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protocols::cyclic_peptide_predict::PNearCalculator Class Reference

A class to compute P_Near and DG_folding. More...

#include <PNearCalculator.hh>

Inheritance diagram for protocols::cyclic_peptide_predict::PNearCalculator:
Inheritance graph
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Public Member Functions

 PNearCalculator ()=delete
 Default constructor (deleted). More...
 
 PNearCalculator (core::Real const lambda, core::Real const kbt)
 Options constructor. More...
 
 ~PNearCalculator () override
 Destructor. More...
 
PNearCalculatorOP clone () const
 Clone operation: make a copy of this object, and return an owning pointer to the copy. More...
 
void add_data_point (core::Real const energy, core::Real const rmsd)
 Add a data point to the set used to compute PNear. More...
 
void compute_pnear_and_dgfolding (core::Real &pnear, core::Real &Keq, core::Real &dgfolding) const
 Compute PNear and DeltaG_folding given the data points that have been added previously using add_data_point(). More...
 

Private Attributes

core::Real numerator_ = 0.0
 Accumulator for the numerator. More...
 
core::Real denominator_ = 0.0
 Accumulator for the denominator. More...
 
core::Real lambda_ = 0.5
 Lambda parameter (see PNear equation). More...
 
core::Real kbt_ = 1.0
 k_B*t parameter (see PNear equation). More...
 

Detailed Description

A class to compute P_Near and DG_folding.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Constructor & Destructor Documentation

protocols::cyclic_peptide_predict::PNearCalculator::PNearCalculator ( )
delete

Default constructor (deleted).

protocols::cyclic_peptide_predict::PNearCalculator::PNearCalculator ( core::Real const  lambda,
core::Real const  kbt 
)

Options constructor.

References kbt_, protocols::antibody::lambda, lambda_, and core::id::to_string().

protocols::cyclic_peptide_predict::PNearCalculator::~PNearCalculator ( )
overridedefault

Destructor.

Member Function Documentation

void protocols::cyclic_peptide_predict::PNearCalculator::add_data_point ( core::Real const  energy,
core::Real const  rmsd 
)

Add a data point to the set used to compute PNear.

References denominator_, kbt_, lambda_, and numerator_.

PNearCalculatorOP protocols::cyclic_peptide_predict::PNearCalculator::clone ( ) const

Clone operation: make a copy of this object, and return an owning pointer to the copy.

void protocols::cyclic_peptide_predict::PNearCalculator::compute_pnear_and_dgfolding ( core::Real pnear,
core::Real Keq,
core::Real dgfolding 
) const

Compute PNear and DeltaG_folding given the data points that have been added previously using add_data_point().

The pnear, Keq, and dgfolding values are overwritten by this operation. (These are the outputs.)

References denominator_, kbt_, and numerator_.

Member Data Documentation

core::Real protocols::cyclic_peptide_predict::PNearCalculator::denominator_ = 0.0
private

Accumulator for the denominator.

Referenced by add_data_point(), and compute_pnear_and_dgfolding().

core::Real protocols::cyclic_peptide_predict::PNearCalculator::kbt_ = 1.0
private

k_B*t parameter (see PNear equation).

Defaults to 1.0.

Referenced by add_data_point(), compute_pnear_and_dgfolding(), and PNearCalculator().

core::Real protocols::cyclic_peptide_predict::PNearCalculator::lambda_ = 0.5
private

Lambda parameter (see PNear equation).

Defaults to 0.5.

Referenced by add_data_point(), and PNearCalculator().

core::Real protocols::cyclic_peptide_predict::PNearCalculator::numerator_ = 0.0
private

Accumulator for the numerator.

Referenced by add_data_point(), and compute_pnear_and_dgfolding().


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