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

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

#include <DirectReadoutPotential.hh>

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

typedef std::string core::scoring::dna::DirectReadoutPotential::string

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, core::chemical::aa_from_oneletter_code(), aas_at_grid, C_bins, fill_bins(), G_bins, get_pairs(), log(), 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

References utility::io::izstream::close(), getline(), utility::io::izstream::good(), l, basic::database::open(), and utility_exit_with_message.

Referenced by DirectReadoutPotential().

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

private

References utility::io::izstream::close(), getline(), utility::io::izstream::good(), l, num_pairs, basic::database::open(), and utility_exit_with_message.

Referenced by DirectReadoutPotential().

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

private

References bin, and core::pack::dunbrack::c.

Referenced by rsd_rsd_energy().

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

private

References bin, and 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

References core::conformation::Residue::aa(), numeric::xyzVector< class >::cross(), dot(), core::chemical::first_DNA_aa, get_xy_bin(), core::scoring::dna::get_z_axis(), get_z_bin(), core::conformation::Residue::is_DNA(), core::conformation::Residue::is_protein(), core::chemical::na_ade, core::chemical::na_gua, score, and core::conformation::Residue::xyz().

Referenced by core::scoring::methods::DirectReadoutEnergy::my_residue_pair_energy().

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

Referenced by DirectReadoutPotential(), and get_pairs().

const Real core::scoring::dna::DirectReadoutPotential::RT

private

Referenced by DirectReadoutPotential().

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

private

Referenced by DirectReadoutPotential(), and rsd_rsd_energy().

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().

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

• src/core/scoring/dna/DirectReadoutPotential.hh
• src/core/scoring/dna/DirectReadoutPotential.cc