VTK  9.3.20240615
vtkMolecule.h
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1// SPDX-FileCopyrightText: Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
2// SPDX-License-Identifier: BSD-3-Clause
60#ifndef vtkMolecule_h
61#define vtkMolecule_h
62
63#include "vtkCommonDataModelModule.h" // For export macro
64#include "vtkSmartPointer.h" // For vtkSmartPointer
65#include "vtkUndirectedGraph.h"
66
67#include "vtkAtom.h" // Simple proxy class dependent on vtkMolecule
68#include "vtkBond.h" // Simple proxy class dependent on vtkMolecule
69
70#include "vtkVector.h" // Small templated vector convenience class
71
72VTK_ABI_NAMESPACE_BEGIN
74class vtkDataArray;
75class vtkInformation;
77class vtkMatrix3x3;
78class vtkPlane;
79class vtkPoints;
82
83class VTKCOMMONDATAMODEL_EXPORT vtkMolecule : public vtkUndirectedGraph
84{
85public:
86 static vtkMolecule* New();
88 void PrintSelf(ostream& os, vtkIndent indent) override;
89 void Initialize() override;
90
94 int GetDataObjectType() override { return VTK_MOLECULE; }
95
100 vtkAtom AppendAtom() { return this->AppendAtom(0, 0., 0., 0.); }
101
103
107 vtkAtom AppendAtom(unsigned short atomicNumber, double x, double y, double z);
108 vtkAtom AppendAtom(unsigned short atomicNumber, const vtkVector3f& pos)
109 {
110 return this->AppendAtom(atomicNumber, pos[0], pos[1], pos[2]);
111 }
112
113 vtkAtom AppendAtom(unsigned short atomicNumber, double pos[3])
114 {
115 return this->AppendAtom(atomicNumber, pos[0], pos[1], pos[2]);
116 }
118
123
128
130
135 vtkBond AppendBond(vtkIdType atom1, vtkIdType atom2, unsigned short order = 1);
136 vtkBond AppendBond(const vtkAtom& atom1, const vtkAtom& atom2, unsigned short order = 1)
137 {
138 return this->AppendBond(atom1.Id, atom2.Id, order);
139 }
141
146
151
155 unsigned short GetAtomAtomicNumber(vtkIdType atomId);
156
160 void SetAtomAtomicNumber(vtkIdType atomId, unsigned short atomicNum);
161
163
166 void SetAtomPosition(vtkIdType atomId, const vtkVector3f& pos);
167 void SetAtomPosition(vtkIdType atomId, double x, double y, double z);
168 void SetAtomPosition(vtkIdType atomId, double pos[3])
169 {
170 this->SetAtomPosition(atomId, pos[0], pos[1], pos[2]);
171 }
173
175
179 void GetAtomPosition(vtkIdType atomId, float pos[3]);
180 void GetAtomPosition(vtkIdType atomId, double pos[3]);
182
184
187 void SetBondOrder(vtkIdType bondId, unsigned short order);
188 unsigned short GetBondOrder(vtkIdType bondId);
190
200 double GetBondLength(vtkIdType bondId);
201
203
210
212
215 vtkGetObjectMacro(ElectronicData, vtkAbstractElectronicData);
218
224 bool CheckedShallowCopy(vtkGraph* g) override;
225
231 bool CheckedDeepCopy(vtkGraph* g) override;
232
236 void ShallowCopy(vtkDataObject* obj) override;
237
241 void DeepCopy(vtkDataObject* obj) override;
242
247
252
258
264
266
293 static bool GetPlaneFromBond(const vtkBond& bond, const vtkVector3f& normal, vtkPlane* plane);
294 static bool GetPlaneFromBond(
295 const vtkAtom& atom1, const vtkAtom& atom2, const vtkVector3f& normal, vtkPlane* plane);
297
302
307
309
314 void SetLattice(const vtkVector3d& a, const vtkVector3d& b, const vtkVector3d& c);
316
324
326
332
334
337 vtkGetMacro(LatticeOrigin, vtkVector3d);
338 vtkSetMacro(LatticeOrigin, vtkVector3d);
340
345
350
355
360
366 vtkPoints* atomPositions, vtkDataArray* atomicNumberArray, vtkDataSetAttributes* atomData);
367
371 int Initialize(vtkPoints* atomPositions, vtkDataSetAttributes* atomData)
372 {
373 return this->Initialize(atomPositions, nullptr, atomData);
374 }
375
379 int Initialize(vtkMolecule* molecule);
380
382
388
393
398
402 vtkIdType GetBondId(vtkIdType a, vtkIdType b) { return this->GetEdgeId(a, b); }
403
405
408 vtkSetStringMacro(AtomicNumberArrayName);
409 vtkGetStringMacro(AtomicNumberArrayName);
411
413
416 vtkSetStringMacro(BondOrdersArrayName);
417 vtkGetStringMacro(BondOrdersArrayName);
419
427 unsigned long GetActualMemorySize() override;
428
429protected:
431 ~vtkMolecule() override;
432
436 virtual void CopyStructureInternal(vtkMolecule* m, bool deep);
437
441 virtual void CopyAttributesInternal(vtkMolecule* m, bool deep);
442
444
451 void SetBondListDirty() { this->BondListIsDirty = true; }
455
456 friend class vtkAtom;
457 friend class vtkBond;
458
462
465
468
469private:
470 vtkMolecule(const vtkMolecule&) = delete;
471 void operator=(const vtkMolecule&) = delete;
472};
473
474VTK_ABI_NAMESPACE_END
475#endif
Provides access to and storage of chemical electronic data.
convenience proxy for vtkMolecule
Definition vtkAtom.h:24
vtkIdType Id
Definition vtkAtom.h:64
convenience proxy for vtkMolecule
Definition vtkBond.h:23
abstract superclass for arrays of numeric data
general representation of visualization data
represent and manipulate attribute data in a dataset
Base class for graph data types.
Definition vtkGraph.h:340
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:108
Store zero or more vtkInformation instances.
Store vtkAlgorithm input/output information.
represent and manipulate 3x3 transformation matrices
class describing a molecule
Definition vtkMolecule.h:84
vtkAbstractElectronicData * ElectronicData
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.
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).
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
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.
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.
vtkIdType GetBondId(vtkIdType a, vtkIdType b)
Return the edge id from the underlying graph.
vtkUnsignedCharArray * AtomGhostArray
void GetLattice(vtkVector3d &a, vtkVector3d &b, vtkVector3d &c)
Get the unit cell lattice vectors, and optionally, the origin.
vtkUnsignedCharArray * BondGhostArray
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:94
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
bool HasLattice()
Return true if a unit cell lattice is defined.
~vtkMolecule() override
vtkDataSetAttributes * GetAtomData()
Return the VertexData of the underlying graph.
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.
bool BondListIsDirty
The graph superclass does not provide fast random access to the edge (bond) data.
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
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.
vtkDataSetAttributes * GetBondData()
Return the EdgeData of the underlying graph.
vtkIdType GetNumberOfAtoms()
Return the number of atoms in the molecule.
vtkVector3d LatticeOrigin
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.
vtkIdTypeArray * GetBondList()
The graph superclass does not provide fast random access to the edge (bond) data.
perform various plane computations
Definition vtkPlane.h:135
represent and manipulate 3D points
Definition vtkPoints.h:139
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:315
#define VTK_MOLECULE
Definition vtkType.h:98