vtkMolecule.h

/*=========================================================================

  Program:   Visualization Toolkit
  Module:    vtkMolecule.h

  Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
  All rights reserved.
  See Copyright.txt or http://www.kitware.com/Copyright.htm for details.

     This software is distributed WITHOUT ANY WARRANTY; without even
     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
     PURPOSE.  See the above copyright notice for more information.

=========================================================================*/
/**
 * @class   vtkMolecule
 * @brief   class describing a molecule
 *
 *
 *
 * vtkMolecule and the convenience classes vtkAtom and vtkBond
 * describe the geometry and connectivity of a molecule. The molecule
 * can be constructed using the AppendAtom() and AppendBond() methods in one
 * of two ways; either by fully specifying the atom/bond in a single
 * call, or by incrementally setting the various attributes using the
 * convenience vtkAtom and vtkBond classes:
 *
 * Single call:
 * \code
 * vtkMolecule *mol = vtkMolecule::New();
 * vtkAtom h1 = mol->AppendAtom(1, 0.0, 0.0, -0.5);
 * vtkAtom h2 = mol->AppendAtom(1, 0.0, 0.0,  0.5);
 * vtkBond b  = mol->AppendBond(h1, h2, 1);
 * \endcode
 *
 * Incremental:
 * \code
 * vtkMolecule *mol = vtkMolecule::New();
 *
 * vtkAtom h1 = mol->AppendAtom();
 * h1.SetAtomicNumber(1);
 * h1.SetPosition(0.0, 0.0, -0.5);
 *
 * vtkAtom h2 = mol->AppendAtom();
 * h2.SetAtomicNumber(1);
 * vtkVector3d displacement (0.0, 0.0, 1.0);
 * h2.SetPosition(h1.GetPositionAsVector3d() + displacement);
 *
 * vtkBond b  = mol->AppendBond(h1, h2, 1);
 * \endcode
 *
 * Both of the above methods will produce the same molecule, two
 * hydrogens connected with a 1.0 Angstrom single bond, aligned to the
 * z-axis. The second example also demonstrates the use of VTK's
 * vtkVector class, which is fully supported by the Chemistry kit.
 *
 * The vtkMolecule object is intended to be used with the
 * vtkMoleculeMapper class for visualizing molecular structure using
 * common rendering techniques.
 *
 * \warning While direct use of the underlying vtkUndirectedGraph
 * structure is possible due to vtkMolecule's public inheritance, this
 * should not be relied upon and may change in the future.
 *
 * @sa
 * vtkAtom vtkBond vtkMoleculeMapper vtkPeriodicTable
*/

#ifndef vtkMolecule_h
#define vtkMolecule_h

#include "vtkCommonDataModelModule.h" // For export macro
#include "vtkUndirectedGraph.h"
#include "vtkSmartPointer.h" // For vtkSmartPointer

#include "vtkAtom.h" // Simple proxy class dependent on vtkMolecule
#include "vtkBond.h" // Simple proxy class dependent on vtkMolecule

#include "vtkVector.h" // Small templated vector convenience class

class vtkAbstractElectronicData;
class vtkDataArray;
class vtkInformation;
class vtkInformationVector;
class vtkMatrix3x3;
class vtkPlane;
class vtkPoints;
class vtkUnsignedCharArray;
class vtkUnsignedShortArray;

class VTKCOMMONDATAMODEL_EXPORT vtkMolecule : public vtkUndirectedGraph
{
public:
  static vtkMolecule *New();
  vtkTypeMacro(vtkMolecule,vtkUndirectedGraph);
  void PrintSelf(ostream &os, vtkIndent indent) override;
  void Initialize() override;

  /**
   * Return what type of dataset this is.
   */
  int GetDataObjectType() override {return VTK_MOLECULE;}

  /**
   * Add new atom with atomic number 0 (dummy atom) at origin. Return
   * a vtkAtom that refers to the new atom.
   */
  vtkAtom AppendAtom()
  {
    return this->AppendAtom(0, vtkVector3f(0, 0, 0));
  }

  /**
   * Add new atom with the specified atomic number and position. Return a
   * vtkAtom that refers to the new atom.
   */
  vtkAtom AppendAtom(unsigned short atomicNumber, const vtkVector3f &pos);

  /**
   * Convenience methods to append a new atom with the specified atomic number
   * and position.
   */
  vtkAtom AppendAtom(unsigned short atomicNumber, double x, double y, double z)
  {
    return this->AppendAtom(atomicNumber, vtkVector3f(x, y, z));
  }

  /**
   * Return a vtkAtom that refers to the atom with the specified id.
   */
  vtkAtom GetAtom(vtkIdType atomId);

  /**
   * Return the number of atoms in the molecule.
   */
  vtkIdType GetNumberOfAtoms();

  //@{
  /**
   * Add a bond between the specified atoms, optionally setting the
   * bond order (default: 1). Return a vtkBond object referring to the
   * new bond.
   */
  vtkBond AppendBond(vtkIdType atom1, vtkIdType atom2,
                     unsigned short order = 1);
  vtkBond AppendBond(const vtkAtom &atom1, const vtkAtom &atom2,
                     unsigned short order = 1)
  {
    return this->AppendBond(atom1.Id, atom2.Id, order);
  }
  //@}

  /**
   * Return a vtkAtom that refers to the bond with the specified id.
   */
  vtkBond GetBond(vtkIdType bondId);

  /**
   * Return the number of bonds in the molecule.
   */
  vtkIdType GetNumberOfBonds();

  /**
   * Return the atomic number of the atom with the specified id.
   */
  unsigned short GetAtomAtomicNumber(vtkIdType atomId);

  /**
   * Set the atomic number of the atom with the specified id.
   */
  void SetAtomAtomicNumber(vtkIdType atomId,
                           unsigned short atomicNum);

  //@{
  /**
   * Set the position of the atom with the specified id.
   */
  void SetAtomPosition(vtkIdType atomId, const vtkVector3f &pos);
  void SetAtomPosition(vtkIdType atomId, double x, double y, double z);
  //@}

  //@{
  /**
   * Get the position of the atom with the specified id.
   */
  vtkVector3f GetAtomPosition(vtkIdType atomId);
  void GetAtomPosition(vtkIdType atomId, float pos[3]);
  //@}

  //@{
  /**
   * Get/Set the bond order of the bond with the specified id
   */
  void SetBondOrder(vtkIdType bondId, unsigned short order);
  unsigned short GetBondOrder(vtkIdType bondId);
  //@}

  /**
   * Get the bond length of the bond with the specified id

   * \note If the associated vtkBond object is already available,
   * vtkBond::GetBondLength is potentially much faster than this
   * function, as a list of all bonds may need to be constructed to
   * locate the appropriate bond.
   * \sa UpdateBondList()
   */
  double GetBondLength(vtkIdType bondId);

  //@{
  /**
   * Access the raw arrays used in this vtkMolecule instance
   */
  vtkPoints * GetAtomicPositionArray();
  vtkUnsignedShortArray * GetAtomicNumberArray();
  vtkUnsignedShortArray * GetBondOrdersArray();
  //@}

  //@{
  /**
   * Set/Get the AbstractElectronicData-subclassed object for this molecule.
   */
  vtkGetObjectMacro(ElectronicData, vtkAbstractElectronicData);
  virtual void SetElectronicData(vtkAbstractElectronicData*);
  //@}

  /**
   * Performs the same operation as ShallowCopy(),
   * but instead of reporting an error for an incompatible graph,
   * returns false.
   */
  bool CheckedShallowCopy(vtkGraph *g) override;

  /**
   * Performs the same operation as DeepCopy(),
   * but instead of reporting an error for an incompatible graph,
   * returns false.
   */
  bool CheckedDeepCopy(vtkGraph *g) override;

  /**
   * Shallow copies the data object into this molecule.
   */
  void ShallowCopy(vtkDataObject *obj) override;

  /**
   * Deep copies the data object into this molecule.
   */
  void DeepCopy(vtkDataObject *obj) override;

  /**
   * Shallow copies the atoms and bonds from @a m into @a this.
   */
  virtual void ShallowCopyStructure(vtkMolecule *m);

  /**
   * Deep copies the atoms and bonds from @a m into @a this.
   */
  virtual void DeepCopyStructure(vtkMolecule *m);

  /**
   * Shallow copies attributes (i.e. everything besides atoms and bonds) from
   * @a m into @a this.
   */
  virtual void ShallowCopyAttributes(vtkMolecule *m);

  /**
   * Deep copies attributes (i.e. everything besides atoms and bonds) from
   * @a m into @a this.
   */
  virtual void DeepCopyAttributes(vtkMolecule *m);

  //@{
  /**
   * Obtain the plane that passes through the indicated bond with the given
   * normal. If the plane is set successfully, the function returns true.

   * If the normal is not orthogonal to the bond, a new normal will be
   * constructed in such a way that the plane will be orthogonal to
   * the plane spanned by the bond vector and the input normal vector.

   * This ensures that the plane passes through the bond, and the
   * normal is more of a "hint" indicating the orientation of the plane.

   * The new normal (n) is defined as the input normal vector (n_i) minus
   * the projection of itself (proj[n_i]_v) onto the bond vector (v):

   * @verbatim
   * v ^
   * |  n = (n_i - proj[n_j]_v)
   * proj[n_i]_v ^  |----x
   * |  |   /
   * |  |  / n_i
   * |  | /
   * |  |/
   * @endverbatim

   * If n_i is parallel to v, a warning will be printed and no plane will be
   * added. Obviously, n_i must not be parallel to v.
   */
  static bool GetPlaneFromBond(const vtkBond &bond, const vtkVector3f &normal,
                               vtkPlane *plane);
  static bool GetPlaneFromBond(const vtkAtom &atom1, const vtkAtom &atom2,
                               const vtkVector3f &normal, vtkPlane *plane);
  //@}

  /**
   * Return true if a unit cell lattice is defined.
   */
  bool HasLattice();

  /**
   * Remove any unit cell lattice information from the molecule.
   */
  void ClearLattice();

  //@{
  /**
   * The unit cell vectors. The matrix is stored using a row-major layout, with
   * the vectors encoded as columns.
   */
  void SetLattice(vtkMatrix3x3 *matrix);
  void SetLattice(const vtkVector3d &a,
                  const vtkVector3d &b,
                  const vtkVector3d &c);
  //@}

  /**
   * Get the unit cell lattice vectors. The matrix is stored using a row-major
   * layout, with the vectors encoded as columns. Will return nullptr if no
   * unit cell information is available.
   * @sa GetLatticeOrigin
   */
  vtkMatrix3x3* GetLattice();

  //@{
  /**
   * Get the unit cell lattice vectors, and optionally, the origin.
   */
  void GetLattice(vtkVector3d &a, vtkVector3d &b, vtkVector3d &c);
  void GetLattice(vtkVector3d &a, vtkVector3d &b, vtkVector3d &c,
                  vtkVector3d &origin);
  //@}

  //@{
  /**
   * Get the unit cell origin (for rendering purposes).
   */
  vtkGetMacro(LatticeOrigin, vtkVector3d)
  vtkSetMacro(LatticeOrigin, vtkVector3d)
  //@}

  /**
   * Get the array that defines the ghost type of each atom.
   */
  vtkUnsignedCharArray* GetAtomGhostArray();

  /**
   * Allocate ghost array for atoms.
   */
  void AllocateAtomGhostArray();

  /**
   * Get the array that defines the ghost type of each bond.
   */
  vtkUnsignedCharArray* GetBondGhostArray();

  /**
   * Allocate ghost array for bonds.
   */
  void AllocateBondGhostArray();

  /**
   * Initialize a molecule with an atom per input point.
   * Parameters atomPositions and atomicNumberArray should have the same size.
   */
  int Initialize(vtkPoints* atomPositions,
    vtkDataArray* atomicNumberArray,
    vtkDataSetAttributes* atomData);

  /**
   * Overloads Initialize method.
   */
  int Initialize(vtkPoints* atomPositions,
    vtkDataSetAttributes* atomData)
  {
    return this->Initialize(atomPositions, nullptr, atomData);
  }

  /**
   * Use input molecule points, atomic number and atomic data to initialize the new molecule.
   */
  int Initialize(vtkMolecule* molecule);

  //@{
  /**
   * Retrieve a molecule from an information vector.
   */
  static vtkMolecule* GetData(vtkInformation *info);
  static vtkMolecule* GetData(vtkInformationVector *v, int i=0);
  //@}

  /**
   * Return the VertexData of the underlying graph
   */
  vtkDataSetAttributes* GetAtomData()
  {
    return this->GetVertexData();
  }

  /**
   * Return the EdgeData of the underlying graph
   */
  vtkDataSetAttributes* GetBondData()
  {
    return this->GetEdgeData();
  }

  /**
   * Return the edge id from the underlying graph.
   */
  vtkIdType GetBondId(vtkIdType a, vtkIdType b)
  {
    return this->GetEdgeId(a, b);
  }

  //@{
  /**
   * Get/Set the atomic number array name.
   */
  vtkSetStringMacro(AtomicNumberArrayName);
  vtkGetStringMacro(AtomicNumberArrayName);
  //@}

  //@{
  /**
   * Get/Set the bond orders array name.
   */
  vtkSetStringMacro(BondOrdersArrayName);
  vtkGetStringMacro(BondOrdersArrayName);
  //@}

 protected:
  vtkMolecule();
  ~vtkMolecule() override;

  /**
   * Copy bonds and atoms.
   */
  virtual void CopyStructureInternal(vtkMolecule *m, bool deep);

  /**
   * Copy everything but bonds and atoms.
   */
  virtual void CopyAttributesInternal(vtkMolecule *m, bool deep);

  //@{
  /**
   * The graph superclass does not provide fast random access to the
   * edge (bond) data. All random access is performed using a lookup
   * table that must be rebuilt periodically. These allow for lazy
   * building of the lookup table
   */
  bool BondListIsDirty;
  void SetBondListDirty() {this->BondListIsDirty = true;}
  void UpdateBondList();
  vtkIdTypeArray* GetBondList();
  //@}

  friend class vtkAtom;
  friend class vtkBond;

  vtkAbstractElectronicData *ElectronicData;
  vtkSmartPointer<vtkMatrix3x3> Lattice;
  vtkVector3d LatticeOrigin;

  vtkUnsignedCharArray* AtomGhostArray;
  vtkUnsignedCharArray* BondGhostArray;

  char* AtomicNumberArrayName;
  char* BondOrdersArrayName;

private:
  vtkMolecule(const vtkMolecule&) = delete;
  void operator=(const vtkMolecule&) = delete;
};

#endif