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protocols::helical_bundle::parameters::OmegaBundleParameter Class Reference

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

#include <OmegaBundleParameter.hh>

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

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: