Random perturbation, followed by minimization. More...

#include <PertMinMover.hh>

Inheritance diagram for protocols::minimization_packing::PertMinMover:

Public Member Functions
	PertMinMover ()

	PertMinMover (PertMinMover const &src)

	~PertMinMover () override

core::Real	pert_size () const

bool	uniform () const

bool	sc_only () const

core::select::residue_selector::ResidueSelectorCOP	residues () const

core::scoring::ScoreFunctionCOP	scorefxn () const

core::select::movemap::MoveMapFactoryCOP	movemap () const

void	pert_size (core::Real setting)

void	uniform (bool setting)

void	sc_only (bool setting)

void	residues (core::select::residue_selector::ResidueSelectorCOP setting)

void	scorefxn (core::scoring::ScoreFunctionCOP setting)

void	movemap_factory (core::select::movemap::MoveMapFactoryCOP setting)

void	apply (core::pose::Pose &pose) override
	Main Method. More...

void	pert (core::pose::Pose &pose, utility::vector1< bool > const &resi) const

void	min (core::pose::Pose &pose) const

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

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

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	parse XML tag (to use this Mover in Rosetta Scripts) More...

moves::MoverOP	fresh_instance () const override
	required in the context of the parser/scripting scheme More...

protocols::moves::MoverOP	clone () const override
	required in the context of the parser/scripting scheme 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 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...

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. 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 Attributes
core::Real	pert_size_
	The size of the random perturbation. More...

bool	uniform_
	Do a uniform perturbation (default is Gaussian) More...

bool	sc_only_
	Don't perturb the backbone coordinates. More...

core::select::residue_selector::ResidueSelectorCOP	residues_
	Only perturb the selected residues. More...

core::scoring::ScoreFunctionCOP	scorefxn_
	the score function to use in minimization More...

core::select::movemap::MoveMapFactoryCOP	movemap_factory_
	The movemap factory to be used in minimization. More...

Additional Inherited Members
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

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...

Detailed Description

Random perturbation, followed by minimization.

Constructor & Destructor Documentation

protocols::minimization_packing::PertMinMover::PertMinMover ( )

protocols::minimization_packing::PertMinMover::PertMinMover ( PertMinMover const & src )

default

protocols::minimization_packing::PertMinMover::~PertMinMover ( )

overridedefault

Member Function Documentation

void protocols::minimization_packing::PertMinMover::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References min(), pert(), residues_, scorefxn_, core::pose::Pose::total_residue(), and protocols::minimization_packing::TR().

protocols::moves::MoverOP protocols::minimization_packing::PertMinMover::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

moves::MoverOP protocols::minimization_packing::PertMinMover::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

std::string protocols::minimization_packing::PertMinMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

void protocols::minimization_packing::PertMinMover::min ( core::pose::Pose & pose ) const

References core::scoring::get_score_function(), movemap_factory_, core::optimization::CartesianMinimizer::run(), scorefxn(), and protocols::minimization_packing::TR().

Referenced by apply().

core::select::movemap::MoveMapFactoryCOP protocols::minimization_packing::PertMinMover::movemap ( ) const

inline

References movemap_factory_.

void protocols::minimization_packing::PertMinMover::movemap_factory ( core::select::movemap::MoveMapFactoryCOP setting )

inline

References movemap_factory_.

Referenced by parse_my_tag().

std::string protocols::minimization_packing::PertMinMover::mover_name ( )

static

Referenced by protocols::minimization_packing::PertMinMoverCreator::keyname(), and provide_xml_schema().

void protocols::minimization_packing::PertMinMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

parse XML tag (to use this Mover in Rosetta Scripts)

Reimplemented from protocols::moves::Mover.

References movemap_factory(), protocols::rosetta_scripts::parse_movemap_factory_legacy(), core::select::residue_selector::parse_residue_selector(), core::scoring::parse_score_function(), pert_size(), residues(), sc_only(), scorefxn(), and uniform().

void protocols::minimization_packing::PertMinMover::pert	(	core::pose::Pose &	pose,
		utility::vector1< bool > const &	resi
	)		const

References pert_size_, core::pose::Pose::residue(), sc_only_, core::pose::Pose::set_xyz(), core::pose::Pose::total_residue(), uniform_, and core::pose::Pose::xyz().

Referenced by apply().

core::Real protocols::minimization_packing::PertMinMover::pert_size ( ) const

inline

References pert_size_.

Referenced by parse_my_tag().

void protocols::minimization_packing::PertMinMover::pert_size ( core::Real setting )

inline

References pert_size_.

void protocols::minimization_packing::PertMinMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::rosetta_scripts::append_subelement_for_parse_movemap_factory_legacy(), protocols::rosetta_scripts::attributes_for_parse_residue_selector(), core::scoring::attributes_for_parse_score_function(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes_and_repeatable_subelements().

Referenced by protocols::minimization_packing::PertMinMoverCreator::provide_xml_schema().

core::select::residue_selector::ResidueSelectorCOP protocols::minimization_packing::PertMinMover::residues ( ) const

inline

References residues_.

Referenced by parse_my_tag().

void protocols::minimization_packing::PertMinMover::residues ( core::select::residue_selector::ResidueSelectorCOP setting )

inline

References residues_.

bool protocols::minimization_packing::PertMinMover::sc_only ( ) const

inline

References sc_only_.

Referenced by parse_my_tag().

void protocols::minimization_packing::PertMinMover::sc_only ( bool setting )

inline

References sc_only_.

core::scoring::ScoreFunctionCOP protocols::minimization_packing::PertMinMover::scorefxn ( ) const

inline

References scorefxn_.

Referenced by min(), and parse_my_tag().

void protocols::minimization_packing::PertMinMover::scorefxn ( core::scoring::ScoreFunctionCOP setting )

inline

References scorefxn_.

void protocols::minimization_packing::PertMinMover::show ( std::ostream & output = std::cout ) const

overridevirtual

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.

Reimplemented from protocols::moves::Mover.

References protocols::moves::Mover::show().

Referenced by protocols::minimization_packing::operator<<().

bool protocols::minimization_packing::PertMinMover::uniform ( ) const

inline

References uniform_.

Referenced by parse_my_tag().

void protocols::minimization_packing::PertMinMover::uniform ( bool setting )

inline

References uniform_.

Member Data Documentation

core::select::movemap::MoveMapFactoryCOP protocols::minimization_packing::PertMinMover::movemap_factory_

private

The movemap factory to be used in minimization.

Referenced by min(), movemap(), and movemap_factory().

core::Real protocols::minimization_packing::PertMinMover::pert_size_

private

The size of the random perturbation.

Referenced by pert(), and pert_size().

core::select::residue_selector::ResidueSelectorCOP protocols::minimization_packing::PertMinMover::residues_

private

Only perturb the selected residues.

Referenced by apply(), and residues().

bool protocols::minimization_packing::PertMinMover::sc_only_

private

Don't perturb the backbone coordinates.

Referenced by pert(), and sc_only().

core::scoring::ScoreFunctionCOP protocols::minimization_packing::PertMinMover::scorefxn_

private

the score function to use in minimization

Referenced by apply(), and scorefxn().

bool protocols::minimization_packing::PertMinMover::uniform_

private

Do a uniform perturbation (default is Gaussian)

Referenced by pert(), and uniform().

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

src/protocols/minimization_packing/PertMinMover.hh
src/protocols/minimization_packing/PertMinMover.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation