loos::DensityTools Namespace Reference

Namespace for Density package. More...

Classes
class	BulkedWaterFilter
	Add bulk water back into the mask/map. More...
class	BulkEstimator
class	DensityGrid
	A simple 3D grid class of arbitrary types. More...
class	DensityGridIterator
	Random access iterator using the BOOST facade. More...
class	DensityGridPlane
	Encapsulates an i,j-plane from an DensityGrid. More...
class	DensityGridRow
	Encapsulates a j-row from an DensityGrid. More...
class	NonzeroDensity
	Functor that is true for any non-zero density. More...
class	NullEstimator
class	SimpleMeta
	Simple class for handling metadata. More...
class	Threshold
	Functor that is true if value is greater than or equal to threshold. More...
class	ThresholdRange
	Functor that is true if value is between low and hi, inclusive. More...
class	WaterFilterAxis
	Pick waters that are within a radius of the principal axis for a molecule. More...
class	WaterFilterBase
	Base interface for water filter/picker. More...
class	WaterFilterBlob
	Pick waters based on a grid-mask. More...
class	WaterFilterBox
	Pick waters inside a bounding box. More...
class	WaterFilterContacts
	Pick waters with a minimum number of contacts to protein atoms. More...
class	WaterFilterCore
	Pick waters that are within a radius of the core axis for a molecule. More...
class	WaterFilterDecorator
	Decorator base class for "decorating" the core water filters... More...
class	WaterFilterRadius
	Pick waters within a given radius of a group of atoms. More...
class	WaterHistogrammer
struct	XEDMWriter
	Functor for writing out ASCII formatted X-Plor electron density maps. More...
class	ZClipEstimator
class	ZClippedWaterFilter
	Restrict waters to be within a given z-range. More...
class	ZSliceEstimator

Typedefs
typedef Coord< int >	DensityGridpoint

Functions
std::vector< double >	gaussian1d (const int, const double)
	Construct a 1D gaussian.
template<typename T , class Functor >
std::vector< DensityGridpoint >	floodFill (const DensityGridpoint seed, const DensityGrid< T > &data_grid, const int id, DensityGrid< int > &blob_grid, const Functor &op)
	Flood-fill a grid.
template<typename T , class Functor >
int	floodFill (const DensityGridpoint seed, const DensityGrid< T > &data_grid, const Functor &op)
	Flood-fill a grid, returning a list of points filled in.
template<typename T , class Functor >
std::vector< loos::GCoord >	findPeaks (const DensityGrid< T > &grid, DensityGrid< int > &blobs, const Functor &op)
	Find peaks in a grid given the criteria defined by the passed functor.
template<typename T , class Functor >
std::vector< loos::GCoord >	findPeaks (const DensityGrid< T > &grid, const Functor &op)
	Find peaks in a grid based on the functor.
template<class T , class Functor >
loos::AtomicGroup	gridToAtomicGroup (const DensityGrid< T > &grid, const Functor &op)
	Converts grid points (determined by functor) into an AtomicGroup of pseudo-atoms.
template<class T >
void	gridConvolve (DensityGrid< T > &grid, DensityGrid< T > &kernel)
	Convolve a grid with another grid (kernel)
template<class T >
void	gridConvolve (DensityGrid< T > &grid, std::vector< T > &kernel)
	Convolve a grid with a 1D kernel stored in a vector.
std::vector< GCoord >	getBounds (pTraj &traj, AtomicGroup &group, const std::vector< uint > &frames)
	Get the max bounding box for a group over the trajectory.
template<class T >
void	writeXplorEDM (std::ostream &os, DensityTools::DensityGrid< T > &grid)
	Write out an DensityTools::DensityGrid as an ASCII formatted X-PLOR electron density map.

Detailed Description

Namespace for Density package.

Function Documentation

findPeaks()

template<typename T , class Functor >

std::vector< loos::GCoord > loos::DensityTools::findPeaks	(	const DensityGrid< T > &	grid,
		DensityGrid< int > &	blobs,
		const Functor &	op )

Find peaks in a grid given the criteria defined by the passed functor.

Requires a data-grid, a grid to contain the flood-filled assignments, and a functor that determines what points in the data-grid to operate on.

This function segments the grid into a blobs based on the functor. For each unique blob, it returns the center of mass of the blob as a vector of GCoords. The vector index corresponds to the blob_id - 1 in the blobs grid.

floodFill()

template<typename T , class Functor >

std::vector< DensityGridpoint > loos::DensityTools::floodFill	(	const DensityGridpoint	seed,
		const DensityGrid< T > &	data_grid,
		const int	id,
		DensityGrid< int > &	blob_grid,
		const Functor &	op )

Flood-fill a grid.

Requires a seed-point to start the grid at. The data_grid is untouched by the fill. Instead, a grid of ints (id's) is filled it using the passed id value. The functor op determines the criteria for filling (i.e. using a threshold, range, or non-zero points).

Returns a list of grindpoints that were filled in.