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:

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().

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

• src/protocols/cyclic_peptide_predict/PNearCalculator.hh
• src/protocols/cyclic_peptide_predict/PNearCalculator.cc