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core::scoring::dna::DNA_BasePotential Class Reference

#include <DNA_BasePotential.hh>

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

typedef numeric::xyzMatrix< RealMatrix
 
typedef utility::vector1< RealParams
 
typedef conformation::Residue Residue
 
typedef ObjexxFCL::FArray3D< RealFArray3D_Real
 
typedef ObjexxFCL::FArray4D< RealFArray4D_Real
 

Public Member Functions

 ~DNA_BasePotential () override
 Automatically generated virtual destructor for class deriving directly from VirtualBase. More...
 
 DNA_BasePotential ()
 ctor More...
 
Real base_step_score (Residue const &rsd1, Residue const &rsd2) const
 
Real base_pair_score (Residue const &rsd1, Residue const &rsd2) const
 
void eval_base_step_derivative (Residue const &rsd1, Residue const &rsd2, Vector &F1, Vector &F2, Real const external_sign_factor) const
 
void eval_base_pair_derivative (Residue const &rsd1, Residue const &rsd2, Vector &F1, Vector &F2, Real const sign_factor) const
 
void eval_base_pair_Z_scores (Residue const &rsd1, Residue const &rsd2, utility::vector1< Real > &z_scores) const
 
void eval_base_step_Z_scores (Residue const &rsd1, Residue const &rsd2, utility::vector1< Real > &z_scores) const
 

Private Types

enum  InteractionType { BP_type = 1, BS_type }
 

Private Member Functions

Real mean (InteractionType const &t, std::string const &bases, int const p) const
 
Real stddev (InteractionType const &t, std::string const &bases, int const p) const
 
Real stiffness (InteractionType const &t, std::string const &bases, int const p1, int const p2) const
 
std::string base_string (Residue const &rsd) const
 "A","C","T","G" More...
 
void get_array_indices (InteractionType const &t, std::string const &bases, int &i1, int &i2) const
 
void load_score_tables ()
 
void set_mean_and_stddev (InteractionType const &type, std::string const &bases, int const index, Real mean, Real stddev)
 
void set_stiffness (InteractionType const &type, std::string const &bases, int const index1, int const index2, Real const val)
 
Real base_score (InteractionType const &type, std::string const &bases, utility::vector1< Real > const &params) const
 

Private Attributes

FArray3D_Real mean_
 
FArray3D_Real stddev_
 
FArray4D_Real stiffness_
 

Member Typedef Documentation

typedef numeric::xyzMatrix< Real > core::scoring::dna::DNA_BasePotential::Matrix

Member Enumeration Documentation

Enumerator
BP_type 
BS_type 

Constructor & Destructor Documentation

core::scoring::dna::DNA_BasePotential::~DNA_BasePotential ( )
overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

core::scoring::dna::DNA_BasePotential::DNA_BasePotential ( )

ctor

References load_score_tables().

Member Function Documentation

Real core::scoring::dna::DNA_BasePotential::base_pair_score ( Residue const &  rsd1,
Residue const &  rsd2 
) const
Real core::scoring::dna::DNA_BasePotential::base_score ( InteractionType const &  type,
std::string const &  bases,
utility::vector1< Real > const &  params 
) const
private
Real core::scoring::dna::DNA_BasePotential::base_step_score ( Residue const &  rsd1,
Residue const &  rsd2 
) const
std::string core::scoring::dna::DNA_BasePotential::base_string ( Residue const &  rsd) const
inlineprivate
void core::scoring::dna::DNA_BasePotential::eval_base_pair_derivative ( Residue const &  rsd1,
Residue const &  rsd2,
Vector F1,
Vector F2,
Real const  sign_factor 
) const
void core::scoring::dna::DNA_BasePotential::eval_base_pair_Z_scores ( Residue const &  rsd1,
Residue const &  rsd2,
utility::vector1< Real > &  z_scores 
) const
void core::scoring::dna::DNA_BasePotential::eval_base_step_derivative ( Residue const &  rsd1,
Residue const &  rsd2,
Vector F1,
Vector F2,
Real const  external_sign_factor 
) const
void core::scoring::dna::DNA_BasePotential::eval_base_step_Z_scores ( Residue const &  rsd1,
Residue const &  rsd2,
utility::vector1< Real > &  z_scores 
) const
void core::scoring::dna::DNA_BasePotential::get_array_indices ( InteractionType const &  t,
std::string const &  bases,
int &  i1,
int &  i2 
) const
private

i1 = 1,2 i2 = 1,16

References BP_type.

Referenced by mean(), set_mean_and_stddev(), set_stiffness(), stddev(), and stiffness().

void core::scoring::dna::DNA_BasePotential::load_score_tables ( )
private
Real core::scoring::dna::DNA_BasePotential::mean ( InteractionType const &  t,
std::string const &  bases,
int const  p 
) const
inlineprivate
void core::scoring::dna::DNA_BasePotential::set_mean_and_stddev ( InteractionType const &  type,
std::string const &  bases,
int const  index,
Real  mean,
Real  stddev 
)
private
void core::scoring::dna::DNA_BasePotential::set_stiffness ( InteractionType const &  type,
std::string const &  bases,
int const  index1,
int const  index2,
Real const  val 
)
private
Real core::scoring::dna::DNA_BasePotential::stddev ( InteractionType const &  t,
std::string const &  bases,
int const  p 
) const
inlineprivate
Real core::scoring::dna::DNA_BasePotential::stiffness ( InteractionType const &  t,
std::string const &  bases,
int const  p1,
int const  p2 
) const
inlineprivate

Member Data Documentation

FArray3D_Real core::scoring::dna::DNA_BasePotential::mean_
private

Referenced by mean(), and set_mean_and_stddev().

FArray3D_Real core::scoring::dna::DNA_BasePotential::stddev_
private

Referenced by set_mean_and_stddev(), and stddev().

FArray4D_Real core::scoring::dna::DNA_BasePotential::stiffness_
private

Referenced by set_stiffness(), and stiffness().


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