#include <GeneralizedKICselector.hh>

Inheritance diagram for protocols::generalized_kinematic_closure::selector::GeneralizedKICselector:

Public Member Functions
	GeneralizedKICselector ()
	Constructor for GeneralizedKICselector. More...

	GeneralizedKICselector (GeneralizedKICselector const &src)
	Copy constructor for GeneralizedKICselector. More...

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

GeneralizedKICselectorOP	clone () const
	Clone function for GeneralizedKICselector: More...

std::string	get_name () const
	Returns the name of this class. More...

std::string	get_selector_type_name (core::Size const selector_type) const
	Given a selector type, return its name. Returns "unknown_selector" if not recognized. More...

selector_type	get_selector_type_by_name (std::string const &selectorname) const
	Given the name of a selector type, return the selector type enum. Returns unknown_selector if not recognized. More...

void	set_selector_type (selector_type const &stype)
	Sets the selector type for this selector. More...

void	set_selector_type (std::string const &stypename)
	Sets the selector type for this selector by name. More...

selector_type	get_selector_type () const
	Returns the selector type for this selector. More...

void	set_scorefunction (core::scoring::ScoreFunctionOP sfxn)
	Set the scorefunction used by this selector. More...

core::scoring::ScoreFunctionOP	scorefunction () const
	Get the scorefunction used by this selector. More...

void	set_boltzmann_temp (core::Real const &temp)
	Set the Boltzmann temperature used by this selector. More...

core::Real	get_boltzmann_temp () const
	Returns the Boltzmann temperature used by this selector. More...

core::Size	apply (core::pose::Pose const &pose, core::pose::Pose const &original_pose, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map, utility::vector1< std::pair< core::Size, core::Size > > const &tail_residue_map, utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &atomlist, utility::vector1< utility::vector1< utility::vector1< core::Real > > > const &torsions, utility::vector1< utility::vector1< utility::vector1< core::Real > > > const &bondangles, utility::vector1< utility::vector1< utility::vector1< core::Real > > > const &bondlengths, utility::vector1< core::Size > const &nsol_for_attempt, core::Size const total_solutions, utility::vector1< core::pose::PoseCOP > const &solutions, bool const low_memory_mode, utility::vector1< core::Real > const &energies_for_solution) const
	Applies a selector type to choose a solution, and returns index of chosen solution. More...

Static Public Member Functions
static void	define_valid_selector_name_enumeration (utility::tag::XMLSchemaDefinition &xsd)

Private Member Functions
void	apply_random_selector (core::Size const total_solutions, core::Size &chosen_solution) const
	Applies a random_selector selector. More...

void	apply_lowest_energy_selector (utility::vector1< core::Size > const &nsol_for_attempt, core::Size const total_solutions, core::Size &chosen_solution, core::scoring::ScoreFunctionOP sfxn, core::pose::Pose const &ref_loop_pose, core::pose::Pose const &ref_pose, core::Real const &boltzmann_kbt, bool const use_boltzmann, utility::vector1< core::pose::PoseCOP > const &solutions, bool const low_memory_mode, utility::vector1< core::Real > const &energies_for_solution) const
	Applies a lowest_energy_selector selector. More...

void	apply_lowest_rmsd_selector (utility::vector1< core::Size > const &nsol_for_attempt, core::Size const , core::Size &chosen_solution, utility::vector1< std::pair< core::Size, core::Size > > const &, utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &atomlist, utility::vector1< utility::vector1< utility::vector1< core::Real > > > const &torsions, utility::vector1< utility::vector1< utility::vector1< core::Real > > > const &bondangles, utility::vector1< utility::vector1< utility::vector1< core::Real > > > const &bondlengths, core::pose::Pose const &ref_loop_pose) const
	Applies a lowest_rmsd_selector selector. More...

void	apply_lowest_delta_torsion_selector (utility::vector1< core::Size > const &nsol_for_attempt, core::Size const , core::Size &chosen_solution, utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &atomlist, utility::vector1< utility::vector1< utility::vector1< core::Real > > > const &torsions, core::pose::Pose const &ref_pose) const
	Applies a lowest_delta_torsion_selector. More...

Private Attributes
selector_type	selectortype_
	The selector type for this selector (see the selector_type enum for all types). More...

core::scoring::ScoreFunctionOP	selector_sfxn_
	An owning pointer to a scoring function that a selector can use. More...

core::Real	boltzmann_kbt_
	A Boltzmann temperature (kbt, in Rosetta energy units) that some selectors can use. More...

Constructor & Destructor Documentation

protocols::generalized_kinematic_closure::selector::GeneralizedKICselector::GeneralizedKICselector ( )

Constructor for GeneralizedKICselector.

protocols::generalized_kinematic_closure::selector::GeneralizedKICselector::GeneralizedKICselector ( GeneralizedKICselector const & src )

Copy constructor for GeneralizedKICselector.

protocols::generalized_kinematic_closure::selector::GeneralizedKICselector::~GeneralizedKICselector ( )

overridedefault

Destructor for GeneralizedKICselector mover.

Member Function Documentation

core::Size protocols::generalized_kinematic_closure::selector::GeneralizedKICselector::apply	(	core::pose::Pose const &	pose,
		core::pose::Pose const &	original_pose,
		utility::vector1< std::pair< core::Size, core::Size > > const &	residue_map,
		utility::vector1< std::pair< core::Size, core::Size > > const &	tail_residue_map,
		utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &	atomlist,
		utility::vector1< utility::vector1< utility::vector1< core::Real > > > const &	torsions,
		utility::vector1< utility::vector1< utility::vector1< core::Real > > > const &	bondangles,
		utility::vector1< utility::vector1< utility::vector1< core::Real > > > const &	bondlengths,
		utility::vector1< core::Size > const &	nsol_for_attempt,
		core::Size const	total_solutions,
		utility::vector1< core::pose::PoseCOP > const &	solutions,
		bool const	low_memory_mode,
		utility::vector1< core::Real > const &	energies_for_solution
	)		const

Applies a selector type to choose a solution, and returns index of chosen solution.

Returns zero if some error occurs. Should always return a nonzero integer, though.

Parameters

[in,out]	pose	– The loop to be closed.
[in]	original_pose	– The original pose. Can be used for reference by selectors.
[in]	residue_map	– Mapping of (loop residue, original pose residue).
[in]	tail_residue_map	– Mapping of (tail residue index in pose, tail residue index in original_pose).
[in]	atomlist	– The list of (AtomID, original XYZ coordinates of atoms) representing the chain that was closed.
[in]	torsions	– Matrix of [closure attempt #][solution #][torsion #] with torsion values for each torsion angle in the chain. A selector will pick one solution.
[in]	bondangles	– Matrix of [closure attempt #][solution #][angle #] with bond angle values for each bond angle in the chain. A selector will pick one solution.
[in]	bondlengths	– Matrix of [closure attempt #][solution #][bondlength #] with bond length for each bond in the chain. A selector will pick one solution.
[in]	nsol_for_attempt	– List of the number of solutions for each attempt.
[in]	total_solutions	– Total number of solutions found.
[in]	solutions	– Reference to vector of owning pointers of poses representing solutions, with pre-selection filters already applied.
[in]	low_memory_mode	– Are we running in low memory mode (where vectors of torsions/bondangles/bondlengths are used to store solutions), or default mode (where full poses are stored)?
[in]	energies_for_solution	– Vector of energies for each solution. Used only in low-memory mode.

Returns zero if some error occurs. Should always return a nonzero integer, though.

Parameters

[in,out]	pose	– The loop to be closed.
[in]	original_pose	– The original pose. Can be used for reference by selectors.
[in]	residue_map	– Mapping of (loop residue, original pose residue).
[in]	tail_residue_map	– Mapping of (tail residue index in pose, tail residue index in original_pose).
[in]	atomlist	– The list of (AtomID, original XYZ coordinates of atoms) representing the chain that was closed.
[in]	torsions	– Matrix of [closure attempt #][solution #][torsion #] with torsion values for each torsion angle in the chain. A selector will pick one solution.
[in]	bondangles	– Matrix of [closure attempt #][solution #][angle #] with bond angle values for each bond angle in the chain. A selector will pick one solution.
[in]	bondlengths	– Matrix of [closure attempt #][solution #][bondlength #] with bond length for each bond in the chain. A selector will pick one solution.
[in]	nsol_for_attempt	– List of the number of solutions for each attempt.
[in]	total_solutions	– Total number of solutions found.
[in]	solutions	– Reference to vector of owning pointers of poses representing solutions, with pre-selection filters already applied.
[in]	energies_for_solution	– Vector of energies for each solution. Used only in low-memory mode.

References apply_lowest_delta_torsion_selector(), apply_lowest_energy_selector(), apply_lowest_rmsd_selector(), apply_random_selector(), protocols::generalized_kinematic_closure::selector::boltzmann_energy_selector, boltzmann_kbt_, protocols::generalized_kinematic_closure::selector::lowest_delta_torsion_selector, protocols::generalized_kinematic_closure::selector::lowest_energy_selector, protocols::generalized_kinematic_closure::selector::lowest_rmsd_selector, protocols::generalized_kinematic_closure::selector::random_selector, selector_sfxn_, and selectortype_.

void protocols::generalized_kinematic_closure::selector::GeneralizedKICselector::apply_lowest_delta_torsion_selector	(	utility::vector1< core::Size > const &	nsol_for_attempt,
		core::Size const	,
		core::Size &	chosen_solution,
		utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &	atomlist,
		utility::vector1< utility::vector1< utility::vector1< core::Real > > > const &	torsions,
		core::pose::Pose const &	ref_pose
	)		const

private

Applies a lowest_delta_torsion_selector.

Applies a lowest_delta_torsion_selector selector.

This picks the solution with the lowest RMSD from the starting pose.

This picks the solution with the lowest delta torsion from the starting pose.

References core::pose::Pose::conformation(), and core::conformation::Conformation::torsion_angle().

Referenced by apply().

void protocols::generalized_kinematic_closure::selector::GeneralizedKICselector::apply_lowest_energy_selector	(	utility::vector1< core::Size > const &	nsol_for_attempt,
		core::Size const	total_solutions,
		core::Size &	chosen_solution,
		core::scoring::ScoreFunctionOP	sfxn,
		core::pose::Pose const &	ref_loop_pose,
		core::pose::Pose const &	ref_pose,
		core::Real const &	boltzmann_kbt,
		bool const	use_boltzmann,
		utility::vector1< core::pose::PoseCOP > const &	solutions,
		bool const	low_memory_mode,
		utility::vector1< core::Real > const &	energies_for_solution
	)		const

private

Applies a lowest_energy_selector selector.

This picks the lowest-energy solution, as scored with sfxn. It's a good idea to use a modified scorefunction for this (something that just has the backbone conformation and H-bonding terms, for example, since side-chains will not be repacked by default prior to invoking this selector).

This picks the lowest-energy solution, as scored with sfxn. It's a good idea to use a modified scorefunction for this (something that just has the backbone conformation and H-bonding terms, for example, since side-chains will not be repacked by default prior to invoking this selector). If the use_boltzmann parameter is set to true, the function randomly selects a solution weighted by exp(-E/kbt).

References clone(), core::scoring::get_score_function(), and core::scoring::rg.

Referenced by apply().

void protocols::generalized_kinematic_closure::selector::GeneralizedKICselector::apply_lowest_rmsd_selector	(	utility::vector1< core::Size > const &	nsol_for_attempt,
		core::Size const	,
		core::Size &	chosen_solution,
		utility::vector1< std::pair< core::Size, core::Size > > const &	,
		utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &	atomlist,
		utility::vector1< utility::vector1< utility::vector1< core::Real > > > const &	torsions,
		utility::vector1< utility::vector1< utility::vector1< core::Real > > > const &	bondangles,
		utility::vector1< utility::vector1< utility::vector1< core::Real > > > const &	bondlengths,
		core::pose::Pose const &	ref_loop_pose
	)		const

private

Applies a lowest_rmsd_selector selector.

This picks the solution with the lowest RMSD from the starting pose.

References protocols::generalized_kinematic_closure::set_loop_pose().

Referenced by apply().

void protocols::generalized_kinematic_closure::selector::GeneralizedKICselector::apply_random_selector	(	core::Size const	total_solutions,
		core::Size &	chosen_solution
	)		const

private

Applies a random_selector selector.

This picks a solution randomly from the solutions that passed filters.

References core::scoring::rg.

Referenced by apply().

GeneralizedKICselectorOP protocols::generalized_kinematic_closure::selector::GeneralizedKICselector::clone ( ) const

Clone function for GeneralizedKICselector:

Returns an owning pointer to a copy of this selector.

Referenced by apply_lowest_energy_selector().

void protocols::generalized_kinematic_closure::selector::GeneralizedKICselector::define_valid_selector_name_enumeration ( utility::tag::XMLSchemaDefinition & xsd )

static

Referenced by protocols::generalized_kinematic_closure::GeneralizedKIC::provide_xml_schema().

core::Real protocols::generalized_kinematic_closure::selector::GeneralizedKICselector::get_boltzmann_temp ( ) const

inline

Returns the Boltzmann temperature used by this selector.

References boltzmann_kbt_.

std::string protocols::generalized_kinematic_closure::selector::GeneralizedKICselector::get_name ( ) const

Returns the name of this class.

Returns the name of this class ("GeneralizedKICselector").

selector_type protocols::generalized_kinematic_closure::selector::GeneralizedKICselector::get_selector_type ( ) const

inline

Returns the selector type for this selector.

References selectortype_.

selector_type protocols::generalized_kinematic_closure::selector::GeneralizedKICselector::get_selector_type_by_name ( std::string const & selectorname ) const

Given the name of a selector type, return the selector type enum. Returns unknown_selector if not recognized.

References protocols::generalized_kinematic_closure::selector::end_of_selector_list, get_selector_type_name(), and protocols::generalized_kinematic_closure::selector::unknown_selector.

Referenced by set_selector_type().

std::string protocols::generalized_kinematic_closure::selector::GeneralizedKICselector::get_selector_type_name ( core::Size const selector_type ) const

Given a selector type, return its name. Returns "unknown_selector" if not recognized.

References protocols::generalized_kinematic_closure::selector::boltzmann_energy_selector, protocols::generalized_kinematic_closure::selector::lowest_delta_torsion_selector, protocols::generalized_kinematic_closure::selector::lowest_energy_selector, protocols::generalized_kinematic_closure::selector::lowest_rmsd_selector, protocols::generalized_kinematic_closure::selector::no_selector, and protocols::generalized_kinematic_closure::selector::random_selector.

Referenced by get_selector_type_by_name().

core::scoring::ScoreFunctionOP protocols::generalized_kinematic_closure::selector::GeneralizedKICselector::scorefunction ( ) const

inline

Get the scorefunction used by this selector.

References selector_sfxn_.

void protocols::generalized_kinematic_closure::selector::GeneralizedKICselector::set_boltzmann_temp ( core::Real const & temp )

inline

Set the Boltzmann temperature used by this selector.

References boltzmann_kbt_.

void protocols::generalized_kinematic_closure::selector::GeneralizedKICselector::set_scorefunction ( core::scoring::ScoreFunctionOP sfxn )

inline

Set the scorefunction used by this selector.

References selector_sfxn_.

void protocols::generalized_kinematic_closure::selector::GeneralizedKICselector::set_selector_type ( selector_type const & stype )

Sets the selector type for this selector.

References protocols::generalized_kinematic_closure::selector::end_of_selector_list, and selectortype_.

void protocols::generalized_kinematic_closure::selector::GeneralizedKICselector::set_selector_type ( std::string const & stypename )

Sets the selector type for this selector by name.

References protocols::generalized_kinematic_closure::selector::end_of_selector_list, get_selector_type_by_name(), and selectortype_.

Member Data Documentation

core::Real protocols::generalized_kinematic_closure::selector::GeneralizedKICselector::boltzmann_kbt_

private

A Boltzmann temperature (kbt, in Rosetta energy units) that some selectors can use.

Referenced by apply(), get_boltzmann_temp(), and set_boltzmann_temp().

core::scoring::ScoreFunctionOP protocols::generalized_kinematic_closure::selector::GeneralizedKICselector::selector_sfxn_

private

An owning pointer to a scoring function that a selector can use.

This must be set explicitly; otherwise, it's set to NULL by default.

Referenced by apply(), scorefunction(), and set_scorefunction().

selector_type protocols::generalized_kinematic_closure::selector::GeneralizedKICselector::selectortype_

private

The selector type for this selector (see the selector_type enum for all types).

Referenced by apply(), get_selector_type(), and set_selector_type().

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

src/protocols/generalized_kinematic_closure/selector/GeneralizedKICselector.hh
src/protocols/generalized_kinematic_closure/selector/GeneralizedKICselector.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation