/******************************************************************************
  This source file is part of the Avogadro project.
  This source code is released under the 3-Clause BSD License, (see "LICENSE").
******************************************************************************/

#ifndef AVOGADRO_QTGUI_RWMOLECULE_H
#define AVOGADRO_QTGUI_RWMOLECULE_H

#include "avogadroqtguiexport.h"
#include <QtCore/QObject>

#include "molecule.h" //qtgui::Molecule
#include "persistentatom.h"
#include "persistentbond.h"

#include <avogadro/core/array.h>
#include <avogadro/core/atom.h>
#include <avogadro/core/avogadrocore.h>
#include <avogadro/core/bond.h>
#include <avogadro/core/crystaltools.h>
#include <avogadro/core/residue.h>
#include <avogadro/core/unitcell.h>
#include <avogadro/core/vector.h>

#include <QUndoStack>

namespace Avogadro {
namespace QtGui {

/** Concrete atom/bond proxy classes for RWMolecule. @{ */
class RWAtom;
class RWBond;
/** @} */

/**
 * @class RWMolecule rwmolecule.h <avogadro/qtgui/rwmolecule.h>
 * @brief The RWMolecule class is an editable molecule class that automatically
 * populates an undo stack.
 *
 * This class implements the molecule API and composes a QUndoStack
 * (undoStack()). New undo commands are automatically generated and push each
 * time a non-const method is called.
 *
 * An interactive mode is supported that causes "noisy" commands, such as
 * atom position changes, to be merged into a single command, saving memory
 * keeping the stack usable during interactive editing of the molecule. Use
 * setInteractive(bool) to toggle interactive mode.
 *
 * Similarly, multiple sequences of commands can be compressed into a single
 * named action using the QUndoStack's macro capability. Call
 * undoStack().beginMacro(tr("User Description Of Change")) to begin a macro,
 * and undoStack().endMacro() when finished.
 */
class AVOGADROQTGUI_EXPORT RWMolecule : public QObject
{
  Q_OBJECT

public:
  /** Typedef for Atom class. */
  typedef RWAtom AtomType;

  /** Typedef for PersistentAtom class. */
  typedef PersistentAtom<RWMolecule> PersistentAtomType;

  /** Typedef for Bond class. */
  typedef RWBond BondType;

  /** Typedef for PersistentBond class. */
  typedef PersistentBond<RWMolecule> PersistentBondType;

  /** Construct a molecule with the atoms/bonds of mol. */
  explicit RWMolecule(Molecule& mol, QObject* parent = nullptr);

  ~RWMolecule() override;

  Molecule& molecule() { return m_molecule; }
  const Molecule& molecule() const { return m_molecule; }

  /**
   * Add a new atom to the molecule.
   * @param atomicNumber The atomic number of the new atom.
   * @param usingPositions Whether or not to use positions for this atom.
   *                       Default is true. Set to false if the atom
   *                       will not be using coordinates.
   * @return The new Atom object.
   */
  AtomType addAtom(unsigned char atomicNumber, bool usingPositions = true);

  /**
   * Add a new atom to the molecule and set its position.
   * @param atomicNumber The atomic number of the new atom.
   * @param position3d The position of the atom.
   * @return The new Atom object.
   */
  AtomType addAtom(unsigned char atomicNumber, const Vector3& position3d);

  /**
   * Obtain an atom object.
   * @param atomId The index of the atom to return.
   * @return The requested atom object. Will be invalid if @a atomId >= @a
   * atomCount().
   */
  AtomType atom(Index atomId) const;

  /**
   * Obtain an atom object from it's unique id.
   * @param atomUId The unique of the requested atom.
   * @return The requested atom object. Will be invalid if @a atomUId is not
   * in use.
   */
  AtomType atomByUniqueId(Index atomUId) const;

  /**
   * @return The unique id of the atom.
   * @{
   */
  Index atomUniqueId(Index atomId) const;
  Index atomUniqueId(const AtomType& atom) const;
  /** @} */

  /**
   * @return The number of atoms in the molecule.
   */
  Index atomCount() const;

  /**
   * @return The number of atoms in the molecule with the atomic number @a
   * atomicNumber.
   */
  Index atomCount(unsigned char atomicNumber) const;

  /**
   * Delete the specified atom from this molecule.
   * @return True on success, false otherwise.
   * @note This also removes all bonds connected to the atom.
   * @{
   */
  bool removeAtom(Index atomId);
  bool removeAtom(const AtomType& atom);
  /** @} */

  /**
   * Delete all atoms from this molecule.
   * @note This also removes all bonds.
   */
  void clearAtoms();

  /**
   * Adjust hydrogens for an atom.
   * @param atomId The index of the atom.
   * @note Checks to make sure the atom is valid before adjusting the hydrogens.
   */
  void adjustHydrogens(Index atomId);

  /**
   * Adjust hydrogens for multiple atoms.
   * @param atomIds The indices for the atoms.
   * @note Checks to make sure the atoms are valid before adjusting the
   * hydrogens.
   */
  void adjustHydrogens(const Core::Array<Index>& atomIds);

  /**
   * @return An array containing atomic numbers for all atoms in the molecule,
   * indexed by atom index.
   */
  const Core::Array<unsigned char>& atomicNumbers() const;

  /**
   * Get the atomic number for the requested atom.
   * @param atomId The index of the atom.
   * @return The atomic number of the atom indexed at @a atomId, or
   * Avogadro::InvalidElement if @a atomId is invalid.
   */
  unsigned char atomicNumber(Index atomId) const;

  /**
   * Replace the current array of atomic numbers.
   * @param nums The new atomic number array. Must be of length atomCount().
   * @return True on success, false otherwise.
   */
  bool setAtomicNumbers(const Core::Array<unsigned char>& nums);

  /**
   * Set the atomic number of a single atom.
   * @param atomId The index of the atom to modify.
   * @param atomicNumber The new atomic number.
   * @return True on success, false otherwise.
   */
  bool setAtomicNumber(Index atomId, unsigned char atomicNumber);

  /**
   * @return An array containing 3D coordinates for all atoms in the molecule,
   * indexed by atom index.
   * @note May be empty if position information has not been set for any atoms.
   */
  const Core::Array<Vector3>& atomPositions3d() const;

  /**
   * Get the 3D position of a single atom.
   * @param atomId The index of the atom.
   * @return The position of the atom, or Vector3::Zero() if no position
   * information has been set.
   */
  Vector3 atomPosition3d(Index atomId) const;

  /**
   * Replace the current array of 3D atomic coordinates.
   * @param pos The new coordinate array. Must be of length atomCount().
   * @param undoText The undo text to be displayed for undo commands.
   * @return True on success, false otherwise.
   */
  bool setAtomPositions3d(
    const Core::Array<Vector3>& pos,
    const QString& undoText = tr("Change Atom Positions"));

  /**
   * Set the 3D position of a single atom.
   * @param atomId The index of the atom to modify.
   * @param pos The new position of the atom.
   * @param undoText The undo text to be displayed for undo commands.
   * @return True on success, false otherwise.
   */
  bool setAtomPosition3d(Index atomId, const Vector3& pos,
                         const QString& undoText = tr("Change Atom Position"));

  /**
   * Get the label on an atom.
   * @param atomId The index of the atom.
   * @return The label of the atom indexed at @a atomId, or an empty string if
   * @a atomId is invalid or has no label.
   */
  std::string atomLabel(Index atomId) const;

  /**
   * Set the label of a single atom.
   * @param atomId The index of the atom to modify.
   * @param label The new label.
   * @param undoText The undo text to be displayed for undo commands.
   * @return True on success, false otherwise.
   */
  bool setAtomLabel(Index atomId, const std::string& label,
                    const QString& undoText = tr("Change Atom Label"));

  /**
   * Get the label on a bond
   * @param bondId The index of the bond.
   * @return The label of the bond indexed at @a bondId, or an empty string if
   * @a bondId is invalid or has no label.
   */
  std::string bondLabel(Index bondId) const;

  /**
   * Set the label of a single bond.
   * @param bondId The index of the bond to modify.
   * @param label The new label.
   * @param undoText The undo text to be displayed for undo commands.
   * @return True on success, false otherwise.
   */
  bool setBondLabel(Index bondId, const std::string& label,
                    const QString& undoText = tr("Change Bond Label"));

  /**
   * Set whether the specified atom is selected or not.
   */
  void setAtomSelected(Index atomId, bool selected,
                       const QString& undoText = tr("Change Selection"));

  /**
   * Query whether the supplied atom index has been selected.
   */
  bool atomSelected(Index atomId) const;

  bool setAtomPosition2d(Index, const Vector2&) { return false; }
  Vector2 atomPosition2d(Index) { return Vector2(0, 0); }
  const Core::Array<Vector2>& atomPositions2d() const
  {
    return m_molecule.m_positions2d;
  }

  /**
   * 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;

  /**
   * 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);

  /**
   * Get the isotope for the requested atom.
   * @param atomId The index of the atom.
   * @return The isotope of the atom indexed at @a atomId, or
   * 0 if @a atomId is invalid. (default is 0 for most common isotope)
   */
  unsigned short isotope(Index atomId) const;

  /**
   * Set the isotope of a single atom.
   * @param atomId The index of the atom to modify.
   * @param isotope The new isotope
   * @return True on success, false otherwise.
   */
  bool setIsotope(Index atomId, unsigned short isotope);

  /**
   * Get the color for the requested atom.
   * @param atomId The index of the atom.
   * @return The color of the atom indexed at @a atomId, or
   * (0, 0, 0) if @a atomId is invalid. If no color is set for the
   * given atomId, the default color for the atomic number of
   * the atomId is returned.
   */
  Vector3ub color(Index atomId) const;

  /**
   * Set the color of a single atom.
   * @param atomId The index of the atom to modify.
   * @param color The new color.
   * @return True on success, false otherwise.
   */
  bool setColor(Index atomId, Vector3ub color);

  /**
   * Set the color of a single residue.
   * @param residueId The index of the residue to modify.
   * @param color The new color.
   * @return True on success, false otherwise.
   */
  bool setResidueColor(Index residueId, Vector3ub color);

  bool setLayer(Index atomId, size_t layer);
  size_t layer(Index atomId) const;

  /**
   * Create a new bond in the molecule.
   * @param atom1 The first atom in the bond.
   * @param atom2 The second order in the bond.
   * @param order The bond order.
   * @return The new bond object. Will be invalid if @a atom1 or @a atom2 does
   * not exist.
   * @{
   */
  BondType addBond(Index atom1, Index atom2, unsigned char order = 1);
  BondType addBond(const AtomType& atom1, const AtomType& atom2,
                   unsigned char order = 1);
  /** @} */

  /**
   * Get a bond object.
   * @param bondId The index of the requested bond.
   * @return The requested bond object. Will be invalid if @a bondId >=
   * @a bondCount().
   */
  BondType bond(Index bondId) const;

  /**
   * Get a bond object.
   * @param atom1 The index of one atom in the bond.
   * @param atom2 The index of the other atom in bond.
   * @return The requested bond object. Will be invalid if @a atom1 or @a atom2
   * do not exist.
   */
  BondType bond(Index atom1, Index atom2) const;

  /**
   * Get a bond object.
   * @param atom1 One atom in the bond.
   * @param atom2 The other atom in bond.
   * @return The requested bond object. Will be invalid if @a atom1 or @a atom2
   * are invalid.
   */
  BondType bond(const AtomType& atom1, const AtomType& atom2) const;

  /**
   * Get a bond object from its unique id.
   * @param bondUid The unique id of the bond.
   * @return The requested bond object. Will be invalid if @a bondUid is not in
   * use.
   */
  BondType bondByUniqueId(Index bondUid) const;

  /**
   * Get the unique id of a bond.
   * @param bondId The index of the requested bond.
   * @return The unique id currently assigned to the bond at index @a bondId
   */
  Index bondUniqueId(Index bondId) const;

  /**
   * Get the unique id of a bond.
   * @param bond The requested bond object.
   * @return The unique id currently assigned to @a bond.
   */
  Index bondUniqueId(const BondType& bond) const;

  /**
   * @return The number of bonds in the molecule.
   */
  Index bondCount() const;

  /**
   * Remove the requested bond.
   * @return True on success, false otherwise.
   * @{
   */
  bool removeBond(Index bondId);
  bool removeBond(const BondType& bond);
  bool removeBond(Index atom1, Index atom2);
  bool removeBond(const AtomType& atom1, const AtomType& atom2);
  /** @} */

  /**
   * Remove all bonds from the molecule.
   */
  void clearBonds();

  /**
   * Find bonds connected to an atom.
   * @param atom The atom of interest.
   * @return An array of bond objects that are attached to the specified atom.
   */
  Core::Array<BondType> bonds(const AtomType& atom) const;

  /**
   * Find bonds connected to an atom.
   * @param atomId The index for the atom of interest.
   * @return An array of bond objects that are attached to the specified atom.
   */
  Core::Array<BondType> bonds(const Index& atomId) const;

  /**
   * @return An array of bond orders for all bonds in the molecule, indexed by
   * bond index.
   */
  const Core::Array<unsigned char>& bondOrders() const;

  /**
   * Get the order of a bond.
   * @param bondId The id of the bond.
   * @return The bond order.
   */
  unsigned char bondOrder(Index bondId) const;

  /**
   * Replace the current array of bond orders.
   * @param orders The new array.
   * @return True on success, false on failure.
   */
  bool setBondOrders(const Core::Array<unsigned char>& orders);

  /**
   * Set the order of a bond in the molecule.
   * @param bondId The bond's index.
   * @param order The new order of the bond.
   * @return True on success, false on failure.
   */
  bool setBondOrder(Index bondId, unsigned char order);

  /**
   * @return An array of all bonded atoms in the molecule, indexed by bond
   * index.
   * Each bond pair is represented by a pair of atom indices.
   */
  const Core::Array<std::pair<Index, Index>>& bondPairs() const;

  /**
   * Get the set of bonded atoms corresponding to @a bondId.
   * @param bondId The index of the requested bond.
   * @return The bonded atom pair, represented as a pair of atom indices.
   */
  std::pair<Index, Index> bondPair(Index bondId) const;

  /**
   * Replace the current array of bonded atoms.
   * @param pairs The array.
   * @return True on success, false on failure.
   * @note The bonded atoms are represented as a pair of bond indices.
   * @note If needed, the elements in @a pairs will be modified to ensure that
   * the first atom index is less than the second.
   */
  bool setBondPairs(const Core::Array<std::pair<Index, Index>>& pairs);

  /**
   * Set the bonded atoms for a bond.
   * @param bondId The bond to modify.
   * @param pair The new bond pair.
   * @return True on success, false otherwise.
   * @note If needed, @a pair will be modified to ensure that the first atom
   * index is less than the second.
   */
  bool setBondPair(Index bondId, const std::pair<Index, Index>& pair);

  /**
   * Add a default unit cell to the molecule. Does nothing if there already
   * is a unit cell. Changes are emitted.
   */
  void addUnitCell();

  /**
   * Remove the unit cell from the molecule. Does nothing if there is
   * no unit cell. Changes are emitted.
   */
  void removeUnitCell();

  /**
   * Add a residue to the molecule.
   * @param residue The residue to be added.
   * @param offset The atomic index offset for the new residue.
   */
  void addResidue(const Core::Residue& residue, Index offset = 0);

  /**
   * Generic edit that changes the current molecule to be @a newMolecule.
   * Also sets the text for the undo command to be @a undoText. Changes are
   * emitted.
   * @param newMolecule The new molecule to be set.
   * @param changes The changes to be emitted.
   * @param undoText The text description for the undo command.
   */
  void modifyMolecule(
    const Molecule& newMolecule, Molecule::MoleculeChanges changes,
    const QString& undoText = QStringLiteral("Modify Molecule"));

  /**
   * Generic edit that adds @a newMolecule to the current molecule.
   * Also sets the text for the undo command to be @a undoText. Changes are
   * emitted.
   * @param addMolecule The new molecule to be set.
   * @param undoText The text description for the undo command.
   */
  void appendMolecule(
    const Molecule& addMolecule,
    const QString& undoText = QStringLiteral("Append Molecule"));

  /**
   * Edit the unit cell by replacing the current cell matrix with a new cell
   * matrix. Changes are emitted.
   * @param cellMatrix The new cell matrix to be set.
   * @param opts If TransformAtoms is specified, the atoms in @a molecule are
   * adjusted so that their fractional (lattice) coordinates are preserved. This
   * option is ignored if the input molecule has no unit cell.
   */
  void editUnitCell(Matrix3 cellMatrix, Core::CrystalTools::Options opts);

  /**
   * Wrap atoms to the unit cell. Changes are emitted.
   */
  void wrapAtomsToCell();

  /**
   * Rotate cell to standard orientation. Changes are emitted.
   */
  void rotateCellToStandardOrientation();

  /**
   * Scale a cell's volume. Changes are emitted.
   * @param newVolume The new volume to be set.
   * @param options If CrystalTools::TransformAtoms is set, then
   *                the atoms will be transformed during the scaling.
   */
  void setCellVolume(double newVolume, Core::CrystalTools::Options options);

  /**
   * Build a supercell. Changes are emitted.
   * @param a The final number of units along the A vector (at least 1).
   * @param b The final number of units along the B vector (at least 1).
   * @param c The final number of units along the C vector (at least 1).
   */
  void buildSupercell(unsigned int a, unsigned int b, unsigned int c);

  /**
   * Perform a Niggli reduction on the cell. Changes are emitted.
   */
  void niggliReduceCell();

  /**
   * Use spglib to reduce the cell to its primitive form. Changes are emitted.
   * @param cartTol Cartesian tolerance for primitive reduction.
   * @param copyTol If > 0, add translational boundary copies with this
   *   tolerance in the same undo step.
   * @return True if the algorithm succeeded, and false if it failed.
   */
  bool reduceCellToPrimitive(double cartTol = 1e-5, double copyTol = 0.0);

  /**
   * Use spglib to convert the cell to its conventional form. Changes are
   * emitted.
   * @param cartTol Cartesian tolerance for conventionalization.
   * @param copyTol If > 0, add translational boundary copies with this
   *   tolerance in the same undo step.
   * @return True if the algorithm succeeded, and false if it failed.
   */
  bool conventionalizeCell(double cartTol = 1e-5, double copyTol = 0.0);

  /**
   * Use spglib to symmetrize the cell. Changes are emitted.
   * @param cartTol Cartesian tolerance for symmetrization.
   * @param copyTol If > 0, add translational boundary copies with this
   *   tolerance in the same undo step.
   * @return True if the algorithm succeeded, and false if it failed.
   */
  bool symmetrizeCell(double cartTol = 1e-5, double copyTol = 0.0);

  /**
   * Fill unit cell using transforms for the space group. Changes are emitted.
   * @param hallNumber The hall number to be used for transforming the cell.
   * @param cartTol Cartesian tolerance for comparing atom positions.
   * @param allCopies If true, all copies will be filled (i.e. edges and
   * corners)
   * @return True if the algorithm succeeded, and false if it failed.
   */
  bool fillUnitCell(unsigned short hallNumber, double cartTol = 1e-5,
                    bool allCopies = false);

  /**
   * Add translational copies of atoms on the unit cell boundary without
   * applying symmetry operations. Changes are emitted.
   * @param cartTol Cartesian tolerance for comparing atom positions.
   * @return True if the algorithm succeeded, and false if it failed.
   */
  bool fillTranslationalCopies(double cartTol = 1e-5);

  /**
   * Use transforms to reduce a cell to its asymmetric unit. Changes are
   * emitted.
   * @param hallNumber The hall number to be used for obtaining the transforms.
   * @param cartTol Cartesian tolerance for comparing atom positions.
   * @return True if the algorithm succeeded, and false if it failed.
   */
  bool reduceCellToAsymmetricUnit(unsigned short hallNumber,
                                  double cartTol = 1e-5);

  /**
   * Call this function when you wish to merge all undo commands.
   * It turns on interactive mode to merge similar undo commands in a series
   * (in order to save space), and it uses QUndoStack's beginMacro() to merge
   * dissimilar undo commands together. You must call endMergeMode() to end
   * the merging section (undo and redo are unavailable while merge mode is
   * on).
   * @param undoName The name of the undo command
   */
  void beginMergeMode(const QString& undoName = QStringLiteral("Draw"));

  /**
   * Call this function when you wish merge mode to end. This will turn off
   * interactive mode, and it will call QUndoStack's endMacro(). All of the
   * undo commands pushed between beginMergeMode() and endMergeMode() will be
   * merged into one undo command. beginMergeMode() should have been called
   * before this is called.
   */
  void endMergeMode();

  /**
   * @brief Begin or end an interactive edit.
   *
   * If enabled, certain undo operations will be merged together. For instance,
   * an editor dragging an atom through space in response to mouse movement will
   * only generate a single undo command containing the initial and final
   * positions and discard the intermediate states. If disabled, each
   * intermediate action will appear in the undo log.
   */
  void setInteractive(bool b);

