IMP::score_functor::Statistical< Key, BIPARTITE, INTERPOLATE, SPARSE > Class Template Reference

#include <IMP/score_functor/Statistical.h>

Inheritance diagram for IMP::score_functor::Statistical< Key, BIPARTITE, INTERPOLATE, SPARSE >:

Detailed Description

template<class Key, bool BIPARTITE, bool INTERPOLATE, bool SPARSE = false>
class IMP::score_functor::Statistical< Key, BIPARTITE, INTERPOLATE, SPARSE >

Create a pairwise statistical potential from a file. The Keys passed as a template argument are used to determine how to map the names of the types as described in the loaded file to indexes. That is, if atom::ResidueKey is passed as the Keys, the potential will expect a file which has one line for each pair of residue names.

The expected file format is:

    bin_width number_a number_b [offset]
    key_0a key_0b bin0 bin1 bin2...
    key_1a key_1b bin0 bin1 bin2...

The order of the lines (after the first one) does not matter.
The bin_width is how much distance is allocated per bin (the distance used
is that between the points). number_a and number_b are the numbers of
particle types (number_b should only be specified if BIPARTITE is set).

\note The values read in the file are for bins. That is, the first bin
is from offset to offset+width. The second is offset+width to offset+
2width.
As a result, when interpolation is used, the function achieves the
bin value at the center of the bin.

\param[in] Key is an IMP::Key which maps between names and indices
\param[in] BIPARTITE If true, the two sets of particles being stored are
different (e.g. a protein atom and a ligand atom), otherwise they are
assumed to both be the same. Appropriate values must be provided
in the file.
\param[in] INTERPOLATE If true, even the scores without derivatives are
spline interpolated. If false, only the evaluation of derivatives is
interpolated with a spline.

Definition at line 53 of file Statistical.h.

Public Member Functions
	Statistical (IntKey k, double threshold, base::TextInput data_file)
	Statistical (IntKey k, double threshold, base::TextInput data_file, unsigned int shift)
bool	get_is_trivially_zero (kernel::Model *m, const ParticleIndexPair &p, double squared_distance) const
double	get_maximum_range (kernel::Model *, const ParticleIndexPair &) const
double	get_score (kernel::Model *m, const ParticleIndexPair &pp, double distance) const
DerivativePair	get_score_and_derivative (kernel::Model *m, const base::Array< 2, kernel::ParticleIndex > &pp, double distance) const
Public Member Functions inherited from IMP::score_functor::Score
kernel::ModelObjectsTemp	get_inputs (kernel::Model *m, const kernel::ParticleIndexes &pis) const
template<unsigned int D>
bool	get_is_trivially_zero (kernel::Model *m, const base::Array< D, kernel::ParticleIndex > &p, double squared_distance) const
template<unsigned int D>
double	get_maximum_range (kernel::Model *m, const base::Array< D, kernel::ParticleIndex > &p) const
template<unsigned int D>
double	get_score (kernel::Model *m, const base::Array< D, kernel::ParticleIndex > &p, double distance) const
	Return the score at the passed feature size (eg distance). More...
template<unsigned int D>
DerivativePair	get_score_and_derivative (kernel::Model *m, const base::Array< D, kernel::ParticleIndex > &p, double distance) const
	Return the score and derivative at the passed feature size (eg distance). More...
void	show (std::ostream &) const

Constructor & Destructor Documentation

template<class Key, bool BIPARTITE, bool INTERPOLATE, bool SPARSE = false>

IMP::score_functor::Statistical< Key, BIPARTITE, INTERPOLATE, SPARSE >::Statistical	(	IntKey	k,
		double	threshold,
		base::TextInput	data_file
	)

Parameters

[in]	k	The attribute to use for determining the particle types
[in]	threshold	The maximum distance to score
[in]	data_file	Where to load the file from.

Definition at line 64 of file Statistical.h.

template<class Key, bool BIPARTITE, bool INTERPOLATE, bool SPARSE = false>

IMP::score_functor::Statistical< Key, BIPARTITE, INTERPOLATE, SPARSE >::Statistical	(	IntKey	k,
		double	threshold,
		base::TextInput	data_file,
		unsigned int	shift
	)

Parameters

[in]	k	The attribute to use for determining the particle types
[in]	threshold	The maximum distance to score
[in]	data_file	Where to load the file from.
[in]	shift	The offset for the types of the second set of types. eg, if the score is on protein and ligand atoms, the ligand atom types start with the value shift.

Definition at line 76 of file Statistical.h.

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

• Statistical.h