NetChargeEnergySetup, a helper class for the NetChargeEnergy energy method that stores all of its setup data. More...

#include <NetChargeEnergySetup.hh>

Inheritance diagram for core::scoring::netcharge_energy::NetChargeEnergySetup:

Public Member Functions
	NetChargeEnergySetup ()
	Default constructor for NetChargeEnergySetup. More...

	~NetChargeEnergySetup () override
	Default destructor for NetChargeEnergySetup. More...

virtual NetChargeEnergySetupOP	clone () const
	Clone: create a copy of this object, and return an owning pointer to the copy. More...

void	reset ()
	Reset all data in this data storage object. More...

void	initialize_from_file (std::string const &filename)
	Initialize from a .charge file. More...

void	initialize_from_file_contents (std::string const &filecontents)
	Initialize from a string in the format of a .charge file. More...

std::string	get_tailfunction_name (TailFunction const tf) const
	Get tail function name from enum. More...

TailFunction	get_tailfunction_from_name (std::string const &name) const
	Get tail function enum from name. More...

unsigned long int	desired_charge () const
	Get the desired charge. More...

core::Real	penalty (signed long const observed) const
	Look up the penalty given the net charge observed. More...

std::string	report () const
	Get a summary of the data stored in this object. More...

Private Member Functions
void	parse_a_penalty_definition (utility::vector1< std::string > const &lines)
	Parse out penalty definition from a single block of lines from file. More...

void	check_data () const
	Do some final checks to ensure that data were loaded properly. More...

core::Real	out_of_bounds_func (signed long const observed, bool const before) const
	Calculate the out-of-bounds behaviour of the penalty function and return the penalty value. More...

core::Real	const_out_of_bounds_func (bool const before) const
	Return a constant value for an out-of-bounds behaviour. More...

core::Real	linear_out_of_bounds_func (bool const before, signed long const observed) const
	Return a linear value for an out-of-bounds behaviour. More...

core::Real	quadratic_out_of_bounds_func (bool const before, signed long const observed) const
	Return a quadratic value for an out-of-bounds behaviour. More...

Private Attributes
signed long int	desired_charge_
	The desired net charge. More...

std::pair< signed long int, signed long int >	charge_penalties_range_
	The lower and upper ends of the charge range specified in the penalties. More...

utility::vector1< core::Real >	penalties_
	Penalties for each residue count (relative to expected). More...

std::pair< TailFunction, TailFunction >	tailfunctions_
	The behaviours at the end of the user-defined range. More...

Detailed Description

NetChargeEnergySetup, a helper class for the NetChargeEnergy energy method that stores all of its setup data.

Constructor & Destructor Documentation

core::scoring::netcharge_energy::NetChargeEnergySetup::NetChargeEnergySetup ( )

Default constructor for NetChargeEnergySetup.

core::scoring::netcharge_energy::NetChargeEnergySetup::~NetChargeEnergySetup ( )

overridedefault

Default destructor for NetChargeEnergySetup.

Member Function Documentation

void core::scoring::netcharge_energy::NetChargeEnergySetup::check_data ( ) const

private

Do some final checks to ensure that data were loaded properly.

References charge_penalties_range_, desired_charge_, penalties_, report(), and core::scoring::netcharge_energy::TR().

Referenced by initialize_from_file(), initialize_from_file_contents(), and parse_a_penalty_definition().

NetChargeEnergySetupOP core::scoring::netcharge_energy::NetChargeEnergySetup::clone ( ) const

virtual

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

core::Real core::scoring::netcharge_energy::NetChargeEnergySetup::const_out_of_bounds_func ( bool const before ) const

inlineprivate

Return a constant value for an out-of-bounds behaviour.

Inputs are:

Parameters

[in] before If true, this is beyond the low range of penalty values. If false, we're beyond the high range.

References penalties_.

Referenced by out_of_bounds_func().

unsigned long int core::scoring::netcharge_energy::NetChargeEnergySetup::desired_charge ( ) const

inline

Get the desired charge.

References desired_charge_.

Referenced by parse_a_penalty_definition().

TailFunction core::scoring::netcharge_energy::NetChargeEnergySetup::get_tailfunction_from_name ( std::string const & name ) const

Get tail function enum from name.

This is slow; it calls get_tailfunction_name repeatedly. Intended only for use during setup. Returns tf_unknown if tail function couldn't be parsed.

References get_tailfunction_name(), core::scoring::netcharge_energy::tf_end_of_list, and core::scoring::netcharge_energy::tf_unknown.

Referenced by parse_a_penalty_definition().

std::string core::scoring::netcharge_energy::NetChargeEnergySetup::get_tailfunction_name ( TailFunction const tf ) const

Get tail function name from enum.

References core::scoring::netcharge_energy::tf_constant, core::scoring::netcharge_energy::tf_linear, and core::scoring::netcharge_energy::tf_quadratic.

Referenced by get_tailfunction_from_name(), and report().

void core::scoring::netcharge_energy::NetChargeEnergySetup::initialize_from_file ( std::string const & filename )

Initialize from a .charge file.

References check_data(), protocols::abinitio::filename(), parse_a_penalty_definition(), reset(), and core::scoring::netcharge_energy::TR().

void core::scoring::netcharge_energy::NetChargeEnergySetup::initialize_from_file_contents ( std::string const & filecontents )

Initialize from a string in the format of a .charge file.

Allows external code to initialize object without having it read directly from disk.

References check_data(), parse_a_penalty_definition(), reset(), and core::scoring::netcharge_energy::TR().

core::Real core::scoring::netcharge_energy::NetChargeEnergySetup::linear_out_of_bounds_func	(	bool const	before,
		signed long const	observed
	)		const

inlineprivate

Return a linear value for an out-of-bounds behaviour.

This fits the first two or last two points to a straight line, then extends it. Inputs are:

Parameters

[in]	before	If true, this is beyond the low range of penalty values. If false, we're beyond the high range.
[in]	observed	The observed count.

References protocols::match::upstream::b, charge_penalties_range_, and penalties_.

Referenced by out_of_bounds_func().

core::Real core::scoring::netcharge_energy::NetChargeEnergySetup::out_of_bounds_func	(	signed long const	observed,
		bool const	before
	)		const

inlineprivate

Calculate the out-of-bounds behaviour of the penalty function and return the penalty value.

Inputs are:

Parameters

[in]	observed	The observed count.
[in]	before	If true, this is beyond the low range of penalty values. If false, we're beyond the high range.

References const_out_of_bounds_func(), linear_out_of_bounds_func(), quadratic_out_of_bounds_func(), tailfunctions_, core::scoring::netcharge_energy::tf_constant, core::scoring::netcharge_energy::tf_linear, core::scoring::netcharge_energy::tf_quadratic, and core::scoring::netcharge_energy::tf_unknown.

Referenced by penalty().

void core::scoring::netcharge_energy::NetChargeEnergySetup::parse_a_penalty_definition ( utility::vector1< std::string > const & lines )

private

Parse out penalty definition from a single block of lines from file.

The lines vector should be the lines BETWEEN the PENALTY_DEFINITION and END_PENALTY_DEFINITION lines.

References charge_penalties_range_, check_data(), desired_charge(), desired_charge_, get_tailfunction_from_name(), penalties_, tailfunctions_, core::scoring::netcharge_energy::tf_quadratic, and core::scoring::netcharge_energy::tf_unknown.

Referenced by initialize_from_file(), and initialize_from_file_contents().

core::Real core::scoring::netcharge_energy::NetChargeEnergySetup::penalty ( signed long const observed ) const

inline

Look up the penalty given the net charge observed.

References charge_penalties_range_, out_of_bounds_func(), and penalties_.

core::Real core::scoring::netcharge_energy::NetChargeEnergySetup::quadratic_out_of_bounds_func	(	bool const	before,
		signed long const	observed
	)		const

inlineprivate

Return a quadratic value for an out-of-bounds behaviour.

This fits the first two or the last two values to a parabola centred on the origin, then extends it. Inputs are:

Parameters

[in]	before	If true, this is beyond the low range of penalty values. If false, we're beyond the high range.
[in]	observed	The observed count.

References core::pose::motif::a(), protocols::match::upstream::b, charge_penalties_range_, desired_charge_, and penalties_.

Referenced by out_of_bounds_func().

std::string core::scoring::netcharge_energy::NetChargeEnergySetup::report ( ) const

Get a summary of the data stored in this object.

References charge_penalties_range_, desired_charge_, get_tailfunction_name(), penalties_, and tailfunctions_.

Referenced by check_data().

void core::scoring::netcharge_energy::NetChargeEnergySetup::reset ( )

Reset all data in this data storage object.

References charge_penalties_range_, desired_charge_, penalties_, tailfunctions_, and core::scoring::netcharge_energy::tf_quadratic.

Referenced by initialize_from_file(), and initialize_from_file_contents().

Member Data Documentation

std::pair< signed long int, signed long int > core::scoring::netcharge_energy::NetChargeEnergySetup::charge_penalties_range_

private

The lower and upper ends of the charge range specified in the penalties.

Referenced by check_data(), linear_out_of_bounds_func(), parse_a_penalty_definition(), penalty(), quadratic_out_of_bounds_func(), report(), and reset().

signed long int core::scoring::netcharge_energy::NetChargeEnergySetup::desired_charge_

private

The desired net charge.

Referenced by check_data(), desired_charge(), parse_a_penalty_definition(), quadratic_out_of_bounds_func(), report(), and reset().

utility::vector1< core::Real > core::scoring::netcharge_energy::NetChargeEnergySetup::penalties_

private

Penalties for each residue count (relative to expected).

Referenced by check_data(), const_out_of_bounds_func(), linear_out_of_bounds_func(), parse_a_penalty_definition(), penalty(), quadratic_out_of_bounds_func(), report(), and reset().

std::pair<TailFunction, TailFunction > core::scoring::netcharge_energy::NetChargeEnergySetup::tailfunctions_

private

The behaviours at the end of the user-defined range.

By default, past the user-defined range, the energy increases quadratically with increasing deviations from ideal sequence composition. The user can set this to be linear or constant, though.

Referenced by out_of_bounds_func(), parse_a_penalty_definition(), report(), and reset().

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

src/core/scoring/netcharge_energy/NetChargeEnergySetup.hh
src/core/scoring/netcharge_energy/NetChargeEnergySetup.cc

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation