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core::scoring::dna::DNA_EnvPairPotential Class Reference

#include <DNA_EnvPairPotential.hh>

Inheritance diagram for core::scoring::dna::DNA_EnvPairPotential:
Inheritance graph
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Public Types

typedef chemical::AA AA
 

Public Member Functions

 DNA_EnvPairPotential ()
 ctor – read the datafiles More...
 
Real nbr_dis2_threshold () const
 
Vector centroid_xyz (conformation::Residue const &rsd) const
 This is really slow. Could be made faster in many ways, but mostly by adding an explicit centroid atom to centroiddna. More...
 
Real residue_pair_score (AA const &na, AA const &aa, Real const dis2) const
 
Real residue_env_score (AA const &aa, Size const nbr_count) const
 

Private Member Functions

void load_score_tables ()
 
Size get_pair_disbin (Real const dis2) const
 
Size get_env_nbr_bin (Size const nbr_count) const
 

Private Attributes

Size n_pair_disbins_
 
Size max_nbrs_
 
utility::vector1
< utility::vector1
< utility::vector1< Real > > > 
pair_stats_
 
utility::vector1
< utility::vector1< Real > > 
env_stats_
 
utility::vector1< Realpair_bin_lower_bounds_
 
utility::vector0< Sizenbr_bin_
 

Static Private Attributes

static Real const nbr_dis2_threshold_
 
static Real const min_env_enrichment_
 
static Real const max_env_enrichment_
 
static Real const min_pair_enrichment_
 
static Real const max_pair_enrichment_
 

Member Typedef Documentation

Constructor & Destructor Documentation

core::scoring::dna::DNA_EnvPairPotential::DNA_EnvPairPotential ( )

ctor – read the datafiles

ctor, reads data file. Need to configure to allow alternate tables/atom_sets

References load_score_tables().

Member Function Documentation

Vector core::scoring::dna::DNA_EnvPairPotential::centroid_xyz ( conformation::Residue const &  rsd) const
Size core::scoring::dna::DNA_EnvPairPotential::get_env_nbr_bin ( Size const  nbr_count) const
inlineprivate
Size core::scoring::dna::DNA_EnvPairPotential::get_pair_disbin ( Real const  dis2) const
inlineprivate
void core::scoring::dna::DNA_EnvPairPotential::load_score_tables ( )
private
Real core::scoring::dna::DNA_EnvPairPotential::nbr_dis2_threshold ( ) const
inline
Real core::scoring::dna::DNA_EnvPairPotential::residue_env_score ( AA const &  aa,
Size const  nbr_count 
) const
Real core::scoring::dna::DNA_EnvPairPotential::residue_pair_score ( AA const &  na,
AA const &  aa,
Real const  dis2 
) const

Member Data Documentation

utility::vector1< utility::vector1< Real > > core::scoring::dna::DNA_EnvPairPotential::env_stats_
private
Real const core::scoring::dna::DNA_EnvPairPotential::max_env_enrichment_
staticprivate

Referenced by load_score_tables().

Size core::scoring::dna::DNA_EnvPairPotential::max_nbrs_
private
Real const core::scoring::dna::DNA_EnvPairPotential::max_pair_enrichment_
staticprivate

Referenced by load_score_tables().

Real const core::scoring::dna::DNA_EnvPairPotential::min_env_enrichment_
staticprivate

Referenced by load_score_tables().

Real const core::scoring::dna::DNA_EnvPairPotential::min_pair_enrichment_
staticprivate

Referenced by load_score_tables().

Size core::scoring::dna::DNA_EnvPairPotential::n_pair_disbins_
private
utility::vector0< Size > core::scoring::dna::DNA_EnvPairPotential::nbr_bin_
private
Real const core::scoring::dna::DNA_EnvPairPotential::nbr_dis2_threshold_
staticprivate
utility::vector1< Real > core::scoring::dna::DNA_EnvPairPotential::pair_bin_lower_bounds_
private
utility::vector1< utility::vector1< utility::vector1< Real > > > core::scoring::dna::DNA_EnvPairPotential::pair_stats_
private

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