BaseGrid

This class provides discrete representation of the molecule. The molecule is represented by a grid. Each voxel of the grid can be marked with DataT.

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AUTHORS

CHANGES LOG

GOALS

USAGE

Class Summary

class BaseGrid
{

public:

	// Constructors
template< class MoleculeT>	BaseGrid(const MoleculeT& mol, const float inDelta, const float maxRadius);
void	clear();
int	getIndexForPoint( const Vector3& point) const ;
Vector3	getPointForIndex(int index) const ;
bool	isValidIndex(int index) const ;
int	getIntGridRadius( float radius ) const ;
protected:
float	delta ;
vector < int >	neigbor;
vector < float >	neigborDist;
vector < DataT >	grid;

}; // BaseGrid

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AUTHORS

Yuval Inbar Dina Duhovny ,

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CHANGES LOG

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GOALS

The class is designed to represent a molecule as accurate as possible using small amount of space and fast algorithms for grid calculations.

Space Complexity of the Grid: The density of the grid: delta, is specified by the user. Assume that the width of the molecule along each of the axis is: x_width, y_width, z_width. The space used by the grid will be: x_width*y_width*z_width/(delta^3).

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USAGE

The BaseGrid class uses any set of points given by the user (Surface, Molecule ...) to generate the grid object.


  Surface msSurface;
  // ... read msSurface
  
  // initialization of grid
  BaseGrid* grid = new BaseGrid(msSurface, delta, maxDist) ;

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template< class MoleculeT> BaseGrid(const MoleculeT& mol, const float inDelta, const float maxRadius);

The BaseGrid constructor receives Connoly MS Surface, delta - grid density and maxRadius - maximum radius for distance function calculation.

  template< class MoleculeT>
  BaseGrid(const MoleculeT& mol, const float inDelta, const float maxRadius);

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void clear();

clears object (grid becomes empty)

  void clear();

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int getIndexForPoint( const Vector3& point) const ;

computes index in grid for a point.

  int getIndexForPoint( const Vector3& point) const                                                                                                                                                                                                                                                                                                                                          
;

Function is currently defined inline.

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Vector3 getPointForIndex(int index) const ;

computes a point corresponding to an index.

  Vector3 getPointForIndex(int index) const                                                                                                                                                                                                 
;

Function is currently defined inline.

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bool isValidIndex(int index) const ;

checks if the index is valid for the grid

  bool isValidIndex(int index) const                                             
;

Function is currently defined inline.

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int getIntGridRadius( float radius ) const ;

convert radius to grid valid radius (number of voxels)

  int getIntGridRadius( float radius ) const                                                
;

Function is currently defined inline.

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float delta ;

grid resolution

  float delta ;

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vector < int > neigbor;

cube neighbors there are 26 neighbors for each voxel

  vector < int > neigbor;

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vector < float > neigborDist;

cube neighbors' distances

  vector < float > neigborDist;

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vector < DataT > grid;

distances grid

  vector < DataT > grid;

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All Members

public:

	// Constructors
template< class MoleculeT>	BaseGrid(const MoleculeT& mol, const float inDelta, const float maxRadius);
void	clear();
int	getIndexForPoint( const Vector3& point) const ;
Vector3	getPointForIndex(int index) const ;
bool	isValidIndex(int index) const ;
int	getIntGridRadius( float radius ) const ;
protected:
float	delta ;
vector < int >	neigbor;
vector < float >	neigborDist;
vector < DataT >	grid;

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Ancestors

Class does not inherit from any other class.

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Descendants

AtomGrid

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Generated from source by the Cocoon utilities on Tue Jan 5 18:47:29 2010 .

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