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core::scoring::func::GaussianChainGeneralFunc Class Reference

#include <GaussianChainGeneralFunc.hh>

Inheritance diagram for core::scoring::func::GaussianChainGeneralFunc:
Inheritance graph
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Public Member Functions

 GaussianChainGeneralFunc (Real const gaussian_variance_, Real const loop_fixed_cost, utility::vector1< Distance > const &other_distances)
 
FuncOP clone () const override
 This method must return a deep copy of this Func, meaning if this Func holds pointers to other Func objects, that it must clone those Func objects as well. More...
 
bool operator== (Func const &other) const override
 Equality operator. Looks for strict equality. Floating-point comparison is the rule rather than the exception. More...
 
bool same_type_as_me (Func const &other) const override
 Does the input Func, "other", have the same type as me? Necessary for the equality operator to function correctly. All derived Func classes must implement this function. More...
 
Real func (Real const z, bool const calc_deriv, Real &deriv) const
 
Real func (Real const x) const override
 Returns a value representing this function evaluated at a given point. More...
 
Real dfunc (Real const x) const override
 Returns a value representing the derivative of this function evaluated at a given point. More...
 
void read_data (std::istream &in) override
 initialize this Func from the given std::istream. More...
 
void show_definition (std::ostream &out) const override
 shows the definition of this function, usually the string type of function and the parameters passed in to the constructor. More...
 
- Public Member Functions inherited from core::scoring::func::Func
 ~Func () override
 Automatically generated virtual destructor for class deriving directly from VirtualBase. More...
 
bool operator!= (Func const &other) const
 inequality operator – simply the negation of the (virtual) equality operator More...
 
virtual Real estimate_dfunc (Real const r) const
 Estimates the derivative of this function at a given radius by calculating the slope of the secant line from func(r) and func(r+1e-05). More...
 
virtual Real estimate_dfunc (Real const r, Real const h) const
 Estimates the derivative of this function at a given radius by calculating the slope of the secant line from func(r) and func(r+h). More...
 
virtual void show (std::ostream &out) const
 Prints out space-delimited columns for r, func, dfunc and dfunc_est. The values for func, dfunc and dfunc_est are plotted as a function of r, which is varied from 2-20 in steps of 0.5. The value for dfunc_est is the estimated by the method estimate_dfunc( r ). More...
 
virtual Size show_violations (std::ostream &out, Real r, Size verbose_level, Real threshold=1) const
 show some sort of stringified representation of the violations for this constraint. More...
 

Private Member Functions

void initialize_parameters ()
 
void recompute_parameters ()
 
Real erfc_integral (Real const &x, int const N) const
 

Private Attributes

Real gaussian_variance_
 
Real loop_fixed_cost_
 
utility::vector1< Realother_distances_
 
Real kB_T_
 
Real loop_fixed_cost_total_
 
Size N_
 

Constructor & Destructor Documentation

core::scoring::func::GaussianChainGeneralFunc::GaussianChainGeneralFunc ( Real const  gaussian_variance_,
Real const  loop_fixed_cost,
utility::vector1< Distance > const &  other_distances 
)

Member Function Documentation

FuncOP core::scoring::func::GaussianChainGeneralFunc::clone ( ) const
overridevirtual

This method must return a deep copy of this Func, meaning if this Func holds pointers to other Func objects, that it must clone those Func objects as well.

Implements core::scoring::func::Func.

References gaussian_variance_, loop_fixed_cost_, and other_distances_.

Real core::scoring::func::GaussianChainGeneralFunc::dfunc ( Real const  const) const
overridevirtual

Returns a value representing the derivative of this function evaluated at a given point.

Implements core::scoring::func::Func.

References func().

Real core::scoring::func::GaussianChainGeneralFunc::erfc_integral ( Real const &  x,
int const  N 
) const
private

Referenced by func().

Real core::scoring::func::GaussianChainGeneralFunc::func ( Real const  z,
bool const  calc_deriv,
Real deriv 
) const
Real core::scoring::func::GaussianChainGeneralFunc::func ( Real const  const) const
overridevirtual

Returns a value representing this function evaluated at a given point.

Implements core::scoring::func::Func.

References func().

void core::scoring::func::GaussianChainGeneralFunc::initialize_parameters ( )
private
bool core::scoring::func::GaussianChainGeneralFunc::operator== ( Func const &  other) const
overridevirtual

Equality operator. Looks for strict equality. Floating-point comparison is the rule rather than the exception.

Implements core::scoring::func::Func.

References gaussian_variance_, kB_T_, loop_fixed_cost_, loop_fixed_cost_total_, N_, other_distances_, same_type_as_me(), and core::scoring::func::Func::same_type_as_me().

void core::scoring::func::GaussianChainGeneralFunc::read_data ( std::istream &  )
overridevirtual

initialize this Func from the given std::istream.

Reimplemented from core::scoring::func::Func.

References gaussian_variance_, initialize_parameters(), loop_fixed_cost_, and other_distances_.

void core::scoring::func::GaussianChainGeneralFunc::recompute_parameters ( )
private
bool core::scoring::func::GaussianChainGeneralFunc::same_type_as_me ( Func const &  other) const
overridevirtual

Does the input Func, "other", have the same type as me? Necessary for the equality operator to function correctly. All derived Func classes must implement this function.

Implements core::scoring::func::Func.

Referenced by operator==().

void core::scoring::func::GaussianChainGeneralFunc::show_definition ( std::ostream &  out) const
overridevirtual

shows the definition of this function, usually the string type of function and the parameters passed in to the constructor.

Reimplemented from core::scoring::func::Func.

References core::kinematics::distance(), gaussian_variance_, loop_fixed_cost_, and other_distances_.

Member Data Documentation

Real core::scoring::func::GaussianChainGeneralFunc::gaussian_variance_
private
Real core::scoring::func::GaussianChainGeneralFunc::kB_T_
private
Real core::scoring::func::GaussianChainGeneralFunc::loop_fixed_cost_
private
Real core::scoring::func::GaussianChainGeneralFunc::loop_fixed_cost_total_
private
Size core::scoring::func::GaussianChainGeneralFunc::N_
private
utility::vector1< Real > core::scoring::func::GaussianChainGeneralFunc::other_distances_
private

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