Merge pull request cryos#17 from cryos/rwmol-enhancements

RWmol enhancements for formal charges and hybridizations
psavery · May 27, 2015 · 7c4430a · 7c4430a
2 parents 81c26e4 + e6fea7e
commit 7c4430a
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Showing 3 changed files with 136 additions and 10 deletions.
diff --git a/avogadro/core/molecule.h b/avogadro/core/molecule.h
@@ -570,7 +570,7 @@ inline bool Molecule::setAtomicNumber(Index atomId, unsigned char number)
   return hyb;
 }
 
- inline bool Molecule::setHybridizations(const Core::Array<AtomHybridization> &hybs)
+inline bool Molecule::setHybridizations(const Core::Array<AtomHybridization> &hybs)
 {
   if (hybs.size() == atomCount()) {
     m_hybridizations = hybs;
@@ -579,9 +579,11 @@ inline bool Molecule::setAtomicNumber(Index atomId, unsigned char number)
   return false;
 }
 
- inline bool Molecule::setHybridization(Index atomId, AtomHybridization hyb)
+inline bool Molecule::setHybridization(Index atomId, AtomHybridization hyb)
 {
   if (atomId < atomCount()) {
+    if (atomId >= m_hybridizations.size())
+      m_hybridizations.resize(atomCount(), HybridizationUnknown);
     m_hybridizations[atomId] = hyb;
     return true;
   }
@@ -606,6 +608,8 @@ inline bool Molecule::setFormalCharges(const Core::Array<signed char> &charges)
 inline bool Molecule::setFormalCharge(Index atomId, signed char charge)
 {
   if (atomId < atomCount()) {
+    if (atomId >= m_formalCharges.size())
+      m_formalCharges.resize(atomCount(), 0);
     m_formalCharges[atomId] = charge;
     return true;
   }

diff --git a/avogadro/qtgui/rwmolecule.cpp b/avogadro/qtgui/rwmolecule.cpp
@@ -2,7 +2,7 @@
 
   This source file is part of the Avogadro project.
 
-  Copyright 2013 Kitware, Inc.
+  Copyright 2013-2015 Kitware, Inc.
 
   This source code is released under the New BSD License, (the "License").
 
@@ -21,11 +21,12 @@
 #include <algorithm>
 #include <cassert>
 
-using Avogadro::Core::Array;
-
 namespace Avogadro {
 namespace QtGui {
 
+using Core::Array;
+using Core::AtomHybridization;
+
 // Base class for all undo commands used by this class.
 // Used to expose molecule internals without needing to add explicit friendships
 // between all undo commands and the container.
@@ -43,6 +44,8 @@ class RWMolecule::UndoCommand : public QUndoCommand
   Array<Index>& bondUniqueIds() { return m_mol.m_molecule.bondUniqueIds(); }
   Array<unsigned char>& atomicNumbers() { return m_mol.m_molecule.atomicNumbers(); }
   Array<Vector3>& positions3d() { return m_mol.m_molecule.atomPositions3d(); }
+  Array<AtomHybridization>& hybridizations() { return m_mol.m_molecule.hybridizations(); }
+  Array<signed char>& formalCharges() { return m_mol.m_molecule.formalCharges(); }
   Array<std::pair<Index, Index> >& bondPairs() { return m_mol.m_molecule.bondPairs(); }
   Array<unsigned char>& bondOrders() { return m_mol.m_molecule.bondOrders(); }
   RWMolecule &m_mol;
@@ -477,6 +480,89 @@ bool RWMolecule::setAtomPosition3d(Index atomId, const Vector3 &pos)
   return true;
 }
 
+namespace {
+class SetAtomHybridizationCommand : public RWMolecule::UndoCommand
+{
+  Index m_atomId;
+  Core::AtomHybridization m_oldHybridization;
+  Core::AtomHybridization m_newHybridization;
+public:
+  SetAtomHybridizationCommand(RWMolecule &m, Index atomId,
+                              Core::AtomHybridization oldHybridization,
+                              Core::AtomHybridization newHybridization)
+    : UndoCommand(m),
+      m_atomId(atomId),
+      m_oldHybridization(oldHybridization),
+      m_newHybridization(newHybridization)
+  {
+  }
+
+  void redo() AVO_OVERRIDE
+  {
+    hybridizations()[m_atomId] = m_newHybridization;
+  }
+
+  void undo() AVO_OVERRIDE
+  {
+    hybridizations()[m_atomId] = m_oldHybridization;
+  }
+};
+} // end anon namespace
+
+bool RWMolecule::setHybridization(Index atomId, Core::AtomHybridization hyb)
+{
+  if (atomId >= atomCount())
+    return false;
+
+  SetAtomicNumberCommand *comm =
+      new SetAtomicNumberCommand(*this, atomId,
+                                 m_molecule.hybridization(atomId), hyb);
+  comm->setText(tr("Change Atom Hybridization"));
+  m_undoStack.push(comm);
+  return true;
+}
+
+namespace {
+class SetAtomFormalChargeCommand : public RWMolecule::UndoCommand
+{
+  Index m_atomId;
+  signed char m_oldCharge;
+  signed char m_newCharge;
+public:
+  SetAtomFormalChargeCommand(RWMolecule &m, Index atomId,
+                             signed char oldCharge, signed char newCharge)
+    : UndoCommand(m),
+      m_atomId(atomId),
+      m_oldCharge(oldCharge),
+      m_newCharge(newCharge)
+  {
+  }
+
+  void redo() AVO_OVERRIDE
+  {
+    formalCharges()[m_atomId] = m_newCharge;
+  }
+
+  void undo() AVO_OVERRIDE
+  {
+    formalCharges()[m_atomId] = m_oldCharge;
+  }
+};
+} // end anon namespace
+
+bool RWMolecule::setFormalCharge(Index atomId, signed char charge)
+{
+  if (atomId >= atomCount())
+    return false;
+
+  SetAtomFormalChargeCommand *comm =
+      new SetAtomFormalChargeCommand(*this, atomId,
+                                     m_molecule.formalCharge(atomId), charge);
+  comm->setText(tr("Change Atom Formal Charge"));
+  m_undoStack.push(comm);
+  return true;
+}
+
 namespace {
 class AddBondCommand : public RWMolecule::UndoCommand
 {

diff --git a/avogadro/qtgui/rwmolecule.h b/avogadro/qtgui/rwmolecule.h
@@ -2,7 +2,7 @@
 
   This source file is part of the Avogadro project.
 
-  Copyright 2013 Kitware, Inc.
+  Copyright 2013-2015 Kitware, Inc.
 
   This source code is released under the New BSD License, (the "License").
 
@@ -208,11 +208,37 @@ class AVOGADROQTGUI_EXPORT RWMolecule : public QObject
     return m_molecule.m_positions2d;
   }
 
-  Core::AtomHybridization hybridization(Index) const { return Core::HybridizationUnknown; }
-  bool setHybridization(Index, Core::AtomHybridization) { return false; }
+  /**
+   * Get the hybridization for the requested atom.
+   * @param atomId The index of the atom.
+   * @return The hybridization of the atom indexed at @a atomId, or
+   * 0 if @a atomId is invalid.
+   */
+  Core::AtomHybridization hybridization(Index atomId) const;
+
+  /**
+   * Set the hybridization of a single atom.
+   * @param atomId The index of the atom to modify.
+   * @param hyb The new hybridization.
+   * @return True on success, false otherwise.
+   */
+  bool setHybridization(Index atomId, Core::AtomHybridization hyb);
+
+  /**
+   * Get the formal charge for the requested atom.
+   * @param atomId The index of the atom.
+   * @return The formal charge of the atom indexed at @a atomId, or
+   * 0 if @a atomId is invalid.
+   */
+  signed char formalCharge(Index atomId) const;
 
-  signed char formalCharge(Index) const { return 0; }
-  bool setFormalCharge(Index, signed char) { return false; }
+  /**
+   * Set the formal charge of a single atom.
+   * @param atomId The index of the atom to modify.
+   * @param charge The new formal charge.
+   * @return True on success, false otherwise.
+   */
+  bool setFormalCharge(Index atomId, signed char charge);
 
   /**
    * Create a new bond in the molecule.
@@ -502,6 +528,16 @@ inline Vector3 RWMolecule::atomPosition3d(Index atomId) const
   return m_molecule.atomPosition3d(atomId);
 }
 
+inline Core::AtomHybridization RWMolecule::hybridization(Index atomId) const
+{
+  return m_molecule.hybridization(atomId);
+}
+
+inline signed char RWMolecule::formalCharge(Index atomId) const
+{
+  return m_molecule.formalCharge(atomId);
+}
+
 inline RWMolecule::BondType RWMolecule::addBond(const AtomType &atom1,
                                                 const AtomType &atom2,
                                                 unsigned char order)