Labels

avogadro/core/atom.h

@@ -185,6 +185,9 @@ class AtomTemplate
    */
   void setForceVector(const Vector3& force);
   Vector3 forceVector() const;
+
+  void setLabel(const std::string& label);
+  std::string label() const;
   /** @} */
 
 private:
@@ -365,6 +368,18 @@ Vector3 AtomTemplate<Molecule_T>::forceVector() const
            : Vector3::Zero();
 }
 
+template <class Molecule_T>
+void AtomTemplate<Molecule_T>::setLabel(const std::string& label)
+{
+  m_molecule->setLabel(m_index, label);
+}
+
+template <class Molecule_T>
+std::string AtomTemplate<Molecule_T>::label() const
+{
+  return m_molecule->label(m_index);
+}
+
 } // namespace Core
 } // namespace Avogadro
 

avogadro/core/molecule.cpp

@@ -31,8 +31,8 @@ Molecule::Molecule()
 Molecule::Molecule(const Molecule& other)
   : m_data(other.m_data), m_customElementMap(other.m_customElementMap),
     m_positions2d(other.m_positions2d), m_positions3d(other.m_positions3d),
-    m_coordinates3d(other.m_coordinates3d), m_timesteps(other.m_timesteps),
-    m_hybridizations(other.m_hybridizations),
+    m_label(other.m_label), m_coordinates3d(other.m_coordinates3d),
+    m_timesteps(other.m_timesteps), m_hybridizations(other.m_hybridizations),
     m_formalCharges(other.m_formalCharges), m_colors(other.m_colors),
     m_vibrationFrequencies(other.m_vibrationFrequencies),
     m_vibrationIntensities(other.m_vibrationIntensities),
@@ -63,6 +63,7 @@ Molecule::Molecule(Molecule&& other) noexcept
     m_customElementMap(std::move(other.m_customElementMap)),
     m_positions2d(std::move(other.m_positions2d)),
     m_positions3d(std::move(other.m_positions3d)),
+    m_label(std::move(other.m_label)),
     m_coordinates3d(std::move(other.m_coordinates3d)),
     m_timesteps(std::move(other.m_timesteps)),
     m_hybridizations(std::move(other.m_hybridizations)),
@@ -94,6 +95,7 @@ Molecule& Molecule::operator=(const Molecule& other)
     m_customElementMap = other.m_customElementMap;
     m_positions2d = other.m_positions2d;
     m_positions3d = other.m_positions3d;
+    m_label = other.m_label;
     m_coordinates3d = other.m_coordinates3d;
     m_timesteps = other.m_timesteps;
     m_hybridizations = other.m_hybridizations;
@@ -144,6 +146,7 @@ Molecule& Molecule::operator=(Molecule&& other) noexcept
     m_customElementMap = std::move(other.m_customElementMap);
     m_positions2d = std::move(other.m_positions2d);
     m_positions3d = std::move(other.m_positions3d);
+    m_label = std::move(other.m_label);
     m_coordinates3d = std::move(other.m_coordinates3d);
     m_timesteps = std::move(other.m_timesteps);
     m_hybridizations = std::move(other.m_hybridizations);
@@ -397,6 +400,7 @@ void Molecule::clearAtoms()
 {
   m_positions2d.clear();
   m_positions3d.clear();
+  m_label.clear();
   m_hybridizations.clear();
   m_formalCharges.clear();
   m_colors.clear();

avogadro/core/molecule.h

@@ -233,6 +233,10 @@ class AVOGADROCORE_EXPORT Molecule
    */
   bool setAtomPosition3d(Index atomId, const Vector3& pos);
 
+  std::string label(Index atomId) const;
+  bool setLabel(const Core::Array<std::string>& label);
+  bool setLabel(Index atomId, const std::string& label);
+
   /**
    * Set whether the specified atom is selected or not.
    */
@@ -664,6 +668,7 @@ class AVOGADROCORE_EXPORT Molecule
   CustomElementMap m_customElementMap;
   Array<Vector2> m_positions2d;
   Array<Vector3> m_positions3d;
+  Array<std::string> m_label;
   Array<Array<Vector3>> m_coordinates3d; // Used for conformers/trajectories.
   Array<double> m_timesteps;
   Array<AtomHybridization> m_hybridizations;
@@ -857,6 +862,31 @@ inline bool Molecule::setAtomPosition3d(Index atomId, const Vector3& pos)
   return false;
 }
 
+inline std::string Molecule::label(Index atomId) const
+{
+  return atomId < m_label.size() ? m_label[atomId] : "";
+}
+
+inline bool Molecule::setLabel(const Core::Array<std::string>& label)
+{
+  if (label.size() == atomCount() || label.size() == 0) {
+    m_label = label;
+    return true;
+  }
+  return false;
+}
+
+inline bool Molecule::setLabel(Index atomId, const std::string& label)
+{
+  if (atomId < atomCount()) {
+    if (atomId >= m_label.size())
+      m_label.resize(atomCount(), "");
+    m_label[atomId] = label;
+    return true;
+  }
+  return false;
+}
+
 inline void Molecule::setAtomSelected(Index atomId, bool selected)
 {
   if (atomId < atomCount()) {

avogadro/io/cjsonformat.cpp

@@ -143,6 +143,13 @@ bool CjsonFormat::read(std::istream& file, Molecule& molecule)
     }
   }
 
+  // todo? 2d position
+  // labels
+  json labels = atoms["labels"];
+  for (size_t i = 0; i < atomCount; ++i) {
+    molecule.atom(i).setLabel(labels[i]);
+  }
+
   // Check for coordinate sets, and read them in if found, e.g. trajectories.
   json coordSets = atoms["coords"]["3dSets"];
   if (coordSets.is_array() && coordSets.size()) {
@@ -232,8 +239,9 @@ bool CjsonFormat::read(std::istream& file, Molecule& molecule)
           newResidue.addResidueAtom(item.key(), atom);
         }
       }
-
-      // todo colors
+      json color = residue["color"];
+      Vector3ub col = Vector3ub(color[0], color[1], color[2]);
+      newResidue.setColor(col);
     }
   }
 
@@ -725,6 +733,13 @@ bool CjsonFormat::write(std::ostream& file, const Molecule& molecule)
     }
   }
 
+  // labels
+  json labels;
+  for (size_t i = 0; i < molecule.atomCount(); ++i) {
+    labels.push_back(molecule.label(i));
+  }
+  root["atoms"]["labels"] = labels;
+
   auto layer = LayerManager::getMoleculeInfo(&molecule)->layer;
   if (layer.atomCount()) {
     json atomLayer;

avogadro/qtgui/rwmolecule.cpp

@@ -168,6 +168,15 @@ bool RWMolecule::setAtomPositions3d(const Core::Array<Vector3>& pos,
   return true;
 }
 
+bool RWMolecule::setLabel(Index atomId, const std::string& label,
+                          const QString& undoText)
+{
+  ModifyLabelCommand* comm = new ModifyLabelCommand(*this, atomId, label);
+  comm->setText(undoText);
+  m_undoStack.push(comm);
+  return true;
+}
+
 bool RWMolecule::setAtomPosition3d(Index atomId, const Vector3& pos,
                                    const QString& undoText)
 {

avogadro/qtgui/rwmolecule.h

@@ -214,6 +214,9 @@ class AVOGADROQTGUI_EXPORT RWMolecule : public QObject
    */
   Vector3 atomPosition3d(Index atomId) const;
 
+  std::string label(Index atomId) const;
+  bool setLabel(Index atomId, const std::string& label,
+                const QString& undoText = QStringLiteral("Change Atom Label"));
   /**
    * Replace the current array of 3D atomic coordinates.
    * @param pos The new coordinate array. Must be of length atomCount().
@@ -739,6 +742,11 @@ inline Vector3 RWMolecule::atomPosition3d(Index atomId) const
   return m_molecule.atomPosition3d(atomId);
 }
 
+inline std::string RWMolecule::label(Index atomId) const
+{
+  return m_molecule.label(atomId);
+}
+
 inline Core::AtomHybridization RWMolecule::hybridization(Index atomId) const
 {
   return m_molecule.hybridization(atomId);

avogadro/qtgui/rwmolecule_undo.h

@@ -624,6 +624,27 @@ class SetForceVectorCommand : public MergeUndoCommand<SetForceVectorMergeId>
   }
 };
 } // namespace
+
+namespace {
+class ModifyLabelCommand : public RWMolecule::UndoCommand
+{
+  Index m_atomId;
+  std::string m_newLabel;
+  std::string m_oldLabel;
+
+public:
+  ModifyLabelCommand(RWMolecule& m, Index atomId, const std::string& label)
+    : UndoCommand(m), m_atomId(atomId), m_newLabel(label)
+  {
+    m_oldLabel = m_mol.molecule().label(m_atomId);
+  }
+
+  void redo() override { m_mol.molecule().setLabel(m_atomId, m_newLabel); }
+
+  void undo() override { m_mol.molecule().setLabel(m_atomId, m_oldLabel); }
+};
+} // namespace
+
 } // namespace QtGui
 } // namespace Avogadro
 #endif

avogadro/qtplugins/CMakeLists.txt

@@ -106,6 +106,7 @@ add_subdirectory(fetchpdb)
 add_subdirectory(hydrogens)
 add_subdirectory(importpqr)
 add_subdirectory(insertfragment)
+add_subdirectory(label)
 add_subdirectory(lammpsinput)
 add_subdirectory(lineformatinput)
 add_subdirectory(manipulator)

avogadro/qtplugins/label/CMakeLists.txt

@@ -0,0 +1,11 @@
+
+avogadro_plugin(Label
+  "Labels rendering scheme"
+  ScenePlugin
+  label.h
+  Label
+  label.cpp
+  "")
+
+
+target_link_libraries(Label LINK_PRIVATE AvogadroRendering)