#include <CoarseRNA_Fragments.hh>

Inheritance diagram for protocols::rna::denovo::coarse::CoarseRNA_Fragments:

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, SourcePositionsOP >	source_positions_map_

std::map< std::string, core::Size >	coarse_rna_name_to_num_

Constructor & Destructor Documentation

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

References initialize_frag_source_pose().

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

overridedefault

Member Function Documentation

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

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

References insert_fragment(), pick_random_fragment(), and core::pose::Pose::size().

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

private

References core::import_pose::compare_RNA_char(), core::import_pose::compare_RNA_secstruct(), frag_source_pose_, frag_source_secstruct_, source_positions_map_, and protocols::rna::denovo::TR().

Referenced by pick_random_fragment().

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

private

References coarse_rna_name_to_num_, core::pose::rna::figure_out_secstruct(), frag_source_file_, frag_source_pose_, frag_source_secstruct_, core::pose::rna::secstruct_legacy::get_rna_secstruct_legacy(), core::chemical::na_rad, core::import_pose::PDB_file, and core::import_pose::pose_from_file().

Referenced by CoarseRNA_Fragments().

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().

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

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

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

overridevirtual

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

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

References core::import_pose::convert_based_on_match_type(), find_source_positions(), core::scoring::rg, source_positions_map_, and protocols::rna::denovo::TR().

Referenced by apply_random_fragment(), and pick_random_fragment().

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

References core::pose::rna::secstruct_legacy::get_rna_secstruct_legacy(), pick_random_fragment(), and core::pose::Pose::sequence().

Member Data Documentation

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

private

Referenced by initialize_frag_source_pose().

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

private

Referenced by initialize_frag_source_pose().

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

private

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

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

private

Referenced by find_source_positions(), and initialize_frag_source_pose().

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

mutableprivate

Referenced by find_source_positions(), and pick_random_fragment().

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

src/protocols/rna/denovo/coarse/CoarseRNA_Fragments.hh
src/protocols/rna/denovo/coarse/CoarseRNA_Fragments.cc

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation