vtkMolecule.h

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/*=========================================================================
 
  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.
 
=========================================================================*/
#ifndef vtkMolecule_h
#define vtkMolecule_h
 
#include "vtkCommonDataModelModule.h" // For export macro
#include "vtkUndirectedGraph.h"
 
//BTX
#include "vtkAtom.h" // Simple proxy class dependent on vtkMolecule
#include "vtkBond.h" // Simple proxy class dependent on vtkMolecule
//ETX
#include "vtkVector.h" // Small templated vector convenience class
 
class vtkPlane;
class vtkAbstractElectronicData;
class vtkPoints;
class vtkUnsignedShortArray;
 
class VTKCOMMONDATAMODEL_EXPORT vtkMolecule : public vtkUndirectedGraph
{
public:
  static vtkMolecule *New();
  vtkTypeMacro(vtkMolecule,vtkUndirectedGraph);
  void PrintSelf(ostream &os, vtkIndent indent);
  virtual void Initialize();
 
  virtual int GetDataObjectType() {return VTK_MOLECULE;}
 
//BTX
 
  vtkAtom AppendAtom()
  {
    return this->AppendAtom(0, vtkVector3f(0, 0, 0));
  }
 
  vtkAtom AppendAtom(unsigned short atomicNumber, const vtkVector3f &pos);
 
 
  vtkAtom AppendAtom(unsigned short atomicNumber, double x, double y, double z)
  {
    return this->AppendAtom(atomicNumber, vtkVector3f(x, y, z));
  }
 
  vtkAtom GetAtom(vtkIdType atomId);
 
  vtkIdType GetNumberOfAtoms();
 
 
  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);
  }
 
 
  vtkBond GetBond(vtkIdType bondId);
//ETX
 
  vtkIdType GetNumberOfBonds();
 
  unsigned short GetAtomAtomicNumber(vtkIdType atomId);
 
 
  void SetAtomAtomicNumber(vtkIdType atomId,
                           unsigned short atomicNum);
 
 
  void SetAtomPosition(vtkIdType atomId, const vtkVector3f &pos);
  void SetAtomPosition(vtkIdType atomId, double x, double y, double z);
 
 
  vtkVector3f GetAtomPosition(vtkIdType atomId);
  void GetAtomPosition(vtkIdType atomId, float pos[3]);
 
 
  void SetBondOrder(vtkIdType bondId, unsigned short order);
  unsigned short GetBondOrder(vtkIdType bondId);
 
  double GetBondLength(vtkIdType bondId);
 
 
  vtkPoints * GetAtomicPositionArray();
  vtkUnsignedShortArray * GetAtomicNumberArray();
 
//BTX
 
  vtkGetObjectMacro(ElectronicData, vtkAbstractElectronicData);
  virtual void SetElectronicData(vtkAbstractElectronicData*);
//ETX
 
  virtual void ShallowCopy(vtkDataObject *obj);
 
  virtual void DeepCopy(vtkDataObject *obj);
 
  virtual void ShallowCopyStructure(vtkMolecule *m);
 
  virtual void DeepCopyStructure(vtkMolecule *m);
 
  virtual void ShallowCopyAttributes(vtkMolecule *m);
 
  virtual void DeepCopyAttributes(vtkMolecule *m);
 
 
  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);
 
 protected:
  vtkMolecule();
  ~vtkMolecule();
 
  virtual void CopyStructureInternal(vtkMolecule *m, bool deep);
 
  virtual void CopyAttributesInternal(vtkMolecule *m, bool deep);
 
 
  bool BondListIsDirty;
  void SetBondListDirty() {this->BondListIsDirty = true;}
  void UpdateBondList();
 
  friend class vtkAtom;
  friend class vtkBond;
 
  vtkAbstractElectronicData *ElectronicData;
 
private:
  vtkMolecule(const vtkMolecule&);    // Not implemented.
  void operator=(const vtkMolecule&); // Not implemented.
};
 
#endif