Warning, file /education/kalzium/src/tools/moleculeview.cpp was not indexed or was modified since last indexation (in which case cross-reference links may be missing, inaccurate or erroneous).

 /*
     SPDX-FileCopyrightText: 2006 Carsten Niehaus <cniehaus@kde.org>
     SPDX-FileCopyrightText: 2007-2008 Marcus D. Hanwell <marcus@cryos.org>
     SPDX-FileCopyrightText: 2016 Andreas Cord-Landwehr <cordlandwehr@kde.org>
     SPDX-License-Identifier: GPL-2.0-or-later
 */
 
 #include "moleculeview.h"
 
 #include <avogadro/qtgui/elementtranslator.h>
 #include <avogadro/qtgui/periodictableview.h>
 #include <avogadro/qtgui/scenepluginmodel.h>
 #include <avogadro/qtgui/toolplugin.h>
 
 #include <QDebug>
 #include <QFileInfo>
 #include <QGLFormat>
 #include <QUrl>
 
 #include <KIO/Job>
 #include <KJob>
 #include <KLocalizedString>
 #include <KMessageBox>
 #include <KNS3/DownloadDialog>
 
 #include "iowrapper.h"
 
 #include <openbabel/mol.h>
 #include <openbabel/obiter.h>
 // This is needed to ensure that the forcefields are set up right with GCC vis
 #ifdef __KDE_HAVE_GCC_VISIBILITY
 #define HAVE_GCC_VISIBILITY
 #endif
 #include <KGuiItem>
 #include <QDialogButtonBox>
 #include <QFileDialog>
 #include <QPushButton>
 #include <QStandardPaths>
 #include <QVBoxLayout>
 #include <openbabel/forcefield.h>
 
 using namespace OpenBabel;
 using namespace Avogadro::QtGui;
 
 MoleculeDialog::MoleculeDialog(QWidget *parent)
     : QDialog(parent)
     , m_path(QString())
     , m_periodicTable(nullptr)
 {
     // use multi-sample (anti-aliased) OpenGL if available
     QGLFormat defFormat = QGLFormat::defaultFormat();
     defFormat.setSampleBuffers(true);
     QGLFormat::setDefaultFormat(defFormat);
 
     setWindowTitle(i18nc("@title:window", "Molecular Editor"));
     QDialogButtonBox *buttonBox = new QDialogButtonBox(QDialogButtonBox::Close);
     QWidget *mainWidget = new QWidget(this);
     QVBoxLayout *mainLayout = new QVBoxLayout;
     setLayout(mainLayout);
     mainLayout->addWidget(mainWidget);
     QPushButton *user1Button = new QPushButton;
     buttonBox->addButton(user1Button, QDialogButtonBox::ActionRole);
     QPushButton *user2Button = new QPushButton;
     buttonBox->addButton(user2Button, QDialogButtonBox::ActionRole);
     QPushButton *user3Button = new QPushButton;
     buttonBox->addButton(user3Button, QDialogButtonBox::ActionRole);
     connect(buttonBox, &QDialogButtonBox::rejected, this, &MoleculeDialog::reject);
 
     user1Button->setDefault(true);
 
     KGuiItem::assign(user1Button, KGuiItem(i18n("Load Molecule")));
 
     KGuiItem::assign(user2Button, KGuiItem(i18n("Download New Molecules")));
 
     KGuiItem::assign(user3Button, KGuiItem(i18n("Save Molecule")));
 
     ui.setupUi(mainWidget);
 
     // Attempt to set up the UFF forcefield
     //     m_forceField = OBForceField::FindForceField("UFF");
     //     if (!m_forceField) {
     //         ui.optimizeButton->setEnabled(false);
     //     }
 
     ui.styleCombo->addItems({"Ball and Stick", "Licorice", "Van der Waals", "Van der Waals (AO)", "Wireframe"});
     connect(ui.styleCombo, static_cast<void (QComboBox::*)(int)>(&QComboBox::currentIndexChanged), this, &MoleculeDialog::slotUpdateScenePlugin);
     slotUpdateScenePlugin();
 
     connect(ui.tabWidget, &QTabWidget::currentChanged, this, &MoleculeDialog::setViewEdit);
 
     // Editing parameters
     // commented out until we find new API for pumbling to OpenBabel
     //     connect(ui.optimizeButton, &QPushButton::clicked,
     //             this, &MoleculeDialog::slotGeometryOptimize);
     connect(ui.clearDrawingButton, &QPushButton::clicked, this, &MoleculeDialog::clearAllElementsInEditor);
 
     connect(ui.glWidget->molecule(), &Avogadro::QtGui::Molecule::changed, this, &MoleculeDialog::slotUpdateStatistics);
 
     connect(user1Button, &QPushButton::clicked, this, &MoleculeDialog::slotLoadMolecule);
     connect(user2Button, &QPushButton::clicked, this, &MoleculeDialog::slotDownloadNewStuff);
     connect(user3Button, &QPushButton::clicked, this, &MoleculeDialog::slotSaveMolecule);
 
     mainLayout->addWidget(buttonBox);
 
     // Check that we have managed to load up some tools and engines
     int nTools = ui.glWidget->tools().size();
     if (!nTools) {
         QString error = i18n("No tools loaded - it is likely that the Avogadro plugins could not be located.");
         // use parent as parent for the messagebix, as this dialog is not shown yet
         // and thus not known to the window system to position to dialog relative to it
         KMessageBox::error(parent, error, i18n("Kalzium"));
     }
 
     // objectName is also used in Avogadro2 for identifying tools
     foreach (auto *tool, ui.glWidget->tools()) {
         if (tool->objectName() == QLatin1String("Editor")) {
             ui.editTabLayout->insertWidget(0, tool->toolWidget());
             break;
         }
     }
 }
 
 void MoleculeDialog::slotLoadMolecule()
 {
     // Check that we have managed to load up some tools and engines
     int nTools = ui.glWidget->tools().size();
 
     if (!nTools) {
         QString error = i18n(
             "No tools loaded - it is likely that the Avogadro plugins could not be located. "
             "No molecules can be viewed until this issue is resolved.");
         KMessageBox::information(this, error);
     }
 
     m_path = QStandardPaths::locate(QStandardPaths::AppLocalDataLocation, QStringLiteral("data/molecules/"), QStandardPaths::LocateDirectory);
 
     QString commonMoleculeFormats = i18n("Common molecule formats");
     QString allFiles = i18n("All files");
 
     QString filename = QFileDialog::getOpenFileName(
                        this,
                        i18n("Choose a file to open"),
                        m_path,
                        commonMoleculeFormats + "(*.cml *.xyz *.ent *.pdb *.alc *.chm *.cdx *.cdxml *.c3d1 *.c3d2"
                        " *.gpr *.mdl *.mol *.sdf *.sd *.crk3d *.cht *.dmol *.bgf"
                        " *.gam *.inp *.gamin *.gamout *.tmol *.fract"
                        " *.mpd *.mol2);;" + allFiles + "(*)");
 
     loadMolecule(filename);
 }
 
 void MoleculeDialog::slotUpdateScenePlugin()
 {
     const QString text = ui.styleCombo->currentText();
     for (int i = 0; i < ui.glWidget->sceneModel().rowCount(QModelIndex()); ++i) {
         QModelIndex index = ui.glWidget->sceneModel().index(i, 0);
         if (text == ui.glWidget->sceneModel().data(index, Qt::DisplayRole)) {
             ui.glWidget->sceneModel().setData(index, Qt::Checked, Qt::CheckStateRole);
         } else {
             ui.glWidget->sceneModel().setData(index, Qt::Unchecked, Qt::CheckStateRole);
         }
     }
 }
 
 void MoleculeDialog::loadMolecule(const QString &filename)
 {
     if (filename.isEmpty()) {
         return;
     }
 
     // 1. workaround for missing copy-constructor: fixed in Avogadro2 > 0.9
     // 2. another workaround for broken copy-constructor that does not
     //    initialize the m_undoMolecule private member variable;
     //    this molecule should be created on the heap instead of the stack
     auto molecule_ptr = IoWrapper::readMolecule(filename);
     if (!molecule_ptr) {
         KMessageBox::error(this, i18n("Could not load molecule"), i18n("Loading the molecule failed."));
         return;
     }
 
     m_molecule = *molecule_ptr;
 
     if (m_molecule.atomCount() != 0) {
         disconnect(ui.glWidget->molecule(), nullptr, this, nullptr);
         ui.glWidget->setMolecule(&m_molecule);
         ui.glWidget->update();
         slotUpdateStatistics();
         connect(&m_molecule, &Avogadro::QtGui::Molecule::changed, this, &MoleculeDialog::slotUpdateStatistics);
     }
     ui.glWidget->resetCamera();
     ui.glWidget->updateScene();
 }
 
 void MoleculeDialog::clearAllElementsInEditor()
 {
     ui.glWidget->molecule()->clearBonds();
     ui.glWidget->molecule()->clearAtoms();
     ui.glWidget->updateScene();
 }
 
 void MoleculeDialog::slotSaveMolecule()
 {
     QString commonMoleculeFormats = i18n("Common molecule formats");
     QString allFiles = i18n("All files");
     QString filename = QFileDialog::getSaveFileName(this,
                                                     i18n("Choose a file to save to"),
                                                     QString(),
                                                     commonMoleculeFormats
                                                         + QStringLiteral(" (*.cml *.xyz *.ent *.pdb *.alc *.chm *.cdx *.cdxml *.c3d1 *.c3d2"
                                                                          " *.gpr *.mdl *.mol *.sdf *.sd *.crk3d *.cht *.dmol *.bgf"
                                                                          " *.gam *.inp *.gamin *.gamout *.tmol *.fract"
                                                                          " *.mpd *.mol2);;")
                                                         + allFiles + QStringLiteral(" (*)"));
 
     if (!filename.contains(QLatin1String("."))) {
         filename.append(QLatin1String(".cml"));
     }
 
