Merge pull request OpenChemistry#1863 from ghutchis/alchemy

Add a quick "change elements" command (e.g., setting to dummy)

avogadro/qtplugins/CMakeLists.txt

@@ -96,20 +96,26 @@ endfunction()
 
 # Now to make the plugins.
 add_subdirectory(3dmol)
-add_subdirectory(applycolors)
+add_subdirectory(alchemy)
 add_subdirectory(aligntool)
+add_subdirectory(apbs)
+add_subdirectory(applycolors)
 add_subdirectory(bondcentrictool)
 add_subdirectory(bonding)
 add_subdirectory(cartoons)
 add_subdirectory(centroid)
 add_subdirectory(configurepython)
+add_subdirectory(coordinateeditor)
 add_subdirectory(copypaste)
+add_subdirectory(cp2kinput)
 add_subdirectory(crystal)
 add_subdirectory(customelements)
 # add_subdirectory(dipole)
 add_subdirectory(editor)
 add_subdirectory(fetchpdb)
 add_subdirectory(focus)
+add_subdirectory(forcefield)
+add_subdirectory(gamessinput)
 add_subdirectory(hydrogens)
 add_subdirectory(importpqr)
 add_subdirectory(insertdna)
@@ -135,20 +141,11 @@ if(USE_SPGLIB)
   add_subdirectory(spacegroup)
 endif()
 add_subdirectory(surfaces)
+add_subdirectory(svg)
 add_subdirectory(templatetool)
 add_subdirectory(vibrations)
 add_subdirectory(vrml)
 
-# These should work after the QRegExp migration
-add_subdirectory(apbs)
-add_subdirectory(coordinateeditor)
-add_subdirectory(cp2kinput)
-add_subdirectory(forcefield)
-add_subdirectory(gamessinput)
-
-# The SVG library changed in Qt6
-add_subdirectory(svg)
-
 # Plugins that require VTK
 if(USE_VTK)
   add_subdirectory(coloropacitymap)

avogadro/qtplugins/alchemy/CMakeLists.txt

@@ -0,0 +1,10 @@
+include_directories(${CMAKE_CURRENT_BINARY_DIR})
+
+avogadro_plugin(Alchemy
+  "Change elements"
+  ExtensionPlugin
+  alchemy.h
+  Alchemy
+  "alchemy.cpp"
+  ""
+)

avogadro/qtplugins/alchemy/alchemy.cpp

@@ -0,0 +1,89 @@
+/******************************************************************************
+  This source file is part of the Avogadro project.
+  This source code is released under the 3-Clause BSD License, (see "LICENSE").
+******************************************************************************/
+
+#include "alchemy.h"
+
+#include <avogadro/core/elements.h>
+#include <avogadro/qtgui/molecule.h>
+
+#include <QAction>
+#include <QtCore/QSettings>
+#include <QtWidgets/QDialog>
+#include <QtWidgets/QInputDialog>
+
+#include <vector>
+
+namespace Avogadro::QtPlugins {
+
+using Core::Array;
+using Core::Elements;
+
+Alchemy::Alchemy(QObject* parent_)
+  : Avogadro::QtGui::ExtensionPlugin(parent_),
+    m_action(new QAction(tr("Change Elements…"), this)), m_molecule(nullptr)
+{
+  m_action->setProperty("menu priority", 750);
+
+  connect(m_action, &QAction::triggered, this, &Alchemy::changeElements);
+}
+
+Alchemy::~Alchemy() {}
+
+QList<QAction*> Alchemy::actions() const
+{
+  QList<QAction*> result;
+  return result << m_action;
+}
+
+QStringList Alchemy::menuPath(QAction*) const
+{
+  return QStringList() << tr("&Build");
+}
+
+void Alchemy::setMolecule(QtGui::Molecule* mol)
+{
+  m_molecule = mol;
+}
+
+void Alchemy::changeElements()
+{
+  if (!m_molecule)
+    return;
+
+  // assemble the list of elements
+  QStringList choices;
+  for (unsigned char i = 0; i < Elements::elementCount(); ++i) {
+    QString choice("%1: %2");
+    choice = choice.arg(i).arg(Elements::name(i));
+    choices << choice;
+  }
+
+  // get the element of the first selected atom
+  unsigned char firstElement = 0;
+  for (Index i = 0; i < m_molecule->atomCount(); ++i) {
+    if (m_molecule->atomSelected(i)) {
+      firstElement = m_molecule->atom(i).atomicNumber();
+      break;
+    }
+  }
+
+  bool ok = false;
+  QString currentChoice = QInputDialog::getItem(
+    qobject_cast<QWidget*>(parent()), tr("Change Elements"), tr("Element:"),
+    choices, static_cast<int>(firstElement), false, &ok);
+  if (!ok)
+    return;
+
+  unsigned char newElement = currentChoice.section(':', 0, 0).toUShort();
+  // loop through the selected atoms and change their elements
+  for (Index i = 0; i < m_molecule->atomCount(); ++i) {
+    if (m_molecule->atomSelected(i))
+      m_molecule->atom(i).setAtomicNumber(newElement);
+  }
+
+  m_molecule->emitChanged(QtGui::Molecule::Atoms);
+}
+
+} // namespace Avogadro::QtPlugins

avogadro/qtplugins/alchemy/alchemy.h

@@ -0,0 +1,57 @@
+/******************************************************************************
+  This source file is part of the Avogadro project.
+  This source code is released under the 3-Clause BSD License, (see "LICENSE").
+******************************************************************************/
+
+#ifndef AVOGADRO_QTPLUGINS_ALCHEMY_H
+#define AVOGADRO_QTPLUGINS_ALCHEMY_H
+
+#include <avogadro/core/avogadrocore.h>
+#include <avogadro/qtgui/extensionplugin.h>
+
+#include <QtWidgets/QDialog>
+
+namespace Ui {
+class BondingDialog;
+}
+
+namespace Avogadro {
+namespace QtPlugins {
+
+/**
+ * @brief The Bonding class performs bonding operations on demand.
+ */
+class Alchemy : public QtGui::ExtensionPlugin
+{
+  Q_OBJECT
+public:
+  explicit Alchemy(QObject* parent_ = nullptr);
+  ~Alchemy() override;
+
+  QString name() const override { return tr("Alchemy"); }
+
+  QString description() const override
+  {
+    return tr("Change elements of atoms.");
+  }
+
+  QList<QAction*> actions() const override;
+
+  QStringList menuPath(QAction* action) const override;
+
+public slots:
+  void setMolecule(QtGui::Molecule* mol) override;
+
+private slots:
+  void changeElements();
+
+private:
+  QtGui::Molecule* m_molecule;
+
+  QAction* m_action;
+};
+
+} // namespace QtPlugins
+} // namespace Avogadro
+
+#endif // AVOGADRO_QTPLUGINS_ALCHEMY_H