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core::scoring::dna::DirectReadoutPotential Class Reference

1st pass implementation of Kono + Sarai's protein-DNA interaction potential More...

#include <DirectReadoutPotential.hh>

Inheritance diagram for core::scoring::dna::DirectReadoutPotential:
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Public Types

typedef std::string string
 

Public Member Functions

 DirectReadoutPotential ()
 ctor, reads data file More...
 
Real rsd_rsd_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2) const
 

Private Member Functions

void fill_bins (string(&my_array)[9][9][4], char const base)
 
void get_pairs ()
 
int get_xy_bin (Real coord) const
 
int get_z_bin (Real coord) const
 

Private Attributes

Real score [9][9][4][20][4]
 
int num_pairs [4][20]
 
string A_bins [9][9][4]
 
string G_bins [9][9][4]
 
string T_bins [9][9][4]
 
string C_bins [9][9][4]
 
int aas_at_grid
 
const Real wt
 
const Real RT
 

Detailed Description

1st pass implementation of Kono + Sarai's protein-DNA interaction potential

Needs polishing, converting to mini standards in some respects, but still in trial stage.

Member Typedef Documentation

Constructor & Destructor Documentation

core::scoring::dna::DirectReadoutPotential::DirectReadoutPotential ( )

ctor, reads data file

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

References A_bins, protocols::cluster::calibur::aa, core::chemical::aa_from_oneletter_code(), aas_at_grid, C_bins, fill_bins(), G_bins, get_pairs(), num_pairs, RT, score, T_bins, and wt.

Member Function Documentation

void core::scoring::dna::DirectReadoutPotential::fill_bins ( string(&)  my_array[9][9][4],
char const  base 
)
private

Referenced by DirectReadoutPotential().

void core::scoring::dna::DirectReadoutPotential::get_pairs ( )
private

References num_pairs.

Referenced by DirectReadoutPotential().

int core::scoring::dna::DirectReadoutPotential::get_xy_bin ( Real  coord) const
private

References core::pack::dunbrack::c.

Referenced by rsd_rsd_energy().

int core::scoring::dna::DirectReadoutPotential::get_z_bin ( Real  coord) const
private

References core::pack::dunbrack::c.

Referenced by rsd_rsd_energy().

Real core::scoring::dna::DirectReadoutPotential::rsd_rsd_energy ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2 
) const

Member Data Documentation

string core::scoring::dna::DirectReadoutPotential::A_bins[9][9][4]
private

Referenced by DirectReadoutPotential().

int core::scoring::dna::DirectReadoutPotential::aas_at_grid
private

Referenced by DirectReadoutPotential().

string core::scoring::dna::DirectReadoutPotential::C_bins[9][9][4]
private

Referenced by DirectReadoutPotential().

string core::scoring::dna::DirectReadoutPotential::G_bins[9][9][4]
private

Referenced by DirectReadoutPotential().

int core::scoring::dna::DirectReadoutPotential::num_pairs[4][20]
private
const Real core::scoring::dna::DirectReadoutPotential::RT
private

Referenced by DirectReadoutPotential().

Real core::scoring::dna::DirectReadoutPotential::score[9][9][4][20][4]
private
string core::scoring::dna::DirectReadoutPotential::T_bins[9][9][4]
private

Referenced by DirectReadoutPotential().

const Real core::scoring::dna::DirectReadoutPotential::wt
private

Referenced by DirectReadoutPotential().


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