VTK
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class describing a molecule More...
#include <vtkMolecule.h>
Inherits vtkUndirectedGraph.
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typedef vtkUndirectedGraph | Superclass |
Public Member Functions | |
virtual int | IsA (const char *type) |
vtkMolecule * | NewInstance () 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) |
vtkPoints * | GetAtomicPositionArray () |
vtkUnsignedShortArray * | GetAtomicNumberArray () |
virtual vtkAbstractElectronicData * | GetElectronicData () |
virtual void | SetElectronicData (vtkAbstractElectronicData *) |
Static Public Member Functions | |
static vtkMolecule * | New () |
static int | IsTypeOf (const char *type) |
static vtkMolecule * | SafeDownCast (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 vtkObjectBase * | NewInstanceInternal () 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 () |
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:
Incremental:
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.
Definition at line 88 of file vtkMolecule.h.
typedef vtkUndirectedGraph vtkMolecule::Superclass |
Definition at line 92 of file vtkMolecule.h.
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vtkMolecule* vtkMolecule::NewInstance | ( | ) | const |
void vtkMolecule::PrintSelf | ( | ostream & | os, |
vtkIndent | indent | ||
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Return what type of dataset this is.
Definition at line 97 of file vtkMolecule.h.
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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 | ||
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Add new atom with the specified atomic number and position. Return a vtkAtom that refers to the new atom.
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Convenience methods to append a new atom with the specified atomic number and position.
Definition at line 116 of file vtkMolecule.h.
Return a vtkAtom that refers to the atom with the specified id.
vtkIdType vtkMolecule::GetNumberOfAtoms | ( | ) |
Return the number of atoms in the molecule.
Add a bond between the specified atoms, optionally setting the bond order (default: 1). Return a vtkBond object referring to the new bond.
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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.
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 | ||
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Set the position of the atom with the specified id.
void vtkMolecule::SetAtomPosition | ( | vtkIdType | atomId, |
double | x, | ||
double | y, | ||
double | z | ||
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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] | ||
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Get the position of the atom with the specified id.
void vtkMolecule::SetBondOrder | ( | vtkIdType | bondId, |
unsigned short | order | ||
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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
vtkPoints* vtkMolecule::GetAtomicPositionArray | ( | ) |
Access the raw arrays used in this vtkMolecule instance
vtkUnsignedShortArray* vtkMolecule::GetAtomicNumberArray | ( | ) |
Access the raw arrays used in this vtkMolecule instance
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Set/Get the AbstractElectronicData-subclassed object for this molecule.
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Set/Get the AbstractElectronicData-subclassed object for this molecule.
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Shallow copies the data object into this molecule.
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Deep copies the data object into this molecule.
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Shallow copies the atoms and bonds from m into this.
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Deep copies the atoms and bonds from m into this.
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Shallow copies attributes (i.e. everything besides atoms and bonds) from m into this.
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Deep copies attributes (i.e. everything besides atoms and bonds) from m into this.
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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.
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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.
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Copy bonds and atoms.
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Copy everything but bonds and atoms.
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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.
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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
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Definition at line 259 of file vtkMolecule.h.
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Definition at line 260 of file vtkMolecule.h.
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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.
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Definition at line 262 of file vtkMolecule.h.