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protocols::generalized_kinematic_closure::selector::GeneralizedKICselector Class Reference

#include <GeneralizedKICselector.hh>

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

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: