VTK  9.3.20240328
vtkMoleculeReaderBase.h
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1 // SPDX-FileCopyrightText: Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
2 // SPDX-License-Identifier: BSD-3-Clause
15 #ifndef vtkMoleculeReaderBase_h
16 #define vtkMoleculeReaderBase_h
17 
18 #include "vtkIOChemistryModule.h" // For export macro
19 #include "vtkPolyDataAlgorithm.h"
20 
21 VTK_ABI_NAMESPACE_BEGIN
22 class vtkCellArray;
23 class vtkFloatArray;
24 class vtkDataArray;
25 class vtkIdTypeArray;
28 class vtkPoints;
29 class vtkStringArray;
30 class vtkMolecule;
31 class vtkPeriodicTable;
32 
33 class VTKIOCHEMISTRY_EXPORT vtkMoleculeReaderBase : public vtkPolyDataAlgorithm
34 {
35 public:
37  void PrintSelf(ostream& os, vtkIndent indent) override;
38 
41 
43 
46  vtkSetMacro(BScale, double);
47  vtkGetMacro(BScale, double);
49 
51 
54  vtkSetMacro(HBScale, double);
55  vtkGetMacro(HBScale, double);
57 
61  vtkGetMacro(NumberOfAtoms, vtkIdType);
62 
66  vtkGetMacro(NumberOfModels, unsigned int);
67 
68 protected:
71 
72  char* FileName;
73  double BScale;
74  double HBScale;
76  unsigned int NumberOfModels;
77 
80 
89  int ReadMolecule(FILE* fp, vtkPolyData* output);
90 
99  unsigned int MakeAtomType(const char* atomType);
100 
110  unsigned int MakeBonds(vtkPoints* points, vtkIdTypeArray* atomTypes, vtkCellArray* newBonds);
111 
126 
127  virtual void ReadSpecificMolecule(FILE* fp) = 0;
128 
129 private:
131  void operator=(const vtkMoleculeReaderBase&) = delete;
132 };
133 
134 VTK_ABI_NAMESPACE_END
135 #endif
object to represent cell connectivity
Definition: vtkCellArray.h:285
abstract superclass for arrays of numeric data
Definition: vtkDataArray.h:154
dynamic, self-adjusting array of float
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.
Read molecular data files.
unsigned int MakeBonds(vtkPoints *points, vtkIdTypeArray *atomTypes, vtkCellArray *newBonds)
Creates molecular bonds (VTK cells) given atomic coordinates (VTK points) and atom types.
vtkSmartPointer< vtkStringArray > AtomTypeStrings
vtkSmartPointer< vtkUnsignedCharArray > SecondaryStructures
int FillOutputPortInformation(int, vtkInformation *) override
Fill the output port information objects for this algorithm.
void PrintSelf(ostream &os, vtkIndent indent) override
Methods invoked by print to print information about the object including superclasses.
vtkSmartPointer< vtkIdTypeArray > Residue
vtkSetFilePathMacro(FileName)
int RequestData(vtkInformation *, vtkInformationVector **, vtkInformationVector *) override
This is called by the superclass.
vtkGetFilePathMacro(FileName)
unsigned int MakeAtomType(const char *atomType)
Given a string for the type (name) of an atom, returns a unique number for that atom.
vtkSmartPointer< vtkUnsignedCharArray > RGB
virtual void ReadSpecificMolecule(FILE *fp)=0
vtkSmartPointer< vtkUnsignedCharArray > SecondaryStructuresEnd
vtkSmartPointer< vtkPoints > Points
int ReadMolecule(FILE *fp, vtkPolyData *output)
Reads a molecule from the passed file pointer and creates a vtkPolyData.
vtkNew< vtkPeriodicTable > PeriodicTable
vtkSmartPointer< vtkUnsignedCharArray > SecondaryStructuresBegin
vtkSmartPointer< vtkIdTypeArray > AtomType
vtkSmartPointer< vtkUnsignedIntArray > Model
vtkSmartPointer< vtkUnsignedCharArray > IsHetatm
vtkSmartPointer< vtkUnsignedCharArray > Chain
vtkSmartPointer< vtkMolecule > Molecule
~vtkMoleculeReaderBase() override
vtkSmartPointer< vtkFloatArray > Radii
class describing a molecule
Definition: vtkMolecule.h:84
Access to information about the elements.
represent and manipulate 3D points
Definition: vtkPoints.h:138
Superclass for algorithms that produce only polydata as output.
concrete dataset represents vertices, lines, polygons, and triangle strips
Definition: vtkPolyData.h:180
a vtkAbstractArray subclass for strings
dynamic, self-adjusting array of unsigned char
dynamic, self-adjusting array of unsigned int
@ points
Definition: vtkX3D.h:446
int vtkIdType
Definition: vtkType.h:315