Merge pull request #1495 from ghutchis/add-bond-labels

Adding support for bond label in base classes and CJSON

avogadro/core/atom.h

@@ -380,13 +380,13 @@ Vector3 AtomTemplate<Molecule_T>::forceVector() const
 template <class Molecule_T>
 void AtomTemplate<Molecule_T>::setLabel(const std::string& label)
 {
-  m_molecule->setLabel(m_index, label);
+  m_molecule->setAtomLabel(m_index, label);
 }
 
 template <class Molecule_T>
 std::string AtomTemplate<Molecule_T>::label() const
 {
-  return m_molecule->label(m_index);
+  return m_molecule->atomLabel(m_index);
 }
 
 } // namespace Core

avogadro/core/molecule.cpp

@@ -38,9 +38,9 @@ Molecule::Molecule(const Molecule& other)
   : m_data(other.m_data), m_partialCharges(other.m_partialCharges),
     m_spectra(other.m_spectra), m_customElementMap(other.m_customElementMap),
     m_elements(other.m_elements), 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),
+    m_positions3d(other.m_positions3d), m_atomLabels(other.m_atomLabels),
+    m_bondLabels(other.m_bondLabels), 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_vibrationIRIntensities(other.m_vibrationIRIntensities),
@@ -79,7 +79,8 @@ Molecule::Molecule(const Molecule& other)
 
 void Molecule::readProperties(const Molecule& other)
 {
-  m_label = other.m_label;
+  m_atomLabels = other.m_atomLabels;
+  m_bondLabels = other.m_bondLabels;
   m_colors = other.m_colors;
   // merge data maps by iterating through other's map
   for (auto it = other.m_data.constBegin(); it != other.m_data.constEnd();
@@ -134,9 +135,9 @@ Molecule::Molecule(Molecule&& other) noexcept
     m_spectra(other.m_spectra),
     m_customElementMap(std::move(other.m_customElementMap)),
     m_elements(other.m_elements), 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),
+    m_positions3d(other.m_positions3d), m_atomLabels(other.m_atomLabels),
+    m_bondLabels(other.m_bondLabels), 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_vibrationIRIntensities(other.m_vibrationIRIntensities),
@@ -176,7 +177,8 @@ Molecule& Molecule::operator=(const Molecule& other)
     m_elements = other.m_elements;
     m_positions2d = other.m_positions2d;
     m_positions3d = other.m_positions3d;
-    m_label = other.m_label;
+    m_atomLabels = other.m_atomLabels;
+    m_bondLabels = other.m_bondLabels;
     m_coordinates3d = other.m_coordinates3d;
     m_timesteps = other.m_timesteps;
     m_hybridizations = other.m_hybridizations;
@@ -238,7 +240,8 @@ Molecule& Molecule::operator=(Molecule&& other) noexcept
     m_elements = other.m_elements;
     m_positions2d = other.m_positions2d;
     m_positions3d = other.m_positions3d;
-    m_label = other.m_label;
+    m_atomLabels = other.m_atomLabels;
+    m_bondLabels = other.m_bondLabels;
     m_coordinates3d = other.m_coordinates3d;
     m_timesteps = other.m_timesteps;
     m_hybridizations = other.m_hybridizations;
@@ -646,12 +649,13 @@ void Molecule::clearAtoms()
 {
   m_positions2d.clear();
   m_positions3d.clear();
-  m_label.clear();
+  m_atomLabels.clear();
   m_hybridizations.clear();
   m_formalCharges.clear();
   m_colors.clear();
   m_atomicNumbers.clear();
   m_bondOrders.clear();
+  m_bondLabels.clear();
   m_graph.clear();
   m_partialCharges.clear();
   m_elements.reset();

avogadro/core/molecule.h

@@ -287,9 +287,27 @@ 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);
+  /**
+   * @return Any custom label for the requested atom.
+   * @param atomId The index of the atom.
+   */
+  std::string atomLabel(Index atomId) const;
+  /**
+   * Set the custom label of a single atom.
+   * @param atomId The index of the atom to modify.
+   * @param label The new label of the atom.
+   * @return True on success, false otherwise.
+   */
+  bool setAtomLabel(Index atomId, const std::string& label);
+
+  const Core::Array<std::string> atomLabels() const { return m_atomLabels; }
+
+  /**
+   * Set all the atom labels in the molecule.
+   * @param label The new label array. Must be of length atomCount().
+   * @return True on success, false otherwise.
+   */
+  bool setAtomLabels(const Core::Array<std::string>& label);
 
   /**
    * Set whether the specified atom is selected or not.
@@ -404,6 +422,28 @@ class AVOGADROCORE_EXPORT Molecule
   /** @return the bond between atomId1 and atomId2. */
   BondType bond(Index atomId1, Index atomId2) const;
 
+  /**
+   * @return Any custom label for the requested bond.
+   * @param bondIndex The index of the bond.
+   */
+  std::string bondLabel(Index bondIndex) const;
+  /**
+   * Set the custom label of a single bond.
+   * @param bondIndex The index of the bond to modify.
+   * @param label The new label of the bond.
+   * @return True on success, false otherwise.
+   */
+  bool setBondLabel(Index bondIndex, const std::string& label);
+
+  const Core::Array<std::string> bondLabels() const { return m_bondLabels; }
+
+  /**
+   * Set all the atom labels in the molecule.
+   * @param label The new label array. Must be of length atomCount().
+   * @return True on success, false otherwise.
+   */
+  bool setBondLabels(const Core::Array<std::string>& label);
+
   /**
    * @brief Get all bonds to @p a.
    * @return A vector of bonds to the supplied atom @p a.
@@ -780,7 +820,8 @@ class AVOGADROCORE_EXPORT Molecule
                           //!< force fields)
   Array<Vector2> m_positions2d;
   Array<Vector3> m_positions3d;
-  Array<std::string> m_label;
+  Array<std::string> m_atomLabels;
+  Array<std::string> m_bondLabels;
   Array<Array<Vector3>> m_coordinates3d; //!< Store conformers/trajectories.
   Array<double> m_timesteps;
   Array<AtomHybridization> m_hybridizations;
@@ -989,26 +1030,26 @@ inline bool Molecule::setAtomPosition3d(Index atomId, const Vector3& pos)
   return false;
 }
 
-inline std::string Molecule::label(Index atomId) const
+inline std::string Molecule::atomLabel(Index atomId) const
 {
-  return atomId < m_label.size() ? m_label[atomId] : "";
+  return atomId < m_atomLabels.size() ? m_atomLabels[atomId] : "";
 }
 
-inline bool Molecule::setLabel(const Core::Array<std::string>& label)
+inline bool Molecule::setAtomLabels(const Core::Array<std::string>& labels)
 {
-  if (label.size() == atomCount() || label.size() == 0) {
-    m_label = label;
+  if (labels.size() == atomCount() || labels.size() == 0) {
+    m_atomLabels = labels;
     return true;
   }
   return false;
 }
 
-inline bool Molecule::setLabel(Index atomId, const std::string& label)
+inline bool Molecule::setAtomLabel(Index atomId, const std::string& label)
 {
   if (atomId < atomCount()) {
-    if (atomId >= m_label.size())
-      m_label.resize(atomCount(), "");
-    m_label[atomId] = label;
+    if (atomId >= m_atomLabels.size())
+      m_atomLabels.resize(atomCount(), "");
+    m_atomLabels[atomId] = label;
     return true;
   }
   return false;
@@ -1086,6 +1127,30 @@ inline const Array<unsigned char>& Molecule::bondOrders() const
   return m_bondOrders;
 }
 
+inline std::string Molecule::bondLabel(Index bondId) const
+{
+  return bondId < m_bondLabels.size() ? m_bondLabels[bondId] : "";
+}
+
+inline bool Molecule::setBondLabels(const Core::Array<std::string>& labels)
+{
+  if (labels.size() == atomCount() || labels.size() == 0) {
+    m_bondLabels = labels;
+    return true;
+  }
+  return false;
+}
+
+inline bool Molecule::setBondLabel(Index bondId, const std::string& label)
+{
+  if (bondId < bondCount()) {
+    if (bondId >= m_bondLabels.size())
+      m_bondLabels.resize(bondCount(), "");
+    m_bondLabels[bondId] = label;
+    return true;
+  }
+  return false;
+}
 inline const Graph& Molecule::graph() const
 {
   return m_graph;

avogadro/io/cjsonformat.cpp

@@ -164,7 +164,7 @@ bool CjsonFormat::deserialize(std::istream& file, Molecule& molecule,
   json labels = atoms["labels"];
   if (labels.is_array() && labels.size() == atomCount) {
     for (size_t i = 0; i < atomCount; ++i) {
-      molecule.atom(i).setLabel(labels[i]);
+      molecule.setAtomLabel(i, labels[i]);
     }
   }
 
@@ -239,6 +239,14 @@ bool CjsonFormat::deserialize(std::istream& file, Molecule& molecule,
         molecule.bond(i).setOrder(static_cast<int>(order[i]));
       }
     }
+
+    // are there bond labels?
+    json bondLabels = bonds["labels"];
+    if (bondLabels.is_array() && bondLabels.size() == molecule.bondCount()) {
+      for (unsigned int i = 0; i < molecule.bondCount(); ++i) {
+        molecule.setBondLabel(i, bondLabels[i]);
+      }
+    }
   }
 
   // residues are optional, but should be loaded
@@ -1051,12 +1059,15 @@ bool CjsonFormat::serialize(std::ostream& file, const Molecule& molecule,
     }
   }
 
-  // labels
-  json labels;
-  for (size_t i = 0; i < molecule.atomCount(); ++i) {
-    labels.push_back(molecule.label(i));
+  // check for atom labels
+  Array atomLabels = molecule.atomLabels();
+  if (atomLabels.size() == molecule.atomCount()) {
+    json labels;
+    for (Index i = 0; i < molecule.atomCount(); ++i) {
+      labels.push_back(atomLabels[i]);
+    }
+    root["atoms"]["labels"] = labels;
   }
-  root["atoms"]["labels"] = labels;
 
   // formal charges
   json formalCharges;
@@ -1086,6 +1097,16 @@ bool CjsonFormat::serialize(std::ostream& file, const Molecule& molecule,
     }
     root["bonds"]["connections"]["index"] = connections;
     root["bonds"]["order"] = order;
+
+    // check if there are bond labels
+    Array bondLabels = molecule.bondLabels();
+    if (bondLabels.size() == molecule.bondCount()) {
+      json labels;
+      for (Index i = 0; i < molecule.bondCount(); ++i) {
+        labels.push_back(bondLabels[i]);
+      }
+      root["bonds"]["labels"] = labels;
+    }
   }
 
   // Create and populate any residue arrays