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Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::rna::denovo::coarse::CoarseRNA_Fragments Class Reference

#include <CoarseRNA_Fragments.hh>

Inheritance diagram for protocols::rna::denovo::coarse::CoarseRNA_Fragments:
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Public Member Functions

 CoarseRNA_Fragments (std::string const &filename)
 
 ~CoarseRNA_Fragments () override
 
void apply_random_fragment (core::pose::Pose &pose, core::Size const position, core::Size const size, core::Size const type, core::fragment::rna::RNA_FragmentHomologyExclusionCOP const &homology_exclusion, core::pose::toolbox::AtomLevelDomainMapCOP atom_level_domain_map, core::Size const symm_hack_arity) const override
 
bool is_fullatom () override
 
- Public Member Functions inherited from core::fragment::rna::RNA_Fragments
 RNA_Fragments ()
 
 ~RNA_Fragments () override
 
virtual void apply_best_fragment (core::scoring::ScoreFunctionOP sfxn, core::pose::Pose &pose, core::Size const position, core::Size const size, core::Size const type, RNA_FragmentHomologyExclusionCOP const &homology_exclusion, core::pose::toolbox::AtomLevelDomainMapCOP atom_level_domain_map, core::Size const symm_hack_arity, core::Size const exhaustive) const
 
virtual FragmentLibraryOP get_fragment_library_pointer (std::string const &, std::string const &, RNA_FragmentHomologyExclusionCOP const &, utility::vector1< SYN_ANTI_RESTRICTION > const &, Size const) const
 

Private Member Functions

void insert_fragment (core::pose::Pose &, core::Size const, core::fragment::rna::TorsionSet const &, core::pose::toolbox::AtomLevelDomainMapCOP) const override
 
virtual void insert_fragment (core::pose::Pose &pose, core::Size const &insert_res, core::Size const &source_res, core::Size const &frag_size, core::fragment::rna::RNA_FragmentHomologyExclusionCOP const &homology_exclusion, core::pose::toolbox::AtomLevelDomainMapCOP atom_level_domain_map) const
 
void find_source_positions (SequenceSecStructPair const &key) const
 
core::Size pick_random_fragment (std::string const &RNA_string, std::string const &RNA_secstruct_string, core::Size const type) const
 
core::Size pick_random_fragment (core::pose::Pose &pose, core::Size const position, core::Size const size, core::Size const type) const
 
void initialize_frag_source_pose ()
 

Private Attributes

std::string frag_source_secstruct_
 
std::string const frag_source_file_
 
core::pose::MiniPoseOP frag_source_pose_
 
std::map< SequenceSecStructPair, SourcePositionsOPsource_positions_map_
 
std::map< std::string, core::Sizecoarse_rna_name_to_num_
 

Constructor & Destructor Documentation

◆ CoarseRNA_Fragments()

protocols::rna::denovo::coarse::CoarseRNA_Fragments::CoarseRNA_Fragments ( std::string const &  filename)

◆ ~CoarseRNA_Fragments()

protocols::rna::denovo::coarse::CoarseRNA_Fragments::~CoarseRNA_Fragments ( )
overridedefault

Member Function Documentation

◆ apply_random_fragment()

void protocols::rna::denovo::coarse::CoarseRNA_Fragments::apply_random_fragment ( core::pose::Pose pose,
core::Size const  position,
core::Size const  size,
core::Size const  type,
core::fragment::rna::RNA_FragmentHomologyExclusionCOP const &  homology_exclusion,
core::pose::toolbox::AtomLevelDomainMapCOP  atom_level_domain_map,
core::Size const  symm_hack_arity 
) const
overridevirtual

◆ find_source_positions()

void protocols::rna::denovo::coarse::CoarseRNA_Fragments::find_source_positions ( SequenceSecStructPair const &  key) const
private

◆ initialize_frag_source_pose()

void protocols::rna::denovo::coarse::CoarseRNA_Fragments::initialize_frag_source_pose ( )
private

◆ insert_fragment() [1/2]

void protocols::rna::denovo::coarse::CoarseRNA_Fragments::insert_fragment ( core::pose::Pose ,
core::Size const  ,
core::fragment::rna::TorsionSet const &  ,
core::pose::toolbox::AtomLevelDomainMapCOP   
) const
inlineoverrideprivatevirtual

Reimplemented from core::fragment::rna::RNA_Fragments.

Referenced by apply_random_fragment().

◆ insert_fragment() [2/2]

void protocols::rna::denovo::coarse::CoarseRNA_Fragments::insert_fragment ( core::pose::Pose pose,
core::Size const &  insert_res,
core::Size const &  source_res,
core::Size const &  frag_size,
core::fragment::rna::RNA_FragmentHomologyExclusionCOP const &  homology_exclusion,
core::pose::toolbox::AtomLevelDomainMapCOP  atom_level_domain_map 
) const
privatevirtual

◆ is_fullatom()

bool protocols::rna::denovo::coarse::CoarseRNA_Fragments::is_fullatom ( )
overridevirtual

◆ pick_random_fragment() [1/2]

Size protocols::rna::denovo::coarse::CoarseRNA_Fragments::pick_random_fragment ( core::pose::Pose pose,
core::Size const  position,
core::Size const  size,
core::Size const  type 
) const
private

◆ pick_random_fragment() [2/2]

Size protocols::rna::denovo::coarse::CoarseRNA_Fragments::pick_random_fragment ( std::string const &  RNA_string,
std::string const &  RNA_secstruct_string,
core::Size const  type 
) const
private

Member Data Documentation

◆ coarse_rna_name_to_num_

std::map< std::string, core::Size > protocols::rna::denovo::coarse::CoarseRNA_Fragments::coarse_rna_name_to_num_
private

◆ frag_source_file_

std::string const protocols::rna::denovo::coarse::CoarseRNA_Fragments::frag_source_file_
private

◆ frag_source_pose_

core::pose::MiniPoseOP protocols::rna::denovo::coarse::CoarseRNA_Fragments::frag_source_pose_
private

◆ frag_source_secstruct_

std::string protocols::rna::denovo::coarse::CoarseRNA_Fragments::frag_source_secstruct_
private

◆ source_positions_map_

std::map< SequenceSecStructPair, SourcePositionsOP > protocols::rna::denovo::coarse::CoarseRNA_Fragments::source_positions_map_
mutableprivate

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