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vtkMolecule.h
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1 /*=========================================================================
2 
3  Program: Visualization Toolkit
4  Module: vtkMolecule.h
5 
6  Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
7  All rights reserved.
8  See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
9 
10  This software is distributed WITHOUT ANY WARRANTY; without even
11  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
12  PURPOSE. See the above copyright notice for more information.
13 
14 =========================================================================*/
91 #ifndef vtkMolecule_h
92 #define vtkMolecule_h
93 
94 #include "vtkCommonDataModelModule.h" // For export macro
95 #include "vtkSmartPointer.h" // For vtkSmartPointer
96 #include "vtkUndirectedGraph.h"
97 
98 #include "vtkAtom.h" // Simple proxy class dependent on vtkMolecule
99 #include "vtkBond.h" // Simple proxy class dependent on vtkMolecule
100 
101 #include "vtkVector.h" // Small templated vector convenience class
102 
104 class vtkDataArray;
105 class vtkInformation;
107 class vtkMatrix3x3;
108 class vtkPlane;
109 class vtkPoints;
112 
113 class VTKCOMMONDATAMODEL_EXPORT vtkMolecule : public vtkUndirectedGraph
114 {
115 public:
116  static vtkMolecule* New();
118  void PrintSelf(ostream& os, vtkIndent indent) override;
119  void Initialize() override;
120 
124  int GetDataObjectType() override { return VTK_MOLECULE; }
125 
130  vtkAtom AppendAtom() { return this->AppendAtom(0, 0., 0., 0.); }
131 
133 
137  vtkAtom AppendAtom(unsigned short atomicNumber, double x, double y, double z);
138  vtkAtom AppendAtom(unsigned short atomicNumber, const vtkVector3f& pos)
139  {
140  return this->AppendAtom(atomicNumber, pos[0], pos[1], pos[2]);
141  }
142 
143  vtkAtom AppendAtom(unsigned short atomicNumber, double pos[3])
144  {
145  return this->AppendAtom(atomicNumber, pos[0], pos[1], pos[2]);
146  }
148 
153 
158 
160 
165  vtkBond AppendBond(vtkIdType atom1, vtkIdType atom2, unsigned short order = 1);
166  vtkBond AppendBond(const vtkAtom& atom1, const vtkAtom& atom2, unsigned short order = 1)
167  {
168  return this->AppendBond(atom1.Id, atom2.Id, order);
169  }
171 
176 
181 
185  unsigned short GetAtomAtomicNumber(vtkIdType atomId);
186 
190  void SetAtomAtomicNumber(vtkIdType atomId, unsigned short atomicNum);
191 
193 
196  void SetAtomPosition(vtkIdType atomId, const vtkVector3f& pos);
197  void SetAtomPosition(vtkIdType atomId, double x, double y, double z);
198  void SetAtomPosition(vtkIdType atomId, double pos[3])
199  {
200  this->SetAtomPosition(atomId, pos[0], pos[1], pos[2]);
201  }
203 
205 
209  void GetAtomPosition(vtkIdType atomId, float pos[3]);
210  void GetAtomPosition(vtkIdType atomId, double pos[3]);
212 
214 
217  void SetBondOrder(vtkIdType bondId, unsigned short order);
218  unsigned short GetBondOrder(vtkIdType bondId);
220 
230  double GetBondLength(vtkIdType bondId);
231 
233 
240 
242 
245  vtkGetObjectMacro(ElectronicData, vtkAbstractElectronicData);
248 
254  bool CheckedShallowCopy(vtkGraph* g) override;
255 
261  bool CheckedDeepCopy(vtkGraph* g) override;
262 
266  void ShallowCopy(vtkDataObject* obj) override;
267 
271  void DeepCopy(vtkDataObject* obj) override;
272 
277 
281  virtual void DeepCopyStructure(vtkMolecule* m);
282 
288 
293  virtual void DeepCopyAttributes(vtkMolecule* m);
294 
296 
323  static bool GetPlaneFromBond(const vtkBond& bond, const vtkVector3f& normal, vtkPlane* plane);
324  static bool GetPlaneFromBond(
325  const vtkAtom& atom1, const vtkAtom& atom2, const vtkVector3f& normal, vtkPlane* plane);
327 
331  bool HasLattice();
332 
336  void ClearLattice();
337 
339 
343  void SetLattice(vtkMatrix3x3* matrix);
344  void SetLattice(const vtkVector3d& a, const vtkVector3d& b, const vtkVector3d& c);
346 
354 
356 
362 
364 
367  vtkGetMacro(LatticeOrigin, vtkVector3d);
368  vtkSetMacro(LatticeOrigin, vtkVector3d);
370 
375 
380 
385 
390 
396  vtkPoints* atomPositions, vtkDataArray* atomicNumberArray, vtkDataSetAttributes* atomData);
397 
401  int Initialize(vtkPoints* atomPositions, vtkDataSetAttributes* atomData)
402  {
403  return this->Initialize(atomPositions, nullptr, atomData);
404  }
405 
409  int Initialize(vtkMolecule* molecule);
410 
412 
416  static vtkMolecule* GetData(vtkInformationVector* v, int i = 0);
418 
423 
428 
432  vtkIdType GetBondId(vtkIdType a, vtkIdType b) { return this->GetEdgeId(a, b); }
433 
435 
438  vtkSetStringMacro(AtomicNumberArrayName);
439  vtkGetStringMacro(AtomicNumberArrayName);
441 
443 
446  vtkSetStringMacro(BondOrdersArrayName);
447  vtkGetStringMacro(BondOrdersArrayName);
449 
457  unsigned long GetActualMemorySize() override;
458 
459 protected:
461  ~vtkMolecule() override;
462 
466  virtual void CopyStructureInternal(vtkMolecule* m, bool deep);
467 
471  virtual void CopyAttributesInternal(vtkMolecule* m, bool deep);
472 
474 
481  void SetBondListDirty() { this->BondListIsDirty = true; }
485 
486  friend class vtkAtom;
487  friend class vtkBond;
488 
492 
495 
498 
499 private:
500  vtkMolecule(const vtkMolecule&) = delete;
501  void operator=(const vtkMolecule&) = delete;
502 };
503 
504 #endif
Provides access to and storage of chemical electronic data.
convenience proxy for vtkMolecule
Definition: vtkAtom.h:35
vtkIdType Id
Definition: vtkAtom.h:75
convenience proxy for vtkMolecule
Definition: vtkBond.h:34
friend class vtkMolecule
Definition: vtkBond.h:81
abstract superclass for arrays of numeric data
Definition: vtkDataArray.h:165
general representation of visualization data
represent and manipulate attribute data in a dataset
Base class for graph data types.
Definition: vtkGraph.h:345
virtual vtkDataSetAttributes * GetEdgeData()
Get the vertex or edge data.
void Initialize() override
Initialize to an empty graph.
virtual vtkDataSetAttributes * GetVertexData()
Get the vertex or edge data.
vtkIdType GetEdgeId(vtkIdType a, vtkIdType b)
Returns the Id of the edge between vertex a and vertex b.
dynamic, self-adjusting array of vtkIdType
a simple class to control print indentation
Definition: vtkIndent.h:119
Store zero or more vtkInformation instances.
Store vtkAlgorithm input/output information.
represent and manipulate 3x3 transformation matrices
Definition: vtkMatrix3x3.h:66
class describing a molecule
Definition: vtkMolecule.h:114
vtkAbstractElectronicData * ElectronicData
Definition: vtkMolecule.h:489
void GetAtomPosition(vtkIdType atomId, float pos[3])
Get the position of the atom with the specified id.
vtkAtom AppendAtom()
Add new atom with atomic number 0 (dummy atom) at origin.
Definition: vtkMolecule.h:130
vtkVector3f GetAtomPosition(vtkIdType atomId)
Get the position of the atom with the specified id.
vtkIdTypeArray * GetBondList()
The graph superclass does not provide fast random access to the edge (bond) data.
void SetLattice(vtkMatrix3x3 *matrix)
The unit cell vectors.
vtkDataSetAttributes * GetAtomData()
Return the VertexData of the underlying graph.
Definition: vtkMolecule.h:422
void PrintSelf(ostream &os, vtkIndent indent) override
Methods invoked by print to print information about the object including superclasses.
int Initialize(vtkPoints *atomPositions, vtkDataArray *atomicNumberArray, vtkDataSetAttributes *atomData)
Initialize a molecule with an atom per input point.
vtkBond AppendBond(const vtkAtom &atom1, const vtkAtom &atom2, unsigned short order=1)
Add a bond between the specified atoms, optionally setting the bond order (default: 1).
Definition: vtkMolecule.h:166
void SetBondOrder(vtkIdType bondId, unsigned short order)
Get/Set the bond order of the bond with the specified id.
vtkAtom AppendAtom(unsigned short atomicNumber, double x, double y, double z)
Add new atom with the specified atomic number and position.
vtkAtom GetAtom(vtkIdType atomId)
Return a vtkAtom that refers to the atom with the specified id.
virtual void DeepCopyStructure(vtkMolecule *m)
Deep copies the atoms and bonds from m into this.
void GetLattice(vtkVector3d &a, vtkVector3d &b, vtkVector3d &c, vtkVector3d &origin)
Get the unit cell lattice vectors, and optionally, the origin.
void Initialize() override
Initialize to an empty graph.
void ClearLattice()
Remove any unit cell lattice information from the molecule.
vtkUnsignedCharArray * GetAtomGhostArray()
Get the array that defines the ghost type of each atom.
virtual void ShallowCopyAttributes(vtkMolecule *m)
Shallow copies attributes (i.e.
void SetAtomAtomicNumber(vtkIdType atomId, unsigned short atomicNum)
Set the atomic number of the atom with the specified id.
virtual void ShallowCopyStructure(vtkMolecule *m)
Shallow copies the atoms and bonds from m into this.
void GetAtomPosition(vtkIdType atomId, double pos[3])
Get the position of the atom with the specified id.
unsigned long GetActualMemorySize() override
Return the actual size of the data in kibibytes (1024 bytes).
double GetBondLength(vtkIdType bondId)
Get the bond length of the bond with the specified id.
vtkSmartPointer< vtkMatrix3x3 > Lattice
Definition: vtkMolecule.h:490
virtual void DeepCopyAttributes(vtkMolecule *m)
Deep copies attributes (i.e.
static bool GetPlaneFromBond(const vtkBond &bond, const vtkVector3f &normal, vtkPlane *plane)
Obtain the plane that passes through the indicated bond with the given normal.
int Initialize(vtkPoints *atomPositions, vtkDataSetAttributes *atomData)
Overloads Initialize method.
Definition: vtkMolecule.h:401
void ShallowCopy(vtkDataObject *obj) override
Shallow copies the data object into this molecule.
vtkPoints * GetAtomicPositionArray()
Access the raw arrays used in this vtkMolecule instance.
void SetBondListDirty()
The graph superclass does not provide fast random access to the edge (bond) data.
Definition: vtkMolecule.h:481
vtkIdType GetBondId(vtkIdType a, vtkIdType b)
Return the edge id from the underlying graph.
Definition: vtkMolecule.h:432
vtkUnsignedShortArray * GetAtomicNumberArray()
Access the raw arrays used in this vtkMolecule instance.
vtkUnsignedCharArray * AtomGhostArray
Definition: vtkMolecule.h:493
void GetLattice(vtkVector3d &a, vtkVector3d &b, vtkVector3d &c)
Get the unit cell lattice vectors, and optionally, the origin.
vtkUnsignedCharArray * BondGhostArray
Definition: vtkMolecule.h:494
void SetAtomPosition(vtkIdType atomId, double x, double y, double z)
Set the position of the atom with the specified id.
void UpdateBondList()
The graph superclass does not provide fast random access to the edge (bond) data.
virtual void CopyAttributesInternal(vtkMolecule *m, bool deep)
Copy everything but bonds and atoms.
void DeepCopy(vtkDataObject *obj) override
Deep copies the data object into this molecule.
int GetDataObjectType() override
Return what type of dataset this is.
Definition: vtkMolecule.h:124
static bool GetPlaneFromBond(const vtkAtom &atom1, const vtkAtom &atom2, const vtkVector3f &normal, vtkPlane *plane)
Obtain the plane that passes through the indicated bond with the given normal.
void AllocateAtomGhostArray()
Allocate ghost array for atoms.
void SetAtomPosition(vtkIdType atomId, const vtkVector3f &pos)
Set the position of the atom with the specified id.
virtual void SetElectronicData(vtkAbstractElectronicData *)
Set/Get the AbstractElectronicData-subclassed object for this molecule.
unsigned short GetAtomAtomicNumber(vtkIdType atomId)
Return the atomic number of the atom with the specified id.
vtkIdType GetNumberOfBonds()
Return the number of bonds in the molecule.
char * BondOrdersArrayName
Definition: vtkMolecule.h:497
bool HasLattice()
Return true if a unit cell lattice is defined.
~vtkMolecule() override
vtkBond AppendBond(vtkIdType atom1, vtkIdType atom2, unsigned short order=1)
Add a bond between the specified atoms, optionally setting the bond order (default: 1).
void SetLattice(const vtkVector3d &a, const vtkVector3d &b, const vtkVector3d &c)
The unit cell vectors.
unsigned short GetBondOrder(vtkIdType bondId)
Get/Set the bond order of the bond with the specified id.
vtkAtom AppendAtom(unsigned short atomicNumber, const vtkVector3f &pos)
Add new atom with the specified atomic number and position.
Definition: vtkMolecule.h:138
bool BondListIsDirty
The graph superclass does not provide fast random access to the edge (bond) data.
Definition: vtkMolecule.h:480
vtkBond GetBond(vtkIdType bondId)
Return a vtkAtom that refers to the bond with the specified id.
static vtkMolecule * GetData(vtkInformationVector *v, int i=0)
Retrieve a molecule from an information vector.
int Initialize(vtkMolecule *molecule)
Use input molecule points, atomic number and atomic data to initialize the new molecule.
char * AtomicNumberArrayName
Definition: vtkMolecule.h:496
void AllocateBondGhostArray()
Allocate ghost array for bonds.
vtkUnsignedShortArray * GetBondOrdersArray()
Access the raw arrays used in this vtkMolecule instance.
virtual void CopyStructureInternal(vtkMolecule *m, bool deep)
Copy bonds and atoms.
static vtkMolecule * New()
static vtkMolecule * GetData(vtkInformation *info)
Retrieve a molecule from an information vector.
vtkUnsignedCharArray * GetBondGhostArray()
Get the array that defines the ghost type of each bond.
void SetAtomPosition(vtkIdType atomId, double pos[3])
Set the position of the atom with the specified id.
Definition: vtkMolecule.h:198
vtkIdType GetNumberOfAtoms()
Return the number of atoms in the molecule.
vtkVector3d LatticeOrigin
Definition: vtkMolecule.h:491
bool CheckedShallowCopy(vtkGraph *g) override
Performs the same operation as ShallowCopy(), but instead of reporting an error for an incompatible g...
bool CheckedDeepCopy(vtkGraph *g) override
Performs the same operation as DeepCopy(), but instead of reporting an error for an incompatible grap...
vtkDataSetAttributes * GetBondData()
Return the EdgeData of the underlying graph.
Definition: vtkMolecule.h:427
vtkMatrix3x3 * GetLattice()
Get the unit cell lattice vectors.
vtkAtom AppendAtom(unsigned short atomicNumber, double pos[3])
Add new atom with the specified atomic number and position.
Definition: vtkMolecule.h:143
perform various plane computations
Definition: vtkPlane.h:146
represent and manipulate 3D points
Definition: vtkPoints.h:149
An undirected graph.
dynamic, self-adjusting array of unsigned char
dynamic, self-adjusting array of unsigned short
@ order
Definition: vtkX3D.h:446
@ info
Definition: vtkX3D.h:382
int vtkIdType
Definition: vtkType.h:332
#define VTK_MOLECULE
Definition: vtkType.h:110