BundleParametrizationCalculator class, used for parametric helical bundle backbone generation. More...

#include <BundleParametrizationCalculator.hh>

Inheritance diagram for protocols::helical_bundle::BundleParametrizationCalculator:

[legend]

Public Types
typedef core::conformation::parametric::ParameterizationCalculatorProperties	ParameterizationCalculatorProperties

Public Member Functions
	BundleParametrizationCalculator (bool const use_degrees=false)
	constructors More...

	BundleParametrizationCalculator (bool const use_degrees, protocols::helical_bundle::parameters::BundleParametersCOP params_in)
	Params constructor. More...

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

	~BundleParametrizationCalculator () override
	Destructor. More...

core::conformation::parametric::ParametrizationCalculatorOP	clone () const override
	Copy this object ( allocate actual memory for it ) More...

void	init_from_file (std::string const &filename)
	Read a Crick params file and initialize this calculator. More...

void	copy_unset_params_from_globals (BundleParametrizationCalculatorCOP global_calculator)
	Copy the parameter values for parameters that have not been set from the global parameters. More...

bool	copy_params_from_previous_helices_makebundlehelix_style (core::pose::Pose const &prev_helices_pose)
	Copy the parameter values for parameters that copy values from previous helices, from the previous helices. More...

bool	build_helix (core::pose::Pose &pose) const
	Attempts to build a helix based on the current Crick parameters. More...

bool	build_helix (core::pose::Pose &pose, core::Size const helix_start, core::Size const helix_end) const
	Attempts to build a helix based on the current Crick parameters. More...

void	set_use_degrees (bool const setting)
	Set whether this calculator uses degrees or radians for the user-set angles. More...

bool	use_degrees () const
	Get whether this calculator expects input in degrees or radians for user-set angles. More...

void	set_perturbation_type_globally (std::string const &perturbation_type_in)
	Set the perturbation type for all parameters. More...

core::Size	repeats_per_turn () const
	Get the number of repeats needed to go one full turn. More...

core::Size	residues_per_repeat () const
	The number of residues per repeating unit. More...

core::Size	residues_per_turn () const
	The number of residues needed for one full turn. More...

Public Member Functions inherited from core::conformation::parametric::ParametrizationCalculator
	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...

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...

Static Public Member Functions
static bool	copy_params_from_previous_helices_perturbbundle_style (parameters::BundleParametersSetCOP paramset, core::Size const copy_from_helix_index, BPC_Parameters const parameter_type, core::conformation::parametric::RealValuedParameterOP parameter_to_copy_to, protocols::helical_bundle::parameters::BundleParametersCOP current_helix_params)
	Copy the parameter values for parameters that copy values from previous helices, from the previous helices. More...

static core::conformation::parametric::ParameterType	parameter_type_from_enum (BPC_Parameters param_enum)
	Get the parameter type from the BPC_Parameters enum. More...

static std::string const &	parameter_description_from_enum (BPC_Parameters param_enum)
	Given a BPC_Parameters enum, get a short lay-language description (used for annotating output) of the parameter. More...

static std::string const &	short_parameter_description_from_enum (BPC_Parameters param_type)
	Get the short parameter name from the BPC_Parameters enum. More...

static std::string const &	parameter_units_from_enum (BPC_Parameters param_type)
	Get the parameter units from the BPC_Parameters enum. More...

static ParameterizationCalculatorProperties const &	parameter_properties_from_enum (BPC_Parameters param_enum)
	Given a BPC_Parameters enum, get whether this parameter is one that the user can set, whether it can be sampled, whether it can be perturbed, and whether it's global for a ParametersSet (helical bundle). More...

static std::string const &	parameter_name_from_enum (BPC_Parameters param_type)
	Get the parameter name from the BPC_Parameters enum. More...

static BPC_Parameters	parameter_enum_from_name (std::string const &name)
	Get the BPC_Parameters enum from the parameter name. More...

Private Member Functions
void	set_use_degrees_for_parameters ()
	Update whether certain parameters expect their inputs in degrees. More...

Private Attributes
bool	use_degrees_

Additional Inherited Members
Protected Member Functions inherited from core::conformation::parametric::ParametrizationCalculator
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...

Detailed Description

BundleParametrizationCalculator class, used for parametric helical bundle backbone generation.

