IMP::core::StatisticalPairScore< Key, BIPARTITE, INTERPOLATE, SPARSE > Class Template Reference

#include <IMP/core/StatisticalPairScore.h>

Inheritance diagram for IMP::core::StatisticalPairScore< Key, BIPARTITE, INTERPOLATE, SPARSE >:

Detailed Description

template<class Key, bool BIPARTITE, bool INTERPOLATE, bool SPARSE = false>
class IMP::core::StatisticalPairScore< 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 59 of file StatisticalPairScore.h.

Public Member Functions
	StatisticalPairScore (IntKey k, double threshold, base::TextInput data_file)
	StatisticalPairScore (IntKey k, double threshold, base::TextInput data_file, unsigned int shift)
Public Member Functions inherited from IMP::score_functor::DistancePairScore< score_functor::Statistical< Key, BIPARTITE, INTERPOLATE, SPARSE > >
	DistancePairScore (const DistanceScore &t0, std::string name="FunctorDistancePairScore %1%")
virtual kernel::ModelObjectsTemp	do_get_inputs (kernel::Model *m, const kernel::ParticleIndexes &pis) const
double	evaluate_if_good_indexes (kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
virtual double	evaluate_index (kernel::Model *m, const kernel::ParticleIndexPair &pip, DerivativeAccumulator *da) const
	Compute the score and the derivative if needed. More...
double	evaluate_indexes (kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
	Compute the score and the derivative if needed over a set. More...
score_functor::Statistical < Key, BIPARTITE, INTERPOLATE, SPARSE > &	get_score_functor ()
virtual std::string	get_type_name () const
virtual ::IMP::base::VersionInfo	get_version_info () const
	Get information about the module and version of the object. More...
Public Member Functions inherited from IMP::kernel::PairScore
	PairScore (std::string name="PairScore %1%")
Restraints	create_current_decomposition (kernel::Model *m, const kernel::ParticleIndexPair &vt) const
virtual double	evaluate (const kernel::ParticlePair &vt, DerivativeAccumulator *da) const
	Compute the score and the derivative if needed. More...
virtual double	evaluate_if_good_index (kernel::Model *m, const kernel::ParticleIndexPair &vt, DerivativeAccumulator *da, double max) const
	Compute the score and the derivative if needed. More...
Public Member Functions inherited from IMP::kernel::ParticleInputs
virtual ContainersTemp	get_input_containers (Particle *p) const
virtual ParticlesTemp	get_input_particles (Particle *p) const
ModelObjectsTemp	get_inputs (kernel::Model *m, const ParticleIndexes &pis) const
Public Member Functions inherited from IMP::base::Object
virtual void	clear_caches ()
CheckLevel	get_check_level () const
LogLevel	get_log_level () const
void	set_check_level (CheckLevel l)
void	set_log_level (LogLevel l)
	Set the logging level used in this object. More...
void	set_was_used (bool tf) const
void	show (std::ostream &out=std::cout) const
const std::string &	get_name () const
void	set_name (std::string name)

Additional Inherited Members
Public Types inherited from IMP::score_functor::DistancePairScore< score_functor::Statistical< Key, BIPARTITE, INTERPOLATE, SPARSE > >
typedef score_functor::Statistical < Key, BIPARTITE, INTERPOLATE, SPARSE >	DistanceScore
Public Types inherited from IMP::kernel::PairScore
typedef kernel::ParticlePair	Argument
typedef kernel::ParticleIndexPair	IndexArgument
typedef PairModifier	Modifier
typedef const kernel::ParticlePair &	PassArgument
typedef const kernel::ParticleIndexPair &	PassIndexArgument
Protected Member Functions inherited from IMP::kernel::PairScore
virtual Restraints	do_create_current_decomposition (kernel::Model *m, const kernel::ParticleIndexPair &vt) const
Protected Member Functions inherited from IMP::base::Object
	Object (std::string name)
	Construct an object with the given name. More...
virtual void	do_destroy ()

Constructor & Destructor Documentation

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

IMP::core::StatisticalPairScore< Key, BIPARTITE, INTERPOLATE, SPARSE >::StatisticalPairScore	(	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 70 of file StatisticalPairScore.h.

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

IMP::core::StatisticalPairScore< Key, BIPARTITE, INTERPOLATE, SPARSE >::StatisticalPairScore	(	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 79 of file StatisticalPairScore.h.

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

• StatisticalPairScore.h