BackboneGridSamplerHelper class, which stores options for the PerturbBundle mover. More...

#include <BackboneGridSamplerHelper.hh>

Inheritance diagram for protocols::helical_bundle::BackboneGridSamplerHelper:

Public Member Functions
	BackboneGridSamplerHelper ()
	constructors More...

virtual BackboneGridSamplerHelperOP	clone () const
	Copy this BackboneGridSamplerHelper object( allocate actual memory for it ) More...

void	reset ()
	Reset this BackboneGridSamplerHelper object. More...

BackboneGridSamplerHelperCOP	get_self_ptr () const
	self pointers More...

BackboneGridSamplerHelperOP	get_self_ptr ()

BackboneGridSamplerHelperCAP	get_self_weak_ptr () const

BackboneGridSamplerHelperAP	get_self_weak_ptr ()

core::Size	residues_per_repeat () const
	Returns the number of residues per repeat, set by the initialize_data() function. More...

core::Size	n_torsions_total () const
	Returns the total number of mainchain torsions over which we will sample. More...

core::Size	n_torsions (core::Size const res_index) const
	Returns the number of different mainchain torsions that the BackboneGridSampler will sample over. More...

core::Size	residue_index (core::Size const index) const
	Returns the residue index in the repeating unit (1st, 2nd, 3rd etc.) corresponding to a given torsion index. More...

core::Size	torsion_id (core::Size const index) const
	Returns the torsion ID for the specified torsion index. More...

core::Real	torsion_sample_value (core::Size const &index) const
	Returns the current sample value for the specified torsion. More...

void	increment_cur_indices ()
	RECURSIVE function that increments the current sample index. More...

void	initialize_data (utility::vector1< utility::vector1< std::pair< core::Size, std::pair< std::pair< core::Real, core::Real >, core::Size > > > > const &torsions_to_sample)
	Initialize this object from an object passed from the BackboneGridSampler mover. More...

Private Member Functions
void	initialize_samples ()
	Perform the pre-calculation that sets up the lists of mainchain torsion values to be sampled. More...

void	increment_cur_indices (core::Size const index_to_increment)
	RECURSIVE function that increments the current sample index. More...

Private Attributes
core::Size	residues_per_repeat_
	Number of residues in the repeating unit. More...

utility::vector1< core::Size >	n_torsions_
	Number of mainchain torsions that will be sampled by the BackboneGridSampler mover. More...

core::Size	n_torsions_total_
	Total number of mainchain torsions over which we will sample. This is the sum of the n_torsions_ entries for each residue in the repeating unit, and is initialized by the initialize_samples() function. More...

utility::vector1< core::Size >	residue_indices_
	Residue indicies. More...

utility::vector1< core::Size >	allowed_torsion_indices_
	Allowed mainchain torsion indices. More...

utility::vector1< core::Size >	torsion_samples_
	Number of samples for each mainchain torsion. More...

utility::vector1< core::Real >	torsion_lower_vals_
	Lower bound of the range sampled for each mainchain torsion torsion. More...

utility::vector1< core::Real >	torsion_upper_vals_
	Upper bound of the range sampled for each mainchain torsion. More...

utility::vector1 < utility::vector1< core::Real > >	torsion_sample_vals_
	The vector of vectors of sample values for each mainchain torsion. More...

utility::vector1< core::Size >	cur_indices_
	The vector indicating the current set of values that we're sampling. More...

Detailed Description

BackboneGridSamplerHelper class, which stores options for the PerturbBundle mover.

Constructor & Destructor Documentation

protocols::helical_bundle::BackboneGridSamplerHelper::BackboneGridSamplerHelper ( )

constructors

Constructor.

References n_torsions_.

Member Function Documentation

BackboneGridSamplerHelperOP protocols::helical_bundle::BackboneGridSamplerHelper::clone ( ) const

virtual

Copy this BackboneGridSamplerHelper object( allocate actual memory for it )

make a copy of this BackboneGridSamplerHelper object (allocate actual memory for it)

BackboneGridSamplerHelperCOP protocols::helical_bundle::BackboneGridSamplerHelper::get_self_ptr ( ) const

inline

self pointers

BackboneGridSamplerHelperOP protocols::helical_bundle::BackboneGridSamplerHelper::get_self_ptr ( )

inline

BackboneGridSamplerHelperCAP protocols::helical_bundle::BackboneGridSamplerHelper::get_self_weak_ptr ( ) const

inline

BackboneGridSamplerHelperAP protocols::helical_bundle::BackboneGridSamplerHelper::get_self_weak_ptr ( )

inline

void protocols::helical_bundle::BackboneGridSamplerHelper::increment_cur_indices ( )

RECURSIVE function that increments the current sample index.

This function adds 1 to the last torsion index. If the last torsion index value exceeds the number of samples for that torsion, it resets that torsion index and increments the second-last torsion index by 1 by recursively calling itself. This function is overloaded; the public version by default tries to increment the last index, while the private version can be called recursively.

This function adds 1 to the last mainchain torsion index. If the last torsion index value exceeds the number of samples for that torsion, it resets that torsion index and increments the second-last torsion index by 1 by recursively calling itself. This function is overloaded; the public version by default tries to increment the last index, while the private version can be called recursively.

References torsion_sample_vals_.

Referenced by increment_cur_indices().

void protocols::helical_bundle::BackboneGridSamplerHelper::increment_cur_indices ( core::Size const index_to_increment )

private

RECURSIVE function that increments the current sample index.

This function adds 1 to the last torsion index. If the last torsion index value exceeds the number of samples for that torsion, it resets that torsion index and increments the second-last torsion index by 1 by recursively calling itself.

References cur_indices_, increment_cur_indices(), and torsion_sample_vals_.

void protocols::helical_bundle::BackboneGridSamplerHelper::initialize_data ( utility::vector1< utility::vector1< std::pair< core::Size, std::pair< std::pair< core::Real, core::Real >, core::Size > > > > const & torsions_to_sample )

Initialize this object from an object passed from the BackboneGridSampler mover.

References allowed_torsion_indices_, initialize_samples(), n_torsions_, reset(), residue_indices_, residues_per_repeat_, torsion_lower_vals_, torsion_samples_, and torsion_upper_vals_.

void protocols::helical_bundle::BackboneGridSamplerHelper::initialize_samples ( )

private

Perform the pre-calculation that sets up the lists of mainchain torsion values to be sampled.

Perform the pre-calculation that sets up the lists of torsion values to be sampled.

Called by the initialize_data() function.

References allowed_torsion_indices_, cur_indices_, n_torsions_total_, residue_indices_, torsion_lower_vals_, torsion_sample_vals_, torsion_samples_, torsion_upper_vals_, and protocols::helical_bundle::TR().

Referenced by initialize_data().

core::Size protocols::helical_bundle::BackboneGridSamplerHelper::n_torsions ( core::Size const res_index ) const

inline

Returns the number of different mainchain torsions that the BackboneGridSampler will sample over.

Returns a value for the residue in the repeating unit with index res_index.

References n_torsions_.

core::Size protocols::helical_bundle::BackboneGridSamplerHelper::n_torsions_total ( ) const

inline

Returns the total number of mainchain torsions over which we will sample.

This is the sum of the n_torsions_ entries for each residue in the repeating unit, and is initialized by the initialize_samples() function.

References n_torsions_total_.

void protocols::helical_bundle::BackboneGridSamplerHelper::reset ( void )

Reset this BackboneGridSamplerHelper object.

Clears all internal data.

References allowed_torsion_indices_, cur_indices_, n_torsions_, n_torsions_total_, residue_indices_, residues_per_repeat_, torsion_lower_vals_, torsion_sample_vals_, torsion_samples_, and torsion_upper_vals_.

Referenced by initialize_data().

core::Size protocols::helical_bundle::BackboneGridSamplerHelper::residue_index ( core::Size const index ) const

inline

Returns the residue index in the repeating unit (1st, 2nd, 3rd etc.) corresponding to a given torsion index.

References residue_indices_.

core::Size protocols::helical_bundle::BackboneGridSamplerHelper::residues_per_repeat ( ) const

inline

Returns the number of residues per repeat, set by the initialize_data() function.

References residues_per_repeat_.

core::Size protocols::helical_bundle::BackboneGridSamplerHelper::torsion_id ( core::Size const index ) const

inline

Returns the torsion ID for the specified torsion index.

References allowed_torsion_indices_.

core::Real protocols::helical_bundle::BackboneGridSamplerHelper::torsion_sample_value ( core::Size const & index ) const

inline

Returns the current sample value for the specified torsion.

References cur_indices_, and torsion_sample_vals_.

Member Data Documentation

utility::vector1< core::Size > protocols::helical_bundle::BackboneGridSamplerHelper::allowed_torsion_indices_

private

Allowed mainchain torsion indices.

This stores a list of mainchain torsion indices that will be sampled over.

Referenced by initialize_data(), initialize_samples(), reset(), and torsion_id().

utility::vector1< core::Size > protocols::helical_bundle::BackboneGridSamplerHelper::cur_indices_

private

The vector indicating the current set of values that we're sampling.

Entries in this vector represent indices in the torsion_sample_vals_ vector.

Referenced by increment_cur_indices(), initialize_samples(), reset(), and torsion_sample_value().

utility::vector1< core::Size > protocols::helical_bundle::BackboneGridSamplerHelper::n_torsions_

private

Number of mainchain torsions that will be sampled by the BackboneGridSampler mover.

This is a vector with an entry for each residue in the repeating unit.

Referenced by BackboneGridSamplerHelper(), initialize_data(), n_torsions(), and reset().

core::Size protocols::helical_bundle::BackboneGridSamplerHelper::n_torsions_total_

private

Total number of mainchain torsions over which we will sample. This is the sum of the n_torsions_ entries for each residue in the repeating unit, and is initialized by the initialize_samples() function.

Referenced by initialize_samples(), n_torsions_total(), and reset().

utility::vector1< core::Size > protocols::helical_bundle::BackboneGridSamplerHelper::residue_indices_

private

Residue indicies.

This stores indices of residues (in the repeating unit – 1, 2, 3, etc.) with corresponding entries to the allowed_torsion_indicies vector.

Referenced by initialize_data(), initialize_samples(), reset(), and residue_index().

core::Size protocols::helical_bundle::BackboneGridSamplerHelper::residues_per_repeat_

private

Number of residues in the repeating unit.

Referenced by initialize_data(), reset(), and residues_per_repeat().

utility::vector1< core::Real > protocols::helical_bundle::BackboneGridSamplerHelper::torsion_lower_vals_

private

Lower bound of the range sampled for each mainchain torsion torsion.

This class stores a list of allowed mainchain torsion that will be sampled by the BackboneGridSampler mover. It does this in several vectors. This one lists the lower bound of the range sampled for each mainchain torsion.

Referenced by initialize_data(), initialize_samples(), and reset().

utility::vector1< utility::vector1 < core::Real > > protocols::helical_bundle::BackboneGridSamplerHelper::torsion_sample_vals_

private

The vector of vectors of sample values for each mainchain torsion.

This is pre-computed by the initialize_samples() function. Order of the outer vector is the order of mainchain torsion indices in the allowed_torsion_indices_ vector. Note that the residue_indices_ vector tells us which residue in the repeating unit each mainchain torsion is in.

Referenced by increment_cur_indices(), initialize_samples(), reset(), and torsion_sample_value().

utility::vector1< core::Size > protocols::helical_bundle::BackboneGridSamplerHelper::torsion_samples_

private

Number of samples for each mainchain torsion.

This class stores a list of allowed mainchain torsions that will be sampled by the BackboneGridSampler mover. It does this in several vectors. This one lists the number of samples for each mainchain torsion.

Referenced by initialize_data(), initialize_samples(), and reset().

utility::vector1< core::Real > protocols::helical_bundle::BackboneGridSamplerHelper::torsion_upper_vals_

private

Upper bound of the range sampled for each mainchain torsion.

This class stores a list of allowed mainchain torsions that will be sampled by the BackboneGridSampler mover. It does this in several vectors. This one lists the upper bound of the range sampled for each mainchain torsion.

Referenced by initialize_data(), initialize_samples(), and reset().

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

src/protocols/helical_bundle/BackboneGridSamplerHelper.hh
src/protocols/helical_bundle/BackboneGridSamplerHelper.cc

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation