Parameter class, used to store a single parameter for parametric backbone generation. More...

#include <Parameter.hh>

Inheritance diagram for core::conformation::parametric::Parameter:

Public Member Functions
	Parameter ()
	constructors More...

virtual ParameterOP	clone () const =0
	Make a copy of this object ( allocate actual memory for it ) 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...

virtual void	set_parameter_type (ParameterType const type_in)
	Set the parameter type. 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 bool	copy_value_from_parameter (ParameterCOP other_parameter, ParametersCOP other_parameter_collection, ParametersCOP this_parameter_collection)=0
	Given another parameter of the same type, copy its value. This does not set value_set_ to true. More...

virtual void	parse_setting (utility::tag::TagCOP tag, bool const parse_setting, bool const parse_grid_sampling, bool const parse_perturbation, bool const parse_copying)=0
	Given a tag, parse out the setting for this parameter. More...

virtual 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 =0
	Return the XSD information for this parameter. More...

virtual void	reset_sampling_and_perturbation_settings ()=0
	Reset the sampling and perturbation options before storing this Parameter object in a parametric Conformation. More...

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

virtual void	reset_value_settings ()=0
	Reset the value settings for this Parameter object. More...

Protected Member Functions
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 Attributes
std::string	parameter_name_
	The name of the parameter (e.g. "r0", "omega0", etc.) More...

std::string	parameter_description_
	Parameter description. More...

std::string	short_parameter_description_
	A shorter, lay-language descriptoin used for annotating user output. Should be a word or two, with the first word captialized. More...

std::string	parameter_units_
	A word or two for the units. Defaults to "dimensionless". More...

ParameterType	parameter_type_
	The type of data associated with the parameter (e.g. generic real, angle, integer, boolean). More...

bool	can_be_set_
	Is this parameter one that can be set directly by the user? More...

bool	can_be_copied_
	Is this parameter one that can be copied from another parameter? More...

bool	can_be_sampled_
	Is this parameter one that can be sampled? More...

bool	can_be_perturbed_
	Is this parameter one that can be perturbed? More...

bool	global_for_parameters_set_
	Is this a parameter that is intended to be global for a ParametersSet? More...

std::string	copy_suffix_
	A string appended to the parameter name for options related to copying the parameter value. More...

core::Size	copy_from_parameters_index_
	Index of the Parameters object from which we should copy this parameter's value. More...

bool	value_set_
	Was the value set? More...

Detailed Description

Parameter class, used to store a single parameter for parametric backbone generation.

Constructor & Destructor Documentation

core::conformation::parametric::Parameter::Parameter ( )

constructors

Constructor.

Member Function Documentation

bool core::conformation::parametric::Parameter::can_be_copied ( ) const

inline

Is this parameter one that can be copied from another parameter?

Default true.

References can_be_copied_.

Referenced by set_can_be_set_sampled_perturbed_copied().

bool core::conformation::parametric::Parameter::can_be_perturbed ( ) const

inline

Is this parameter one that can be perturbed?

Default true. If false, it must be read from the database, e.g. from a Crick parameters file.

References can_be_perturbed_.

Referenced by set_can_be_set_sampled_perturbed_copied().

bool core::conformation::parametric::Parameter::can_be_sampled ( ) const

inline

Is this parameter one that can be sampled?

Default true. If false, it must be read from the database, e.g. from a Crick parameters file.

References can_be_sampled_.

Referenced by set_can_be_set_sampled_perturbed_copied().

bool core::conformation::parametric::Parameter::can_be_set ( ) const

inline

Is this parameter one that can be set directly by the user?

Default true. If false, it must be read from the database, e.g. from a Crick parameters file.

References can_be_set_.

Referenced by set_can_be_set_sampled_perturbed_copied().

virtual ParameterOP core::conformation::parametric::Parameter::clone ( ) const

pure virtual

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

Implemented in core::conformation::parametric::RealValuedParameter, core::conformation::parametric::BooleanValuedParameter, core::conformation::parametric::RealVectorValuedParameter, core::conformation::parametric::SizeValuedParameter, core::conformation::parametric::SizeVectorValuedParameter, and protocols::helical_bundle::parameters::OmegaBundleParameter.

core::Size core::conformation::parametric::Parameter::copy_from_parameters_index ( ) const

inline

Get the index of the Parameters object from which we will copy this parameter's value.

A setting of zero means no copying.

References copy_from_parameters_index_.

std::string const& core::conformation::parametric::Parameter::copy_suffix ( ) const

inline

Get the suffix for the copy tag (e.g. "copies_helix" in the case of helical bundles).

Does not include the leading underscore.

References copy_suffix_.

Referenced by protocols::helical_bundle::parameters::OmegaBundleParameter::parse_setting_only(), core::conformation::parametric::RealValuedParameter::parse_setting_only(), core::conformation::parametric::RealValuedParameter::provide_xsd_copying_information(), and core::conformation::parametric::RealValuedParameter::set_copy_information().

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

pure virtual

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

Must be implemented by derived classes. Type checking can be performed by derived classes.

Returns TRUE for failure and FALSE for success.

Implemented in core::conformation::parametric::RealValuedParameter, core::conformation::parametric::BooleanValuedParameter, core::conformation::parametric::RealVectorValuedParameter, core::conformation::parametric::SizeValuedParameter, core::conformation::parametric::SizeVectorValuedParameter, and protocols::helical_bundle::parameters::OmegaBundleParameter.

bool core::conformation::parametric::Parameter::copying_information_was_set ( ) const

inline

Has the copying information been set?

References copy_from_parameters_index_.

ParameterCOP core::conformation::parametric::Parameter::get_self_ptr ( ) const

inline

Self pointers (const shared pointer).

ParameterOP core::conformation::parametric::Parameter::get_self_ptr ( )

inline

Self pointers (nonconst shared pointer).

ParameterCAP core::conformation::parametric::Parameter::get_self_weak_ptr ( ) const

inline

Self pointers (const weak pointer).

ParameterAP core::conformation::parametric::Parameter::get_self_weak_ptr ( )

inline

Self pointers (nonconst weak pointer).

bool core::conformation::parametric::Parameter::global_for_parameters_set ( ) const

inline

Get whether this property is meant to be global for a parameters set.

References global_for_parameters_set_.

std::string const& core::conformation::parametric::Parameter::parameter_description ( ) const

inline

Get parameter description.

This is a lay-language description used for annotating user output. It should be a short phrase with no capitals.

References parameter_description_.

Referenced by core::conformation::parametric::BooleanValuedParameter::provide_xsd_information(), core::conformation::parametric::SizeVectorValuedParameter::provide_xsd_information(), core::conformation::parametric::SizeValuedParameter::provide_xsd_information(), core::conformation::parametric::RealVectorValuedParameter::provide_xsd_information(), and core::conformation::parametric::RealValuedParameter::provide_xsd_setting_information().

std::string const& core::conformation::parametric::Parameter::parameter_name ( ) const

inline

Get parameter name.

References parameter_name_.

ParameterType core::conformation::parametric::Parameter::parameter_type ( ) const

inline

Get the parameter type.

References parameter_type_.

Referenced by core::conformation::parametric::SizeValuedParameter::correct_range(), core::conformation::parametric::SizeVectorValuedParameter::correct_range(), core::conformation::parametric::RealValuedParameter::correct_range(), core::conformation::parametric::RealVectorValuedParameter::correct_values(), core::conformation::parametric::RealValuedParameter::generate_perturbed_value(), core::conformation::parametric::SizeVectorValuedParameter::provide_xsd_information(), and core::conformation::parametric::SizeValuedParameter::provide_xsd_information().

std::string const& core::conformation::parametric::Parameter::parameter_units ( ) const

inline

Get units.

References parameter_units_.

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

pure virtual

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. If parse_copying is true, this parses options for copying. Note that, if multiple options are true an error should be thrown if more than one of these is provided.

Note: Must be implemented by derived classes.

Implemented in core::conformation::parametric::RealValuedParameter, core::conformation::parametric::RealVectorValuedParameter, core::conformation::parametric::BooleanValuedParameter, core::conformation::parametric::SizeValuedParameter, and core::conformation::parametric::SizeVectorValuedParameter.

virtual void core::conformation::parametric::Parameter::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

pure virtual

Return the XSD information for this parameter.

Note: Must be implemented by derived classes.

Implemented in core::conformation::parametric::RealValuedParameter, core::conformation::parametric::RealVectorValuedParameter, core::conformation::parametric::BooleanValuedParameter, core::conformation::parametric::SizeValuedParameter, core::conformation::parametric::SizeVectorValuedParameter, and protocols::helical_bundle::parameters::OmegaBundleParameter.

void core::conformation::parametric::Parameter::reset_copying_settings ( )

virtual

Reset the copying options.

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

References copy_from_parameters_index_.

Referenced by core::conformation::parametric::RealValuedParameter::parse_setting_only(), core::conformation::parametric::RealValuedParameter::set_perturbation_options(), and core::conformation::parametric::RealValuedParameter::set_sampling_options().

virtual void core::conformation::parametric::Parameter::reset_sampling_and_perturbation_settings ( )

pure virtual

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

Pure virtual. Must be implemented by derived classes.

Implemented in core::conformation::parametric::RealValuedParameter, core::conformation::parametric::RealVectorValuedParameter, core::conformation::parametric::BooleanValuedParameter, core::conformation::parametric::SizeValuedParameter, and core::conformation::parametric::SizeVectorValuedParameter.

Referenced by set_copy_from_parameters_index().

virtual void core::conformation::parametric::Parameter::reset_value_settings ( )

pure virtual

Reset the value settings for this Parameter object.

Pure virtual. Must be implemented by derived classes.

Implemented in core::conformation::parametric::RealValuedParameter, core::conformation::parametric::RealVectorValuedParameter, core::conformation::parametric::BooleanValuedParameter, core::conformation::parametric::SizeValuedParameter, and core::conformation::parametric::SizeVectorValuedParameter.

Referenced by set_copy_from_parameters_index().

void core::conformation::parametric::Parameter::reset_value_was_set ( )

inlineprotected

Allows derived classes to indicate that the value has not been set.

References value_set_.

Referenced by core::conformation::parametric::BooleanValuedParameter::reset_value_settings(), core::conformation::parametric::SizeVectorValuedParameter::reset_value_settings(), core::conformation::parametric::SizeValuedParameter::reset_value_settings(), core::conformation::parametric::RealVectorValuedParameter::reset_value_settings(), and core::conformation::parametric::RealValuedParameter::reset_value_settings().

void core::conformation::parametric::Parameter::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.

Default true in all cases. If setting is false, the parameter value must be read from the database, e.g. from a Crick parameters file.

References can_be_copied(), can_be_copied_, can_be_perturbed(), can_be_perturbed_, can_be_sampled(), can_be_sampled_, can_be_set(), and can_be_set_.

Referenced by core::conformation::parametric::BooleanValuedParameter::BooleanValuedParameter(), core::conformation::parametric::RealValuedParameter::RealValuedParameter(), core::conformation::parametric::RealVectorValuedParameter::RealVectorValuedParameter(), core::conformation::parametric::SizeValuedParameter::SizeValuedParameter(), and core::conformation::parametric::SizeVectorValuedParameter::SizeVectorValuedParameter().

void core::conformation::parametric::Parameter::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.

A setting of zero means no copying.

References copy_from_parameters_index_, reset_sampling_and_perturbation_settings(), and reset_value_settings().

Referenced by core::conformation::parametric::RealValuedParameter::set_copy_information(), and protocols::helical_bundle::parameters::OmegaBundleParameter::set_pitch_copying_information().

void core::conformation::parametric::Parameter::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).

The leading underscore should be omitted.

References copy_suffix_.

void core::conformation::parametric::Parameter::set_global_for_parameters_set ( bool const setting )

Set whether this property is meant to be global for a parameters set.

References global_for_parameters_set_.

void core::conformation::parametric::Parameter::set_parameter_description ( std::string const & description_in )

Set parameter description.

This is a lay-language description used for annotating user output. It should be a short phrase with no capitals.

References parameter_description_.

void core::conformation::parametric::Parameter::set_parameter_name ( std::string const & name_in )

Set parameter name.

References parameter_name_.

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

virtual

Set the parameter type.

Reimplemented in core::conformation::parametric::RealValuedParameter, core::conformation::parametric::BooleanValuedParameter, core::conformation::parametric::RealVectorValuedParameter, core::conformation::parametric::SizeValuedParameter, and core::conformation::parametric::SizeVectorValuedParameter.

References parameter_type_.

void core::conformation::parametric::Parameter::set_parameter_units ( std::string const & units_in )

Set parameter units.

References parameter_units_.

void core::conformation::parametric::Parameter::set_short_parameter_description ( std::string const & short_description_in )

Set short parameter description.

This is a one or two word lay-language description used for annotating user output. The first word should be capitalized.

References short_parameter_description_.

void core::conformation::parametric::Parameter::set_value_was_set ( )

inlineprotected

Allows derived classes to indicate that the value has been set.

References value_set_.

Referenced by core::conformation::parametric::BooleanValuedParameter::set_value(), core::conformation::parametric::SizeVectorValuedParameter::set_value(), core::conformation::parametric::SizeValuedParameter::set_value(), core::conformation::parametric::RealVectorValuedParameter::set_value(), and core::conformation::parametric::RealValuedParameter::set_value().

std::string const& core::conformation::parametric::Parameter::short_parameter_description ( ) const

inline

Get short parameter description.

This is a one or two word lay-language description used for annotating user output. The first word should be capitalized.

References short_parameter_description_.

bool core::conformation::parametric::Parameter::value_was_set ( ) const

inline

Has the value been set?

References value_set_.

Referenced by core::conformation::parametric::BooleanValuedParameter::set_default_value(), core::conformation::parametric::RealVectorValuedParameter::set_default_value(), core::conformation::parametric::SizeValuedParameter::set_default_value(), core::conformation::parametric::SizeVectorValuedParameter::set_default_value(), core::conformation::parametric::RealValuedParameter::set_default_value(), and core::conformation::parametric::RealValuedParameter::set_input_is_angle_in_degrees().

Member Data Documentation

bool core::conformation::parametric::Parameter::can_be_copied_

private

Is this parameter one that can be copied from another parameter?

Default true.

Referenced by can_be_copied(), and set_can_be_set_sampled_perturbed_copied().

bool core::conformation::parametric::Parameter::can_be_perturbed_

private

Is this parameter one that can be perturbed?

Default true.

Referenced by can_be_perturbed(), and set_can_be_set_sampled_perturbed_copied().

bool core::conformation::parametric::Parameter::can_be_sampled_

private

Is this parameter one that can be sampled?

Default true.

Referenced by can_be_sampled(), and set_can_be_set_sampled_perturbed_copied().

bool core::conformation::parametric::Parameter::can_be_set_

private

Is this parameter one that can be set directly by the user?

Default true. If false, it must be read from the database, e.g. from a Crick parameters file.

Referenced by can_be_set(), and set_can_be_set_sampled_perturbed_copied().

core::Size core::conformation::parametric::Parameter::copy_from_parameters_index_

private

Index of the Parameters object from which we should copy this parameter's value.

Referenced by copy_from_parameters_index(), copying_information_was_set(), reset_copying_settings(), and set_copy_from_parameters_index().

std::string core::conformation::parametric::Parameter::copy_suffix_

private

A string appended to the parameter name for options related to copying the parameter value.

For example, "copies_helix" in the case of parametric helices.

Referenced by copy_suffix(), and set_copy_suffix().

bool core::conformation::parametric::Parameter::global_for_parameters_set_

private

Is this a parameter that is intended to be global for a ParametersSet?

Default false.

Referenced by global_for_parameters_set(), and set_global_for_parameters_set().

std::string core::conformation::parametric::Parameter::parameter_description_

private

Parameter description.

This is a lay-language description used for annotating user output. It should be a short phrase with no capitals.

Referenced by parameter_description(), and set_parameter_description().

std::string core::conformation::parametric::Parameter::parameter_name_

private

The name of the parameter (e.g. "r0", "omega0", etc.)

Referenced by parameter_name(), and set_parameter_name().

ParameterType core::conformation::parametric::Parameter::parameter_type_

private

The type of data associated with the parameter (e.g. generic real, angle, integer, boolean).

Referenced by parameter_type(), and set_parameter_type().

std::string core::conformation::parametric::Parameter::parameter_units_

private

A word or two for the units. Defaults to "dimensionless".

Referenced by parameter_units(), and set_parameter_units().

std::string core::conformation::parametric::Parameter::short_parameter_description_

private

A shorter, lay-language descriptoin used for annotating user output. Should be a word or two, with the first word captialized.

Referenced by set_short_parameter_description(), and short_parameter_description().

bool core::conformation::parametric::Parameter::value_set_

private

Was the value set?

Referenced by reset_value_was_set(), set_value_was_set(), and value_was_set().

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

src/core/conformation/parametric/Parameter.hh
src/core/conformation/parametric/Parameter.cc

Public Member Functions

Protected Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation