IMP  2.0.1
The Integrative Modeling Platform
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 >:

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 void do_show (std::ostream &out) const
 
- Public Member Functions inherited from IMP::kernel::PairScore
 PairScore (std::string name="PairScore %1%")
 
Restraints create_current_decomposition (Model *m, const ParticleIndexPair &vt) const
 
virtual double evaluate (const ParticlePair &vt, DerivativeAccumulator *da) const
 Compute the score and the derivative if needed.
 
virtual double evaluate_if_good_index (Model *m, const ParticleIndexPair &vt, DerivativeAccumulator *da, double max) const
 Compute the score and the derivative if needed.
 
virtual double evaluate_if_good_indexes (Model *m, const ParticleIndexPairs &o, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
 
virtual double evaluate_index (Model *m, const ParticleIndexPair &vt, DerivativeAccumulator *da) const
 Compute the score and the derivative if needed.
 
virtual double evaluate_indexes (Model *m, const ParticleIndexPairs &o, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
 
ContainersTemp get_input_containers (Particle *p) const
 
ParticlesTemp get_input_particles (Particle *p) const
 
ModelObjectsTemp get_inputs (Model *m, const ParticleIndexes &pis) const
 
- Public Member Functions inherited from IMP::base::Object
virtual void clear_caches ()
 
virtual IMP::base::VersionInfo get_version_info () const =0
 Get information about the module and version of the object.
 
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
 
- Protected Member Functions inherited from IMP::kernel::PairScore
virtual Restraints do_create_current_decomposition (Model *m, const ParticleIndexPair &vt) const
 
virtual ModelObjectsTemp do_get_inputs (Model *m, const ParticleIndexes &pis) const =0
 

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.
Parameters
[in]Keyis an IMP::Key which maps between names and indices
[in]BIPARTITEIf 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.
[in]INTERPOLATEIf 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.

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]kThe attribute to use for determining the particle types
[in]thresholdThe maximum distance to score
[in]data_fileWhere to load the file from.

Definition at line 74 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]kThe attribute to use for determining the particle types
[in]thresholdThe maximum distance to score
[in]data_fileWhere to load the file from.
[in]shiftThe 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 86 of file StatisticalPairScore.h.


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