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core::conformation::parametric::Parameter Class Referenceabstract

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

#include <Parameter.hh>

Inheritance diagram for core::conformation::parametric::Parameter:
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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
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
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
std::string const& core::conformation::parametric::Parameter::parameter_name ( ) const
inline
ParameterType core::conformation::parametric::Parameter::parameter_type ( ) const
inline
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
void core::conformation::parametric::Parameter::reset_copying_settings ( )
virtual
virtual void core::conformation::parametric::Parameter::reset_sampling_and_perturbation_settings ( )
pure virtual
virtual void core::conformation::parametric::Parameter::reset_value_settings ( )
pure virtual
void core::conformation::parametric::Parameter::reset_value_was_set ( )
inlineprotected
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 
)
void core::conformation::parametric::Parameter::set_copy_from_parameters_index ( core::Size const  setting)
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
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
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

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: