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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=========================================================================*/
88#ifndef vtkMolecule_h
89#define vtkMolecule_h
90
91#include "vtkCommonDataModelModule.h" // For export macro
92#include "vtkSmartPointer.h" // For vtkSmartPointer
93#include "vtkUndirectedGraph.h"
94
95#include "vtkAtom.h" // Simple proxy class dependent on vtkMolecule
96#include "vtkBond.h" // Simple proxy class dependent on vtkMolecule
97
98#include "vtkVector.h" // Small templated vector convenience class
99
101class vtkDataArray;
102class vtkInformation;
104class vtkMatrix3x3;
105class vtkPlane;
106class vtkPoints;
109
110class VTKCOMMONDATAMODEL_EXPORT vtkMolecule : public vtkUndirectedGraph
111{
112public:
113 static vtkMolecule* New();
115 void PrintSelf(ostream& os, vtkIndent indent) override;
116 void Initialize() override;
117
121 int GetDataObjectType() override { return VTK_MOLECULE; }
122
127 vtkAtom AppendAtom() { return this->AppendAtom(0, 0., 0., 0.); }
128
130
134 vtkAtom AppendAtom(unsigned short atomicNumber, double x, double y, double z);
135 vtkAtom AppendAtom(unsigned short atomicNumber, const vtkVector3f& pos)
136 {
137 return this->AppendAtom(atomicNumber, pos[0], pos[1], pos[2]);
138 }
139
140 vtkAtom AppendAtom(unsigned short atomicNumber, double pos[3])
141 {
142 return this->AppendAtom(atomicNumber, pos[0], pos[1], pos[2]);
143 }
145
150
155
157
162 vtkBond AppendBond(vtkIdType atom1, vtkIdType atom2, unsigned short order = 1);
163 vtkBond AppendBond(const vtkAtom& atom1, const vtkAtom& atom2, unsigned short order = 1)
164 {
165 return this->AppendBond(atom1.Id, atom2.Id, order);
166 }
168
173
178
182 unsigned short GetAtomAtomicNumber(vtkIdType atomId);
183
187 void SetAtomAtomicNumber(vtkIdType atomId, unsigned short atomicNum);
188
190
193 void SetAtomPosition(vtkIdType atomId, const vtkVector3f& pos);
194 void SetAtomPosition(vtkIdType atomId, double x, double y, double z);
195 void SetAtomPosition(vtkIdType atomId, double pos[3])
196 {
197 this->SetAtomPosition(atomId, pos[0], pos[1], pos[2]);
198 }
200
202
206 void GetAtomPosition(vtkIdType atomId, float pos[3]);
207 void GetAtomPosition(vtkIdType atomId, double pos[3]);
209
211
214 void SetBondOrder(vtkIdType bondId, unsigned short order);
215 unsigned short GetBondOrder(vtkIdType bondId);
217
227 double GetBondLength(vtkIdType bondId);
228
230
237
239
242 vtkGetObjectMacro(ElectronicData, vtkAbstractElectronicData);
245
251 bool CheckedShallowCopy(vtkGraph* g) override;
252
258 bool CheckedDeepCopy(vtkGraph* g) override;
259
263 void ShallowCopy(vtkDataObject* obj) override;
264
268 void DeepCopy(vtkDataObject* obj) override;
269
274
279
285
291
293
320 static bool GetPlaneFromBond(const vtkBond& bond, const vtkVector3f& normal, vtkPlane* plane);
321 static bool GetPlaneFromBond(
322 const vtkAtom& atom1, const vtkAtom& atom2, const vtkVector3f& normal, vtkPlane* plane);
324
329
334
336
341 void SetLattice(const vtkVector3d& a, const vtkVector3d& b, const vtkVector3d& c);
343
351
353
359
361
364 vtkGetMacro(LatticeOrigin, vtkVector3d);
365 vtkSetMacro(LatticeOrigin, vtkVector3d);
367
372
377
382
387
393 vtkPoints* atomPositions, vtkDataArray* atomicNumberArray, vtkDataSetAttributes* atomData);
394
398 int Initialize(vtkPoints* atomPositions, vtkDataSetAttributes* atomData)
399 {
400 return this->Initialize(atomPositions, nullptr, atomData);
401 }
402
406 int Initialize(vtkMolecule* molecule);
407
409
415
420
425
429 vtkIdType GetBondId(vtkIdType a, vtkIdType b) { return this->GetEdgeId(a, b); }
430
432
435 vtkSetStringMacro(AtomicNumberArrayName);
436 vtkGetStringMacro(AtomicNumberArrayName);
438
440
443 vtkSetStringMacro(BondOrdersArrayName);
444 vtkGetStringMacro(BondOrdersArrayName);
446
454 unsigned long GetActualMemorySize() override;
455
456protected:
458 ~vtkMolecule() override;
459
463 virtual void CopyStructureInternal(vtkMolecule* m, bool deep);
464
468 virtual void CopyAttributesInternal(vtkMolecule* m, bool deep);
469
471
478 void SetBondListDirty() { this->BondListIsDirty = true; }
482
483 friend class vtkAtom;
484 friend class vtkBond;
485
489
492
495
496private:
497 vtkMolecule(const vtkMolecule&) = delete;
498 void operator=(const vtkMolecule&) = delete;
499};
500
501#endif
Provides access to and storage of chemical electronic data.
convenience proxy for vtkMolecule
Definition: vtkAtom.h:32
vtkIdType Id
Definition: vtkAtom.h:72
convenience proxy for vtkMolecule
Definition: vtkBond.h:31
abstract superclass for arrays of numeric data
Definition: vtkDataArray.h:159
general representation of visualization data
represent and manipulate attribute data in a dataset
Base class for graph data types.
Definition: vtkGraph.h:339
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.
virtual vtkDataSetAttributes * GetEdgeData()
Get the vertex or edge data.
dynamic, self-adjusting array of vtkIdType
a simple class to control print indentation
Definition: vtkIndent.h:113
Store zero or more vtkInformation instances.
Store vtkAlgorithm input/output information.
represent and manipulate 3x3 transformation matrices
Definition: vtkMatrix3x3.h:63
class describing a molecule
Definition: vtkMolecule.h:111
vtkAbstractElectronicData * ElectronicData
Definition: vtkMolecule.h:486
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:127
vtkVector3f GetAtomPosition(vtkIdType atomId)
Get the position of the atom with the specified id.
void SetLattice(vtkMatrix3x3 *matrix)
The unit cell vectors.
void PrintSelf(ostream &os, vtkIndent indent) override
Methods invoked by print to print information about the object including superclasses.
static vtkMolecule * New()
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:163
vtkUnsignedShortArray * GetAtomicNumberArray()
Access the raw arrays used in this vtkMolecule instance.
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.
static vtkMolecule * GetData(vtkInformationVector *v, int i=0)
Retrieve a molecule from an information vector.
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.
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:487
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:398
void ShallowCopy(vtkDataObject *obj) override
Shallow copies the data object into this molecule.
void SetBondListDirty()
The graph superclass does not provide fast random access to the edge (bond) data.
Definition: vtkMolecule.h:478
vtkIdType GetBondId(vtkIdType a, vtkIdType b)
Return the edge id from the underlying graph.
Definition: vtkMolecule.h:429
vtkUnsignedCharArray * AtomGhostArray
Definition: vtkMolecule.h:490
void GetLattice(vtkVector3d &a, vtkVector3d &b, vtkVector3d &c)
Get the unit cell lattice vectors, and optionally, the origin.
vtkUnsignedCharArray * BondGhostArray
Definition: vtkMolecule.h:491
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.
vtkPoints * GetAtomicPositionArray()
Access the raw arrays used in this vtkMolecule instance.
virtual void CopyAttributesInternal(vtkMolecule *m, bool deep)
Copy everything but bonds and atoms.
vtkUnsignedShortArray * GetBondOrdersArray()
Access the raw arrays used in this vtkMolecule instance.
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:121
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.
vtkUnsignedCharArray * GetBondGhostArray()
Get the array that defines the ghost type of each bond.
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:494
bool HasLattice()
Return true if a unit cell lattice is defined.
~vtkMolecule() override
vtkDataSetAttributes * GetAtomData()
Return the VertexData of the underlying graph.
Definition: vtkMolecule.h:419
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.
vtkMatrix3x3 * GetLattice()
Get the unit cell lattice 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:135
bool BondListIsDirty
The graph superclass does not provide fast random access to the edge (bond) data.
Definition: vtkMolecule.h:477
static vtkMolecule * GetData(vtkInformation *info)
Retrieve a molecule from an information vector.
vtkUnsignedCharArray * GetAtomGhostArray()
Get the array that defines the ghost type of each atom.
vtkBond GetBond(vtkIdType bondId)
Return a vtkAtom that refers to the bond with the specified id.
int Initialize(vtkMolecule *molecule)
Use input molecule points, atomic number and atomic data to initialize the new molecule.
char * AtomicNumberArrayName
Definition: vtkMolecule.h:493
void AllocateBondGhostArray()
Allocate ghost array for bonds.
virtual void CopyStructureInternal(vtkMolecule *m, bool deep)
Copy bonds and atoms.
void SetAtomPosition(vtkIdType atomId, double pos[3])
Set the position of the atom with the specified id.
Definition: vtkMolecule.h:195
vtkDataSetAttributes * GetBondData()
Return the EdgeData of the underlying graph.
Definition: vtkMolecule.h:424
vtkIdType GetNumberOfAtoms()
Return the number of atoms in the molecule.
vtkVector3d LatticeOrigin
Definition: vtkMolecule.h:488
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...
vtkAtom AppendAtom(unsigned short atomicNumber, double pos[3])
Add new atom with the specified atomic number and position.
Definition: vtkMolecule.h:140
vtkIdTypeArray * GetBondList()
The graph superclass does not provide fast random access to the edge (bond) data.
perform various plane computations
Definition: vtkPlane.h:143
represent and manipulate 3D points
Definition: vtkPoints.h:143
Hold a reference to a vtkObjectBase instance.
An undirected graph.
dynamic, self-adjusting array of unsigned char
dynamic, self-adjusting array of unsigned short
int vtkIdType
Definition: vtkType.h:332
#define VTK_MOLECULE
Definition: vtkType.h:110