Member Typedef Documentation

◆ ParameterizationCalculatorProperties

typedef core::conformation::parametric::ParameterizationCalculatorProperties protocols::helical_bundle::BundleParametrizationCalculator::ParameterizationCalculatorProperties

Constructor & Destructor Documentation

◆ BundleParametrizationCalculator() [1/3]

protocols::helical_bundle::BundleParametrizationCalculator::BundleParametrizationCalculator ( bool const use_degrees = false )

constructors

Constructor.

References core::conformation::parametric::ParametrizationCalculator::add_custom_parameter(), core::conformation::parametric::ParametrizationCalculator::add_parameter(), core::conformation::parametric::ParametrizationCalculator::boolean_parameter(), protocols::helical_bundle::BPC_end_of_list, protocols::helical_bundle::BPC_epsilon, protocols::helical_bundle::BPC_omega0, protocols::helical_bundle::BPC_set_bondangles, protocols::helical_bundle::BPC_set_bondlengths, protocols::helical_bundle::BPC_set_dihedrals, core::conformation::parametric::ParametrizationCalculator::parameter(), parameter_description_from_enum(), parameter_name_from_enum(), parameter_properties_from_enum(), parameter_type_from_enum(), parameter_units_from_enum(), core::conformation::parametric::ParametrizationCalculator::real_parameter(), set_use_degrees_for_parameters(), and short_parameter_description_from_enum().

◆ BundleParametrizationCalculator() [2/3]

protocols::helical_bundle::BundleParametrizationCalculator::BundleParametrizationCalculator	(	bool const	use_degrees,
		protocols::helical_bundle::parameters::BundleParametersCOP	params_in
	)

Params constructor.

◆ BundleParametrizationCalculator() [3/3]

protocols::helical_bundle::BundleParametrizationCalculator::BundleParametrizationCalculator ( BundleParametrizationCalculator const & src )

Copy constructor.

Deep-copies the stored parameters.

Deep-copies the stored parameters (by calling the copy constructor of the base class).

◆ ~BundleParametrizationCalculator()

protocols::helical_bundle::BundleParametrizationCalculator::~BundleParametrizationCalculator ( )

override

Destructor.

Member Function Documentation

◆ build_helix() [1/2]

bool protocols::helical_bundle::BundleParametrizationCalculator::build_helix ( core::pose::Pose & pose ) const

Attempts to build a helix based on the current Crick parameters.

Returns true for FAILURE and false for SUCCESS. The object "pose" is replaced with a new helix if this operation succeeds.

References core::pose::Pose::total_residue().

Referenced by protocols::helical_bundle::PerturbBundleHelix::apply().

◆ build_helix() [2/2]

bool protocols::helical_bundle::BundleParametrizationCalculator::build_helix	(	core::pose::Pose &	pose,
		core::Size const	helix_start,
		core::Size const	helix_end
	)		const

Attempts to build a helix based on the current Crick parameters.

Returns true for FAILURE and false for SUCCESS. The object "pose" is replaced with a new helix if this operation succeeds.

Note: This version takes parameters for the start and end of the helix.

◆ clone()

core::conformation::parametric::ParametrizationCalculatorOP protocols::helical_bundle::BundleParametrizationCalculator::clone ( ) const

overridevirtual

Copy this object ( allocate actual memory for it )

Implements core::conformation::parametric::ParametrizationCalculator.

◆ copy_params_from_previous_helices_makebundlehelix_style()

bool protocols::helical_bundle::BundleParametrizationCalculator::copy_params_from_previous_helices_makebundlehelix_style ( core::pose::Pose const & prev_helices_pose )

Copy the parameter values for parameters that copy values from previous helices, from the previous helices.

This function should be called before build_helix().

Note: This function assumes that the input pose consists only of previous helices, and stores N ParametersSet objects for N helices, each with 1 Parameters object contained.

Returns: Returns true for failure, false for success.

This function should be called before build_helix().

Returns: Returns true for failure, false for success.

References protocols::helical_bundle::BPC_end_of_list, core::pose::Pose::conformation(), core::conformation::Conformation::n_parameters_sets(), core::conformation::parametric::ParametrizationCalculator::parameter(), and core::conformation::Conformation::parameters_set().

◆ copy_params_from_previous_helices_perturbbundle_style()

bool protocols::helical_bundle::BundleParametrizationCalculator::copy_params_from_previous_helices_perturbbundle_style	(	parameters::BundleParametersSetCOP	paramset,
		core::Size const	copy_from_helix_index,
		BPC_Parameters const	parameter_type,
		core::conformation::parametric::RealValuedParameterOP	parameter_to_copy_to,
		protocols::helical_bundle::parameters::BundleParametersCOP	current_helix_params
	)

static

Copy the parameter values for parameters that copy values from previous helices, from the previous helices.

This function should be called before build_helix().

Note: This function assumes that the input pose is the whole shebang passed to the PerturbBundle mover. Unlike copy_params_from_previous_helices_makebundlehelix_style(), this functon does not modify the BundleParametrizationCalculator. Instead it copies the parameter value for the given parameter from the indicated previous helix to the indicated parameter object.

Returns: Returns true for failure, false for success.

Referenced by protocols::helical_bundle::PerturbBundle::perturb_values().

◆ copy_unset_params_from_globals()

void protocols::helical_bundle::BundleParametrizationCalculator::copy_unset_params_from_globals ( BundleParametrizationCalculatorCOP global_calculator )

Copy the parameter values for parameters that have not been set from the global parameters.

This function should be called before build_helix().

References protocols::helical_bundle::BPC_end_of_list, and core::conformation::parametric::ParametrizationCalculator::parameter().

◆ init_from_file()

void protocols::helical_bundle::BundleParametrizationCalculator::init_from_file ( std::string const & filename )

Read a Crick params file and initialize this calculator.

Triggers a read from disk!

◆ parameter_description_from_enum()

std::string const & protocols::helical_bundle::BundleParametrizationCalculator::parameter_description_from_enum ( BPC_Parameters param_enum )

static

Given a BPC_Parameters enum, get a short lay-language description (used for annotating output) of the parameter.

Returns "INVALID!!!" if invalid.

Referenced by BundleParametrizationCalculator().

◆ parameter_enum_from_name()

BPC_Parameters protocols::helical_bundle::BundleParametrizationCalculator::parameter_enum_from_name ( std::string const & name )

static

Get the BPC_Parameters enum from the parameter name.

Returns BPC_unknown_parameter if this can't be parsed.

References protocols::helical_bundle::BPC_end_of_list, protocols::helical_bundle::BPC_unknown_parameter, and parameter_name_from_enum().

◆ parameter_name_from_enum()

std::string const & protocols::helical_bundle::BundleParametrizationCalculator::parameter_name_from_enum ( BPC_Parameters param_type )

static

Get the parameter name from the BPC_Parameters enum.

Referenced by protocols::helical_bundle::BundleGridSampler::apply(), BundleParametrizationCalculator(), protocols::helical_bundle::BundleGridSamplerHelper::DoF_name(), and parameter_enum_from_name().

◆ parameter_properties_from_enum()

core::conformation::parametric::ParameterizationCalculatorProperties const & protocols::helical_bundle::BundleParametrizationCalculator::parameter_properties_from_enum ( BPC_Parameters param_enum )

static

Given a BPC_Parameters enum, get whether this parameter is one that the user can set, whether it can be sampled, whether it can be perturbed, and whether it's global for a ParametersSet (helical bundle).

Referenced by BundleParametrizationCalculator().

◆ parameter_type_from_enum()

core::conformation::parametric::ParameterType protocols::helical_bundle::BundleParametrizationCalculator::parameter_type_from_enum ( BPC_Parameters param_enum )

static

Get the parameter type from the BPC_Parameters enum.

Returns PT_invalid_type if invalid.

Referenced by BundleParametrizationCalculator().

◆ parameter_units_from_enum()

std::string const & protocols::helical_bundle::BundleParametrizationCalculator::parameter_units_from_enum ( BPC_Parameters param_type )

static

Get the parameter units from the BPC_Parameters enum.

Given a BPC_Parameters enum, units for the parameter.

Referenced by BundleParametrizationCalculator().

◆ repeats_per_turn()

core::Size protocols::helical_bundle::BundleParametrizationCalculator::repeats_per_turn ( ) const

Get the number of repeats needed to go one full turn.

This is rounded UP. So for an alpha helix, with about 3.6 repeating units (residues) per turn, this function returns 4.

References protocols::helical_bundle::BPC_omega1, and core::conformation::parametric::ParametrizationCalculator::real_parameter_cop().

Referenced by residues_per_turn().

◆ residues_per_repeat()

core::Size protocols::helical_bundle::BundleParametrizationCalculator::residues_per_repeat ( ) const

The number of residues per repeating unit.

References protocols::helical_bundle::BPC_residues_per_repeat, and core::conformation::parametric::ParametrizationCalculator::size_parameter_cop().

Referenced by init_from_file(), and residues_per_turn().

◆ residues_per_turn()

core::Size protocols::helical_bundle::BundleParametrizationCalculator::residues_per_turn ( ) const

The number of residues needed for one full turn.

This is repeats_per_turn() * residues_per_repeat().

References repeats_per_turn(), and residues_per_repeat().

◆ set_perturbation_type_globally()

void protocols::helical_bundle::BundleParametrizationCalculator::set_perturbation_type_globally ( std::string const & perturbation_type_in )

Set the perturbation type for all parameters.

References protocols::helical_bundle::BPC_last_parameter_to_be_sampled, core::conformation::parametric::RealValuedParameter::perturbation_type_enum_from_string(), core::conformation::parametric::ParametrizationCalculator::real_parameter(), and core::conformation::parametric::RPT_unknown_type.

◆ set_use_degrees()

void protocols::helical_bundle::BundleParametrizationCalculator::set_use_degrees ( bool const setting )

Set whether this calculator uses degrees or radians for the user-set angles.

Defaults to radians (false).

References set_use_degrees_for_parameters(), and use_degrees_.

◆ set_use_degrees_for_parameters()

void protocols::helical_bundle::BundleParametrizationCalculator::set_use_degrees_for_parameters ( )

private

Update whether certain parameters expect their inputs in degrees.

References protocols::helical_bundle::BPC_delta_omega0, protocols::helical_bundle::BPC_delta_omega1, protocols::helical_bundle::BPC_omega0, core::conformation::parametric::ParametrizationCalculator::real_parameter(), and use_degrees_.

Referenced by BundleParametrizationCalculator(), and set_use_degrees().

◆ short_parameter_description_from_enum()

std::string const & protocols::helical_bundle::BundleParametrizationCalculator::short_parameter_description_from_enum ( BPC_Parameters param_enum )

static

Get the short parameter name from the BPC_Parameters enum.

Given a BPC_Parameters enum, get a one- or two-word lay-language description (used for annotating output) of the parameter.

Returns "INVALID!!!" if invalid.

Referenced by BundleParametrizationCalculator().

◆ use_degrees()

bool protocols::helical_bundle::BundleParametrizationCalculator::use_degrees ( ) const

inline

Get whether this calculator expects input in degrees or radians for user-set angles.

References use_degrees_.

Member Data Documentation

◆ use_degrees_

bool protocols::helical_bundle::BundleParametrizationCalculator::use_degrees_

private

Referenced by set_use_degrees(), set_use_degrees_for_parameters(), and use_degrees().

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

src/protocols/helical_bundle/BundleParametrizationCalculator.hh
src/protocols/helical_bundle/BundleParametrizationCalculator.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ ParameterizationCalculatorProperties

Constructor & Destructor Documentation

◆ BundleParametrizationCalculator() [1/3]

◆ BundleParametrizationCalculator() [2/3]

◆ BundleParametrizationCalculator() [3/3]

◆ ~BundleParametrizationCalculator()

Member Function Documentation

◆ build_helix() [1/2]

◆ build_helix() [2/2]

◆ clone()

◆ copy_params_from_previous_helices_makebundlehelix_style()

◆ copy_params_from_previous_helices_perturbbundle_style()

◆ copy_unset_params_from_globals()

◆ init_from_file()

◆ parameter_description_from_enum()

◆ parameter_enum_from_name()

◆ parameter_name_from_enum()

◆ parameter_properties_from_enum()

◆ parameter_type_from_enum()

◆ parameter_units_from_enum()

◆ repeats_per_turn()

◆ residues_per_repeat()

◆ residues_per_turn()

◆ set_perturbation_type_globally()

◆ set_use_degrees()

◆ set_use_degrees_for_parameters()

◆ short_parameter_description_from_enum()

◆ use_degrees()

Member Data Documentation

◆ use_degrees_