#include <DEEROptimizeCoordsMover.hh>

Inheritance diagram for protocols::simple_moves::DEEROptimizeCoordsMover:

[legend]

Public Member Functions
	DEEROptimizeCoordsMover ()
	Default constructor. More...

	~DEEROptimizeCoordsMover () override
	Default constructor. More...

moves::MoverOP	clone () const override
	Makes a new, identical version of itself. More...

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

std::map< PairSizeString, utility::vector1< PseudoSL > >	init_coords (core::pose::Pose &pose, core::scoring::epr_deer::DEERDataCache const &datacache)
	Initializes coords used throughout method. More...

std::map< ResPair, std::map< SizePair, utility::vector1< core::Real > > >	init_data (std::map< PairSizeString, utility::vector1< PseudoSL > > const &default_coords, core::scoring::epr_deer::DEERDataCache &datacache)
	Initializes the data saved in the Mover. More...

CoordModel	init_model (std::map< PairSizeString, utility::vector1< PseudoSL > > const &coords, core::scoring::epr_deer::DEERDataCache &datacache)
	Initialize and run the optimization procedure. More...

void	initial_search (CoordModel &model, core::Real &resolution, std::map< ResPair, std::map< SizePair, utility::vector1< core::Real > > > const &trace_map, core::scoring::epr_deer::DEERDataCache &datacache)
	Performs an initial search (for non-3D backgrounds) More...

core::Real	minimize (CoordModel &model, core::Real &resolution, std::map< ResPair, std::map< SizePair, utility::vector1< core::Real > > > const &trace_map, core::scoring::epr_deer::DEERDataCache &datacache)
	Minimizes the model to fit the data. More...

bool	boltzmann (core::Real const &diff, core::Real const &temp=1.0) const

void	normalize (CoordModel &model, PairSizeString const &res=std::make_pair(0, "")) const
	Recursive function to normalize the weights of a model. More...

core::Real	score (CoordModel const &coords, std::map< ResPair, std::map< SizePair, utility::vector1< core::Real > > > const &trace_map, core::scoring::epr_deer::DEERDataCache &datacache, bool const print=false)

void	print_coords (CoordModel const &model, std::map< PairSizeString, utility::vector1< PseudoSL > > const &default_coords, core::Real const &current_score, core::scoring::epr_deer::DEERDataCache &datacache, std::map< ResPair, std::map< SizePair, utility::vector1< core::Real > > > const &trace_map, core::pose::Pose &pose)

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

std::string	mover_name () const

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

void	parse_my_tag (utility::tag::TagCOP, basic::datacache::DataMap &) override
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

std::string	keyname () const

moves::MoverOP	create_mover () const

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

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...

virtual MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. 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...

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...

Private Types
using	PairSizeString = std::pair< core::Size, std::string >

using	ResPair = std::pair< PairSizeString, PairSizeString >

using	SizePair = std::pair< core::Size, core::Size >

using	PseudoSL = std::pair< numeric::xyzVector< core::Real >, core::Real >

using	CoordModel = std::map< PairSizeString, utility::vector1< core::Real > >

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

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...

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

◆ CoordModel

using protocols::simple_moves::DEEROptimizeCoordsMover::CoordModel = std::map< PairSizeString, utility::vector1< core::Real > >

private

◆ PairSizeString

using protocols::simple_moves::DEEROptimizeCoordsMover::PairSizeString = std::pair< core::Size, std::string >

private

◆ PseudoSL

using protocols::simple_moves::DEEROptimizeCoordsMover::PseudoSL = std::pair< numeric::xyzVector< core::Real >, core::Real >

private

◆ ResPair

using protocols::simple_moves::DEEROptimizeCoordsMover::ResPair = std::pair< PairSizeString, PairSizeString >

private

◆ SizePair

using protocols::simple_moves::DEEROptimizeCoordsMover::SizePair = std::pair< core::Size, core::Size >

private

Constructor & Destructor Documentation

◆ DEEROptimizeCoordsMover()

protocols::simple_moves::DEEROptimizeCoordsMover::DEEROptimizeCoordsMover ( )

Default constructor.

◆ ~DEEROptimizeCoordsMover()

protocols::simple_moves::DEEROptimizeCoordsMover::~DEEROptimizeCoordsMover ( )

override

Default constructor.

Member Function Documentation

◆ apply()

void protocols::simple_moves::DEEROptimizeCoordsMover::apply ( core::pose::Pose & pose )

overridevirtual

Main function.

Parameters

pose	Input pose to be modified (in this case it isn't)

Implements protocols::moves::Mover.

References core::scoring::epr_deer::DEERDataCache::clone(), core::pose::Pose::data(), core::pose::datacache::CacheableDataType::EPR_DEER_DATA, core::scoring::epr_deer::DEERDataCache::fetch_and_organize_data(), and protocols::antibody::design::minimize.

◆ boltzmann()

bool protocols::simple_moves::DEEROptimizeCoordsMover::boltzmann	(	core::Real const &	diff,
		core::Real const &	temp = `1.0`
	)		const

◆ clone()

moves::MoverOP protocols::simple_moves::DEEROptimizeCoordsMover::clone ( ) const

overridevirtual

Makes a new, identical version of itself.

Reimplemented from protocols::moves::Mover.

◆ create_mover()

moves::MoverOP protocols::simple_moves::DEEROptimizeCoordsMover::create_mover ( ) const

◆ get_name()

std::string protocols::simple_moves::DEEROptimizeCoordsMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

◆ init_coords()

std::map< PairSizeString, utility::vector1< PseudoSL > > protocols::simple_moves::DEEROptimizeCoordsMover::init_coords	(	core::pose::Pose &	pose,
		core::scoring::epr_deer::DEERDataCache const &	datacache
	)

Initializes coords used throughout method.

Parameters

pose	Pose being labeled

Returns: Coords that pass clash evaluation

References core::scoring::epr_deer::EPRSpinLabel::cutoff(), core::scoring::epr_deer::EPRSpinLabel::label(), core::scoring::epr_deer::DEERDataCache::labeled_residues(), and core::pose::Pose::update_residue_neighbors().

◆ init_data()

std::map< DEEROptimizeCoordsMover::ResPair, std::map< DEEROptimizeCoordsMover::SizePair, utility::vector1< core::Real > > > protocols::simple_moves::DEEROptimizeCoordsMover::init_data	(	std::map< PairSizeString, utility::vector1< PseudoSL > > const &	default_coords,
		core::scoring::epr_deer::DEERDataCache &	datacache
	)

Initializes the data saved in the Mover.

Parameters

pose	Pose being modified
datacache	Datacache @detail ResPair is std::pair< PairSizeString, PairSizeString > @detail PairSizeString is std::pair< core::Size, std::string > @detail SizePair is std::pair< core::Size, core::Size > @detail Map used: data[ resPair ][ std::make_pair( res1_id, res2_id ) ]

References core::scoring::epr_deer::metrics::DEERData::bins_per_a(), core::sequence::end, core::scoring::gauss, core::scoring::epr_deer::DEERDataCache::indices(), protocols::hybridization::r1, protocols::hybridization::r2, protocols::noesy_assign::round(), protocols::loops::start, and protocols::analysis::total.

◆ init_model()

DEEROptimizeCoordsMover::CoordModel protocols::simple_moves::DEEROptimizeCoordsMover::init_model	(	std::map< PairSizeString, utility::vector1< PseudoSL > > const &	coords,
		core::scoring::epr_deer::DEERDataCache &	datacache
	)

Initialize and run the optimization procedure.

Parameters

start_resolution	Starting resolution for modifications
end_resolution	End resolution for modifications

Returns: Best coordinate model obtained (by sum of squared residuals)

References protocols::simple_filters::coords(), and core::scoring::epr_deer::DEERDataCache::labeled_residues().

◆ initial_search()

void protocols::simple_moves::DEEROptimizeCoordsMover::initial_search	(	CoordModel &	model,
		core::Real &	resolution,
		std::map< ResPair, std::map< SizePair, utility::vector1< core::Real > > > const &	trace_map,
		core::scoring::epr_deer::DEERDataCache &	datacache
	)

Performs an initial search (for non-3D backgrounds)

Parameters

model	Model to refine
resolution	Refinement resolution
trace_map	Map of DEER traces for calculation
datacache	Datacache with data

References core::scoring::epr_deer::Simulated4PDEERTraceFactory::bckg_type(), core::scoring::epr_deer::metrics::DEERDecayData::factory(), core::scoring::epr_deer::DEERDataCache::indices(), and protocols::antibody::design::minimize.

◆ keyname()

std::string protocols::simple_moves::DEEROptimizeCoordsMover::keyname ( ) const

◆ minimize()

core::Real protocols::simple_moves::DEEROptimizeCoordsMover::minimize	(	CoordModel &	model,
		core::Real &	resolution,
		std::map< ResPair, std::map< SizePair, utility::vector1< core::Real > > > const &	trace_map,
		core::scoring::epr_deer::DEERDataCache &	datacache
	)

Minimizes the model to fit the data.

Parameters

model	Model to refine
resolution	Refinement resolution
trace_map	Map of DEER traces for calculation
datacache	Datacache with data

Returns: Score of the model

References core::scoring::epr_deer::DEERDataCache::labeled_residues(), protocols::mean_field::max(), protocols::hybridization::score, core::scoring::epr_deer::DEERDataCache::size(), protocols::hybridization::t, and protocols::simple_moves::TR().

◆ mover_name()

std::string protocols::simple_moves::DEEROptimizeCoordsMover::mover_name ( ) const

Referenced by protocols::simple_moves::DEEROptimizeCoordsMoverCreator::keyname().

◆ normalize()

void protocols::simple_moves::DEEROptimizeCoordsMover::normalize	(	CoordModel &	model,
		PairSizeString const &	res = `std::make_pair( 0, "" )`
	)		const

Recursive function to normalize the weights of a model.

Parameters

model	The model being normalized
res	Residue to normalize @detail If residue is zero, the function calls itself for each residue

References protocols::analysis::total.

◆ parse_my_tag()

void protocols::simple_moves::DEEROptimizeCoordsMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

◆ print_coords()

void protocols::simple_moves::DEEROptimizeCoordsMover::print_coords	(	CoordModel const &	model,
		std::map< PairSizeString, utility::vector1< PseudoSL > > const &	default_coords,
		core::Real const &	current_score,
		core::scoring::epr_deer::DEERDataCache &	datacache,
		std::map< ResPair, std::map< SizePair, utility::vector1< core::Real > > > const &	trace_map,
		core::pose::Pose &	pose
	)

References core::scoring::epr_deer::EPRSpinLabel::label(), core::pose::Pose::residue(), protocols::hybridization::score, core::scoring::epr_deer::DEERDataCache::set_labels(), core::scoring::epr_deer::DEERDataCache::set_sl_weights(), protocols::simple_moves::TR(), and core::conformation::Residue::xyz().

◆ provide_xml_schema() [1/2]

void protocols::simple_moves::DEEROptimizeCoordsMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

References protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::simple_moves::DEEROptimizeCoordsMoverCreator::provide_xml_schema().

◆ provide_xml_schema() [2/2]

void protocols::simple_moves::DEEROptimizeCoordsMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd ) const

◆ score()

core::Real protocols::simple_moves::DEEROptimizeCoordsMover::score	(	CoordModel const &	coords,
		std::map< ResPair, std::map< SizePair, utility::vector1< core::Real > > > const &	trace_map,
		core::scoring::epr_deer::DEERDataCache &	datacache,
		bool const	print = `false`
	)

References protocols::simple_filters::coords(), core::scoring::epr_deer::DEERDataCache::indices(), protocols::mean_field::max(), protocols::hybridization::r1, protocols::hybridization::r2, core::scoring::total_score, and protocols::simple_moves::TR().

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

src/protocols/simple_moves/DEEROptimizeCoordsMover.hh
src/protocols/simple_moves/DEEROptimizeCoordsMover.cc

Public Member Functions

Private Types

Additional Inherited Members

Member Typedef Documentation

◆ CoordModel

◆ PairSizeString

◆ PseudoSL

◆ ResPair

◆ SizePair

Constructor & Destructor Documentation

◆ DEEROptimizeCoordsMover()

◆ ~DEEROptimizeCoordsMover()

Member Function Documentation

◆ apply()

◆ boltzmann()

◆ clone()

◆ create_mover()

◆ get_name()

◆ init_coords()

◆ init_data()

◆ init_model()

◆ initial_search()

◆ keyname()

◆ minimize()

◆ mover_name()

◆ normalize()

◆ parse_my_tag()

◆ print_coords()

◆ provide_xml_schema() [1/2]

◆ provide_xml_schema() [2/2]

◆ score()