VTK  9.1.0
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=========================================================================*/
69#ifndef vtkMolecule_h
70#define vtkMolecule_h
71
72#include "vtkCommonDataModelModule.h" // For export macro
73#include "vtkSmartPointer.h" // For vtkSmartPointer
74#include "vtkUndirectedGraph.h"
75
76#include "vtkAtom.h" // Simple proxy class dependent on vtkMolecule
77#include "vtkBond.h" // Simple proxy class dependent on vtkMolecule
78
79#include "vtkVector.h" // Small templated vector convenience class
80
82class vtkDataArray;
83class vtkInformation;
85class vtkMatrix3x3;
86class vtkPlane;
87class vtkPoints;
90
91class VTKCOMMONDATAMODEL_EXPORT vtkMolecule : public vtkUndirectedGraph
92{
93public:
94 static vtkMolecule* New();
96 void PrintSelf(ostream& os, vtkIndent indent) override;
97 void Initialize() override;
98
102 int GetDataObjectType() override { return VTK_MOLECULE; }
103
108 vtkAtom AppendAtom() { return this->AppendAtom(0, 0., 0., 0.); }
109
111
115 vtkAtom AppendAtom(unsigned short atomicNumber, double x, double y, double z);
116 vtkAtom AppendAtom(unsigned short atomicNumber, const vtkVector3f& pos)
117 {
118 return this->AppendAtom(atomicNumber, pos[0], pos[1], pos[2]);
119 }
120
121 vtkAtom AppendAtom(unsigned short atomicNumber, double pos[3])
122 {
123 return this->AppendAtom(atomicNumber, pos[0], pos[1], pos[2]);
124 }
126
131
136
138
143 vtkBond AppendBond(vtkIdType atom1, vtkIdType atom2, unsigned short order = 1);
144 vtkBond AppendBond(const vtkAtom& atom1, const vtkAtom& atom2, unsigned short order = 1)
145 {
146 return this->AppendBond(atom1.Id, atom2.Id, order);
147 }
149
154
159
163 unsigned short GetAtomAtomicNumber(vtkIdType atomId);
164
168 void SetAtomAtomicNumber(vtkIdType atomId, unsigned short atomicNum);
169
171
174 void SetAtomPosition(vtkIdType atomId, const vtkVector3f& pos);
175 void SetAtomPosition(vtkIdType atomId, double x, double y, double z);
176 void SetAtomPosition(vtkIdType atomId, double pos[3])
177 {
178 this->SetAtomPosition(atomId, pos[0], pos[1], pos[2]);
179 }
181
183
187 void GetAtomPosition(vtkIdType atomId, float pos[3]);
188 void GetAtomPosition(vtkIdType atomId, double pos[3]);
190
192
195 void SetBondOrder(vtkIdType bondId, unsigned short order);
196 unsigned short GetBondOrder(vtkIdType bondId);
198
208 double GetBondLength(vtkIdType bondId);
209
211
218
220
223 vtkGetObjectMacro(ElectronicData, vtkAbstractElectronicData);
226
232 bool CheckedShallowCopy(vtkGraph* g) override;
233
239 bool CheckedDeepCopy(vtkGraph* g) override;
240
244 void ShallowCopy(vtkDataObject* obj) override;
245
249 void DeepCopy(vtkDataObject* obj) override;
250
255
260
266
272
274
301 static bool GetPlaneFromBond(const vtkBond& bond, const vtkVector3f& normal, vtkPlane* plane);
302 static bool GetPlaneFromBond(
303 const vtkAtom& atom1, const vtkAtom& atom2, const vtkVector3f& normal, vtkPlane* plane);
305
310
315
317
322 void SetLattice(const vtkVector3d& a, const vtkVector3d& b, const vtkVector3d& c);
324
332
334
340
342
345 vtkGetMacro(LatticeOrigin, vtkVector3d);
346 vtkSetMacro(LatticeOrigin, vtkVector3d);
348
353
358
363
368
374 vtkPoints* atomPositions, vtkDataArray* atomicNumberArray, vtkDataSetAttributes* atomData);
375
379 int Initialize(vtkPoints* atomPositions, vtkDataSetAttributes* atomData)
380 {
381 return this->Initialize(atomPositions, nullptr, atomData);
382 }
383
387 int Initialize(vtkMolecule* molecule);
388
390
396
401
406
410 vtkIdType GetBondId(vtkIdType a, vtkIdType b) { return this->GetEdgeId(a, b); }
411
413
416 vtkSetStringMacro(AtomicNumberArrayName);
417 vtkGetStringMacro(AtomicNumberArrayName);
419
421
424 vtkSetStringMacro(BondOrdersArrayName);
425 vtkGetStringMacro(BondOrdersArrayName);
427
435 unsigned long GetActualMemorySize() override;
436
437protected:
439 ~vtkMolecule() override;
440
444 virtual void CopyStructureInternal(vtkMolecule* m, bool deep);
445
449 virtual void CopyAttributesInternal(vtkMolecule* m, bool deep);
450
452
459 void SetBondListDirty() { this->BondListIsDirty = true; }
463
464 friend class vtkAtom;
465 friend class vtkBond;
466
470
473
476
477private:
478 vtkMolecule(const vtkMolecule&) = delete;
479 void operator=(const vtkMolecule&) = delete;
480};
481
482#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:50
general representation of visualization data
Definition: vtkDataObject.h:60
represent and manipulate attribute data in a dataset
Base class for graph data types.
Definition: vtkGraph.h:290
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:34
Store zero or more vtkInformation instances.
Store vtkAlgorithm input/output information.
represent and manipulate 3x3 transformation matrices
Definition: vtkMatrix3x3.h:34
class describing a molecule
Definition: vtkMolecule.h:92
vtkAbstractElectronicData * ElectronicData
Definition: vtkMolecule.h:467
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:108
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:144
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:468
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:379
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:459
vtkIdType GetBondId(vtkIdType a, vtkIdType b)
Return the edge id from the underlying graph.
Definition: vtkMolecule.h:410
vtkUnsignedCharArray * AtomGhostArray
Definition: vtkMolecule.h:471
void GetLattice(vtkVector3d &a, vtkVector3d &b, vtkVector3d &c)
Get the unit cell lattice vectors, and optionally, the origin.
vtkUnsignedCharArray * BondGhostArray
Definition: vtkMolecule.h:472
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:102
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:475
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:400
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:116
bool BondListIsDirty
The graph superclass does not provide fast random access to the edge (bond) data.
Definition: vtkMolecule.h:458
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:474
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:176
vtkDataSetAttributes * GetBondData()
Return the EdgeData of the underlying graph.
Definition: vtkMolecule.h:405
vtkIdType GetNumberOfAtoms()
Return the number of atoms in the molecule.
vtkVector3d LatticeOrigin
Definition: vtkMolecule.h:469
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:121
vtkIdTypeArray * GetBondList()
The graph superclass does not provide fast random access to the edge (bond) data.
perform various plane computations
Definition: vtkPlane.h:34
represent and manipulate 3D points
Definition: vtkPoints.h:34
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