ParametrizationCalculator class, used for parametric backbone generation. More...

#include <ParametrizationCalculator.hh>

Inheritance diagram for core::conformation::parametric::ParametrizationCalculator:

Public Member Functions
	ParametrizationCalculator ()
	Constructor. More...

	ParametrizationCalculator (ParametersOP parameters)
	Constructor with input Parameters object. More...

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

	~ParametrizationCalculator () override=0
	Pure virtual destructor means don't instantiate this base class!. More...

virtual ParametrizationCalculatorOP	clone () const =0
	Copy this object ( allocate actual memory for it ) More...

ParametrizationCalculatorCOP	get_self_ptr () const
	self pointers More...

ParametrizationCalculatorOP	get_self_ptr ()

ParametrizationCalculatorCAP	get_self_weak_ptr () const

ParametrizationCalculatorAP	get_self_weak_ptr ()

ParametersCOP	parameters_cop () const
	Get a const-owning pointer to the Parameters object. More...

ParameterOP	parameter (core::Size const index)
	Access a parameter. More...

ParameterCOP	parameter_cop (core::Size const index) const
	Access a parameter. More...

RealValuedParameterOP	real_parameter (core::Size const index)
	Accesses a real-valued parameter. More...

RealVectorValuedParameterOP	realvector_parameter (core::Size const index)
	Accesses a realvector-valued parameter. More...

SizeValuedParameterOP	size_parameter (core::Size const index)
	Accesses a size-valued parameter. More...

SizeVectorValuedParameterOP	sizevector_parameter (core::Size const index)
	Accesses a sizevector-valued parameter. More...

BooleanValuedParameterOP	boolean_parameter (core::Size const index)
	Accesses a boolean-valued parameter. More...

RealValuedParameterCOP	real_parameter_cop (core::Size const index) const
	Accesses a real-valued parameter (const-access). More...

RealVectorValuedParameterCOP	realvector_parameter_cop (core::Size const index) const
	Accesses a realvector-valued parameter (const-access). More...

SizeValuedParameterCOP	size_parameter_cop (core::Size const index) const
	Accesses a size-valued parameter (const-access). More...

SizeVectorValuedParameterCOP	sizevector_parameter_cop (core::Size const index) const
	Accesses a sizevector-valued parameter (const-access). More...

BooleanValuedParameterCOP	boolean_parameter_cop (core::Size const index) const
	Accesses a boolean-valued parameter (const-access). More...

Protected Member Functions
void	add_parameter (std::string const &parameter_name, ParameterType type, std::string const &description, std::string const &short_description, std::string const &units, ParameterizationCalculatorProperties const &properties)
	Add a parameter to this calculator, automatically determining the type. More...

void	add_real_parameter (std::string const &parameter_name, ParameterType type, std::string const &description, std::string const &short_description, std::string const &units, ParameterizationCalculatorProperties const &properties)
	Add a real-valued parameter to this calculator. More...

void	add_realvector_parameter (std::string const &parameter_name, ParameterType type, std::string const &description, std::string const &short_description, std::string const &units, ParameterizationCalculatorProperties const &properties)
	Add a vector-valued parameter to this calculator. More...

void	add_size_parameter (std::string const &parameter_name, ParameterType type, std::string const &description, std::string const &short_description, std::string const &units, ParameterizationCalculatorProperties const &properties)
	Add a core::Size-valued parameter to this calculator. More...

void	add_sizevector_parameter (std::string const &parameter_name, ParameterType type, std::string const &description, std::string const &short_description, std::string const &units, ParameterizationCalculatorProperties const &properties)
	Add a integer vector-valued parameter to this calculator. More...

void	add_boolean_parameter (std::string const &parameter_name, ParameterType type, std::string const &description, std::string const &short_description, std::string const &units, ParameterizationCalculatorProperties const &properties)
	Add a Boolean-valued parameter to this calculator. More...

void	add_custom_parameter (std::string const &parameter_name, ParameterType const type, std::string const &description, std::string const &short_description, std::string const &units, ParameterizationCalculatorProperties const &properties, ParameterOP parameter_in)
	Add a custom parameter. More...

Private Member Functions
void	add_parameter (ParameterOP parameter_in)
	Add a parameter to this calculator. More...

Private Attributes
ParametersOP	parameters_
	The container of parameters that the user can twiddle given a particular parametrization. More...

