RealValuedParameter class, used to store a single real-valued parameter for parametric backbone generation. More...

#include <RealValuedParameter.hh>

Inheritance diagram for core::conformation::parametric::RealValuedParameter:

Public Member Functions
	RealValuedParameter ()
	constructors More...

	RealValuedParameter (RealValuedParameter const &src)

	~RealValuedParameter () override

ParameterOP	clone () const override
	Make a copy of this object ( allocate actual memory for it ) More...

core::Real const &	value () const
	Get the value of this parameter. More...

core::Real const &	default_value () const
	Get the default value of this parameter. More...

core::Real const &	value_min () const
	Get the minimum value of this parameter. More...

core::Real const &	value_max () const
	Get the maximum value of this parameter. More...

core::Size	value_samples () const
	Get the samples. More...

RealPerturbationType	perturbation_type () const
	Get the perturbation type. More...

core::Real const &	perturbation_magnitude () const
	Get the perturbation magnitude of this parameter. More...

void	set_input_is_angle_in_degrees (bool const setting)
	Set whether this parameter expects that its input is an angle in degrees. More...

void	set_value (core::Real const &value_in, bool const ignore_use_degrees=false)
	Set the value of this parameter. More...

void	set_default_value (core::Real const &value_in)
	Sets the initial value of this parameter, keeping the value_set_ boolean false. More...

void	set_parameter_type (ParameterType const type_in) override
	Sets the parameter type. More...

void	set_sampling_options (core::Real const &value_min_in, core::Real const &value_max_in, core::Size const samples_in)
	Set the options for sampling this parameter. More...

void	set_perturbation_type (std::string const &pert_type_in)
	Set the perturbation type, by string. More...

void	set_perturbation_type (RealPerturbationType const pert_type_in)
	Set the perturbation type, by enum. More...

void	set_perturbation_options (core::Real const &pert_magnitude_in, std::string const &pert_type_in)
	Set the options for perturbing this parameter (with perturbation type set by string). More...

void	set_perturbation_options (core::Real const &pert_magnitude_in, RealPerturbationType const pert_type_in)
	Set the options for perturbing this parameter (with perturbation type set by enum). More...

bool	copy_value_from_parameter (ParameterCOP other_parameter, ParametersCOP other_parameter_collection, ParametersCOP this_parameter_collection) override
	Given another parameter of the same type, copy its value. This does not set value_set_ to true. More...

void	parse_setting (utility::tag::TagCOP tag, bool const parse_setting, bool const parse_grid_sampling, bool const parse_perturbation, bool const parse_copying) override
	Given a tag, parse out the setting for this parameter. More...

void	provide_xsd_information (utility::tag::AttributeList &xsd, bool const provide_setting, bool const provide_copying, bool const provide_grid_sampling, bool const provide_perturbation) const override
	Return the XSD information for this parameter. More...

void	reset_sampling_and_perturbation_settings () override
	Reset the sampling and perturbation options before storing this Parameter object in a parametric Conformation. More...

void	reset_value_settings () override
	Reset the value settings for this Parameter object. More...

bool	perturbation_set () const
	Has the perturbation information for this parameter been set? More...

bool	sampling_set () const
	Has the sampling information for this parameter been set? More...

core::Real	generate_perturbed_value (core::Real const &current_value) const
	Given the current value of this parameter and the current perturbation settings, return a perturbed value. More...

Public Member Functions inherited from core::conformation::parametric::Parameter
	Parameter ()
	constructors More...

ParameterCOP	get_self_ptr () const
	Self pointers (const shared pointer). More...

ParameterOP	get_self_ptr ()
	Self pointers (nonconst shared pointer). More...

ParameterCAP	get_self_weak_ptr () const
	Self pointers (const weak pointer). More...

ParameterAP	get_self_weak_ptr ()
	Self pointers (nonconst weak pointer). More...

std::string const &	parameter_name () const
	Get parameter name. More...

std::string const &	parameter_description () const
	Get parameter description. More...

std::string const &	short_parameter_description () const
	Get short parameter description. More...

std::string const &	parameter_units () const
	Get units. More...

ParameterType	parameter_type () const
	Get the parameter type. More...

bool	can_be_set () const
	Is this parameter one that can be set directly by the user? More...

bool	can_be_copied () const
	Is this parameter one that can be copied from another parameter? More...

bool	can_be_sampled () const
	Is this parameter one that can be sampled? More...

bool	can_be_perturbed () const
	Is this parameter one that can be perturbed? More...

bool	global_for_parameters_set () const
	Get whether this property is meant to be global for a parameters set. More...

std::string const &	copy_suffix () const
	Get the suffix for the copy tag (e.g. "copies_helix" in the case of helical bundles). More...

core::Size	copy_from_parameters_index () const
	Get the index of the Parameters object from which we will copy this parameter's value. More...

bool	value_was_set () const
	Has the value been set? More...

bool	copying_information_was_set () const
	Has the copying information been set? More...

void	set_parameter_name (std::string const &name_in)
	Set parameter name. More...

void	set_parameter_description (std::string const &description_in)
	Set parameter description. More...

void	set_short_parameter_description (std::string const &short_description_in)
	Set short parameter description. More...

void	set_parameter_units (std::string const &units_in)
	Set parameter units. More...

void	set_can_be_set_sampled_perturbed_copied (bool const can_be_set, bool const can_be_copied, bool const can_be_sampled, bool const can_be_perturbed)
	Set whether this parameter is one that can be set directly by the user, whether it can be sampled, and whether it can be perturbed. More...

void	set_global_for_parameters_set (bool const setting)
	Set whether this property is meant to be global for a parameters set. More...

void	set_copy_suffix (std::string const &suffix_in)
	Set the suffix for the copy tag (e.g. "copies_helix" in the case of helical bundles). More...

void	set_copy_from_parameters_index (core::Size const setting)
	Set the index of the Parameters object from which we will copy this parameter's value. More...

virtual void	reset_copying_settings ()
	Reset the copying options. More...

Static Public Member Functions
static std::string const &	perturbation_type_string_from_enum (RealPerturbationType const type_enum)
	Given a perturbation type enum, get the string for that enum. More...

static RealPerturbationType	perturbation_type_enum_from_string (std::string const &type_string)
	Given a perturbation type string, get the enum for that string. More...

Protected Member Functions
void	set_value_sneakily (core::Real const &value_in)
	Set the value without setting value_was_set_ = true. More...

void	set_copy_information (utility::tag::TagCOP tag)
	Parse copy information from the tag, and set it. More...

virtual bool	parse_setting_only (utility::tag::TagCOP tag, bool const parse_copying_too)
	Parse a setting for this parameter (e.g. r0="12.5"). More...

Protected Member Functions inherited from core::conformation::parametric::Parameter
void	set_value_was_set ()
	Allows derived classes to indicate that the value has been set. More...

void	reset_value_was_set ()
	Allows derived classes to indicate that the value has not been set. More...

Private Member Functions
core::Real	convert_angle (core::Real const &val) const
	Ensure that an angle value is in radians. More...

void	provide_xsd_grid_sampling_information (utility::tag::AttributeList &xsd) const
	Return the XSD information for grid-sampling this parameter. More...

void	provide_xsd_perturbation_information (utility::tag::AttributeList &xsd) const
	Return the XSD information for perturbing this parameter. More...

void	provide_xsd_setting_information (utility::tag::AttributeList &xsd) const
	Return the XSD information for setting this parameter. More...

void	provide_xsd_copying_information (utility::tag::AttributeList &xsd) const
	Return the XSD information for copying this parameter from another. More...

void	correct_range ()
	If this is a parameter storing an angle, correct the value to be (-Pi:Pi]. Also, check that the value is positive if it is meant to be, or nonnegative if it is meant to be. More...

bool	parse_grid_sampling_options (utility::tag::TagCOP tag)
	Parse a sampling range for this parameter (e.g. r0_min="12.3" r0_max="14.3" r0_samples="5"). More...

bool	parse_perturbation_options (utility::tag::TagCOP tag)
	Parse perturbation options for this parameter (e.g. r0_perturbation="5.0" r0_perturbation_type="gaussian"). More...

Private Attributes
core::Real	value_
	The value of this parameter. More...

core::Real	default_value_
	The default value of this parameter. More...

bool	default_value_was_set_
	Has the default value been set? More...

core::Real	value_min_
	The min value to be sampled for this parameter. More...

core::Real	value_max_
	The max value to be sampled for this parameter. More...

core::Size	value_samples_
	The number of samples for this parameter. More...

core::Real	perturbation_magnitude_
	The magnitude of the perturbation of this parameter. More...

RealPerturbationType	perturbation_type_
	The perturbation type for this parameter. More...

bool	sampling_set_
	Was the sampling range set? More...

bool	perturbation_set_
	Were perturbation options set? More...

bool	input_is_angle_in_degrees_
	Does this parameter expect that its input will be an angle in degrees? More...

Detailed Description

RealValuedParameter class, used to store a single real-valued parameter for parametric backbone generation.

Constructor & Destructor Documentation

core::conformation::parametric::RealValuedParameter::RealValuedParameter ( )

constructors

Constructor.

References core::conformation::parametric::PT_generic_real, core::conformation::parametric::Parameter::set_can_be_set_sampled_perturbed_copied(), and core::conformation::parametric::Parameter::set_parameter_type().

core::conformation::parametric::RealValuedParameter::RealValuedParameter ( RealValuedParameter const & src )

core::conformation::parametric::RealValuedParameter::~RealValuedParameter ( )

override

Member Function Documentation

ParameterOP core::conformation::parametric::RealValuedParameter::clone ( ) const

overridevirtual

Make a copy of this object ( allocate actual memory for it )

Implements core::conformation::parametric::Parameter.

Reimplemented in protocols::helical_bundle::parameters::OmegaBundleParameter.

core::Real core::conformation::parametric::RealValuedParameter::convert_angle ( core::Real const & val ) const

inlineprivate

Ensure that an angle value is in radians.

Checks the use_degrees_ boolean. If true, converts degrees to radians; if false, returns input value.

References input_is_angle_in_degrees_, and protocols::hybridization::val.

Referenced by set_default_value(), set_perturbation_options(), set_sampling_options(), and set_value().

bool core::conformation::parametric::RealValuedParameter::copy_value_from_parameter	(	ParameterCOP	other_parameter,
		ParametersCOP	other_parameter_collection,
		ParametersCOP	this_parameter_collection
	)

overridevirtual

Given another parameter of the same type, copy its value. This does not set value_set_ to true.

Performs type checking in debug mode.

Returns: Returns TRUE for failure, FALSE for success.

Implements core::conformation::parametric::Parameter.

Reimplemented in protocols::helical_bundle::parameters::OmegaBundleParameter.

References value_.

Referenced by protocols::helical_bundle::parameters::OmegaBundleParameter::copy_value_from_parameter().

void core::conformation::parametric::RealValuedParameter::correct_range ( )

private

If this is a parameter storing an angle, correct the value to be (-Pi:Pi]. Also, check that the value is positive if it is meant to be, or nonnegative if it is meant to be.

Also checks sampling and perturbing options to ensure that these are reasonable.

References core::conformation::parametric::Parameter::parameter_type(), perturbation_magnitude_, perturbation_type_, core::conformation::parametric::PT_angle, core::conformation::parametric::PT_generic_nonnegative_valued_real, core::conformation::parametric::PT_generic_positive_valued_real, core::conformation::parametric::RPT_end_of_list, core::id::swap(), value_, value_max_, and value_min_.

Referenced by set_default_value(), set_parameter_type(), set_perturbation_options(), set_sampling_options(), and set_value().

core::Real const& core::conformation::parametric::RealValuedParameter::default_value ( ) const

inline

Get the default value of this parameter.

References default_value_.

Referenced by provide_xsd_setting_information(), and reset_value_settings().

core::Real core::conformation::parametric::RealValuedParameter::generate_perturbed_value ( core::Real const & current_value ) const

Given the current value of this parameter and the current perturbation settings, return a perturbed value.

Note: Does not alter the value of this parameter.

References core::conformation::parametric::Parameter::parameter_type(), perturbation_magnitude_, perturbation_type_, core::conformation::parametric::PT_angle, core::conformation::parametric::PT_generic_nonnegative_valued_real, core::conformation::parametric::PT_generic_positive_valued_real, core::conformation::parametric::RPT_gaussian, and core::conformation::parametric::RPT_uniform.

bool core::conformation::parametric::RealValuedParameter::parse_grid_sampling_options ( utility::tag::TagCOP tag )

private

Parse a sampling range for this parameter (e.g. r0_min="12.3" r0_max="14.3" r0_samples="5").

Returns false if none of these parameters is provided.

References core::conformation::parametric::Parameter::parameter_name(), and set_sampling_options().

Referenced by parse_setting().

bool core::conformation::parametric::RealValuedParameter::parse_perturbation_options ( utility::tag::TagCOP tag )

private

Parse perturbation options for this parameter (e.g. r0_perturbation="5.0" r0_perturbation_type="gaussian").

Returns false if the _perturbation option is not provided.

References core::conformation::parametric::Parameter::parameter_name(), perturbation_type_, perturbation_type_string_from_enum(), and set_perturbation_options().

Referenced by parse_setting().

void core::conformation::parametric::RealValuedParameter::parse_setting	(	utility::tag::TagCOP	tag,
		bool const	parse_setting,
		bool const	parse_grid_sampling,
		bool const	parse_perturbation,
		bool const	parse_copying
	)

overridevirtual

Given a tag, parse out the setting for this parameter.

If parse_setting is true, this tries to parse the value for this parameter. If parse_grid_sampling is true, this tries to parse a range of values to sample, and a number of samples. If parse_perturbation is true, this parses options for perturbing the value of the parameter. Note that, if multiple options are true, grid sampling or perturbation options are given priority over a flat setting (and an error is thrown if more than one of these is provided).

Note: Must be implemented by derived classes.

Implements core::conformation::parametric::Parameter.

References parse_grid_sampling_options(), parse_perturbation_options(), and parse_setting_only().

bool core::conformation::parametric::RealValuedParameter::parse_setting_only	(	utility::tag::TagCOP	tag,
		bool const	parse_copying_too
	)

protectedvirtual

Parse a setting for this parameter (e.g. r0="12.5").

Returns false if this parameter isn't provided. Also parses copying.

Note: May be overridden by derived classes.

Reimplemented in protocols::helical_bundle::parameters::OmegaBundleParameter.

References core::conformation::parametric::Parameter::copy_suffix(), core::conformation::parametric::Parameter::parameter_name(), core::conformation::parametric::Parameter::reset_copying_settings(), reset_sampling_and_perturbation_settings(), reset_value_settings(), set_copy_information(), and set_value().

Referenced by parse_setting().

core::Real const& core::conformation::parametric::RealValuedParameter::perturbation_magnitude ( ) const

inline

Get the perturbation magnitude of this parameter.

References perturbation_magnitude_.

bool core::conformation::parametric::RealValuedParameter::perturbation_set ( ) const

inline

Has the perturbation information for this parameter been set?

References perturbation_set_.

RealPerturbationType core::conformation::parametric::RealValuedParameter::perturbation_type ( ) const

inline

Get the perturbation type.

References perturbation_type_.

RealPerturbationType core::conformation::parametric::RealValuedParameter::perturbation_type_enum_from_string ( std::string const & type_string )

static

Given a perturbation type string, get the enum for that string.

Returns RPT_unknown_type if unknown string provided.

References perturbation_type_string_from_enum(), core::conformation::parametric::RPT_end_of_list, and core::conformation::parametric::RPT_unknown_type.

Referenced by set_perturbation_options(), set_perturbation_type(), and protocols::helical_bundle::BundleParametrizationCalculator::set_perturbation_type_globally().

std::string const & core::conformation::parametric::RealValuedParameter::perturbation_type_string_from_enum ( RealPerturbationType const type_enum )

static

Given a perturbation type enum, get the string for that enum.

Throws an error for an invalid enum.

References core::conformation::parametric::RPT_end_of_list.

Referenced by parse_perturbation_options(), and perturbation_type_enum_from_string().

void core::conformation::parametric::RealValuedParameter::provide_xsd_copying_information ( utility::tag::AttributeList & xsd ) const

private

Return the XSD information for copying this parameter from another.

References core::conformation::parametric::Parameter::copy_suffix(), and core::conformation::parametric::Parameter::parameter_name().

Referenced by provide_xsd_information().

void core::conformation::parametric::RealValuedParameter::provide_xsd_grid_sampling_information ( utility::tag::AttributeList & xsd ) const

private

Return the XSD information for grid-sampling this parameter.

References core::conformation::parametric::Parameter::parameter_name().

Referenced by provide_xsd_information().

void core::conformation::parametric::RealValuedParameter::provide_xsd_information	(	utility::tag::AttributeList &	xsd,
		bool const	provide_setting,
		bool const	provide_copying,
		bool const	provide_grid_sampling,
		bool const	provide_perturbation
	)		const

overridevirtual

Return the XSD information for this parameter.

Note: Must be implemented by derived classes.

Implements core::conformation::parametric::Parameter.

Reimplemented in protocols::helical_bundle::parameters::OmegaBundleParameter.

References provide_xsd_copying_information(), provide_xsd_grid_sampling_information(), provide_xsd_perturbation_information(), and provide_xsd_setting_information().

Referenced by protocols::helical_bundle::parameters::OmegaBundleParameter::provide_xsd_information().

void core::conformation::parametric::RealValuedParameter::provide_xsd_perturbation_information ( utility::tag::AttributeList & xsd ) const

private

Return the XSD information for perturbing this parameter.

References core::conformation::parametric::Parameter::parameter_name().

Referenced by provide_xsd_information().

void core::conformation::parametric::RealValuedParameter::provide_xsd_setting_information ( utility::tag::AttributeList & xsd ) const

private

Return the XSD information for setting this parameter.

References default_value(), core::conformation::parametric::Parameter::parameter_description(), core::conformation::parametric::Parameter::parameter_name(), and core::id::to_string().

Referenced by provide_xsd_information().

void core::conformation::parametric::RealValuedParameter::reset_sampling_and_perturbation_settings ( )

overridevirtual

Reset the sampling and perturbation options before storing this Parameter object in a parametric Conformation.

Pure virtual. Must be implemented by derived classes.

Implements core::conformation::parametric::Parameter.

References perturbation_magnitude_, perturbation_set_, perturbation_type_, core::conformation::parametric::RPT_gaussian, sampling_set_, value_max_, value_min_, and value_samples_.

Referenced by parse_setting_only(), set_perturbation_options(), protocols::helical_bundle::parameters::OmegaBundleParameter::set_pitch_copying_information(), and set_sampling_options().

void core::conformation::parametric::RealValuedParameter::reset_value_settings ( )

overridevirtual

Reset the value settings for this Parameter object.

Implements core::conformation::parametric::Parameter.

References default_value(), core::conformation::parametric::Parameter::reset_value_was_set(), and set_value().

Referenced by parse_setting_only(), set_perturbation_options(), protocols::helical_bundle::parameters::OmegaBundleParameter::set_pitch_copying_information(), and set_sampling_options().

bool core::conformation::parametric::RealValuedParameter::sampling_set ( ) const

inline

Has the sampling information for this parameter been set?

References sampling_set_.

void core::conformation::parametric::RealValuedParameter::set_copy_information ( utility::tag::TagCOP tag )

protected

Parse copy information from the tag, and set it.

References core::conformation::parametric::Parameter::copy_suffix(), core::conformation::parametric::Parameter::parameter_name(), and core::conformation::parametric::Parameter::set_copy_from_parameters_index().

Referenced by protocols::helical_bundle::parameters::OmegaBundleParameter::parse_setting_only(), and parse_setting_only().

void core::conformation::parametric::RealValuedParameter::set_default_value ( core::Real const & value_in )

Sets the initial value of this parameter, keeping the value_set_ boolean false.

Also sets default_value_.

References convert_angle(), correct_range(), default_value_, default_value_was_set_, value_, and core::conformation::parametric::Parameter::value_was_set().

void core::conformation::parametric::RealValuedParameter::set_input_is_angle_in_degrees ( bool const setting )

Set whether this parameter expects that its input is an angle in degrees.

Must be set before any values are set.

References default_value_was_set_, input_is_angle_in_degrees_, perturbation_set_, sampling_set_, and core::conformation::parametric::Parameter::value_was_set().

void core::conformation::parametric::RealValuedParameter::set_parameter_type ( ParameterType const type_in )

overridevirtual

Sets the parameter type.

Override is limited to real types.

Reimplemented from core::conformation::parametric::Parameter.

References correct_range(), core::conformation::parametric::PT_angle, core::conformation::parametric::PT_generic_nonnegative_valued_real, core::conformation::parametric::PT_generic_positive_valued_real, core::conformation::parametric::PT_generic_real, and core::conformation::parametric::Parameter::set_parameter_type().

void core::conformation::parametric::RealValuedParameter::set_perturbation_options	(	core::Real const &	pert_magnitude_in,
		std::string const &	pert_type_in
	)

Set the options for perturbing this parameter (with perturbation type set by string).

References perturbation_type_enum_from_string().

Referenced by parse_perturbation_options().

void core::conformation::parametric::RealValuedParameter::set_perturbation_options	(	core::Real const &	pert_magnitude_in,
		RealPerturbationType const	pert_type_in
	)

Set the options for perturbing this parameter (with perturbation type set by enum).

References convert_angle(), correct_range(), perturbation_magnitude_, perturbation_set_, perturbation_type_, core::conformation::parametric::Parameter::reset_copying_settings(), reset_sampling_and_perturbation_settings(), reset_value_settings(), and core::conformation::parametric::RPT_unknown_type.

void core::conformation::parametric::RealValuedParameter::set_perturbation_type ( std::string const & pert_type_in )

Set the perturbation type, by string.

Throws an error if not a valid type.

References perturbation_type_enum_from_string().

void core::conformation::parametric::RealValuedParameter::set_perturbation_type ( RealPerturbationType const pert_type_in )

Set the perturbation type, by enum.

Throws an error if invalid enum.

References perturbation_type_, and core::conformation::parametric::RPT_unknown_type.

void core::conformation::parametric::RealValuedParameter::set_sampling_options	(	core::Real const &	value_min_in,
		core::Real const &	value_max_in,
		core::Size const	samples_in
	)

Set the options for sampling this parameter.

References convert_angle(), correct_range(), core::conformation::parametric::Parameter::reset_copying_settings(), reset_sampling_and_perturbation_settings(), reset_value_settings(), sampling_set_, value_max_, value_min_, and value_samples_.

Referenced by parse_grid_sampling_options().

void core::conformation::parametric::RealValuedParameter::set_value	(	core::Real const &	value_in,
		bool const	ignore_use_degrees = `false`
	)

Set the value of this parameter.

If ignore_use_degrees is true, this will just set the value to the input value. Otherwise, it convert from degrees to radians if input_is_angle_in_degrees_ is true.