shelxlPath, Window *parent): QWidget(parent) {
  m_shelxle = parent;
  m_molecule = mole;
  m_shelxlPath = shelxlPath;
  this->setWindowFlags(Qt::Window|Qt::WindowStaysOnTopHint);
  //printf("I am DSR and this are my flags:%d\n",windowFlags ());
  setWindowTitle(QString(tr("DSR GUI")));
  if (mysystem == QString("win")) {
    dsrpath = getDSRDir()+"/dsr.bat";
    dsr_db_path = getDSRdbDir();
  } else if (mysystem == QString("unix")){
    dsrpath = QDir::cleanPath(getDSRDir()+"/dsr");
    dsr_db_path = QDir::cleanPath(getDSRdbDir());
  }
  this->hide();
  dsrVersion = "";
  replace = false;
  norefine = false; // this has to stay here
  runext = false;
  invert = false;
  rigid = false;
  cf3 = false;
  splitmode = false;
  fragmentsList = new QVector<QStringList>;
  fragmentNameTag.clear();
  header = new DSRMol;
  mainLayout = new QGridLayout(this);
  editLayout = new QHBoxLayout();
  //chooserLayout = new QGridLayout;
  searchLayout = new QHBoxLayout();
  //partLayout = new QHBoxLayout();
  //fvarLayout = new QHBoxLayout();
  //occLayout = new QHBoxLayout();
  resclassLayout = new QHBoxLayout();
  optionsLayout2 = new QVBoxLayout();
  optionsLayout3 = new QVBoxLayout();
  groupBox1 = new QGroupBox();
  optionsLayout1 = new QGridLayout(groupBox1);
  groupBox2 = new QGroupBox();
  residueOptionsBox = new QGroupBox(tr("Use a Residue"));
  buttonLayout = new QVBoxLayout();
  optionboxes = new QHBoxLayout();
  fitDSRButton = new QPushButton(tr("Fit Fragment!"));
  splitButton = new QPushButton(tr("Split Atoms"));
  fitDSRButton->setStyleSheet("QPushButton {"
                              "font-weight: bold; "
                              "color: #209920}");
  exportFragButton = new QPushButton(tr("Export Fragment"));
  editButton = new QPushButton(tr("Edit Fragment"));
  editButton->setStyleSheet("QPushButton {"
                            "font-weight: bold; "
                            "color: rgb(8, 82, 182)}");
  openLastButton = new QPushButton(tr("Restore last .res"));
  runExtBox = new QCheckBox(tr("External Restraints"));
  invertFragBox = new QCheckBox(tr("Invert Coordinates"));
  dfixBox = new QCheckBox(tr("Calculate DFIX"));
  rigidBox = new QCheckBox(tr("Rigid Group (no restraints)"));
  replaceModeBox = new QCheckBox(tr("Replace Target"));
  splitModeBox = new QCheckBox(tr("Split Target"));
  searchLabel = new QLabel(tr("Search:"));
  SearchInp = new QLineEdit;//(tr("Search a fragment here"));
  partLabel = new QLabel(tr("PART"));
  fvarLabel = new QPushButton(tr("Free Variable"));  // Is a QPushbutton to have a clicked() signal
  fvarLabel->setStyleSheet("QPushButton {border-style: outset; border-width: 0px; text-align:left;}");  // remove border to appear like a label
  fvarLabel->setToolTip("Click here to invert the current free variable");
  occLabel = new QLabel(tr("Occupancy"));
  classLabel = new QLabel(tr("Residue Class"));
  usermanualLabel = new QLabel(tr("<a href=\"https://github.com/dkratzert/DSR/raw/master/manuals/DSR-manual.pdf\"> DSR User Manual </a>"));
  usermanualLabel->setOpenExternalLinks(true);
  resnumbertext = new QString(tr("A residue number will be\nchosen automatically."));
  resiTextLabel = new QLabel();
  resiTextLabel->setText(*resnumbertext);
  outtext = new QTextBrowser;
  outtext->setOpenExternalLinks(true);
  info = new QTextBrowser;
  //this->move(-this->width(), -this->height());
  info->setMinimumWidth(235);  
  info->hide();
  //info->setMaximumWidth(235);
  fragmentTableView = new QTableView;
  occEdit = new QLineEdit;
  partspinner = new QSpinBox;
  fvarspinner = new QSpinBox;
  resiclassEdit = new QLineEdit;
  // layout for the interactions
  optionboxes->addWidget(groupBox1);
  //optionboxes->addStretch();
  optionboxes->addWidget(groupBox2);
  //optionboxes->addStretch();
  optionboxes->addWidget(residueOptionsBox);
  //optionboxes->addStretch();
  optionboxes->addLayout(buttonLayout);
  //buttonLayout->setSizeConstraint(QLayout::SetMaximumSize);
  // The search field:

  SearchInp->setFocus();  // searching should be the default
  SearchInp->setMinimumWidth(getCharWidth(9));
  fragmentNameTag.clear();
  // The OpenGL widget with the molecule:
  mygl = new DSRGlWindow(this, m_molecule, *header, fragmentNameTag);
  m_molecule->loadSettings();
  mygl->showFit = new QCheckBox(tr("show fitted target overlay"));
  mygl->showFit->setChecked(true);
  mygl->showFitLabel = new QCheckBox(tr("labels on target overlay"));
  mygl->showFitLabel->setChecked(true);
  // Table of fragments and 3D window:

  editLayout->addWidget(outtext);
  editLayout->addWidget(info);
  editLayout->setStretchFactor(outtext, 2);
  editLayout->setStretchFactor(info, 1);
  outtext->setReadOnly(true);
  QFont font("Courier");
  font.setStyleHint(QFont::TypeWriter);
  outtext->setFont(font);
  outtext->setMinimumHeight(170);
  partspinner->setRange(-99, 99);
  partspinner->setValue(0);
  fvarspinner->setRange(-99, 99);
  fvarspinner->setValue(1);
  occEdit->setValidator(new QDoubleValidator(0, 99, 5, occEdit));
  occEdit->setMaximumWidth(getCharWidth(5));
  occEdit->setMinimumWidth(getCharWidth(5));
  // box1
  optionsLayout1->addWidget(partspinner,0,0);
  optionsLayout1->addWidget(partLabel,0,1);

  optionsLayout1->addWidget(fvarspinner,1,0);
  optionsLayout1->addWidget(fvarLabel  ,1,1);

  optionsLayout1->addWidget(occEdit ,2,0);
  optionsLayout1->addWidget(occLabel,2,1);

  optionsLayout1->addWidget(replaceModeBox, 3,0,1,2  );
  optionsLayout1->addWidget(splitModeBox,   4,0,1,2  );
  splitModeBox->hide();
  //optionsLayout1->addStretch();
  groupBox1->setLayout(optionsLayout1);
  // box2
  optionsLayout2->addWidget(invertFragBox);
  optionsLayout2->addWidget(runExtBox);
  optionsLayout2->addWidget(dfixBox);
  optionsLayout2->addWidget(rigidBox);
  //optionsLayout2->addStretch();
  groupBox2->setLayout(optionsLayout2);
  // box3
  resclassLayout->addWidget(resiclassEdit);
  resclassLayout->addWidget(classLabel);
  resiclassEdit->setMaximumWidth(getCharWidth(8));
  resiclassEdit->setMinimumWidth(getCharWidth(6));
  optionsLayout3->addLayout(resclassLayout);
  optionsLayout3->addWidget(resiTextLabel);
  optionsLayout3->addWidget(usermanualLabel);
  optionsLayout3->addStretch();
  residueOptionsBox->setLayout(optionsLayout3);
  residueOptionsBox->setCheckable(true);
  // buttons:
  buttonLayout->addWidget(fitDSRButton);
  buttonLayout->addWidget(exportFragButton);
  exportFragButton->setEnabled(false);
  buttonLayout->addWidget(splitButton);
  splitButton->setDisabled(true);
  splitButton->hide();  // there is no DSR version that can do this until now.
  buttonLayout->addWidget(editButton);
  buttonLayout->addWidget(openLastButton);
  // tooltips:
  setToolTips();
  QPixmap pix = QPixmap(250, 50);
  pix.fill(); // need to fill in order to see the text.
  QPainter painter(&pix);
  QRectF rectangle(0, 0, 250-1, 49);
  painter.setFont(QFont("Sans-Serif", 12));
  painter.drawRect(rectangle);
  painter.drawText(QPoint(12, 30), "Loading fragment list...");
  QGroupBox *glGroupBox = new QGroupBox();
  glo = new QGridLayout(glGroupBox);
  glo->addWidget(mygl,0,0,1,2);
  glo->addWidget(mygl->showFit,1,0,1,1);
  glo->addWidget(mygl->showFitLabel,1,1,1,1);

  glGroupBox->setFlat(true);
  QGroupBox *fGroupBox = new QGroupBox();
  flo = new QGridLayout(fGroupBox);
  mainLayout->addWidget(fGroupBox,          0, 0, 3, 2);
  mainLayout->addWidget(glGroupBox,         0, 2, 3, 5);
  flo->addWidget(fragmentTableView ,0,0,1,2);
  flo->addWidget(searchLabel ,1,0,1,1);
  flo->addWidget(SearchInp   ,1,1,1,1);
  mainLayout->setRowMinimumHeight(3,200);
  mainLayout->addLayout(editLayout,  3,0,1,7);
  mainLayout->addLayout(optionboxes, 6,0,1,7);
  QSplashScreen *splash = new QSplashScreen(pix);
  splash->show();
  splash->showMessage("");
  target_atoms = getSelectedAtomsList(); // must be before signals
  // request version.txt to warn for updates:

#if !defined(Q_OS_MAC) && (QT_VERSION >= 0x050000)
  getVersionFromServer();
#endif  
  // Signal slot connections:
  connect_signals_and_slots();
  splitDecide();
  occEdit->setText("1");
  checkForDSRexecutable(splash);
  splash->finish(this);
  // call last, because keyboard focus is reated to tab order,
  // which is based on the order the widgets are created:
  SearchInp->setFocus();
  // Has to be here, otherwise fragmentTableView is not initialized:
  QItemSelectionModel *sm = fragmentTableView->selectionModel();
  this->show();
  if (!(sm == nullptr)){  // prevents error about missing connection if DSR is not present
    connect(sm, SIGNAL(currentRowChanged(QModelIndex,QModelIndex)),
        this, SLOT(setFragName(QModelIndex)), Qt::UniqueConnection);
  }
  //int scn=QApplication::desktop()->screenNumber(m_shelxle);//find out where the main window is
  QScreen *screen = m_shelxle->window()->windowHandle()->screen();
  //QGuiApplication::screens().at(scn)->geometry()
  this->move(screen->geometry().x()+
             screen->geometry().width()-this->width()-30, 30);

  //printf("test\n");
  //this->resize(this->width()-2, this->height()-2);  // a trick to redraw the gl windows
  // this raises an 'Unable to set geometry' error
  mygl->update();
  //printf("test2\n");
  if (!(dsrVersion.toLatin1() == "0")) {
    outtext->append(QString("\nFound DSR version %1.").arg(dsrVersion));
    if (dsrVersion.toInt() > 9999) {  // To be changed later
        splitButton->show();  // logic turned, because a non-replying web server turned this button on
    }
  }
  update();
}


DSRGui::~DSRGui() {
  delete mygl;
}

void DSRGui::aboutDSR() {
  QMessageBox::about(this, QString(tr("About DSR Plugin")),//only one about dlg in macOS
      QString(
        tr("<p><b>DSR plugin for ShelXle</b></p>"
          "This plugin is a graphical interface for DSR.<br>"
          "The GUI part and the interaction with DSR was developed by <b>Daniel Kratzert</b>, "
          "while the 3D OpenGL part was developed by <b>Christian H&uuml;bschle</b>.<br>"
          "DSR is a refinement tool with a database of molecular fragments and corresponding restraints.<br>"
          "Place these fragments in a molecular structure to model disorder or just quickly rename "
          "groups of atoms.<br><br>"
          "Please cite DSR as:<br>"
          "<a href=https://dkratzert.de/files/dsr/documents/dsr_2_reprint.pdf> D. Kratzert, I. Krossing, <i>J. Appl. Cryst.</i><b> 2018</b>, <i>51</i>, 928-934.<br></a>"
          "<a href=https://doi.org/10.1107/S1600576718004508> doi:10.1107/S1600576718004508 </a><br><br>"
          "If you have additional fragments for the DSR database or a bug to report, please send them to "
          "<a href=\"dkratzert@gmx.de\"> dkratzert@gmx.de </a> <br>"
          "Please find the most recent version of DSR at <br>"
          "<a href=\"https://dkratzert.de/dsr.html\"> https://dkratzert.de/dsr.html </a><br><br>"
          "All DSR related software is developed at GitHub:<br>"
          "<a href=\"https://github.com/dkratzert/DSR\"> https://github.com/dkratzert/DSR </a><br><br>"
          "Please refer to the <a href=\"http://www.xs3-data.uni-freiburg.de/data/DSR-manual.pdf\"> manual </a> if you have any questions."
          )));
}

void DSRGui::connect_signals_and_slots() {
  //! Handles most of the signal slot connections
    connect(this, SIGNAL(fragmentSelected(void)),
            this, SLOT(activateFitButton(void)));
    connect(this, SIGNAL(fragmentSelected()),
            this, SLOT(resetSelection()));
    connect(fitDSRButton, SIGNAL (clicked(bool)),
            this, SLOT (fitDSR()));
    connect(fitDSRButton, SIGNAL (clicked(bool)),
            this->info, SLOT(hide()));
    connect(runExtBox, SIGNAL (clicked(bool)),
            this, SLOT (fitDSRExtern(bool)));
    connect(dfixBox, SIGNAL (clicked(bool)),
            this, SLOT (DFIX(bool)));
    connect(invertFragBox, SIGNAL (clicked(bool)),
            this, SLOT (invertFrag(bool)));
    connect(rigidBox, SIGNAL (clicked(bool)),
            this, SLOT (rigid_group(bool)));
    connect(replaceModeBox, SIGNAL(clicked(bool)),
            this, SLOT(replaceOrNot(bool)));
    connect(SearchInp, SIGNAL(textChanged(QString)),
            this, SLOT(searchFragment(QString)));
    connect(occEdit, SIGNAL(textChanged(QString)),
            this, SLOT(setFvarOcc(void)));
    connect(fvarspinner, SIGNAL(valueChanged(int)),
            this, SLOT(setFvarOcc(void)));
    connect(resiclassEdit, SIGNAL(textChanged(QString)),
            this, SLOT(setResiClass(QString)));
    connect(residueOptionsBox, SIGNAL(toggled(bool)),
            this, SLOT(combineOptionstext()));
    connect(splitModeBox, SIGNAL(toggled(bool)),
            this, SLOT(combineOptionstext()));
    connect(partspinner, SIGNAL(valueChanged(int)),
            this, SLOT(setPART(int)));
    connect(exportFragButton, SIGNAL(clicked(bool)),
            this, SLOT(setExportDirDialog(void)));
    connect(fragmentTableView, SIGNAL(clicked(QModelIndex)),
            this, SLOT(setFragName(QModelIndex)));
    connect(this, SIGNAL(optionTextChanged(void)),
            this, SLOT(combineOptionstext(void)));
    connect(editButton, SIGNAL(clicked(bool)),
            this, SLOT(runEditWindow()));
    connect(openLastButton, SIGNAL(clicked(bool)),
            this, SLOT(open_last_fileversion()));
    connect(this, SIGNAL(exportDirChanged(QString)),
            this, SLOT(exportFrag(QString)));
    // sigslot for uppdating the 3D view
    connect(this, SIGNAL(currentFragmentChanged(DSRMol)),
            mygl, SLOT(display_fragment(DSRMol)));
    connect(m_shelxle->chgl, SIGNAL(selectionChanged()),
            mygl, SLOT(update()));
    connect(m_shelxle->chgl, SIGNAL(selectionChanged()),
            this, SLOT(updateTarget()));
    connect(m_shelxle->chgl, SIGNAL(selectionChanged()),
            this, SLOT(update()));
    connect(mygl->showFitLabel, SIGNAL(stateChanged(int)),
            mygl, SLOT(update()));
    connect(mygl->showFitLabel, SIGNAL(stateChanged(int)),
            mygl, SLOT(update()));
    connect(mygl->showFit, SIGNAL(stateChanged(int)),
            mygl, SLOT(update()));
    connect(mygl->showFit, SIGNAL(stateChanged(int)),
            mygl, SLOT(update()));
    connect(m_shelxle->chgl, SIGNAL(selectionChanged()),
            mygl, SLOT(makeInfo()));
    connect(mygl, SIGNAL(sourceStringChanged()),
            this, SLOT(combineOptionstext()));
    connect(mygl, SIGNAL(updateInfo(QString)),
            this, SLOT(setInfo(QString)));
#if !defined(Q_OS_MAC) && (QT_VERSION >= 0x050000)
    connect(net_manager, SIGNAL(finished(QNetworkReply*)),
            this, SLOT(isDSRUpToDate(QNetworkReply*)));
#endif 
    connect(fvarLabel, SIGNAL(clicked(bool)),
            this, SLOT(invertFvar()));
    connect(m_shelxle->chgl, SIGNAL(selectionChanged()),
            this, SLOT(splitDecide(void)));
    connect(splitButton, SIGNAL(clicked(bool)),
            this, SLOT(splitSelectedAtoms(void)));
}

QSize DSRGui::minimumSizeHint() const {
  return QSize(700, 700);
}

QSize DSRGui::sizeHint() const {
  return QSize(700, 780);
}

void DSRGui::getVersionFromServer() {
  //! Writes the proposed version number of DSR into reply
    net_manager = new QNetworkAccessManager(this);
    QNetworkRequest request;
    request.setUrl(QUrl("http://www.xs3-data.uni-freiburg.de/data/version.txt"));
    request.setRawHeader("User-Agent", "DSRGui");
    reply = net_manager->get(request);
  }

/*
bool DSRGui::runTCPServer() {
  //! Socket server to get messages from DSR. Might be used in future.
  tcpServer = new QTcpServer(this);
  //connect(tcpServer, SIGNAL(newConnection()), this, SLOT(ReadClientData()));
  if (!tcpServer->listen(QHostAddress::LocalHost, 51234)) {
      tcpServer->close();
      return false;
  } else {
    if (tcpServer->waitForNewConnection()) {
      if (tcpServer->hasPendingConnections()) {
        ReadClientData();
      }
    }
  }
  return true;
}
*/
/*
void DSRGui::ReadClientData() {
  //! Reads DSR client data from a tcp soccet connection.
  QByteArray data_buffer;
  QTcpSocket *clientConnection = tcpServer->nextPendingConnection();
  connect(clientConnection, SIGNAL(readyRead()), clientConnection, SLOT(deleteLater()));
  // this wait is essential to retrieve data:
  clientConnection->waitForReadyRead();
  while (clientConnection->bytesAvailable() > 0) {
      data_buffer = clientConnection->readAll();
  }
  //close tcpServer after reading data:
  tcpServer->deleteLater();
  outtext->append(data_buffer);
  //dsrResulttext.append(data_buffer);
}
*/

void DSRGui::isDSRUpToDate(QNetworkReply* reply) {
  /*
   *! Displays a warning if the current DSR version is too old.
  */
  QString latestRev_str = reply->readAll();
  bool ok;
  bool ok2;
  QMessageBox info;
  info.addButton(QMessageBox::Close);
  int dsrv = dsrVersion.toInt(&ok2, 10);
  QPushButton *updateButton = info.addButton(tr("Update now"), QMessageBox::ActionRole);
  if (dsrv < 193) {  // This is the first version with self-update mechanism
    updateButton->hide();
  }
  int latestrev_int = latestRev_str.toInt(&ok,10);
  if ((ok&&ok2)&&(latestrev_int)>(dsrv)){
    info.setText(QString(
                   "<h3>You should probably update DSR!</h3>"
                   "This is revision: <b>%1</b><br> "
                   "The latest version is: <b>%2</b> <br><br>"
                   "New versions can be downloaded here: <br>"
                   "<a href=\"https://dkratzert.de/dsr.html\">"
                   "https://dkratzert.de/dsr.html</a><br><br>"
                   "Please contact the author Daniel Kratzert"
                   " <a href=\"mailto:dkratzert@gmx.de\">dkratzert@gmx.de</a> "
                   "if you find any bugs.<br> Thank you!")
                    .arg(dsrVersion.toInt())
                    .arg(latestrev_int));
    info.exec();
    if (info.clickedButton() == updateButton) {
      updateDSR();
    }
  }
  reply->close();
  reply->deleteLater();
  disconnect(net_manager, SIGNAL(finished(QNetworkReply*)), NULL, NULL);
}

void DSRGui::updateTarget() {
  //! updates the target atoms list
  target_atoms = getSelectedAtomsList();
  combineOptionstext();
}

void DSRGui::writeFavorites(QString name) {
  //! Stores favorites in dsrgui.ini
  QSettings dsr_settings( QSettings::IniFormat, QSettings::UserScope, PROGRAM_NAME, "dsrgui" );
  dsr_settings.beginGroup("LastFragment");
  dsr_settings.setValue("last", name);
  dsr_settings.endGroup();
}

QString DSRGui::loadFavoriteFragment() {
  //! Loads Favorites from dsrgui.ini
  QSettings dsr_settings( QSettings::IniFormat, QSettings::UserScope, PROGRAM_NAME, "dsrgui" );
  dsr_settings.beginGroup("LastFragment");
  QString last = dsr_settings.value("last").toString();
  dsr_settings.endGroup();
  if (last == QString("cf6")) {
    splitModeBox->show();
  }
  if (last == QString("")) {
    last = QString("benzene");
  }
  return last;
}

QStringList DSRGui::which(QString programName) {
  //! Implements a which like method
  //! It returns all paths where programName is found in
  //! the system path variable
  QStringList foundInPath;
  QStringList execlist;
  QStringList pathList;
  pathList.clear();
  foundInPath.clear();
  execlist.clear();
  if (mysystem == "win") {
#if (QT_VERSION >= QT_VERSION_CHECK(5, 10, 0))
    pathList = QString(qEnvironmentVariable("PATH")).split(";");
#else
    pathList = QString(qgetenv("PATH")).split(";");
#endif
  } else {
#if (QT_VERSION >= QT_VERSION_CHECK(5, 10, 0))
    pathList = QString(qEnvironmentVariable("PATH")).split(":");
#else
    pathList = QString(qgetenv("PATH")).split(":");
#endif
    pathList.append("/usr/local/bin/");
  }
  execlist << ".bat" << ".exe" << "";
  foreach (QString exec, execlist) {
    foreach (QString path, pathList) {
      QString fullpath = path+"/"+programName+exec;
      QFileInfo fi(fullpath);
      if (QFile::exists(fullpath) && (fi.isExecutable())){
        foundInPath.append(QDir::cleanPath(fullpath));
      }
    }
  }
  return foundInPath;
}

void DSRGui::checkForDSRexecutable(QSplashScreen *splash) {
  //! list fragments only if the path of dsr installation is found:
  if (QFile::exists(dsrpath)) {
    if (listDSRdbFragments("None")) {
      outtext->append(tr("\n* Please pick a fragment first."));
      outtext->append(tr("* Then select at least three atoms from "
                        "the main structure and the fragment respectively. (STRG+click)"));
      outtext->append(tr("* Do not forget to apply a part number and free "
                         "variable in case of disorder."));
      outtext->append(tr("* The fragment will be placed after FVAR in the SHELX file."));
    }
  } else {
    outtext->clear();
    outtext->append(QString(tr("Unable to find DSR executable."
                "\nIs DSR_DIR environment variable set correctly?")));
    outtext->append(QString(tr("Please find the most recent version of DSR at "
                               "<a href=\"https://dkratzert.de/dsr.html\">"
                               "https://dkratzert.de/dsr.html</a>")));
    splash->finish(this);
  }
}

void DSRGui::setToolTips() {
  partspinner->setToolTip(tr("The PART of a fragment controls the binding of atoms.\n"
                             "For example two fragments in PART 1 and PART 2 do not\n"
                             "bind each other but to PART 0. Negative PARTs only bind themselves."));
  replaceModeBox->setToolTip(tr("Toggle replacement of target atoms and all atoms of "
                             "PART 0 \nin 1.3A distance around the fitted fragment atoms."));
  occEdit->setToolTip(tr("The occupancy of the fragment\n"));
  fvarspinner->setToolTip(tr("The Free Variable for the fragment.\n"
                             "Free Variable and Occupancy will be combined occording to the SHELXL syntax.\n"
                             "For example, 21.0 means second free variable with occupancy of 1."));
  invertFragBox->setToolTip(tr("Invert the fragment coordinates during fit."));
  runExtBox->setToolTip(tr("Write restraints to external file."));
  dfixBox->setToolTip(tr("Calculate DFIX/DANG/FLAT restraints "
                         "\naccording to fragment geometry. \n"
                         "Database restraints will be ignored."));
  rigidBox->setToolTip(tr("Keep the fragment as rigid (AFIX 9) group. \n"
                          "Apply no restraints."));
  residueOptionsBox->setToolTip(tr("Enables residues. Usually, you can leave the default.\n"
                           "It will always take the next free residue number."));
  fitDSRButton->setToolTip("Run DSR to fit the fragment into the structure.");
  exportFragButton->setToolTip("Export the current fragment to a .res file.");
  editButton->setToolTip("Edit the current fragment or create a new one.");
  openLastButton->setToolTip("Opens the .res file state before the last DSR fragment fit.");
}

QString DSRGui::textWrap(QString inText, QString indent) {
  //! returns a SHELXL compatible wrapped string (string =\\n string) in case of over 77 characters
  //! line length.
  //! The default of subsequent_indent is "=\n  "
  int length = 70;  // 70 should be save in any case
  QStringList line_list;
  QStringList wrapped;
  QStringList inText_list = inText.split(" ");
  for (int i=0; i<inText_list.length(); i++) {
    QString word = inText_list.at(i);
    QString testline = line_list.join(" ") + " ";
      if (QString(word + testline + indent).length() >= length) {
        if (i < inText_list.length()-2) {
          line_list.append(word + " " + indent);
        } else {
          line_list.append(word);
        }
        wrapped.append(line_list.join(" "));
        line_list.clear();
      } else{
        line_list.append(word);
      }
  }
  if (!line_list.isEmpty()) {
    wrapped.append(line_list.join(" "));
  }
  //qDebug() << wrapped.join(" ");
  return wrapped.join(" ");
}

bool DSRGui::open_last_fileversion() {
    //! Opens the last res file version before the last DSR action from the save history (./Shelxsaves/SAVEHIST)
    QFileInfo fi(m_shelxle->dirName);
    if (!fi.isReadable()) {
        outtext->append("No last .res file found to load.");
        return false;
    }
    QFile currentpath(fi.absolutePath());
    QString saveHistFileName=QString("%1/%2saves/SAVEHIST").arg(currentpath.fileName()).arg(PROGRAM_NAME);
    QFile savehist(saveHistFileName);
    savehist.open(QIODevice::ReadOnly|QIODevice::Text);
    if (!savehist.isReadable()) {
        outtext->append("No last .res file found to load.");
        return false;
    }
    QString savehist_content = savehist.readAll();  //Entry|@|2011-03-08T13:32:19|@|b11.res|@|
    savehist.close();
    QRegularExpression re = QRegularExpression("Entry\\|@\\|\\w+-\\w+-\\w+:\\w+:\\w+\\|@\\|[^@]+@\\|");
    QStringList entries = savehist_content.split(re, skipEmptyParts);
    QFile f(m_shelxle->dirName);
    bool success = f.open(QIODevice::WriteOnly|QIODevice::Text);
    if (success){
      f.write(entries.last().toLatin1().replace(0, 1, ""));
      f.close();
    } else {
      return false;
    }
    outtext->append("Successfully restored last file version.");
    m_shelxle->loadFile(m_shelxle->dirName);
    return true;
}

void DSRGui::invertFvar(){
    //! Inverts the value of FVAR in the OptionsLayout1
    int fvar;
    fvar = fvarspinner->text().toInt();
    fvarspinner->setValue(-fvar);
}

void DSRGui::resetSelection() {
  //! reset the selection of source atoms
  mygl->source_atoms.clear();
  combineOptionstext();
  info->hide();
}

void DSRGui::setInfo(QString s) {
  //! shows an info table with bond distances
  if (mygl->selFragAt.size()<1) {
    info->hide();
  }
  else {
    info->show();
    info->setText(s);
  }
}

void DSRGui::splitDecide(void) {
    //! Enables the "split atoms" button if at least one atom is selected.
    if (target_atoms.length() >= 1) {
        splitButton->setEnabled(true);
    }
}

void DSRGui::splitSelectedAtoms(void) {
    //! Runs DSR to split the currebtly selected atoms along the principal axis of the ellipsoid.
    QFileInfo resfip(m_shelxle->dirName);
    QString option = " -splt ";
    option = option + getSelectedAtomsList();
    option = option + " -r " + resfip.completeBaseName();
    this->runDSR(option);
}

void DSRGui::runEditWindow(void) {
  //! Starts the edit window in order to edit a fragment
  editwindow = new DSREditWindow(m_molecule, header, dsr_db_path,
                                 fragmentNameTag, *fragmentsList, this);
  editwindow->move(60, 50);
  editwindow->show();
  editwindow->setFocus();
  editwindow->setMinimumWidth(800);
  outtext->clear();
  connect(editwindow, SIGNAL(updated(QString)),
          this, SLOT(listDSRdbFragments(QString)));
}

void DSRGui::closeEvent(QCloseEvent *event) {
//! close event is emmited during DSRGui closing to reset its pointer
  emit closed();
  (void)event; // prevent compiler warning
}

int DSRGui::findFVARlines(QStringList *reslist) {
  //! finds the line number of last FVAR or the first atom
  //! I restrict the use of this plugin to stuctures with a valid
  //! FVAR, because a missing FVAR makes it all too error prone.
  int fvarline;
  // I need lastIndexOf() here, because in case of
  // several FVAR lines indexOf() would fail:
  fvarline = reslist->lastIndexOf(QRegularExpression("^FVAR.*", QRegularExpression::CaseInsensitiveOption));
  if (fvarline > 0) {
    return fvarline;
  } else {
    return 0;
  }
}

QVector<int> DSRGui::findDSRLines(QStringList *reslist) {
  //! Find line with "rem DSR ..." in res file and return line number
  //! if it exists.
  QVector<int> lineNums;
  int Num = 0;
  foreach (QString line, *reslist) {
    if (line.contains(QRegularExpression("^rem\\s{1,6}DSR\\s{1,6}.*", QRegularExpression::CaseInsensitiveOption))) {
      lineNums.append(Num);
    }
    Num++;
  }
  return lineNums;
}

int DSRGui::decideDSRInsertLine(QStringList *reslist) {
  //! decides where to instert the DSR command
  int fvarline = findFVARlines(reslist);
  if (fvarline > 0) {
    return fvarline;
  } else if (m_shelxle->firstAtomLine > 0) {
    // in this case, no FVAR is present and we put the DSR command line
    // before the first atom
    combiDSRline = QString("FVAR 1\n") + combiDSRline; // dummy FVAR is added for DSR
    return m_shelxle->firstAtomLine - 1;
  } else {
    return 0;
  }
}

QStringList DSRGui::readResfile() {
  //! read the entire res file into a stringlist
  QFileInfo fi(m_shelxle->dirName);
  QFile file(fi.absoluteFilePath());
  QStringList stringList;
  if (file.open(QFile::ReadOnly | QFile::Text)) {
    QTextStream textStream(&file);
    while (true) {
      QString line = textStream.readLine();
      if (line.isNull()) {
          break;
      } else {
        stringList.append(line);
      }
    }
  }
  file.close();
  return stringList;
}

QString DSRGui::findFreeResiNumber() {
  //! returns the next free residue number in the structure
  QSet<int> resiset;
  QList<int> resilist;
  int resnum = 0;
  for (int i=0; i < m_molecule->asymm.size(); i++) {
    MyAtom atom;
    atom = m_molecule->asymm.at(i);
    if (atom.resiNr >= 0) {
      resiset.insert(atom.resiNr);
    }
  }
  resilist = resiset.values();//.toList();
#if (QT_VERSION >= QT_VERSION_CHECK(5, 0, 0))
  std::sort(resilist.begin(), resilist.end());
#else
  qSort(resilist);
#endif
  int count = 0;
  foreach (int num, resilist) {
    if (num != count) {
      // a gap in residue numbers is found, use this number:
      resnum = count;
      break;
    }
    count++;
  }
  // no gap found, use next number:
  resnum = count;
  // In this case we have no residue in the file:
  if (resilist.isEmpty()) {
    resnum = 1;
  }
  return QString("%1").arg(resnum);
}


bool DSRGui::getFragmentHeader(QString frag) {
  //! defines Name, residue, comment and unit cell of the fragment
  //! in DSRMol
  /*!
    <tag>
     benze
    </tag>
    <comment>
     Benzene2, Benzol, C6H6
    </comment>
    <source>
     CCDC UGEDEQ
    </source>
    <cell>
     1;;1;;1;;90;;90;;90
    </cell>
    <residue>
     ERT
    </residue>
    <dbtype>
     dsr_user_db
    </dbtype>
    <restr>
     RIGU C1 > C6;;SADI C1 C2 C3 C4
     </restr>
    <atoms>
      C1 6 1.78099 7.14907 12.00423;;C2 6 2.20089 8.30676 11.13758;;C3 6 1.26895 9.02168 10.39032;;C4 6 1.64225 10.07768 9.58845;;C5 6 2.98081 10.44432 9.51725;;C6 6 3.92045 9.74974 10.25408
    </atoms>
   */
  header->atoms.clear();
  header->cell.clear();
  header->comment.clear();
  header->dbtype.clear();
  header->residue.clear();
  header->restr.clear();
  header->tag.clear();
  outtext->clear();
  QString *rawheader = new QString;
  QStringList *headerlist = new QStringList;
  QString options = " -ah " + frag;
  dsrResulttext.clear();
  runDSR(options);
  if (dsrResulttext.isEmpty()) {
    outtext->clear();
    outtext->append(tr("Unable to run DSR."));
    editButton->setDisabled(true); // editing the empty header would crash ShelXle
    return false;
  } else {
    rawheader->append(dsrResulttext);
  }
  // in this case no fragment list returned. Hence, we have an error.
  if (!rawheader->contains(";;")) {
    outtext->clear();
    outtext->append(*rawheader);
    //editButton->setDisabled(true); // editing the empty header would crash ShelXle
    return false;
  }
  headerlist->append(rawheader->split(QRegularExpression("\n|\r\n|\r")));
  QStringList line;
  for (int i=0; i<headerlist->size(); i++) {
    if (headerlist->at(i).size() == 0){
      continue;
    }
    line.clear();
    if (headerlist->at(i).trimmed().startsWith("***")) {
      QString error;
      error = headerlist->at(i).trimmed();
      outtext->append("<b>"+error+"</b>");
    }
    if (headerlist->at(i).trimmed().startsWith("<tag>")) {
      line = headerlist->at(i+1).trimmed().split(" ");
      header->tag = line.join("");
    }
    if (headerlist->at(i).trimmed().startsWith("<comment>")) {
      line = headerlist->at(i+1).trimmed().split(" ");
      header->comment = line.join(" ");
    }
    if (headerlist->at(i).trimmed().startsWith("<source>")) {
      line = headerlist->at(i+1).trimmed().split(" ");
      header->source = line.join(" ");
    }
    if (headerlist->at(i).trimmed().startsWith("<cell>")) {
      line = headerlist->at(i+1).simplified().split(";;");
      foreach (QString item, line) {
        header->cell.append(item.toDouble());
      }
    }
    if (headerlist->at(i).trimmed().startsWith("<residue>")) {
      line = headerlist->at(i+1).trimmed().split(" ");
      header->residue = line.join("");
      resiclass = header->residue;
      resiclassEdit->setText(resiclass);
    }
    if (headerlist->at(i).trimmed().startsWith("<dbtype>")) {
      line = headerlist->at(i+1).trimmed().split(" ");
      header->dbtype = line.join("");
    }
    if (headerlist->at(i).trimmed().startsWith("<restr>")) {
      line = headerlist->at(i+1).simplified().split(";;");
      foreach (QString item, line) {
        header->restr.append(item);
      }
    }
    if (headerlist->at(i).trimmed().contains("<atoms>")) {
      line = headerlist->at(i+1).simplified().split(";;");
      foreach (QString item, line) {
        header->atoms.append(item.split(" "));
      }
    }
  }
  editButton->setEnabled(true);
  return true;
}


int DSRGui::getCharWidth(int numchars) {
  //! returns the width in pixel of numchars times the # character
  QString buchstaben;
  buchstaben.clear();
  for (int i=1; i<=numchars; i++) {
    buchstaben += "#";
  }
#if (QT_VERSION >= QT_VERSION_CHECK(5, 11, 0))
  return QFontMetrics(this->font()).horizontalAdvance(buchstaben);
#else
  return QFontMetrics(this->font()).width(buchstaben);
#endif
}


void DSRGui::activateFitButton(void) {
    fitDSRButton->setEnabled(true);
    exportFragButton->setEnabled(true);
}


void DSRGui::combineOptionstext(void) {
  //! combines all options to a single DSR command line
  //! This method gets invoked if optionTextChanged signal is emmitted
  combiDSRline.clear();
  // Displays error messages from DSR:
  if (!outtext->toPlainText().contains("***")) {
    outtext->clear();
  } //else {
    //return;
  //}
  QString split = "";
  // CF3 groups are dummy entries in the DSR database. They get calculated
  // on ideal positions at the respective carbon atom:
  if (fragmentNameTag == QString("cf6")) {
    splitModeBox->show();
  } else {
    splitModeBox->hide();
  }
  if ( (fragmentNameTag == QString("cf3")) ||
       (fragmentNameTag == QString("cf6")) ||
       (fragmentNameTag == QString("cf9")) ) {
    this->cf3 = true;
    rigidBox->setDisabled(true);
    invertFragBox->setDisabled(true);
    runExtBox->setDisabled(true);
    replaceModeBox->setDisabled(true);
    residueOptionsBox->setDisabled(true);
    if (splitModeBox->isChecked() ) {
      split = "SPLIT";
    }
  } else {
    splitModeBox->hide();
    this->cf3 = false;
    rigidBox->setDisabled(false);
    invertFragBox->setDisabled(false);
    runExtBox->setDisabled(false);
    replaceModeBox->setDisabled(false);
    residueOptionsBox->setDisabled(false);
  }
  target_atoms = getSelectedAtomsList();
  QString putreplace = QString("PUT ");
  if (replace) {
      putreplace = QString("REPLACE ");
  }
  if (!cf3) {
    if (target_atoms.split(" ").length() != 3) {
      target_atoms = "<font color=red> Please select 3 target atoms/q-peaks! </font>";
    }
    if (mygl->source_atoms.split(" ").length() != 3){
      mygl->source_atoms = "<font color=red> Please select 3 fragment atoms! </font>";
    }
  } else {
    if (target_atoms.split(" ").length() != 1) {
      target_atoms = "<font color=red> Please select only <b>a single</b> carbon atom! </font>";
    }
    mygl->source_atoms = "";
  }
  QString resistr = "RESI ";
  if (!residueOptionsBox->isChecked() || !residueOptionsBox->isEnabled()) {
    resistr = "";
    resiTextLabel->setText("");
  } else {
    resiTextLabel->setText(*resnumbertext);
    if (resiclassEdit->text() == resiclass) {
      resistr = "RESI "+resiclass;
    } else {
      resistr = "RESI "+resiclassEdit->text();
    }
  }
  QString with;
  if (cf3) {
    with = QString(" ");
  } else {
    with = QString(" WITH ");
  }
  QString outstring = QString(QString("REM DSR ")+putreplace+fragmentNameTag+" "+
                          with+mygl->source_atoms+" "+QString("ON ")+
                          target_atoms+" "+part+" "+fvarocc+" "+dfix+" "+resistr+split);
  combiDSRline = outstring.simplified().toUpper();
  outtext->append(combiDSRline);

  mygl->selchanged = true;
  //printf("combineOptionstext\n");
}


void DSRGui::setResiClass(QString rclass) {
//! defines the residue class
  if (rclass[0].isLetter()){
    if (rclass.length() > 4) {
      resiclassEdit->setText(QString(rclass.mid(0, 4)));
    }
    emit optionTextChanged();
  } else {
    outtext->append(QString(tr("Please start residue "
                            "class with a letter.")));
    resiclassEdit->clear();
  }
}

void DSRGui::setFragName(QModelIndex name) {
//! set the fragment name variable
  //outtext->clear();
  fragmentNameTag = name.sibling(name.row(), 0).data().toString();
  writeFavorites(fragmentNameTag);
  //outtext->clear();
  if (!getFragmentHeader(fragmentNameTag)) {
    // In this case, the most important thing is missing
    return;
  }
  if (header->comment.isEmpty()){
    outtext->append("You should give this fragment a name.");
  }
  if (header->atoms.isEmpty()){
    return;
  }
  if (header->tag.isEmpty()){
    return;
  }
  if (header->restr.isEmpty()){
    return;
  }
  if (header->cell.isEmpty()){
    return;
  }
  //emit optionTextChanged();
  emit fragmentSelected();
  emit currentFragmentChanged(*header);
}


void DSRGui::DFIX(bool checked) {
//! toggles the dfix option
  outtext->clear();
  if (checked)
  {
    this->dfix = QString("DFIX");
  } else
  {
    this->dfix.clear();
  }
  emit optionTextChanged();
}

void DSRGui::setFvarOcc(void) {
//! defines the FVAR and occupancy option
  outtext->clear();
  int fvar = 0;
  double occ = 0;
  double focc = 0;
  fvar = fvarspinner->value();
  occ = (occEdit->text().replace(',', '.').toDouble());
  if (fvar < 0) {
    focc = -(abs(fvar) * 10 + occ);
  } else {
    focc = fvar * 10 + occ;
  }
  fvarocc = QString("OCC ")+QString::number(focc);
  emit optionTextChanged();
  outtext->append("\nFVAR num  ->  times used");
  foreach (int fvar, m_shelxle->fvarCntr.keys()) {
    if (fvar < 2) continue;
    outtext->append(QString("FVAR %1  -> %2  ").arg(fvar, 3).arg(m_shelxle->fvarCntr.value(fvar), 3));
  }
}

void DSRGui::setPART(int partnum) {
//! defines the PART option
  outtext->clear();
  if (partnum == 0)
  {
    part.clear();
  }
  else
  {
    QString s = QString::number(partnum);
    part = QString("PART ")+s ;
  }
  emit optionTextChanged();
}

void DSRGui::fitDSRExtern(bool checked) {
//! enable write restraints to external file
  if (checked) {
    this->runext = true;
  } else {
    this->runext = false;
  }
}

void DSRGui::invertFrag(bool checked) {
//! Inverts the fragment coordinates.
//! They are also inverted in the 3D view.
  // Invert coordinates in DSR:
  if (checked){
    this->invert = true;
  } else {
    this->invert = false;
  }
  /*
  V3 v1 = V3(-1,  0,  0);
  V3 v2 = V3( 0, -1,  0);
  V3 v3 = V3( 0,  0,  1);
  //rotation matrix to rotate the selection 180deg.
  // for less disturbance of the inverted view:
  // ch: WHY??

  Matrix rmat = Matrix(v1, v2, v3);*/
  // Invert the OpenGL coordinates:
  double coord;
  int index;
  index = 0;
  foreach(QStringList line, header->atoms) {
    for (int n = 2; n<5; n++) {
      coord = line[n].toDouble();
      // rotate fragment 180 deg. if ((n == 2) || (n == 3)) { coord = coord * -1; }
      header->atoms[index][n] = QString("%1").arg(-coord);
    }
    index = index+1;
  }
  //Also invert the selection of the atoms:
  for (int n=0; n<mygl->selFragAt.size(); n++) {
    //this line is essential:    mygl->selFragAt[n].pos = mygl->selFragAt[n].pos * rmat;
    mygl->selFragAt[n].pos *= -1.0;
  }
  mygl->display_fragment(*header, false);
  combineOptionstext();
  mygl->makeInfo();
  mygl->update();
}

void DSRGui::rigid_group(bool checked)
//! toggle rigid group refinenement
{
  if (checked) {
    this->rigid = true;
  } else {
    this->rigid = false;
  }
}

bool DSRGui::exportFrag(QString dirname) {
  //! export the current fragment to a res file+png
  //! change to the current dir here, because dsr exports in current dir:
  QDir::setCurrent(dirname);
  outtext->clear();
  if (fragmentNameTag.isEmpty()) {
      outtext->append("No fragment chosen. Doing nothing!");
      return false;
  }
  //outtext->clear();
  QString options = QString(" -e ") + fragmentNameTag;
  dsrResulttext.clear();
  runDSR(options, true, dirname);
  if (dsrResulttext.isEmpty()) {
    outtext->append("Unable to start DSR.");
    return false;
  }
  return true;
}

void DSRGui::refineOrNot(bool checked) {
//! enable or disable refinement after transfer
  if (checked) {
    this->norefine = true;
  } else {
    this->norefine = false;
  }
}

void DSRGui::replaceOrNot(bool checked) {
//! enable or disable replace mode
  outtext->clear();
  if (checked) {
    this->replace = true;
  } else {
    this->replace = false;
  }
  emit optionTextChanged();
}

QString DSRGui::getSelectedAtomsList() {
  //! returns the Names of the currently selected atoms of the structure
  //! loaded in ShelXle as StringList
  QStringList atoms;
  atoms.clear();
  for (int i=0; i<m_molecule->selectedatoms.size(); i++) {
    atoms.append(QString(m_molecule->selectedatoms.at(i).Label.toLatin1()).replace(QChar(187), ">>"));
  }
  return atoms.join(" ");
}

QString DSRGui::getSelectedAtomsCoords() {
  //! returns the atoms coordinates that are selected inside shelxle as a string
  QString atoms = "";
  QString line = "";
  for (int i = 0; i < m_molecule->selectedatoms.size(); ++i) {
    line = QString(" %1 %2 %3").arg(m_molecule->selectedatoms.at(i).frac.x, 10, 'f', 5)
                               .arg(m_molecule->selectedatoms.at(i).frac.y, 10, 'f', 5)
                               .arg(m_molecule->selectedatoms.at(i).frac.z, 10, 'f', 5);
    atoms.append(line);
  }
  return atoms;
}

bool DSRGui::fitDSR() {
  /*!
   runs DSR from command line

   bool QDir::setCurrent(const QString & path)
   QString QFileInfo::completeBaseName() const : "c:/programme/dsr/p21c.res -> p21c.res
   QString QFileInfo::absolutePath() const : c:/programme/dsr/p21c.res -> c:/programme/dsr/
   QString QFileInfo::absoluteFilePath() const : c:/programme/dsr/p21c.res -> c:/programme/dsr/p21c.res
   QFileInfo fi("c:/temp/foo"); => fi.absoluteFilePath()
  */
  QString atoms = getSelectedAtomsCoords();
  if (!cf3) {
    if (m_molecule->selectedatoms.size() != 3) {
      emit optionTextChanged();
      //return false;
    }
    if (mygl->source_atoms.split(" ").length() != 3) {
      emit optionTextChanged();
      outtext->append("<font color=red> \nPlease select three "
                      "atoms of the fragment! </font>");
      return false;
    }
  }
  info->hide(); // Even if the fit does not work, I want to hide it to better see the output
  QString option;
  QString source_atoms_tmp = mygl->source_atoms;
  if ((m_molecule->selectedatoms.size() != 3) && !cf3) {
    //outtext->clear();
    outtext->append("<font color=red> Please select at least three "
                    "atoms or Q-peaks as target in your structure! </font>");
    return false;
  }
  if ((m_molecule->selectedatoms.size() != 1) && cf3) {
    outtext->clear();
    outtext->append("<font color=red> Please select one carbon"
                    "atom as target in your structure! </font>");
    return false;
  }
  target_atoms = getSelectedAtomsList();
  bool ok;
  int dsrv = dsrVersion.toInt(&ok, 10);
  if (ok && dsrv < 200) {
    // This is obsolete with DSR >= 200 since we fit the fragment to
    // the actual coordinates and not to "names":
    if ( target_atoms.contains(QString(">>"))) {
      outtext->clear();
      outtext->append(QString("<font color=red><b>Symmetrie generated atoms not allowed as target! <br><br>"
                              "Please update DSR.</b></font>"));
      return false;
    }
  }
  emit optionTextChanged();
  bool save_sucess = m_shelxle->fileSave(true, false);
  if (!save_sucess) {
    outtext->append("Could not save the instruction file!");
    return false;
  }
  QStringList *reslist = new QStringList;
  reslist->append(readResfile());
  mygl->source_atoms = source_atoms_tmp;
  int DSRposition = decideDSRInsertLine(reslist);
  if (DSRposition == 0){
    outtext->append("Could not fit fragment. No FVAR command found. \nPlease refine at least one cycle.");
    return false;
  }
  QVector<int> previousLines = findDSRLines(reslist);
  QString wrappedDSRLine = textWrap(combiDSRline);
  m_shelxle->insertDSRLine(wrappedDSRLine, DSRposition, previousLines);
  delete reslist;
  if (rigid) {
    option = "-g ";
  } else {
    option = "";
  }
  if (norefine){
    option += " -n ";
  }
  if (!runext && !invert) // the standard run without extra options
  {
    option += " -r ";
  }
  else if (runext && !invert) {
    option += " -re ";
  }
  else if (!runext && invert)
  {
    option += " -t -r ";
  }
  else if (runext && invert) {
    option += " -t -re ";
  } else {
    qDebug() << "Unhandeled option case in DSRGui occoured!!";
    return false;
  }
  if (!m_shelxlPath.isEmpty() && (dsrVersion.toInt() > 182)) {
    option = " -shx " + m_shelxlPath + " " + option;
  }
  if ((dsrVersion.toInt() >= 200)) {
    option = " -target " + atoms + " " + option;
  }
  QFileInfo resfip(m_shelxle->dirName);
  option = option + resfip.completeBaseName();
  QFileInfo check_res(resfip.completeBaseName()+".res");
  if ( resfip.completeSuffix() == "ins" && check_res.size() == 0) {
    outtext->clear();
    outtext->append("Warning! Something went wrong with your .res file.\n"
                    "You are currently working on the .ins file. Please restore "
                    "the .res file before you continue.");
    return false;
  }
  bool dsr = this->runDSR(option);
  if (!dsr) {
      return false;
  }
  m_shelxle->loadAFile();
  this->show();
  this->raise();
  this->activateWindow();
  return true;
}

void DSRGui::updateDSR(void) {
  //!
  //! Updates DSR to the current version on the web server
  //!
  QString option = " -u";
  outtext->append("Update running...");
  this->runDSR(option);
}

bool DSRGui::runDSR(QString option, bool showresults, QString workdir) {
  //! runs DSR with options and shows the results in outtext if desired.
  dsrResulttext.clear();
  outtext->clear();
  QProcess dsr;
  QFileInfo resfip;
  if (workdir.isEmpty()) {
    // workdir can be the export (fragment) directory for example.
    resfip.setFile(m_shelxle->dirName);
    if (resfip.exists()) {
      // Need to check if path is not empty, because en empty path would cause dsr.start() to fail.
      // absolutePath() truncates the last path part even though its C:\foo\bar --> C:\foo
      dsr.setWorkingDirectory(resfip.absolutePath());
    }
  } else {
    resfip.setFile(workdir);
    dsr.setWorkingDirectory(resfip.absoluteFilePath());
  }
  dsr.setProcessChannelMode(QProcess::MergedChannels);
  dsr.closeWriteChannel();
  // Do not use this with fragment export:
  if (!resfip.absolutePath().isEmpty() && workdir.isEmpty()) {
    // Need to do this, because en empty path would cause dsr.start() to fail.
    dsr.setWorkingDirectory(resfip.absolutePath());
  }
  dsr.start(dsrpath, option.split(" ", skipEmptyParts));
  if (!dsr.waitForFinished()) {
    outtext->append("Unable to start DSR.");
    outtext->append(dsrpath + " " + option);
    outtext->append(dsr.readAll());
    return false;
  } else {
    dsrResulttext.append(dsr.readAll());
    //qDebug() << dsrResulttext;
  }
  /*
  if (dsrResulttext.isEmpty()) {
    bool socket = runTCPServer();
    if (!socket) {
      outtext->append("Unable read DSR output.");
    }
  } */
  if (showresults) {
    // Display the results:
    //outtext->clear();
    outtext->append(combiDSRline);
    outtext->append(dsrResulttext);
  }
  this->show();
  this->raise();
  this->activateWindow();
  //qDebug() << dsrResulttext;
  return true;
}

void DSRGui::searchFragment(QString searchName) {
  //! Searches for fragments in the database
  if ((searchName.length() < 2) && (searchName.length() > 0)){
    return;
  }
  // If search length is zero, restore full list:
  if (searchName.length() == 0){
    if (!listDSRdbFragments("None")) {
      outtext->append("Unable to find DSR fragment database.");
      return;
    }
    return;
  }
  QString option = QString(" -x ") + searchName;
  dsrResulttext.clear();
  this->runDSR(option, false);
  QVector<QStringList> fraglist;
  fraglist.clear();
  foreach (QString line, dsrResulttext.split(QRegularExpression("\n|\r\n|\r"))) {
    if (line.isEmpty()){
      continue;
    }
    if (line.contains(";;")) {
      fraglist.append(line.split(";;"));
    }
  }
  if (fraglist.size() > 0) {
    displayFragmentsList(fraglist, fraglist.at(0).at(0).toLatin1().toUpper());
  } else {
    displayFragmentsList(fraglist, "None");
  }
}

bool DSRGui::isDSRVersionCorrect(QString version) {
  //! checks if the version of DSR found in DSR_DIR
  //! is compatible with this GUI
  bool ok;
  ok = false;
  if (version.trimmed().toInt() >= 182) {
    ok = true;
  }
  return ok;
}

bool DSRGui::listDSRdbFragments(QString fav="None") {
  //! list fragments in DSR database
  //! The -lc parameter of DSR returns a semicolon (;;) separated list
  //! tag;;fullname;;line number;;db
  if (QString("None") == fav) {
    fav = loadFavoriteFragment().toLatin1().toUpper();
  }
  fragmentsList->clear();
  fragmentNameTag.clear();
  QString options = " -lc";
  runDSR(options, true);
  QStringList frag_str_list = dsrResulttext.split(QRegularExpression("\n|\r\n|\r"));
  bool versionOk = false;
  foreach (QString line, frag_str_list) {
    if (line.contains("Duplicate database entry")) {
      outtext->clear();
      outtext->append(dsrResulttext);
      return false;
    }
  }
  // in this case no fragment list returned. Hence, we have an error.
  if (!dsrResulttext.contains(";;")) {
    //outtext->clear();
    outtext->append("Something went wrong with DSR. please tell Daniel Kratzert (dkratzert@gmx.de) about this problem.");
    outtext->append(dsrResulttext);
    return false;
  }
  foreach (QString line, frag_str_list) {
    if (line.isEmpty()){
      continue;
    }
    if ( (line.split(":").size() >= 1) && line.contains("DSR version:")) {
      dsrVersion = line.split(":").at(1).trimmed();
    }
    if (line.trimmed().contains("DSR version:")) {
      versionOk = isDSRVersionCorrect(dsrVersion);
      continue;
    }
    if (line.trimmed().startsWith("***")) {
      outtext->append(line);
      continue;
    }
    if (line.contains(";;")) {
      // collect frags to global list here:
      fragmentsList->append(line.split(";;")); // the global list of all fragments
    }
  }
  if (!versionOk) {
    outtext->clear();
    outtext->append(QString(tr("Detected an old version of DSR.")));
    outtext->append(QString(tr("Please get the most recent version from https://dkratzert.de/dsr.html")));
    return false;
  }
  displayFragmentsList(*fragmentsList, fav);
  return true;
}


void DSRGui::displayFragmentsList(QVector<QStringList> list, QString fav="None") {
  //! displays the list of fragments in a table view
  //! The first column (the tag) is hidden, only the name is displayed.
  QStandardItem *fraglabel = new QStandardItem(QString("Fragment Name"));
  fraglabel->setTextAlignment(Qt::AlignLeft);
  QStandardItemModel *FragListmodel = new QStandardItemModel(list.size(), 2, this); //x Rows and 2 Columns
  FragListmodel->setHorizontalHeaderItem(0, new QStandardItem(QString("tag")));
  FragListmodel->setHorizontalHeaderItem(1, fraglabel);
  QStringList line;
  for (int i = 0; i < list.size(); ++i) {
    line.clear();
    line = list[i];
    if ( line.size() < 3 ) {
      continue;
    }
    QString column1 = line[0];
    QString column2 = line[1];
    QStandardItem *nameItem;
    // Add a bold *user* to all fragments from the user db
    if (line[3].contains("dsr_user_db")) {
      column2.append(" *user*");
      nameItem = new QStandardItem(QString(column2));
      QFont f = nameItem->font();
      f.setBold(true);
      nameItem->setFont(f);
    } else {
      nameItem = new QStandardItem(QString(column2));
    }
    FragListmodel->setItem(i, 0, new QStandardItem(QString(column1)));
    FragListmodel->setItem(i, 1, nameItem);
    // load the last fragment:
    if (fav == line.at(0).toLatin1().toUpper()) {
      if (FragListmodel->hasIndex(i, 0)) {
        setFragName(FragListmodel->index(i, 0));
      }
    }
  }
  fragmentTableView->setModel(FragListmodel);
  fragmentTableView->verticalHeader()->hide();
  fragmentTableView->hideColumn(0);
  fragmentTableView->setColumnWidth(1, 600);
  fragmentTableView->setGridStyle(Qt::PenStyle(Qt::NoPen));
  fragmentTableView->setEditTriggers(QAbstractItemView::NoEditTriggers);
}

QString DSRGui::getDSRDir() {
  //! returns the value of the DSR_DIR variable
  //! in case of error, it returns an empty string
#if (QT_VERSION >= QT_VERSION_CHECK(5, 10, 0))
  QString dsrdir = qEnvironmentVariable("DSR_DIR");
#else
  QString dsrdir = qgetenv("DSR_DIR");
#endif
  if (!QFile::exists(dsrdir)){
    if (!which("dsr").isEmpty()) {
      QFileInfo fi(which("dsr").at(0));
      if (fi.exists()) {
        dsrdir = fi.absolutePath();
      }
    }
    if (QFile::exists("/Applications/DSR")) {
        dsrdir = "/Applications/DSR";
    }
#if (QT_VERSION >= QT_VERSION_CHECK(5, 10, 0))
    QString dsrdir2 = qEnvironmentVariable("DSRDIR");
#else
    QString dsrdir2 = qgetenv("DSRDIR");
#endif
    if (QFile::exists(dsrdir2)) {
      qDebug() << "You are probably using an older version of DSR."
                  "\n Please use version 1.7.7 or above.";
      // return empty string, because dsr.bat will
      // hinder dsr from starting properly:
      return QString("");
    }
  }
  return QDir::fromNativeSeparators(dsrdir);
}

QString DSRGui::getDSRdbDir() {
  //! returns the directory with the userdb -> the home directory
  QString dbdir = QDir::homePath();
  return QDir::fromNativeSeparators(dbdir);;
}


void DSRGui::setExportDirDialog() {
  //! File dialog to define the directory for the res file
  //! exported by DSR
  export_dir = "";
  export_dir = QFileDialog::getExistingDirectory(this, tr("Export Fragment to ..."), tr("Directory"));
  if (QFile::exists(export_dir)){
    emit exportDirChanged(export_dir);
  }
}