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protocols::helical_bundle::BackboneGridSamplerHelper Class Reference

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

#include <BackboneGridSamplerHelper.hh>

Inheritance diagram for protocols::helical_bundle::BackboneGridSamplerHelper:
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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::Sizen_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::Sizeresidue_indices_
 Residue indicies. More...
 
utility::vector1< core::Sizeallowed_torsion_indices_
 Allowed mainchain torsion indices. More...
 
utility::vector1< core::Sizetorsion_samples_
 Number of samples for each mainchain torsion. More...
 
utility::vector1< core::Realtorsion_lower_vals_
 Lower bound of the range sampled for each mainchain torsion torsion. More...
 
utility::vector1< core::Realtorsion_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::Sizecur_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)
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  )
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: