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core::pack::rotamer_set::ContinuousRotamerSet Class Reference

#include <ContinuousRotamerSet.hh>

Inheritance diagram for core::pack::rotamer_set::ContinuousRotamerSet:
Inheritance graph
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Public Member Functions

 ContinuousRotamerSet ()
 
 ~ContinuousRotamerSet () override
 
void build_rotamers (pose::Pose const &pose, Size resid, task::PackerTask const &task)
 
Size get_n_residue_types () const
 
Size get_n_sampling_rotamers_for_rotblock (Size which_restype) const
 
Size get_n_baserotamers_for_rotblock (Size which_restype) const
 
Size get_rotblock_index_for_sampling_rotamer (Size which_rotamer) const
 Rotamers i to i+j of all the same residue type are grouped together. This function returns the index of the residue type in a contiguous block of rotamers. E.g. rotamers 100 to 120 might all be lysine rotamers, and might be the 8th residue type, with the first 7 residue types spanning rotamers 1 to 99. If new lysine rotamers are appended to the end of the rotamer set, they are considered to be in a separate residue type block. Lysine rotamers 200 to 210 might be block 15 while lysine rotamers 100 to 120 are still block 7. More...
 
Size num_base_rotamers_total () const
 
Size num_sampling_rotamers_total () const
 
Size sampling_id_for_current_rotamer () const
 
utility::vector1< Vector > const & current_rotamer_coords () const
 
Size resid () const
 
chemical::ResidueTypeCOP restype_for_rotblock (Size rotblock) const
 
dunbrack::DunbrackRotamerSampleData
const & 
baserotamer_data (Size aa_ind, Size rotid_for_aa) const
 
Size pick_baserotamer_from_rotblock (Size aa_ind, Real rand_btw_0_and_1) const
 

Private Types

typedef utility::VirtualBase parent
 
typedef utility::vector1
< dunbrack::DunbrackRotamerSampleData
RotamersForAA
 

Private Member Functions

void determine_rotcounts_for_restype (Size)
 

Private Attributes

Size resid_
 
Size input_rotamer_samplingrot_index_
 
Size input_rotamer_rotblock_
 
utility::vector1< Vectorinput_rotamer_coords_
 
Size n_restypes_
 
utility::vector1< chemical::AAaa_for_rotblock_
 
utility::vector1
< chemical::ResidueTypeCOP
restype_for_rotblock_
 
Size n_baserots_total_
 
utility::vector1< Sizen_baserotamers_for_rotblock_
 
utility::vector1< Sizebaserots_offsets_
 
utility::vector1< Sizeaa_block_for_baserotamer_
 
Size n_samplingrots_total_
 
utility::vector1< Sizen_samplingrots_for_rotblock_
 
utility::vector1< Sizesamplingrot_offsets_
 
utility::vector1< Sizeaa_block_for_samplingrotamer_
 
utility::vector1< RotamersForAAsamples_
 

Member Typedef Documentation

typedef utility::VirtualBase core::pack::rotamer_set::ContinuousRotamerSet::parent
private

Constructor & Destructor Documentation

core::pack::rotamer_set::ContinuousRotamerSet::ContinuousRotamerSet ( )
core::pack::rotamer_set::ContinuousRotamerSet::~ContinuousRotamerSet ( )
overridedefault

Member Function Documentation

dunbrack::DunbrackRotamerSampleData const & core::pack::rotamer_set::ContinuousRotamerSet::baserotamer_data ( Size  aa_ind,
Size  rotid_for_aa 
) const
void core::pack::rotamer_set::ContinuousRotamerSet::build_rotamers ( pose::Pose const &  pose,
Size  resid,
task::PackerTask const &  task 
)
utility::vector1< Vector > const & core::pack::rotamer_set::ContinuousRotamerSet::current_rotamer_coords ( ) const
void core::pack::rotamer_set::ContinuousRotamerSet::determine_rotcounts_for_restype ( Size  restype_ind)
private
Size core::pack::rotamer_set::ContinuousRotamerSet::get_n_baserotamers_for_rotblock ( Size  which_restype) const
Size core::pack::rotamer_set::ContinuousRotamerSet::get_n_residue_types ( ) const

Note, its entirely possible for two residue types to be the "same amino acid", e.g. HIS and HIS_D.

References n_restypes_.

Size core::pack::rotamer_set::ContinuousRotamerSet::get_n_sampling_rotamers_for_rotblock ( Size  which_restype) const
Size core::pack::rotamer_set::ContinuousRotamerSet::get_rotblock_index_for_sampling_rotamer ( Size  which_rotamer) const

Rotamers i to i+j of all the same residue type are grouped together. This function returns the index of the residue type in a contiguous block of rotamers. E.g. rotamers 100 to 120 might all be lysine rotamers, and might be the 8th residue type, with the first 7 residue types spanning rotamers 1 to 99. If new lysine rotamers are appended to the end of the rotamer set, they are considered to be in a separate residue type block. Lysine rotamers 200 to 210 might be block 15 while lysine rotamers 100 to 120 are still block 7.

References aa_block_for_samplingrotamer_.

Referenced by core::pack::assign_random_continuous_rotamer().

Size core::pack::rotamer_set::ContinuousRotamerSet::num_base_rotamers_total ( ) const

References n_baserots_total_.

Size core::pack::rotamer_set::ContinuousRotamerSet::num_sampling_rotamers_total ( ) const

References n_samplingrots_total_.

Size core::pack::rotamer_set::ContinuousRotamerSet::pick_baserotamer_from_rotblock ( Size  aa_ind,
Real  rand_btw_0_and_1 
) const
Size core::pack::rotamer_set::ContinuousRotamerSet::resid ( ) const

References resid_.

Referenced by build_rotamers().

chemical::ResidueTypeCOP core::pack::rotamer_set::ContinuousRotamerSet::restype_for_rotblock ( Size  rotblock) const
Size core::pack::rotamer_set::ContinuousRotamerSet::sampling_id_for_current_rotamer ( ) const

Member Data Documentation

utility::vector1< Size > core::pack::rotamer_set::ContinuousRotamerSet::aa_block_for_baserotamer_
private

Referenced by build_rotamers().

utility::vector1< Size > core::pack::rotamer_set::ContinuousRotamerSet::aa_block_for_samplingrotamer_
private
utility::vector1< chemical::AA > core::pack::rotamer_set::ContinuousRotamerSet::aa_for_rotblock_
private

Referenced by build_rotamers().

utility::vector1< Size > core::pack::rotamer_set::ContinuousRotamerSet::baserots_offsets_
private

Referenced by build_rotamers().

utility::vector1< Vector > core::pack::rotamer_set::ContinuousRotamerSet::input_rotamer_coords_
private
Size core::pack::rotamer_set::ContinuousRotamerSet::input_rotamer_rotblock_
private
Size core::pack::rotamer_set::ContinuousRotamerSet::input_rotamer_samplingrot_index_
private
utility::vector1< Size > core::pack::rotamer_set::ContinuousRotamerSet::n_baserotamers_for_rotblock_
private
Size core::pack::rotamer_set::ContinuousRotamerSet::n_baserots_total_
private
Size core::pack::rotamer_set::ContinuousRotamerSet::n_restypes_
private
utility::vector1< Size > core::pack::rotamer_set::ContinuousRotamerSet::n_samplingrots_for_rotblock_
private
Size core::pack::rotamer_set::ContinuousRotamerSet::n_samplingrots_total_
private
Size core::pack::rotamer_set::ContinuousRotamerSet::resid_
private

Referenced by build_rotamers(), and resid().

utility::vector1< chemical::ResidueTypeCOP > core::pack::rotamer_set::ContinuousRotamerSet::restype_for_rotblock_
private
utility::vector1< RotamersForAA > core::pack::rotamer_set::ContinuousRotamerSet::samples_
private
utility::vector1< Size > core::pack::rotamer_set::ContinuousRotamerSet::samplingrot_offsets_
private

Referenced by build_rotamers().


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