A class for the omega paremeter, derived from the generic RealValuedParameter class. More...

#include <OmegaBundleParameter.hh>

Inheritance diagram for protocols::helical_bundle::parameters::OmegaBundleParameter:

Public Member Functions
	OmegaBundleParameter ()
	Default constructor. More...

	OmegaBundleParameter (OmegaBundleParameter const &src)
	Copy constructor. More...

	~OmegaBundleParameter () override

core::conformation::parametric::ParameterOP	clone () const override
	Clone operator. More...

bool	copy_value_from_parameter (core::conformation::parametric::ParameterCOP other_parameter, core::conformation::parametric::ParametersCOP other_parameter_collection, core::conformation::parametric::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	set_copies_pitch (bool const setting)
	Set whether we're copying pitch (true) or the twist per residue (false). More...

bool	copies_pitch () const
	Get whether we're copying pitch (true) or the twist per residue (false). 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_copying_settings () override
	Reset the copying options. More...

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

	RealValuedParameter (RealValuedParameter const &src)

	~RealValuedParameter () override

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...

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	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...

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

Protected Member Functions inherited from core::conformation::parametric::RealValuedParameter
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...

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
bool	copy_pitch_from_parameter (core::conformation::parametric::ParameterCOP other_parameter, core::conformation::parametric::ParametersCOP other_parameter_collection, core::conformation::parametric::ParametersCOP this_parameter_collection)
	Given another parameter of the same type, copy its pitch. This does not set value_set_ to true. More...

void	set_pitch_copying_information (utility::tag::TagCOP tag)
	Given a tag, parse out "pitch_from_helix" lines and configure this parameter accordingly. More...

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

Private Attributes
bool	pitch_copying_mode_
	When copying, do we copy pitch (true) or value (false)? More...

Additional Inherited Members
Static Public Member Functions inherited from core::conformation::parametric::RealValuedParameter
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...

Detailed Description

A class for the omega paremeter, derived from the generic RealValuedParameter class.

Omega has a few additional options that can be configured, for pitch-copying vs. value-copying.

Constructor & Destructor Documentation

protocols::helical_bundle::parameters::OmegaBundleParameter::OmegaBundleParameter ( )

Default constructor.

protocols::helical_bundle::parameters::OmegaBundleParameter::OmegaBundleParameter ( OmegaBundleParameter const & src )

Copy constructor.

protocols::helical_bundle::parameters::OmegaBundleParameter::~OmegaBundleParameter ( )

overridedefault

Destructor

Member Function Documentation

core::conformation::parametric::ParameterOP protocols::helical_bundle::parameters::OmegaBundleParameter::clone ( ) const

overridevirtual

Clone operator.

Make a copy of this object and return a smart pointer to the copy.

Reimplemented from core::conformation::parametric::RealValuedParameter.

bool protocols::helical_bundle::parameters::OmegaBundleParameter::copies_pitch ( ) const

inline

Get whether we're copying pitch (true) or the twist per residue (false).

References pitch_copying_mode_.

bool protocols::helical_bundle::parameters::OmegaBundleParameter::copy_pitch_from_parameter	(	core::conformation::parametric::ParameterCOP	other_parameter,
		core::conformation::parametric::ParametersCOP	other_parameter_collection,
		core::conformation::parametric::ParametersCOP	this_parameter_collection
	)

private

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

Performs type checking in debug mode.

Returns: Returns TRUE for failure, FALSE for success.

References protocols::helical_bundle::BPC_omega0, protocols::helical_bundle::BPC_r0, protocols::helical_bundle::BPC_z1, core::conformation::parametric::RealValuedParameter::set_value_sneakily(), protocols::helical_bundle::parameters::TR(), and core::conformation::parametric::RealValuedParameter::value().

Referenced by copy_value_from_parameter().

bool protocols::helical_bundle::parameters::OmegaBundleParameter::copy_value_from_parameter	(	core::conformation::parametric::ParameterCOP	other_parameter,
		core::conformation::parametric::ParametersCOP	other_parameter_collection,
		core::conformation::parametric::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. Note that this version has options for copying pitch or copying the value directly.

Returns: Returns TRUE for failure, FALSE for success.

Reimplemented from core::conformation::parametric::RealValuedParameter.

References copy_pitch_from_parameter(), core::conformation::parametric::RealValuedParameter::copy_value_from_parameter(), and pitch_copying_mode_.

bool protocols::helical_bundle::parameters::OmegaBundleParameter::parse_setting_only	(	utility::tag::TagCOP	tag,
		bool const	parse_copying_too
	)

overrideprotectedvirtual

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 from core::conformation::parametric::RealValuedParameter.

References core::conformation::parametric::Parameter::copy_suffix(), core::conformation::parametric::Parameter::parameter_name(), set_copies_pitch(), core::conformation::parametric::RealValuedParameter::set_copy_information(), set_pitch_copying_information(), and core::conformation::parametric::RealValuedParameter::set_value().

void protocols::helical_bundle::parameters::OmegaBundleParameter::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.

Calls the equivalent function for RealValuedParameter, then adds additional settings for pitch copying.

Note: Must be implemented by derived classes.

Reimplemented from core::conformation::parametric::RealValuedParameter.

References core::conformation::parametric::RealValuedParameter::provide_xsd_information(), and provide_xsd_pitch_copying_information().

void protocols::helical_bundle::parameters::OmegaBundleParameter::provide_xsd_pitch_copying_information ( utility::tag::AttributeList & xsd ) const

private

Return the XSD information for copying the pitch value for this parameter from another.

Return the XSD information for copying this parameter from another.

Referenced by provide_xsd_information().

void protocols::helical_bundle::parameters::OmegaBundleParameter::reset_copying_settings ( )

overridevirtual

Reset the copying options.

This version resets pitch_copying_mode_, and calls the parent reset_copying_settings() function.

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

References pitch_copying_mode_.

void protocols::helical_bundle::parameters::OmegaBundleParameter::set_copies_pitch ( bool const setting )

inline

Set whether we're copying pitch (true) or the twist per residue (false).

References pitch_copying_mode_.

Referenced by parse_setting_only(), and set_pitch_copying_information().

void protocols::helical_bundle::parameters::OmegaBundleParameter::set_pitch_copying_information ( utility::tag::TagCOP tag )

private

Given a tag, parse out "pitch_from_helix" lines and configure this parameter accordingly.

Parse copy information from the tag, and set it.

References core::conformation::parametric::RealValuedParameter::reset_sampling_and_perturbation_settings(), core::conformation::parametric::RealValuedParameter::reset_value_settings(), set_copies_pitch(), and core::conformation::parametric::Parameter::set_copy_from_parameters_index().

Referenced by parse_setting_only().

Member Data Documentation

bool protocols::helical_bundle::parameters::OmegaBundleParameter::pitch_copying_mode_

private

When copying, do we copy pitch (true) or value (false)?

Referenced by copies_pitch(), copy_value_from_parameter(), reset_copying_settings(), and set_copies_pitch().

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

src/protocols/helical_bundle/parameters/OmegaBundleParameter.hh
src/protocols/helical_bundle/parameters/OmegaBundleParameter.cc

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation