protocols::coarse_rna::CoarseRNA_Fragments Class Reference

#include <CoarseRNA_Fragments.hh>

Inheritance diagram for protocols::coarse_rna::CoarseRNA_Fragments:

Collaboration diagram for protocols::coarse_rna::CoarseRNA_Fragments:

Public Member Functions
	CoarseRNA_Fragments (std::string const &filename)
virtual	~CoarseRNA_Fragments ()
virtual void	apply_random_fragment (core::pose::Pose &pose, core::Size const position, core::Size const size, core::Size const type, protocols::toolbox::AllowInsertOP allow_insert)
virtual bool	is_fullatom ()
Public Member Functions inherited from protocols::rna::RNA_Fragments
	RNA_Fragments ()
virtual	~RNA_Fragments ()
	RNA_Fragments (std::string const filename)
void	read_vall_torsions (std::string const filename)
void	pick_random_fragment (TorsionSet &torsion_set, core::pose::Pose &pose, core::Size const position, core::Size const size, core::Size const type=MATCH_YR)
core::Real	torsions (core::Size const &i, core::Size const &j) const
std::string	name (core::Size const &i) const
char	secstruct (core::Size const &i) const
bool	non_main_chain_sugar_coords_defined () const
core::Real	non_main_chain_sugar_coords (core::Size const &i, core::Size const &j, core::Size const &k) const

Private Member Functions
void	insert_fragment (core::pose::Pose &pose, Size const &insert_res, Size const &source_res, Size const &frag_size, protocols::toolbox::AllowInsertOP allow_insert)
void	find_source_positions (SequenceSecStructPair const &key)
Size	pick_random_fragment (std::string const RNA_string, std::string const RNA_secstruct_string, Size const type)
Size	pick_random_fragment (core::pose::Pose &pose, Size const position, Size const size, Size const type)
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, SourcePositionsOP >	source_positions_map_
std::map< std::string, Size >	coarse_rna_name_to_num_

Detailed Description

Definition at line 65 of file CoarseRNA_Fragments.hh.

Constructor & Destructor Documentation

protocols::coarse_rna::CoarseRNA_Fragments::CoarseRNA_Fragments

(

std::string const &

filename)

Definition at line 76 of file CoarseRNA_Fragments.cc.

References initialize_frag_source_pose().

protocols::coarse_rna::CoarseRNA_Fragments::~CoarseRNA_Fragments ( )

virtual

Definition at line 67 of file CoarseRNA_Fragments.cc.

Member Function Documentation

void protocols::coarse_rna::CoarseRNA_Fragments::apply_random_fragment ( core::pose::Pose &  pose, core::Size const  position, core::Size const  size, core::Size const  type, protocols::toolbox::AllowInsertOP  allow_insert  )

virtual

Reimplemented from protocols::rna::RNA_Fragments.

Definition at line 284 of file CoarseRNA_Fragments.cc.

References insert_fragment(), and pick_random_fragment().

void protocols::coarse_rna::CoarseRNA_Fragments::find_source_positions ( SequenceSecStructPair const &  key)

private

Definition at line 176 of file CoarseRNA_Fragments.cc.

References protocols::rna::RNA_Fragments::compare_RNA_char(), protocols::rna::RNA_Fragments::compare_RNA_secstruct(), frag_source_pose_, frag_source_secstruct_, core::io::serialization::size(), and source_positions_map_.

Referenced by pick_random_fragment().

void protocols::coarse_rna::CoarseRNA_Fragments::initialize_frag_source_pose ( )

private

Definition at line 85 of file CoarseRNA_Fragments.cc.

References coarse_rna_name_to_num_, protocols::rna::figure_out_secstruct(), frag_source_file_, frag_source_pose_, frag_source_secstruct_, core::chemical::ChemicalManager::get_instance(), protocols::rna::get_rna_secstruct(), core::chemical::na_rad, and core::import_pose::pose_from_pdb().

Referenced by CoarseRNA_Fragments().

void protocols::coarse_rna::CoarseRNA_Fragments::insert_fragment ( core::pose::Pose &  pose, Size const &  insert_res, Size const &  source_res, Size const &  frag_size, protocols::toolbox::AllowInsertOP  allow_insert  )

private

Definition at line 144 of file CoarseRNA_Fragments.cc.

References core::pose::copy_dofs(), frag_source_pose_, and core::pose::Pose::total_residue().

Referenced by apply_random_fragment().

bool protocols::coarse_rna::CoarseRNA_Fragments::is_fullatom ( )

virtual

Reimplemented from protocols::rna::RNA_Fragments.

Definition at line 298 of file CoarseRNA_Fragments.cc.

Size protocols::coarse_rna::CoarseRNA_Fragments::pick_random_fragment ( std::string const  RNA_string, std::string const  RNA_secstruct_string, Size const  type  )

private

Definition at line 234 of file CoarseRNA_Fragments.cc.

References protocols::rna::convert_based_on_match_type(), find_source_positions(), protocols::coarse_rna::RG(), and source_positions_map_.

Referenced by apply_random_fragment(), and pick_random_fragment().

Size protocols::coarse_rna::CoarseRNA_Fragments::pick_random_fragment ( core::pose::Pose &  pose, Size const  position, Size const  size, Size const  type  )

private

Definition at line 266 of file CoarseRNA_Fragments.cc.

References protocols::rna::get_rna_secstruct(), pick_random_fragment(), and core::pose::Pose::sequence().

Member Data Documentation

std::map< std::string, Size > protocols::coarse_rna::CoarseRNA_Fragments::coarse_rna_name_to_num_

private

Definition at line 119 of file CoarseRNA_Fragments.hh.

Referenced by initialize_frag_source_pose().

std::string const protocols::coarse_rna::CoarseRNA_Fragments::frag_source_file_

private

Definition at line 115 of file CoarseRNA_Fragments.hh.

Referenced by initialize_frag_source_pose().

core::pose::MiniPoseOP protocols::coarse_rna::CoarseRNA_Fragments::frag_source_pose_

private

Definition at line 116 of file CoarseRNA_Fragments.hh.

Referenced by find_source_positions(), initialize_frag_source_pose(), and insert_fragment().

std::string protocols::coarse_rna::CoarseRNA_Fragments::frag_source_secstruct_

private

Definition at line 113 of file CoarseRNA_Fragments.hh.

Referenced by find_source_positions(), and initialize_frag_source_pose().

std::map< SequenceSecStructPair, SourcePositionsOP > protocols::coarse_rna::CoarseRNA_Fragments::source_positions_map_

private

Definition at line 117 of file CoarseRNA_Fragments.hh.

Referenced by find_source_positions(), and pick_random_fragment().

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

• src/protocols/coarse_rna/CoarseRNA_Fragments.hh
• src/protocols/coarse_rna/CoarseRNA_Fragments.cc