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vtkMolecule Class Reference

class describing a molecule More...

#include <vtkMolecule.h>

Inherits vtkUndirectedGraph.

Public Types

typedef vtkUndirectedGraph Superclass
 

Public Member Functions

virtual int IsA (const char *type)
 
vtkMoleculeNewInstance () const
 
void PrintSelf (ostream &os, vtkIndent indent)
 
virtual void Initialize ()
 
virtual int GetDataObjectType ()
 
vtkAtom AppendAtom (unsigned short atomicNumber, const vtkVector3f &pos)
 
vtkAtom GetAtom (vtkIdType atomId)
 
vtkIdType GetNumberOfAtoms ()
 
vtkIdType GetNumberOfBonds ()
 
unsigned short GetAtomAtomicNumber (vtkIdType atomId)
 
double GetBondLength (vtkIdType bondId)
 
virtual void ShallowCopy (vtkDataObject *obj)
 
virtual void DeepCopy (vtkDataObject *obj)
 
virtual void ShallowCopyStructure (vtkMolecule *m)
 
virtual void DeepCopyStructure (vtkMolecule *m)
 
virtual void ShallowCopyAttributes (vtkMolecule *m)
 
virtual void DeepCopyAttributes (vtkMolecule *m)
 
vtkAtom AppendAtom ()
 
vtkAtom AppendAtom (unsigned short atomicNumber, double x, double y, double z)
 
vtkBond AppendBond (vtkIdType atom1, vtkIdType atom2, unsigned short order=1)
 
vtkBond AppendBond (const vtkAtom &atom1, const vtkAtom &atom2, unsigned short order=1)
 
vtkBond GetBond (vtkIdType bondId)
 
void SetAtomAtomicNumber (vtkIdType atomId, unsigned short atomicNum)
 
void SetAtomPosition (vtkIdType atomId, const vtkVector3f &pos)
 
void SetAtomPosition (vtkIdType atomId, double x, double y, double z)
 
vtkVector3f GetAtomPosition (vtkIdType atomId)
 
void GetAtomPosition (vtkIdType atomId, float pos[3])
 
void SetBondOrder (vtkIdType bondId, unsigned short order)
 
unsigned short GetBondOrder (vtkIdType bondId)
 
vtkPointsGetAtomicPositionArray ()
 
vtkUnsignedShortArrayGetAtomicNumberArray ()
 
virtual vtkAbstractElectronicData * GetElectronicData ()
 
virtual void SetElectronicData (vtkAbstractElectronicData *)
 

Static Public Member Functions

static vtkMoleculeNew ()
 
static int IsTypeOf (const char *type)
 
static vtkMoleculeSafeDownCast (vtkObjectBase *o)
 
static bool GetPlaneFromBond (const vtkBond &bond, const vtkVector3f &normal, vtkPlane *plane)
 
static bool GetPlaneFromBond (const vtkAtom &atom1, const vtkAtom &atom2, const vtkVector3f &normal, vtkPlane *plane)
 

Protected Member Functions

virtual vtkObjectBaseNewInstanceInternal () const
 
 vtkMolecule ()
 
 ~vtkMolecule ()
 
virtual void CopyStructureInternal (vtkMolecule *m, bool deep)
 
virtual void CopyAttributesInternal (vtkMolecule *m, bool deep)
 

Protected Attributes

vtkAbstractElectronicData * ElectronicData
 

Friends

class vtkAtom
 
class vtkBond
 
bool BondListIsDirty
 
void SetBondListDirty ()
 
void UpdateBondList ()
 

Detailed Description

class describing a molecule

vtkMolecule and the convenience classes vtkAtom and vtkBond describe the geometry and connectivity of a molecule. The molecule can be constructed using the AppendAtom() and AppendBond() methods in one of two ways; either by fully specifying the atom/bond in a single call, or by incrementally setting the various attributes using the convience vtkAtom and vtkBond classes:

Single call:

vtkAtom h1 = mol->AppendAtom(1, 0.0, 0.0, -0.5);
vtkAtom h2 = mol->AppendAtom(1, 0.0, 0.0, 0.5);
vtkBond b = mol->AppendBond(h1, h2, 1);

Incremental:

vtkAtom h1 = mol->AppendAtom();
h1.SetPosition(0.0, 0.0, -0.5);
vtkAtom h2 = mol->AppendAtom();
vtkVector3d displacement (0.0, 0.0, 1.0);
h2.SetPosition(h1.GetPositionAsVector3d() + displacement);
vtkBond b = mol->AppendBond(h1, h2, 1);

Both of the above methods will produce the same molecule, two hydrogens connected with a 1.0 Angstrom single bond, aligned to the z-axis. The second example also demostrates the use of VTK's vtkVector class, which is fully supported by the Chemistry kit.

The vtkMolecule object is intended to be used with the vtkMoleculeMapper class for visualizing molecular structure using common rendering techniques.

Warning
While direct use of the underlying vtkUndirectedGraph structure is possible due to vtkMolecule's public inheritance, this should not be relied upon and may change in the future.
See Also
vtkAtom vtkBond vtkMoleculeMapper vtkPeriodicTable
Tests:
vtkMolecule (Tests)

Definition at line 88 of file vtkMolecule.h.

Member Typedef Documentation

typedef vtkUndirectedGraph vtkMolecule::Superclass

Definition at line 92 of file vtkMolecule.h.

Constructor & Destructor Documentation

vtkMolecule::vtkMolecule ( )
protected
vtkMolecule::~vtkMolecule ( )
protected

Member Function Documentation

static vtkMolecule* vtkMolecule::New ( )
static
static int vtkMolecule::IsTypeOf ( const char *  type)
static
virtual int vtkMolecule::IsA ( const char *  type)
virtual
static vtkMolecule* vtkMolecule::SafeDownCast ( vtkObjectBase o)
static
virtual vtkObjectBase* vtkMolecule::NewInstanceInternal ( ) const
protectedvirtual
vtkMolecule* vtkMolecule::NewInstance ( ) const
void vtkMolecule::PrintSelf ( ostream &  os,
vtkIndent  indent 
)
virtual void vtkMolecule::Initialize ( )
virtual
virtual int vtkMolecule::GetDataObjectType ( )
inlinevirtual

Return what type of dataset this is.

Definition at line 97 of file vtkMolecule.h.

vtkAtom vtkMolecule::AppendAtom ( )
inline

Add new atom with atomic number 0 (dummy atom) at origin. Return a vtkAtom that refers to the new atom.

Definition at line 103 of file vtkMolecule.h.

vtkAtom vtkMolecule::AppendAtom ( unsigned short  atomicNumber,
const vtkVector3f pos 
)

Add new atom with the specified atomic number and position. Return a vtkAtom that refers to the new atom.

vtkAtom vtkMolecule::AppendAtom ( unsigned short  atomicNumber,
double  x,
double  y,
double  z 
)
inline

Convenience methods to append a new atom with the specified atomic number and position.

Definition at line 116 of file vtkMolecule.h.

vtkAtom vtkMolecule::GetAtom ( vtkIdType  atomId)

Return a vtkAtom that refers to the atom with the specified id.

vtkIdType vtkMolecule::GetNumberOfAtoms ( )

Return the number of atoms in the molecule.

vtkBond vtkMolecule::AppendBond ( vtkIdType  atom1,
vtkIdType  atom2,
unsigned short  order = 1 
)

Add a bond between the specified atoms, optionally setting the bond order (default: 1). Return a vtkBond object referring to the new bond.

vtkBond vtkMolecule::AppendBond ( const vtkAtom atom1,
const vtkAtom atom2,
unsigned short  order = 1 
)
inline

Add a bond between the specified atoms, optionally setting the bond order (default: 1). Return a vtkBond object referring to the new bond.

Definition at line 134 of file vtkMolecule.h.

vtkBond vtkMolecule::GetBond ( vtkIdType  bondId)

Return a vtkAtom that refers to the bond with the specified id.

vtkIdType vtkMolecule::GetNumberOfBonds ( )

Return the number of bonds in the molecule.

unsigned short vtkMolecule::GetAtomAtomicNumber ( vtkIdType  atomId)

Return the atomic number of the atom with the specified id.

void vtkMolecule::SetAtomAtomicNumber ( vtkIdType  atomId,
unsigned short  atomicNum 
)

Set the atomic number of the atom with the specified id.

void vtkMolecule::SetAtomPosition ( vtkIdType  atomId,
const vtkVector3f pos 
)

Set the position of the atom with the specified id.

void vtkMolecule::SetAtomPosition ( vtkIdType  atomId,
double  x,
double  y,
double  z 
)

Set the position of the atom with the specified id.

vtkVector3f vtkMolecule::GetAtomPosition ( vtkIdType  atomId)

Get the position of the atom with the specified id.

void vtkMolecule::GetAtomPosition ( vtkIdType  atomId,
float  pos[3] 
)

Get the position of the atom with the specified id.

void vtkMolecule::SetBondOrder ( vtkIdType  bondId,
unsigned short  order 
)

Get/Set the bond order of the bond with the specified id

unsigned short vtkMolecule::GetBondOrder ( vtkIdType  bondId)

Get/Set the bond order of the bond with the specified id

double vtkMolecule::GetBondLength ( vtkIdType  bondId)

Get the bond length of the bond with the specified id

Note
If the associated vtkBond object is already available, vtkBond::GetBondLength is potentially much faster than this function, as a list of all bonds may need to be constructed to locate the appropriate bond.
See Also
UpdateBondList()
vtkPoints* vtkMolecule::GetAtomicPositionArray ( )

Access the raw arrays used in this vtkMolecule instance

vtkUnsignedShortArray* vtkMolecule::GetAtomicNumberArray ( )

Access the raw arrays used in this vtkMolecule instance

virtual vtkAbstractElectronicData* vtkMolecule::GetElectronicData ( )
virtual

Set/Get the AbstractElectronicData-subclassed object for this molecule.

virtual void vtkMolecule::SetElectronicData ( vtkAbstractElectronicData *  )
virtual

Set/Get the AbstractElectronicData-subclassed object for this molecule.

virtual void vtkMolecule::ShallowCopy ( vtkDataObject obj)
virtual

Shallow copies the data object into this molecule.

virtual void vtkMolecule::DeepCopy ( vtkDataObject obj)
virtual

Deep copies the data object into this molecule.

virtual void vtkMolecule::ShallowCopyStructure ( vtkMolecule m)
virtual

Shallow copies the atoms and bonds from m into this.

virtual void vtkMolecule::DeepCopyStructure ( vtkMolecule m)
virtual

Deep copies the atoms and bonds from m into this.

virtual void vtkMolecule::ShallowCopyAttributes ( vtkMolecule m)
virtual

Shallow copies attributes (i.e. everything besides atoms and bonds) from m into this.

virtual void vtkMolecule::DeepCopyAttributes ( vtkMolecule m)
virtual

Deep copies attributes (i.e. everything besides atoms and bonds) from m into this.

static bool vtkMolecule::GetPlaneFromBond ( const vtkBond bond,
const vtkVector3f normal,
vtkPlane plane 
)
static

Obtain the plane that passes through the indicated bond with the given normal. If the plane is set successfully, the function returns true. If the normal is not orthogonal to the bond, a new normal will be constructed in such a way that the plane will be orthogonal to the plane spanned by the bond vector and the input normal vector. This ensures that the plane passes through the bond, and the normal is more of a "hint" indicating the orientation of the plane. The new normal (n) is defined as the input normal vector (n_i) minus the projection of itself (proj[n_i]_v) onto the bond vector (v):

v ^ |  n = (n_i - proj[n_j]_v) proj[n_i]_v ^  |----x |  |  
/ |  |  / n_i |  | / |  |/ 

If n_i is parallel to v, a warning will be printed and no plane will be added. Obviously, n_i must not be parallel to v.

static bool vtkMolecule::GetPlaneFromBond ( const vtkAtom atom1,
const vtkAtom atom2,
const vtkVector3f normal,
vtkPlane plane 
)
static

Obtain the plane that passes through the indicated bond with the given normal. If the plane is set successfully, the function returns true. If the normal is not orthogonal to the bond, a new normal will be constructed in such a way that the plane will be orthogonal to the plane spanned by the bond vector and the input normal vector. This ensures that the plane passes through the bond, and the normal is more of a "hint" indicating the orientation of the plane. The new normal (n) is defined as the input normal vector (n_i) minus the projection of itself (proj[n_i]_v) onto the bond vector (v):

v ^ |  n = (n_i - proj[n_j]_v) proj[n_i]_v ^  |----x |  |  
/ |  |  / n_i |  | / |  |/ 

If n_i is parallel to v, a warning will be printed and no plane will be added. Obviously, n_i must not be parallel to v.

virtual void vtkMolecule::CopyStructureInternal ( vtkMolecule m,
bool  deep 
)
protectedvirtual

Copy bonds and atoms.

virtual void vtkMolecule::CopyAttributesInternal ( vtkMolecule m,
bool  deep 
)
protectedvirtual

Copy everything but bonds and atoms.

void vtkMolecule::SetBondListDirty ( )
inlineprotected

The graph superclass does not provide fast random access to the edge (bond) data. All random access is performed using a lookup table that must be rebuilt periodically. These allow for lazy building of the lookup table

Definition at line 255 of file vtkMolecule.h.

void vtkMolecule::UpdateBondList ( )
protected

The graph superclass does not provide fast random access to the edge (bond) data. All random access is performed using a lookup table that must be rebuilt periodically. These allow for lazy building of the lookup table

Friends And Related Function Documentation

friend class vtkAtom
friend

Definition at line 259 of file vtkMolecule.h.

friend class vtkBond
friend

Definition at line 260 of file vtkMolecule.h.

Member Data Documentation

bool vtkMolecule::BondListIsDirty
protected

The graph superclass does not provide fast random access to the edge (bond) data. All random access is performed using a lookup table that must be rebuilt periodically. These allow for lazy building of the lookup table

Definition at line 254 of file vtkMolecule.h.

vtkAbstractElectronicData* vtkMolecule::ElectronicData
protected

Definition at line 262 of file vtkMolecule.h.


The documentation for this class was generated from the following file: