#include <PerturbBundle.hh>

Inheritance diagram for protocols::helical_bundle::PerturbBundle:

[legend]

Public Types
typedef core::conformation::parametric::Parameters	Parameters

typedef core::conformation::parametric::ParametersOP	ParametersOP

typedef core::conformation::parametric::ParametersSet	ParametersSet

typedef core::conformation::parametric::ParametersSetOP	ParametersSetOP

typedef protocols::helical_bundle::parameters::BundleParameters	BundleParameters

typedef protocols::helical_bundle::parameters::BundleParametersOP	BundleParametersOP

typedef protocols::helical_bundle::parameters::BundleParametersCOP	BundleParametersCOP

typedef protocols::helical_bundle::parameters::BundleParametersSet	BundleParametersSet

typedef protocols::helical_bundle::parameters::BundleParametersSetOP	BundleParametersSetOP

typedef protocols::helical_bundle::parameters::BundleParametersSetCOP	BundleParametersSetCOP

Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef std::list< std::string >	Strings

Public Member Functions
	PerturbBundle ()
	Creator for PerturbBundle mover. More...

	PerturbBundle (PerturbBundle const &src)
	Copy constructor for PerturbBundle mover. More...

	~PerturbBundle () override
	Destructor for PerturbBundle mover. More...

protocols::moves::MoverOP	clone () const override
	Clone operator to create a pointer to a fresh PerturbBundle object that copies this one. More...

protocols::moves::MoverOP	fresh_instance () const override
	Fresh_instance operator to create a pointer to a fresh PerturbBundle object that does NOT copy this one. More...

void	apply (core::pose::Pose &pose) override
	Actually apply the mover to the pose. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	parse XML (specifically in the context of the parser/Rosetta_scripting scheme) More...

void	set_bundleparametersset_index (core::Size const val)
	Set which bundle parameters set will be used, if more than one is defined in the pose's Conformation object. More...

core::Size	bundleparametersset_index () const
	Returns a value indicating which bundle parameters set will be used, if more than one is defined in the pose's Conformation object. More...

void	reset_helices ()
	Clear the list of helices. More...

BundleParametrizationCalculatorOP	add_helix (core::Size const helix_index)
	Add options for a new helix. More...

BundleParametrizationCalculatorCOP	default_calculator_cop () const
	Access the default calculator (const access). More...

BundleParametrizationCalculatorOP	default_calculator ()
	Access the default calculator (nonconst access). More...

BundleParametrizationCalculatorCOP	individual_helix_calculator_cop (core::Size const helix_calculator_index) const
	Access the calculator for a given helix (const access). More...

BundleParametrizationCalculatorOP	individual_helix_calculator (core::Size const helix_calculator_index)
	Access the calculator for a given helix (nonconst access). More...

core::Size	n_helices () const
	Get the number of individual helices that have been configured (which is not necessarily the number of helices in the pose, since we might only be perturbing a subset). More...

std::string	get_name () const override
	Each derived class must specify its name. The class name. More...

void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
	Provide the citation. More...

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

virtual core::Real	last_proposal_density_ratio ()

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	Overload this static method if you access options within the mover. More...

Private Member Functions
bool	helix_not_defined (core::Size const helix_index) const
	Confirms that a helix has not yet been defined. Returns "true" if the helix has NOT been defined, false otherwise. More...

BundleParametrizationCalculatorCOP	get_calculator_for_helix (core::Size const helix_index) const
	Get a calculator for a particular helix. More...

bool	perturb_values (BundleParametersSetOP params_set) const
	Perturb the helical bundle parameter values in the pose, subject to the options already set. More...

void	rebuild_conformation (core::pose::Pose &pose, BundleParametersSetOP params_set, core::Size const params_set_index, bool &failed) const
	Rebuild the helical bundle conformation using the bundle parameter values in the pose. More...

void	write_report (BundleParametersSetOP params_set, bool const before) const
	Write out the perturbed Crick parameters. More...

Private Attributes
BundleParametrizationCalculatorOP	default_calculator_
	The BundleParametrizationCalculator object that will be used for setting up default parameters. More...

utility::vector1< std::pair< core::Size, BundleParametrizationCalculatorOP > >	individual_helix_calculators_
	The BundleParametrizationCalculator objects for individual helices. Cloned from the default calculator. More...

core::Size	bundleparametersset_index_
	Which set of bundle parameters (if there exists more than one) should the mover alter? More...

Additional Inherited Members
Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Member Typedef Documentation

◆ BundleParameters

typedef protocols::helical_bundle::parameters::BundleParameters protocols::helical_bundle::PerturbBundle::BundleParameters

◆ BundleParametersCOP

typedef protocols::helical_bundle::parameters::BundleParametersCOP protocols::helical_bundle::PerturbBundle::BundleParametersCOP

◆ BundleParametersOP

typedef protocols::helical_bundle::parameters::BundleParametersOP protocols::helical_bundle::PerturbBundle::BundleParametersOP

◆ BundleParametersSet

typedef protocols::helical_bundle::parameters::BundleParametersSet protocols::helical_bundle::PerturbBundle::BundleParametersSet

◆ BundleParametersSetCOP

typedef protocols::helical_bundle::parameters::BundleParametersSetCOP protocols::helical_bundle::PerturbBundle::BundleParametersSetCOP

◆ BundleParametersSetOP

typedef protocols::helical_bundle::parameters::BundleParametersSetOP protocols::helical_bundle::PerturbBundle::BundleParametersSetOP

◆ Parameters

typedef core::conformation::parametric::Parameters protocols::helical_bundle::PerturbBundle::Parameters

◆ ParametersOP

typedef core::conformation::parametric::ParametersOP protocols::helical_bundle::PerturbBundle::ParametersOP

◆ ParametersSet

typedef core::conformation::parametric::ParametersSet protocols::helical_bundle::PerturbBundle::ParametersSet

◆ ParametersSetOP

typedef core::conformation::parametric::ParametersSetOP protocols::helical_bundle::PerturbBundle::ParametersSetOP

Constructor & Destructor Documentation

◆ PerturbBundle() [1/2]

protocols::helical_bundle::PerturbBundle::PerturbBundle ( )

Creator for PerturbBundle mover.

◆ PerturbBundle() [2/2]

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

Copy constructor for PerturbBundle mover.

References individual_helix_calculators_.

◆ ~PerturbBundle()

protocols::helical_bundle::PerturbBundle::~PerturbBundle ( )

overridedefault

Destructor for PerturbBundle mover.

Member Function Documentation

◆ add_helix()

BundleParametrizationCalculatorOP protocols::helical_bundle::PerturbBundle::add_helix ( core::Size const helix_index )

Add options for a new helix.

Return value is a smart pointer to the BundleParametrizationCalculator for the new helix, cloned from the default_calculator_.

References default_calculator_, helix_not_defined(), and individual_helix_calculators_.

Referenced by parse_my_tag().

◆ apply()

void protocols::helical_bundle::PerturbBundle::apply ( core::pose::Pose & pose )

overridevirtual

Actually apply the mover to the pose.

Implements protocols::moves::Mover.

References bundleparametersset_index(), core::pose::Pose::conformation(), core::conformation::Conformation::n_parameters_sets(), core::conformation::Conformation::parameters_set(), perturb_values(), rebuild_conformation(), protocols::helical_bundle::TR(), and write_report().

◆ bundleparametersset_index()

core::Size protocols::helical_bundle::PerturbBundle::bundleparametersset_index ( ) const

inline

Returns a value indicating which bundle parameters set will be used, if more than one is defined in the pose's Conformation object.

A value of n indicates that the nth bundle paramets set encountered will be perturbed.

References bundleparametersset_index_.

Referenced by apply().

◆ clone()

protocols::moves::MoverOP protocols::helical_bundle::PerturbBundle::clone ( ) const

overridevirtual

Clone operator to create a pointer to a fresh PerturbBundle object that copies this one.

Reimplemented from protocols::moves::Mover.

◆ default_calculator()

BundleParametrizationCalculatorOP protocols::helical_bundle::PerturbBundle::default_calculator ( )

inline

Access the default calculator (nonconst access).

References default_calculator_.

Referenced by provide_xml_schema().

◆ default_calculator_cop()

BundleParametrizationCalculatorCOP protocols::helical_bundle::PerturbBundle::default_calculator_cop ( ) const

inline

Access the default calculator (const access).

References default_calculator_.

◆ fresh_instance()

protocols::moves::MoverOP protocols::helical_bundle::PerturbBundle::fresh_instance ( ) const

overridevirtual

Fresh_instance operator to create a pointer to a fresh PerturbBundle object that does NOT copy this one.

Reimplemented from protocols::moves::Mover.

◆ get_calculator_for_helix()

BundleParametrizationCalculatorCOP protocols::helical_bundle::PerturbBundle::get_calculator_for_helix ( core::Size const helix_index ) const

private

Get a calculator for a particular helix.

Returns nullptr if no calculator for this helix has been defined.

References individual_helix_calculators_.

Referenced by perturb_values().

◆ get_name()

std::string protocols::helical_bundle::PerturbBundle::get_name ( ) const

overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

References mover_name().

◆ helix_not_defined()

bool protocols::helical_bundle::PerturbBundle::helix_not_defined ( core::Size const helix_index ) const

private

Confirms that a helix has not yet been defined. Returns "true" if the helix has NOT been defined, false otherwise.

References individual_helix_calculators_.

Referenced by add_helix().

◆ individual_helix_calculator()

BundleParametrizationCalculatorOP protocols::helical_bundle::PerturbBundle::individual_helix_calculator ( core::Size const helix_calculator_index )

Access the calculator for a given helix (nonconst access).

References individual_helix_calculators_.

◆ individual_helix_calculator_cop()

BundleParametrizationCalculatorCOP protocols::helical_bundle::PerturbBundle::individual_helix_calculator_cop ( core::Size const helix_calculator_index ) const

Access the calculator for a given helix (const access).

References individual_helix_calculators_.

◆ mover_name()

std::string protocols::helical_bundle::PerturbBundle::mover_name ( )

static

Referenced by get_name(), protocols::helical_bundle::PerturbBundleCreator::keyname(), and provide_xml_schema().

◆ n_helices()

core::Size protocols::helical_bundle::PerturbBundle::n_helices ( ) const

inline

Get the number of individual helices that have been configured (which is not necessarily the number of helices in the pose, since we might only be perturbing a subset).

References individual_helix_calculators_.

Referenced by perturb_values().

◆ parse_my_tag()

void protocols::helical_bundle::PerturbBundle::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

parse XML (specifically in the context of the parser/Rosetta_scripting scheme)

Reimplemented from protocols::moves::Mover.

References add_helix(), protocols::helical_bundle::BPC_last_parameter_to_be_sampled, default_calculator_, reset_helices(), and protocols::helical_bundle::TR().

◆ perturb_values()

bool protocols::helical_bundle::PerturbBundle::perturb_values ( BundleParametersSetOP params_set ) const

private

Perturb the helical bundle parameter values in the pose, subject to the options already set.

Called by the apply() function. Returns true for success, false for failure.

References protocols::helical_bundle::BPC_delta_omega0, protocols::helical_bundle::BPC_last_parameter_to_be_sampled, protocols::helical_bundle::BundleParametrizationCalculator::copy_params_from_previous_helices_perturbbundle_style(), default_calculator_, get_calculator_for_helix(), n_helices(), and protocols::helical_bundle::TR().

Referenced by apply().

◆ provide_citation_info()

void protocols::helical_bundle::PerturbBundle::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

Provide the citation.

Reimplemented from protocols::moves::Mover.

◆ provide_xml_schema()

void protocols::helical_bundle::PerturbBundle::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::helical_bundle::BPC_end_of_list, default_calculator(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes_and_repeatable_subelements().

Referenced by protocols::helical_bundle::PerturbBundleCreator::provide_xml_schema().

◆ rebuild_conformation()

void protocols::helical_bundle::PerturbBundle::rebuild_conformation	(	core::pose::Pose &	pose,
		BundleParametersSetOP	params_set,
		core::Size const	params_set_index,
		bool &	failed
	)		const

private

Rebuild the helical bundle conformation using the bundle parameter values in the pose.

References protocols::helical_bundle::PerturbBundleHelix::apply(), protocols::helical_bundle::PerturbBundleHelix::last_apply_failed(), protocols::helical_bundle::PerturbBundleHelix::set_parameters_index(), and protocols::helical_bundle::PerturbBundleHelix::set_parameters_set_index().

Referenced by apply().

◆ reset_helices()

void protocols::helical_bundle::PerturbBundle::reset_helices ( )

Clear the list of helices.

Clears the individual_helix_calculators_ list.

References individual_helix_calculators_.

Referenced by parse_my_tag().

◆ set_bundleparametersset_index()

void protocols::helical_bundle::PerturbBundle::set_bundleparametersset_index ( core::Size const val )

inline

Set which bundle parameters set will be used, if more than one is defined in the pose's Conformation object.

A value of n indicates that the nth bundle paramets set encountered will be perturbed.

References bundleparametersset_index_, and protocols::hybridization::val.

◆ write_report()

void protocols::helical_bundle::PerturbBundle::write_report	(	BundleParametersSetOP	params_set,
		bool const	before
	)		const

private

Write out the perturbed Crick parameters.

The "before" parameter determines whether this is a pre-perturbation report or a post-perturbation report.

References protocols::helical_bundle::TR().

Referenced by apply().

Member Data Documentation

◆ bundleparametersset_index_

core::Size protocols::helical_bundle::PerturbBundle::bundleparametersset_index_

private

Which set of bundle parameters (if there exists more than one) should the mover alter?

Defaults to 1. Higher values indicate the nth set encountered in the ParametersSet list.

Referenced by bundleparametersset_index(), and set_bundleparametersset_index().

◆ default_calculator_

BundleParametrizationCalculatorOP protocols::helical_bundle::PerturbBundle::default_calculator_

private

The BundleParametrizationCalculator object that will be used for setting up default parameters.

Referenced by add_helix(), default_calculator(), default_calculator_cop(), parse_my_tag(), and perturb_values().

◆ individual_helix_calculators_

utility::vector1< std::pair< core::Size, BundleParametrizationCalculatorOP > > protocols::helical_bundle::PerturbBundle::individual_helix_calculators_

private

The BundleParametrizationCalculator objects for individual helices. Cloned from the default calculator.

Referenced by add_helix(), get_calculator_for_helix(), helix_not_defined(), individual_helix_calculator(), individual_helix_calculator_cop(), n_helices(), PerturbBundle(), and reset_helices().

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

src/protocols/helical_bundle/PerturbBundle.hh
src/protocols/helical_bundle/PerturbBundle.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ BundleParameters

◆ BundleParametersCOP

◆ BundleParametersOP

◆ BundleParametersSet

◆ BundleParametersSetCOP

◆ BundleParametersSetOP

◆ Parameters

◆ ParametersOP

◆ ParametersSet

◆ ParametersSetOP

Constructor & Destructor Documentation

◆ PerturbBundle() [1/2]

◆ PerturbBundle() [2/2]

◆ ~PerturbBundle()

Member Function Documentation

◆ add_helix()

◆ apply()

◆ bundleparametersset_index()

◆ clone()

◆ default_calculator()

◆ default_calculator_cop()

◆ fresh_instance()

◆ get_calculator_for_helix()

◆ get_name()

◆ helix_not_defined()

◆ individual_helix_calculator()

◆ individual_helix_calculator_cop()

◆ mover_name()

◆ n_helices()

◆ parse_my_tag()

◆ perturb_values()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ rebuild_conformation()

◆ reset_helices()

◆ set_bundleparametersset_index()

◆ write_report()

Member Data Documentation

◆ bundleparametersset_index_

◆ default_calculator_

◆ individual_helix_calculators_