Detailed Description

ParametrizationCalculator class, used for parametric backbone generation.

Constructor & Destructor Documentation

core::conformation::parametric::ParametrizationCalculator::ParametrizationCalculator ( )

Constructor.

core::conformation::parametric::ParametrizationCalculator::ParametrizationCalculator ( ParametersOP parameters )

Constructor with input Parameters object.

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

Copy constructor.

Deep-copies the stored parameters.

core::conformation::parametric::ParametrizationCalculator::~ParametrizationCalculator ( )

overridepure virtual

Pure virtual destructor means don't instantiate this base class!.

Counter-intuitively, C++ requires pure virtual destructors to be implemented.

Member Function Documentation

void core::conformation::parametric::ParametrizationCalculator::add_boolean_parameter	(	std::string const &	parameter_name,
		ParameterType	type,
		std::string const &	description,
		std::string const &	short_description,
		std::string const &	units,
		ParameterizationCalculatorProperties const &	properties
	)

protected

Add a Boolean-valued parameter to this calculator.

References add_parameter(), core::conformation::parametric::ParameterizationCalculatorProperties::can_be_copied, core::conformation::parametric::ParameterizationCalculatorProperties::can_be_perturbed, core::conformation::parametric::ParameterizationCalculatorProperties::can_be_sampled, core::conformation::parametric::ParameterizationCalculatorProperties::can_be_set, and core::conformation::parametric::ParameterizationCalculatorProperties::global_for_parameters_set.

Referenced by add_parameter().

void core::conformation::parametric::ParametrizationCalculator::add_custom_parameter	(	std::string const &	parameter_name,
		ParameterType const	type,
		std::string const &	description,
		std::string const &	short_description,
		std::string const &	units,
		ParameterizationCalculatorProperties const &	properties,
		ParameterOP	parameter_in
	)

protected

Add a custom parameter.

References add_parameter(), core::conformation::parametric::ParameterizationCalculatorProperties::can_be_copied, core::conformation::parametric::ParameterizationCalculatorProperties::can_be_perturbed, core::conformation::parametric::ParameterizationCalculatorProperties::can_be_sampled, core::conformation::parametric::ParameterizationCalculatorProperties::can_be_set, and core::conformation::parametric::ParameterizationCalculatorProperties::global_for_parameters_set.

Referenced by protocols::helical_bundle::BundleParametrizationCalculator::BundleParametrizationCalculator().

void core::conformation::parametric::ParametrizationCalculator::add_parameter	(	std::string const &	parameter_name,
		ParameterType	type,
		std::string const &	description,
		std::string const &	short_description,
		std::string const &	units,
		ParameterizationCalculatorProperties const &	properties
	)

protected

Add a parameter to this calculator, automatically determining the type.

Referenced by add_boolean_parameter(), add_custom_parameter(), add_real_parameter(), add_realvector_parameter(), add_size_parameter(), add_sizevector_parameter(), and protocols::helical_bundle::BundleParametrizationCalculator::BundleParametrizationCalculator().

void core::conformation::parametric::ParametrizationCalculator::add_parameter ( ParameterOP parameter_in )

private

Add a parameter to this calculator.

References parameters_.

void core::conformation::parametric::ParametrizationCalculator::add_real_parameter	(	std::string const &	parameter_name,
		ParameterType	type,
		std::string const &	description,
		std::string const &	short_description,
		std::string const &	units,
		ParameterizationCalculatorProperties const &	properties
	)

protected

Add a real-valued parameter to this calculator.

References add_parameter(), core::conformation::parametric::ParameterizationCalculatorProperties::can_be_copied, core::conformation::parametric::ParameterizationCalculatorProperties::can_be_perturbed, core::conformation::parametric::ParameterizationCalculatorProperties::can_be_sampled, core::conformation::parametric::ParameterizationCalculatorProperties::can_be_set, core::conformation::parametric::ParameterizationCalculatorProperties::global_for_parameters_set, and core::conformation::parametric::PT_generic_positive_valued_real.

Referenced by add_parameter().

void core::conformation::parametric::ParametrizationCalculator::add_realvector_parameter	(	std::string const &	parameter_name,
		ParameterType	type,
		std::string const &	description,
		std::string const &	short_description,
		std::string const &	units,
		ParameterizationCalculatorProperties const &	properties
	)

protected

Add a vector-valued parameter to this calculator.

References add_parameter(), core::conformation::parametric::ParameterizationCalculatorProperties::can_be_copied, core::conformation::parametric::ParameterizationCalculatorProperties::can_be_perturbed, core::conformation::parametric::ParameterizationCalculatorProperties::can_be_sampled, core::conformation::parametric::ParameterizationCalculatorProperties::can_be_set, core::conformation::parametric::ParameterizationCalculatorProperties::global_for_parameters_set, and core::conformation::parametric::PT_generic_positive_valued_real.

Referenced by add_parameter().

void core::conformation::parametric::ParametrizationCalculator::add_size_parameter	(	std::string const &	parameter_name,
		ParameterType	type,
		std::string const &	description,
		std::string const &	short_description,
		std::string const &	units,
		ParameterizationCalculatorProperties const &	properties
	)

protected

Add a core::Size-valued parameter to this calculator.

References add_parameter(), core::conformation::parametric::ParameterizationCalculatorProperties::can_be_copied, core::conformation::parametric::ParameterizationCalculatorProperties::can_be_perturbed, core::conformation::parametric::ParameterizationCalculatorProperties::can_be_sampled, core::conformation::parametric::ParameterizationCalculatorProperties::can_be_set, core::conformation::parametric::ParameterizationCalculatorProperties::global_for_parameters_set, and core::conformation::parametric::PT_generic_natural_number.

Referenced by add_parameter().

void core::conformation::parametric::ParametrizationCalculator::add_sizevector_parameter	(	std::string const &	parameter_name,
		ParameterType	type,
		std::string const &	description,
		std::string const &	short_description,
		std::string const &	units,
		ParameterizationCalculatorProperties const &	properties
	)

protected

Add a integer vector-valued parameter to this calculator.

References add_parameter(), core::conformation::parametric::ParameterizationCalculatorProperties::can_be_copied, core::conformation::parametric::ParameterizationCalculatorProperties::can_be_perturbed, core::conformation::parametric::ParameterizationCalculatorProperties::can_be_sampled, core::conformation::parametric::ParameterizationCalculatorProperties::can_be_set, core::conformation::parametric::ParameterizationCalculatorProperties::global_for_parameters_set, and core::conformation::parametric::PT_generic_natural_number_vector.

Referenced by add_parameter().

BooleanValuedParameterOP core::conformation::parametric::ParametrizationCalculator::boolean_parameter ( core::Size const index )

Accesses a boolean-valued parameter.

Returns nullptr if the parameter with the given index is not a BooleanValuedParameter.

References parameter().

Referenced by protocols::helical_bundle::BundleParametrizationCalculator::BundleParametrizationCalculator().

BooleanValuedParameterCOP core::conformation::parametric::ParametrizationCalculator::boolean_parameter_cop ( core::Size const index ) const

Accesses a boolean-valued parameter (const-access).

Returns nullptr if the parameter with the given index is not a BooleanValuedParameter.

References parameter_cop().

Referenced by protocols::helical_bundle::BundleParametrizationCalculator::build_helix().

virtual ParametrizationCalculatorOP core::conformation::parametric::ParametrizationCalculator::clone ( ) const

pure virtual

Copy this object ( allocate actual memory for it )

Must be implemented by derived classes.

Implemented in protocols::helical_bundle::BundleParametrizationCalculator.

ParametrizationCalculatorCOP core::conformation::parametric::ParametrizationCalculator::get_self_ptr ( ) const

inline

self pointers

ParametrizationCalculatorOP core::conformation::parametric::ParametrizationCalculator::get_self_ptr ( )

inline

ParametrizationCalculatorCAP core::conformation::parametric::ParametrizationCalculator::get_self_weak_ptr ( ) const

inline

ParametrizationCalculatorAP core::conformation::parametric::ParametrizationCalculator::get_self_weak_ptr ( )

inline

ParameterOP core::conformation::parametric::ParametrizationCalculator::parameter ( core::Size const index )

Access a parameter.

References parameters_.

Referenced by boolean_parameter(), protocols::helical_bundle::BundleParametrizationCalculator::BundleParametrizationCalculator(), protocols::helical_bundle::BundleParametrizationCalculator::copy_params_from_previous_helices_makebundlehelix_style(), protocols::helical_bundle::BundleParametrizationCalculator::copy_unset_params_from_globals(), real_parameter(), realvector_parameter(), size_parameter(), and sizevector_parameter().

ParameterCOP core::conformation::parametric::ParametrizationCalculator::parameter_cop ( core::Size const index ) const

Access a parameter.

Const-access

References parameters_.

Referenced by boolean_parameter_cop(), real_parameter_cop(), realvector_parameter_cop(), size_parameter_cop(), and sizevector_parameter_cop().

ParametersCOP core::conformation::parametric::ParametrizationCalculator::parameters_cop ( ) const

inline

Get a const-owning pointer to the Parameters object.

References parameters_.

Referenced by protocols::helical_bundle::BundleParametrizationCalculator::copy_params_from_previous_helices_makebundlehelix_style(), and protocols::helical_bundle::BundleParametrizationCalculator::copy_unset_params_from_globals().

RealValuedParameterOP core::conformation::parametric::ParametrizationCalculator::real_parameter ( core::Size const index )

Accesses a real-valued parameter.

Returns nullptr if the parameter with the given index is not a RealValuedParameter.

References parameter().

Referenced by protocols::helical_bundle::BundleParametrizationCalculator::BundleParametrizationCalculator(), protocols::helical_bundle::BundleParametrizationCalculator::init_from_file(), protocols::helical_bundle::BundleParametrizationCalculator::set_perturbation_type_globally(), and protocols::helical_bundle::BundleParametrizationCalculator::set_use_degrees_for_parameters().

RealValuedParameterCOP core::conformation::parametric::ParametrizationCalculator::real_parameter_cop ( core::Size const index ) const

Accesses a real-valued parameter (const-access).

Returns nullptr if the parameter with the given index is not a RealValuedParameter.

References parameter_cop().

Referenced by protocols::helical_bundle::BundleParametrizationCalculator::build_helix(), and protocols::helical_bundle::BundleParametrizationCalculator::repeats_per_turn().

RealVectorValuedParameterOP core::conformation::parametric::ParametrizationCalculator::realvector_parameter ( core::Size const index )

Accesses a realvector-valued parameter.

Accesses a vector-valued parameter.

Returns nullptr if the parameter with the given index is not a RealVectorValuedParameter.

References parameter().

Referenced by protocols::helical_bundle::BundleParametrizationCalculator::init_from_file().

RealVectorValuedParameterCOP core::conformation::parametric::ParametrizationCalculator::realvector_parameter_cop ( core::Size const index ) const

Accesses a realvector-valued parameter (const-access).

Returns nullptr if the parameter with the given index is not a RealVectorValuedParameter.

References parameter_cop().

Referenced by protocols::helical_bundle::BundleParametrizationCalculator::build_helix().

SizeValuedParameterOP core::conformation::parametric::ParametrizationCalculator::size_parameter ( core::Size const index )

Accesses a size-valued parameter.

Returns nullptr if the parameter with the given index is not a SizeValuedParameter.

References parameter().

Referenced by protocols::helical_bundle::BundleParametrizationCalculator::init_from_file().

SizeValuedParameterCOP core::conformation::parametric::ParametrizationCalculator::size_parameter_cop ( core::Size const index ) const

Accesses a size-valued parameter (const-access).

Returns nullptr if the parameter with the given index is not a SizeValuedParameter.

References parameter_cop().

Referenced by protocols::helical_bundle::BundleParametrizationCalculator::build_helix(), and protocols::helical_bundle::BundleParametrizationCalculator::residues_per_repeat().

SizeVectorValuedParameterOP core::conformation::parametric::ParametrizationCalculator::sizevector_parameter ( core::Size const index )

Accesses a sizevector-valued parameter.

Returns nullptr if the parameter with the given index is not a SizeVectorValuedParameter.

References parameter().

Referenced by protocols::helical_bundle::BundleParametrizationCalculator::init_from_file().

SizeVectorValuedParameterCOP core::conformation::parametric::ParametrizationCalculator::sizevector_parameter_cop ( core::Size const index ) const

Accesses a sizevector-valued parameter (const-access).

Returns nullptr if the parameter with the given index is not a SizeVectorValuedParameter.

References parameter_cop().

Referenced by protocols::helical_bundle::BundleParametrizationCalculator::build_helix().

Member Data Documentation

ParametersOP core::conformation::parametric::ParametrizationCalculator::parameters_

private

The container of parameters that the user can twiddle given a particular parametrization.

Referenced by add_parameter(), parameter(), parameter_cop(), and parameters_cop().

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

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

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation