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

#include <DNA_EnvPairPotential.hh>

Inheritance diagram for core::scoring::dna::DNA_EnvPairPotential:

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< Real >	pair_bin_lower_bounds_
utility::vector0< Size >	nbr_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

typedef chemical::AA core::scoring::dna::DNA_EnvPairPotential::AA

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

This is really slow. Could be made faster in many ways, but mostly by adding an explicit centroid atom to centroiddna.

References core::conformation::Residue::aa(), core::conformation::Residue::is_DNA(), core::chemical::na_ade, core::chemical::na_cyt, core::chemical::na_gua, core::chemical::na_thy, core::conformation::Residue::nbr_atom_xyz(), and core::conformation::Residue::xyz().

Referenced by core::energy_methods::DNA_EnvPairEnergy::finalize_total_energy().

Size core::scoring::dna::DNA_EnvPairPotential::get_env_nbr_bin ( Size const  nbr_count ) const

inlineprivate

References max_nbrs_, protocols::mean_field::min(), and nbr_bin_.

Referenced by residue_env_score().

Size core::scoring::dna::DNA_EnvPairPotential::get_pair_disbin ( Real const  dis2 ) const

inlineprivate

References n_pair_disbins_, nbr_dis2_threshold_, and pair_bin_lower_bounds_.

Referenced by residue_pair_score().

void core::scoring::dna::DNA_EnvPairPotential::load_score_tables ( )

private

References protocols::cluster::calibur::aa, core::chemical::aa_from_oneletter_code(), core::scoring::dna::dna_aa_from_oneletter_code(), env_stats_, core::chemical::first_DNA_aa, core::chemical::last_DNA_aa, protocols::mean_field::max(), max_env_enrichment_, max_nbrs_, max_pair_enrichment_, protocols::mean_field::min(), min_env_enrichment_, min_pair_enrichment_, n_pair_disbins_, nbr_bin_, nbr_dis2_threshold_, core::chemical::num_canonical_aas, pair_bin_lower_bounds_, and pair_stats_.

Referenced by DNA_EnvPairPotential().

Real core::scoring::dna::DNA_EnvPairPotential::nbr_dis2_threshold ( ) const

inline

References nbr_dis2_threshold_.

Referenced by core::energy_methods::DNA_EnvPairEnergy::finalize_total_energy().

Real core::scoring::dna::DNA_EnvPairPotential::residue_env_score	(	AA const &	aa,
		Size const	nbr_count
	)		const

References protocols::cluster::calibur::aa, env_stats_, get_env_nbr_bin(), and core::chemical::num_canonical_aas.

Referenced by core::energy_methods::DNA_EnvPairEnergy::finalize_total_energy().

Real core::scoring::dna::DNA_EnvPairPotential::residue_pair_score	(	AA const &	na,
		AA const &	aa,
		Real const	dis2
	)		const

References protocols::cluster::calibur::aa, core::chemical::first_DNA_aa, get_pair_disbin(), core::chemical::last_DNA_aa, and pair_stats_.

Referenced by core::energy_methods::DNA_EnvPairEnergy::finalize_total_energy().

Member Data Documentation

utility::vector1< utility::vector1< Real > > core::scoring::dna::DNA_EnvPairPotential::env_stats_

private

Referenced by load_score_tables(), and residue_env_score().

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

Referenced by get_env_nbr_bin(), and load_score_tables().

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

Referenced by get_pair_disbin(), and load_score_tables().

utility::vector0< Size > core::scoring::dna::DNA_EnvPairPotential::nbr_bin_

private

Referenced by get_env_nbr_bin(), and load_score_tables().

Real const core::scoring::dna::DNA_EnvPairPotential::nbr_dis2_threshold_

staticprivate

Referenced by get_pair_disbin(), load_score_tables(), and nbr_dis2_threshold().

utility::vector1< Real > core::scoring::dna::DNA_EnvPairPotential::pair_bin_lower_bounds_

private

Referenced by get_pair_disbin(), and load_score_tables().

utility::vector1< utility::vector1< utility::vector1< Real > > > core::scoring::dna::DNA_EnvPairPotential::pair_stats_

private

Referenced by load_score_tables(), and residue_pair_score().

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

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