  /**
   * @return True if interactive mode is enabled, false otherwise.
   * @sa setInteractive
   */
  bool isInteractive() const;

  /**
   * @return The QUndoStack for this molecule.
   * @{
   */
  QUndoStack& undoStack();
  const QUndoStack& undoStack() const;
  /** @} */

  class UndoCommand;
  friend class UndoCommand;

  /** Returns a vector of forces for the atoms in the molecule. */
  const Core::Array<Vector3>& forceVectors() const;

  /**
   * Replace the current array of force vectors.
   * @param pos The new force vector array. Must be of length atomCount().
   * @param undoText The undo text to be displayed for undo commands.
   * @return True on success, false otherwise.
   */
  bool setForceVector(
    Index atomId, const Vector3& pos,
    const QString& undoText = QStringLiteral("Change Force Vectors"));

public slots:
  /**
   * @brief Force the molecule to emit the changed() signal.
   * @param change See changed().
   */
  void emitChanged(unsigned int change);

signals:
  /**
   * @brief Indicates that the molecule has changed.
   * @param change Use the MoleculeChange enum to check what has changed.
   *
   * The @p change variable indicates what has changed, i.e. if
   * change & Atoms == true then atoms were changed in some way, and if
   * change & Removed == true then one or more atoms were removed.
   */
  void changed(unsigned int change);

protected:
  Index findAtomUniqueId(Index atomId) const;
  Index findBondUniqueId(Index bondId) const;

  /**
   * @brief m_molecule still stored all data, this class acts upon it and builds
   * an undo/redo stack that can be used to offer undo and redo.
   */
  Molecule& m_molecule;
  bool m_interactive;

  QUndoStack m_undoStack;

  friend class Molecule;
};

class AVOGADROQTGUI_EXPORT RWAtom : public Core::AtomTemplate<RWMolecule>
{
public:
  RWAtom() : Core::AtomTemplate<RWMolecule>() {}
  RWAtom(RWMolecule* m, Index i) : Core::AtomTemplate<RWMolecule>(m, i) {}
};

class AVOGADROQTGUI_EXPORT RWBond : public Core::BondTemplate<RWMolecule>
{
public:
  RWBond() : Core::BondTemplate<RWMolecule>() {}
  RWBond(RWMolecule* m, Index i) : Core::BondTemplate<RWMolecule>(m, i) {}
};

inline RWMolecule::AtomType RWMolecule::atom(Index atomId) const
{
  return AtomType(const_cast<RWMolecule*>(this), atomId);
}

inline RWMolecule::AtomType RWMolecule::atomByUniqueId(Index atomUId) const
{
  return atomUId < m_molecule.m_atomUniqueIds.size()
           ? AtomType(const_cast<RWMolecule*>(this),
                      m_molecule.m_atomUniqueIds[atomUId])
           : AtomType();
}

inline Index RWMolecule::atomUniqueId(Index atomId) const
{
  return findAtomUniqueId(atomId);
}

inline Index RWMolecule::atomUniqueId(const RWMolecule::AtomType& a) const
{
  return a.molecule() == this ? findAtomUniqueId(a.index()) : MaxIndex;
}

inline Index RWMolecule::atomCount() const
{
  return m_molecule.atomCount();
}

inline bool RWMolecule::removeAtom(const AtomType& a)
{
  return a.molecule() == this ? removeAtom(a.index()) : false;
}

inline const Core::Array<unsigned char>& RWMolecule::atomicNumbers() const
{
  return m_molecule.atomicNumbers();
}

inline unsigned char RWMolecule::atomicNumber(Index atomId) const
{
  return m_molecule.atomicNumber(atomId);
}

inline const Core::Array<Vector3>& RWMolecule::atomPositions3d() const
{
  return m_molecule.atomPositions3d();
}

inline Vector3 RWMolecule::atomPosition3d(Index atomId) const
{
  return m_molecule.atomPosition3d(atomId);
}

inline std::string RWMolecule::atomLabel(Index atomId) const
{
  return m_molecule.atomLabel(atomId);
}

inline std::string RWMolecule::bondLabel(Index bondId) const
{
  return m_molecule.bondLabel(bondId);
}

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 unsigned short RWMolecule::isotope(Index atomId) const
{
  return m_molecule.isotope(atomId);
}

inline Vector3ub RWMolecule::color(Index atomId) const
{
  return m_molecule.color(atomId);
}

inline size_t RWMolecule::layer(Index atomId) const
{
  return m_molecule.layer(atomId);
}

inline RWMolecule::BondType RWMolecule::addBond(const AtomType& atom1,
                                                const AtomType& atom2,
                                                unsigned char order)
{
  if (atom1.molecule() != atom2.molecule() || atom1.molecule() != this)
    return BondType();
  return addBond(atom1.index(), atom2.index(), order);
}

inline RWMolecule::BondType RWMolecule::bond(Index bondId) const
{
  return BondType(const_cast<RWMolecule*>(this), bondId);
}

inline RWMolecule::BondType RWMolecule::bond(
  const RWMolecule::AtomType& atom1, const RWMolecule::AtomType& atom2) const
{
  if (atom1.molecule() == atom2.molecule() && atom1.molecule() == this)
    return bond(atom1.index(), atom2.index());
  return BondType();
}

inline RWMolecule::BondType RWMolecule::bondByUniqueId(Index bondUid) const
{
  return bondUid < m_molecule.m_bondUniqueIds.size()
           ? BondType(const_cast<RWMolecule*>(this),
                      m_molecule.m_bondUniqueIds[bondUid])
           : BondType();
}

inline Index RWMolecule::bondUniqueId(Index bondId) const
{
  return findBondUniqueId(bondId);
}

inline Index RWMolecule::bondUniqueId(const RWMolecule::BondType& b) const
{
  return b.molecule() == this ? findBondUniqueId(b.index()) : MaxIndex;
}

inline Index RWMolecule::bondCount() const
{
  return m_molecule.bondCount();
}

inline bool RWMolecule::removeBond(const RWMolecule::BondType& b)
{
  return b.molecule() == this ? removeBond(b.index()) : false;
}

inline bool RWMolecule::removeBond(Index atom1, Index atom2)
{
  return removeBond(bond(atom1, atom2).index());
}

inline bool RWMolecule::removeBond(const RWMolecule::AtomType& atom1,
                                   const RWMolecule::AtomType& atom2)
{
  if (atom1.molecule() != atom2.molecule() || atom1.molecule() != this)
    return false;
  return removeBond(bond(atom1.index(), atom2.index()).index());
}

inline Core::Array<RWMolecule::BondType> RWMolecule::bonds(
  const RWMolecule::AtomType& a) const
{
  return a.molecule() == this ? bonds(a.index()) : Core::Array<BondType>();
}

inline Core::Array<RWMolecule::BondType> RWMolecule::bonds(
  const Index& atomId) const
{
  auto atomBonds = m_molecule.bonds(atomId);
  Core::Array<RWMolecule::BondType> result;
  for (Index i = 0; i < atomBonds.size(); ++i) {
    result.push_back(
      BondType(const_cast<RWMolecule*>(this), atomBonds[i].index()));
  }
  return result;
}

inline const Core::Array<unsigned char>& RWMolecule::bondOrders() const
{
  return m_molecule.bondOrders();
}

inline unsigned char RWMolecule::bondOrder(Index bondId) const
{
  return m_molecule.bondOrder(bondId);
}

inline const Core::Array<std::pair<Index, Index>>& RWMolecule::bondPairs() const
{
  return m_molecule.bondPairs();
}

inline std::pair<Index, Index> RWMolecule::bondPair(Index bondId) const
{
  return m_molecule.bondPair(bondId);
}

inline void RWMolecule::beginMergeMode(const QString& undoName)
{
  m_interactive = true;
  m_undoStack.beginMacro(undoName);
}

inline void RWMolecule::endMergeMode()
{
  m_interactive = false;
  m_undoStack.endMacro();
}

inline void RWMolecule::setInteractive(bool b)
{
  m_interactive = b;
}

inline bool RWMolecule::isInteractive() const
{
  return m_interactive;
}

inline QUndoStack& RWMolecule::undoStack()
{
  return m_undoStack;
}

inline const QUndoStack& RWMolecule::undoStack() const
{
  return m_undoStack;
}

inline const Core::Array<Vector3>& RWMolecule::forceVectors() const
{
  return m_molecule.forceVectors();
}

} // namespace QtGui
} // namespace Avogadro

#endif // AVOGADRO_QTGUI_RWMOLECULE_H
