Add option for pair interaction highlighting without info window show…

…ing, update info label behaviour when pressing I or ctrl + right click

src/core/CMakeLists.txt

@@ -2,6 +2,7 @@ add_library(cx_core
     "${CMAKE_CURRENT_SOURCE_DIR}/adp.cpp"
     "${CMAKE_CURRENT_SOURCE_DIR}/chemicalstructure.cpp"
     "${CMAKE_CURRENT_SOURCE_DIR}/close_contact_criteria.cpp"
+    "${CMAKE_CURRENT_SOURCE_DIR}/colormap.cpp"
     "${CMAKE_CURRENT_SOURCE_DIR}/dynamicstructure.cpp"
     "${CMAKE_CURRENT_SOURCE_DIR}/element.cpp"
     "${CMAKE_CURRENT_SOURCE_DIR}/elementdata.cpp"

src/core/chemicalstructure.cpp

@@ -1,4 +1,5 @@
 #include "chemicalstructure.h"
+#include "colormap.h"
 #include "elementdata.h"
 #include "mesh.h"
 #include "object_tree_model.h"
@@ -22,7 +23,10 @@ occ::Vec3 ChemicalStructure::atomPosition(GenericAtomIndex idx) const {
   return m_atomicPositions.col(i);
 }
 
-void ChemicalStructure::updateBondGraph() { guessBondsBasedOnDistances(); }
+void ChemicalStructure::updateBondGraph() {
+  guessBondsBasedOnDistances();
+  setAllFragmentColors(FragmentColorSettings{});
+}
 
 void ChemicalStructure::guessBondsBasedOnDistances() {
 
@@ -645,7 +649,7 @@ void ChemicalStructure::resetAtomsAndBonds(bool toSelection) {
   // TODO
 }
 
-void ChemicalStructure::setShowContacts(const ContactSettings & state) {
+void ChemicalStructure::setShowContacts(const ContactSettings &state) {
   // TODO
 }
 
@@ -1081,9 +1085,19 @@ void ChemicalStructure::setFragmentColor(FragmentIndex fragment,
   }
 }
 
-void ChemicalStructure::setAllFragmentColors(const QColor &color) {
-  for (auto &[fragIndex, frag] : m_fragments) {
-    frag.color = color;
+void ChemicalStructure::setAllFragmentColors(
+    const FragmentColorSettings &settings) {
+  if (settings.method == FragmentColorSettings::Method::Constant) {
+    for (auto &[fragIndex, frag] : m_fragments) {
+      frag.color = settings.color;
+    }
+  } else if (settings.method ==
+             FragmentColorSettings::Method::SymmetryUniqueFragment) {
+    size_t nasym = m_symmetryUniqueFragments.size();
+    ColorMapFunc cmap(ColorMapName::Hokusai1, 0, nasym);
+    for (auto &[idx, frag] : m_fragments) {
+      frag.color = cmap(frag.asymmetricFragmentIndex.u);
+    }
   }
   emit atomsChanged();
 }
@@ -1108,6 +1122,44 @@ ChemicalStructure::atomicDisplacementParametersForAtoms(
   return std::vector<AtomicDisplacementParameters>(idxs.size());
 }
 
+QString ChemicalStructure::getFragmentLabel(const FragmentIndex &index) {
+  const auto &fragments = symmetryUniqueFragments();
+  if (m_fragmentLabels.size() != fragments.size()) {
+    ankerl::unordered_dense::map<QString, std::pair<QString, int>>
+        formulaToIndex;
+    char currentLabel = 'A';
+    int labelCount = 0;
+
+    for (const auto &[fragmentIndex, fragment] : fragments) {
+      QString formula = formulaSumForAtoms(fragment.atomIndices, false);
+      auto it = formulaToIndex.find(formula);
+
+      if (it == formulaToIndex.end()) {
+        QString label = QString(1, currentLabel);
+        formulaToIndex[formula] = {label, 1};
+        m_fragmentLabels[fragmentIndex] = "1" + label;
+
+        labelCount++;
+        if (labelCount == 26) {
+          currentLabel = 'A';
+          labelCount = 0;
+        } else {
+          currentLabel++;
+        }
+      } else {
+        auto &[label, count] = it->second;
+        count++;
+        m_fragmentLabels[fragmentIndex] = QString::number(count) + label;
+      }
+    }
+  }
+
+  const auto kv = m_fragmentLabels.find(index);
+  if (kv != m_fragmentLabels.end())
+    return kv->second;
+  return "??";
+}
+
 AtomicDisplacementParameters
 ChemicalStructure::atomicDisplacementParameters(GenericAtomIndex idx) const {
   return AtomicDisplacementParameters{};

src/core/chemicalstructure.h

@@ -103,6 +103,8 @@ class ChemicalStructure : public QObject {
 
   virtual occ::Mat3N convertCoordinates(const occ::Mat3N &pos, CoordinateConversion) const;
 
+  QString getFragmentLabel(const FragmentIndex &);
+
   // colors
   QColor atomColor(GenericAtomIndex atomIndex) const;
   void overrideAtomColor(GenericAtomIndex, const QColor &);
@@ -205,7 +207,7 @@ class ChemicalStructure : public QObject {
 
   virtual QColor getFragmentColor(FragmentIndex) const;
   virtual void setFragmentColor(FragmentIndex, const QColor &);
-  virtual void setAllFragmentColors(const QColor &color);
+  virtual void setAllFragmentColors(const FragmentColorSettings &);
 
   // dynamics data
   inline bool hasFrameData() const { return frameCount() > 0; }
@@ -313,6 +315,7 @@ class ChemicalStructure : public QObject {
 
   // all of these must be updated when the bondGraph is updated
   FragmentMap m_fragments;
+  ankerl::unordered_dense::map<FragmentIndex, QString, FragmentIndexHash> m_fragmentLabels;
   FragmentMap m_symmetryUniqueFragments;
 
   std::vector<FragmentIndex> m_fragmentForAtom;

src/core/fragment.h

@@ -6,12 +6,24 @@
 #include <QVector3D>
 #include <occ/core/linear_algebra.h>
 
+using Transform = Eigen::Isometry3d;
+
 struct DimerAtoms {
   std::vector<GenericAtomIndex> a;
   std::vector<GenericAtomIndex> b;
 };
 
-using Transform = Eigen::Isometry3d;
+struct FragmentColorSettings {
+  enum class Method {
+    UnitCellFragment,
+    SymmetryUniqueFragment,
+    Constant
+  };
+
+  Method method{Method::SymmetryUniqueFragment};
+  QColor color{Qt::gray};
+};
+
 struct Fragment {
 
   struct NearestAtomResult {

src/crystal/crystalstructure.cpp

@@ -1,6 +1,7 @@
 #include "crystalstructure.h"
 #include <iostream>
 #include <occ/core/kabsch.h>
+#include "colormap.h"
 
 using VertexDesc =
     typename occ::core::graph::PeriodicBondGraph::VertexDescriptor;
@@ -154,6 +155,7 @@ void CrystalStructure::updateBondGraph() {
       m_fragmentForAtom[genericIndexToIndex(idx)] = frag.index;
     }
   }
+  setAllFragmentColors(FragmentColorSettings{});
 }
 
 void CrystalStructure::resetAtomsAndBonds(bool toSelection) {
@@ -326,9 +328,18 @@ void CrystalStructure::setFragmentColor(FragmentIndex fragment,
   }
 }
 
-void CrystalStructure::setAllFragmentColors(const QColor &color) {
-  for (auto &[fragIndex, frag] : m_fragments) {
-    frag.color = color;
+void CrystalStructure::setAllFragmentColors(const FragmentColorSettings &settings) {
+  if(settings.method == FragmentColorSettings::Method::Constant) {
+    for (auto &[fragIndex, frag] : m_fragments) {
+      frag.color = settings.color;
+    }
+  }
+  else if(settings.method == FragmentColorSettings::Method::SymmetryUniqueFragment) {
+    size_t nasym = m_symmetryUniqueFragments.size();
+    ColorMapFunc cmap(ColorMapName::Hokusai1, 0, nasym);
+    for(auto &[idx, frag] : m_fragments) {
+      frag.color = cmap(frag.asymmetricFragmentIndex.u);
+    }
   }
   emit atomsChanged();
 }

src/crystal/crystalstructure.h

@@ -88,7 +88,7 @@ class CrystalStructure : public ChemicalStructure {
 
   QColor getFragmentColor(FragmentIndex) const override;
   void setFragmentColor(FragmentIndex, const QColor &) override;
-  void setAllFragmentColors(const QColor &color) override;
+  void setAllFragmentColors(const FragmentColorSettings &) override;
 
   Fragment::State getSymmetryUniqueFragmentState(FragmentIndex) const override;
   void setSymmetryUniqueFragmentState(FragmentIndex, Fragment::State) override;

src/crystalx.cpp

@@ -351,6 +351,8 @@ void Crystalx::initConnections() {
   */
   connect(glWindow, &GLWindow::resetCurrentCrystal, project,
           &Project::resetCurrentCrystal);
+  connect(glWindow, &GLWindow::contextualFilterAtoms,
+          project, &Project::filterAtomsForCurrentScene);
 
   connect(m_taskManager, &TaskManager::taskComplete, this,
           &Crystalx::taskManagerTaskComplete);
@@ -408,6 +410,9 @@ void Crystalx::initMenuConnections() {
   connect(energyFrameworksAction, &QAction::triggered, this,
           &Crystalx::showEnergyFrameworkDialog);
 
+  connect(togglePairHighlightingAction, &QAction::toggled, this,
+          &Crystalx::togglePairInteractionHighlighting);
+
   connect(selectAllAtomsAction, &QAction::triggered, project,
           &Project::selectAllAtoms);
   connect(selectsAtomsInsideCurrentSurfaceAction, &QAction::triggered, project,
@@ -420,8 +425,9 @@ void Crystalx::initMenuConnections() {
           &Project::selectSuppressedAtoms);
   connect(removeIncompleteFragmentsAction, &QAction::triggered, project,
           &Project::removeIncompleteFragmentsForCurrentCrystal);
-  connect(removeSelectedAtomsAction, &QAction::triggered, project,
-          &Project::removeSelectedAtomsForCurrentCrystal);
+  connect(removeSelectedAtomsAction, &QAction::triggered,[this]() {
+    project->filterAtomsForCurrentScene(AtomFlag::Selected, true);
+  });
   connect(suppressSelectedAtomsAction, &QAction::triggered, project,
           &Project::suppressSelectedAtoms);
   connect(unsuppressSelectedAtomsAction, &QAction::triggered, project,
@@ -1926,6 +1932,14 @@ void Crystalx::updateInfo(InfoType infoType) {
   }
 }
 
+void Crystalx::togglePairInteractionHighlighting(bool state) {
+  qDebug() << "Toggle pair interaction highlighting";
+  Scene *scene = project->currentScene();
+  if(!scene) return;
+  scene->togglePairHighlighting(state);
+  glWindow->redraw();
+}
+
 void Crystalx::setInfoTabSpecificViewOptions(InfoType infoType) {
   Scene *scene = project->currentScene();
   Q_ASSERT(scene);

src/crystalx.h

@@ -59,6 +59,7 @@ class Crystalx : public QMainWindow, public Ui::Crystalx {
   void loadExternalFileData(QString);
 
 public slots:
+  void togglePairInteractionHighlighting(bool);
   void handleBusyStateChange(bool);
   void generateSurface(isosurface::Parameters);
   void generateSurfaceRequiringWavefunction(isosurface::Parameters, wfn::Parameters);

src/crystalx.ui

@@ -167,6 +167,7 @@
     <addaction name="optionsMoleculeStylePopup"/>
     <addaction name="enableMultipleUnitCellBoxesAction"/>
     <addaction name="cycleDisorderHighlightingAction"/>
+    <addaction name="togglePairHighlightingAction"/>
     <addaction name="separator"/>
     <addaction name="selectMenu"/>
     <addaction name="removeMenu"/>
@@ -975,10 +976,10 @@
     <bool>true</bool>
    </property>
    <property name="text">
-    <string>Toggle Pair Highlighting</string>
+    <string>Fragment pair colouring</string>
    </property>
    <property name="shortcut">
-    <string>Ctrl+Y</string>
+    <string>Shift+P</string>
    </property>
   </action>
   <action name="calculateVoidDomainsAction">
@@ -1127,6 +1128,14 @@
     <enum>QAction::NoRole</enum>
    </property>
   </action>
+  <action name="removeUnselectedAtomsAction">
+   <property name="text">
+    <string>Remove unselected atoms</string>
+   </property>
+   <property name="toolTip">
+    <string>Show Only Selected Atoms</string>
+   </property>
+  </action>
  </widget>
  <resources>
   <include location="../icons/crystalexplorer.qrc"/>