     IoWrapper io;
     io.writeMolecule(filename, ui.glWidget->molecule());
 }
 
 void MoleculeDialog::setViewEdit(int mode)
 {
     if (mode == 0) {
         ui.glWidget->setActiveTool(QStringLiteral("Navigator"));
     } else if (mode == 1) {
         ui.glWidget->setActiveTool(QStringLiteral("Editor"));
     } else if (mode == 2) {
         ui.glWidget->setActiveTool(QStringLiteral("MeasureTool"));
     }
 }
 
 MoleculeDialog::~MoleculeDialog()
 {
 }
 
 void MoleculeDialog::slotUpdateStatistics()
 {
     Molecule *mol = ui.glWidget->molecule();
     if (!mol) {
         return;
     }
     const std::string name = mol->data(QStringLiteral("name").toStdString()).toString();
     ui.nameLabel->setText(QString::fromStdString(name));
     ui.weightLabel->setText(
         i18nc("This 'u' stands for the chemical unit (u for 'units'). Most likely this does not need to be translated at all!", "%1 u", mol->mass()));
     ui.formulaLabel->setText(IoWrapper::getPrettyFormula(mol));
     ui.glWidget->update();
 }
 
 void MoleculeDialog::slotDownloadNewStuff()
 {
     qDebug() << "Kalzium new stuff";
 
     KNS3::DownloadDialog dialog(this);
     dialog.exec();
     // list of changed entries
     QString destinationDir = QStandardPaths::writableLocation(QStandardPaths::DocumentsLocation);
     QDir dir(destinationDir);
     if (!dir.exists()) {
         destinationDir = QDir::homePath();
     }
     bool anyError = false;
     bool anySuccess = false;
     bool moreOneInstalledFile = false;
     QString exactlyOneFile;
     foreach (const KNS3::Entry &entry, dialog.changedEntries()) {
         // care only about installed ones
         if (entry.status() == KNS3::Entry::Installed) {
             qDebug() << "Changed Entry: " << entry.installedFiles();
             foreach (const QString &origFile, entry.installedFiles()) {
                 const QString destFile = destinationDir + '/' + QFileInfo(origFile).fileName();
                 KJob *job = KIO::file_move(QUrl::fromLocalFile(origFile), QUrl::fromLocalFile(destFile));
                 ;
                 const bool success = job->exec();
                 if (success) {
                     if (exactlyOneFile.isEmpty()) {
                         exactlyOneFile = destFile;
                     } else {
                         moreOneInstalledFile = true;
                     }
                     anySuccess = true;
                 } else {
                     KMessageBox::error(this, i18n("Failed to download molecule %1 to %2.", entry.name(), destFile));
                     anyError = true;
                 }
             }
         }
     }
     if (anySuccess) {
         if (anyError) {
             KMessageBox::information(this, i18n("The molecules that could be downloaded have been saved to %1.", destinationDir));
         } else {
             KMessageBox::information(this, i18n("The molecules have been saved to %1.", destinationDir));
         }
         if (!moreOneInstalledFile) {
             loadMolecule(exactlyOneFile);
         }
     }
 }
 
 // TODO there is currently no API to perform the necessary OpenBabel-Avogadro
 //      conversions, after the migration to Avogadro2; at least with v0.9
 void MoleculeDialog::slotGeometryOptimize()
 {
     //     // Perform a geometry optimization
     //     if (!m_forceField) {
     //         return;
     //     }
     //
     //     Molecule* molecule = ui.glWidget->molecule();
     //     OpenBabel::OBMol obmol;//(molecule->OBMol());
     //
     //     // Warn the user if the force field cannot be set up for the molecule
     //     if (!m_forceField->Setup(obmol)) {
     //         KMessageBox::error(this,
     //                         i18n("Could not set up force field for this molecule"),
     //                         i18n("Kalzium"));
     //         return;
     //     }
     //
     //     // Reasonable default values for most users
     //     m_forceField->SteepestDescentInitialize(500, 1.0e-5);
     //     // Provide some feedback as the optimization runs
     //     while (m_forceField->SteepestDescentTakeNSteps(5)) {
     //         m_forceField->UpdateCoordinates(obmol);
     //         molecule->setOBMol(&obmol);
     //         molecule->update();
     //     }
 }