core::scoring::UnfoldedStatePotential Class Reference

#include <UnfoldedStatePotential.hh>

Inheritance diagram for core::scoring::UnfoldedStatePotential:

Public Member Functions
	UnfoldedStatePotential (std::string const &filename)
	ctor - calls the function which reads in the database file More...
	~UnfoldedStatePotential () override
void	raw_unfolded_state_energymap (std::string const &aa_name3, scoring::EnergyMap &e) const
	returns the database values for an aa in the unfolded state - these are unweighted values! More...
void	pose_raw_unfolded_state_energymap (pose::Pose const &pose, scoring::EnergyMap &e) const
	returns the unweighted unfolded state energy for the whole pose as an emap (i.e. broken up by score type) More...
scoring::EnergyMap	get_unfoled_potential_file_weights () const
	returns an emap of the energy method weights specfied in the unfolded energy file More...

Private Member Functions
void	read_database_file (std::string const &filename)
	Read the amino acid energy file. More...

Private Attributes
std::map< std::string, scoring::EnergyMap >	unfolded_energy_
	Unfolded state energies by residue. More...
scoring::EnergyMap	unfolded_potential_file_weights_
	energy method weights listed in the energies file More...

Detailed Description

Remarks

making this a separate class because it relies on a database file. rather than putting the code to read the database file in the energy method class, it seems like the design we're following is to have a class like this one that reads the file and provides the lookup into the data structure holding the database information and a separate class for the energy method implementation.

Constructor & Destructor Documentation

core::scoring::UnfoldedStatePotential::UnfoldedStatePotential

(

std::string const &

filename

)

ctor - calls the function which reads in the database file

References read_database_file().

core::scoring::UnfoldedStatePotential::~UnfoldedStatePotential ( )

overridedefault

Member Function Documentation

scoring::EnergyMap core::scoring::UnfoldedStatePotential::get_unfoled_potential_file_weights

(

)

const

returns an emap of the energy method weights specfied in the unfolded energy file

References unfolded_potential_file_weights_.

void core::scoring::UnfoldedStatePotential::pose_raw_unfolded_state_energymap	(	pose::Pose const &	pose,
		scoring::EnergyMap &	e
	)		const

returns the unweighted unfolded state energy for the whole pose as an emap (i.e. broken up by score type)

References core::conformation::Residue::is_protein(), core::conformation::Residue::is_RNA(), core::conformation::Residue::name3(), core::pose::Pose::residue(), core::pose::Pose::size(), and unfolded_energy_.

Referenced by protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_mutation_data().

void core::scoring::UnfoldedStatePotential::raw_unfolded_state_energymap	(	std::string const &	aa_name3,
		scoring::EnergyMap &	e
	)		const

returns the database values for an aa in the unfolded state - these are unweighted values!

References unfolded_energy_.

Referenced by protocols::optimize_weights::IterativeOptEDriver::get_nat_aa_opte_data(), protocols::optimize_weights::IterativeOptEDriver::output_weighted_unfolded_energies(), and core::energy_methods::UnfoldedStateEnergy::residue_energy().

void core::scoring::UnfoldedStatePotential::read_database_file ( std::string const &  filename )

private

Read the amino acid energy file.

References core::scoring::ScoreTypeManager::is_score_type(), core::scoring::ScoreTypeManager::score_type_from_name(), protocols::hybridization::t, unfolded_energy_, unfolded_potential_file_weights_, and protocols::hybridization::val.

Referenced by UnfoldedStatePotential().

Member Data Documentation

std::map< std::string, scoring::EnergyMap > core::scoring::UnfoldedStatePotential::unfolded_energy_

private

Unfolded state energies by residue.

Referenced by pose_raw_unfolded_state_energymap(), raw_unfolded_state_energymap(), and read_database_file().

scoring::EnergyMap core::scoring::UnfoldedStatePotential::unfolded_potential_file_weights_

private

energy method weights listed in the energies file

Referenced by get_unfoled_potential_file_weights(), and read_database_file().

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

• src/core/scoring/UnfoldedStatePotential.hh
• src/core/scoring/UnfoldedStatePotential.cc