#include <RNA_FragmentsClasses.hh>

Inheritance diagram for protocols::rna::RNA_Fragments:

Collaboration diagram for protocols::rna::RNA_Fragments:

Public Member Functions
	RNA_Fragments ()

virtual	~RNA_Fragments ()

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

virtual bool	is_fullatom ()

	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	pick_random_fragment (TorsionSet &torsion_set, std::string const RNA_string, std::string const RNA_secstruct_string, core::Size const type=MATCH_YR)

std::string const	convert_based_on_match_type (std::string const RNA_string, core::Size const type)

bool	compare_RNA_char (char const char1, char const char2)

bool	compare_RNA_secstruct (char const char1, char const char2)

void	pick_fragment_library (SequenceSecStructPair const &key)

void	pick_random_fragment (FArray1D< core::Real > &RNA_torsions, std::string const RNA_string)

Private Attributes
FArray2D< core::Real >	vall_torsions_

FArray3D< core::Real >	vall_non_main_chain_sugar_coords_

FArray1D< char >	vall_sequence_

FArray1D< bool >	vall_is_chainbreak_

FArray2D< bool >	vall_edge_is_base_pairing_

FArray1D< bool >	vall_makes_canonical_base_pair_

FArray1D< char >	vall_secstruct_

FArray1D< std::string >	vall_name_

core::Size	vall_size_

bool	vall_non_main_chain_sugar_coords_defined_

FragmentLibraryPointerMap	fragment_library_pointer_map

Constructor & Destructor Documentation

protocols::rna::RNA_Fragments::RNA_Fragments ( )

protocols::rna::RNA_Fragments::~RNA_Fragments ( )

virtual

protocols::rna::RNA_Fragments::RNA_Fragments ( std::string const filename)

inline

Member Function Documentation

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

virtual

Reimplemented in protocols::rna::FullAtomRNA_Fragments, and protocols::coarse_rna::CoarseRNA_Fragments.

bool protocols::rna::RNA_Fragments::compare_RNA_char	(	char const	char1,
		char const	char2
	)

private

Referenced by protocols::coarse_rna::CoarseRNA_Fragments::find_source_positions(), and protocols::rna::FullAtomRNA_Fragments::pick_fragment_library().

bool protocols::rna::RNA_Fragments::compare_RNA_secstruct	(	char const	char1,
		char const	char2
	)

private

Referenced by protocols::coarse_rna::CoarseRNA_Fragments::find_source_positions(), and protocols::rna::FullAtomRNA_Fragments::pick_fragment_library().

std::string const protocols::rna::RNA_Fragments::convert_based_on_match_type	(	std::string const	RNA_string,
		core::Size const	type
	)

private

References protocols::rna::MATCH_ALL, protocols::rna::MATCH_YR, and core::io::serialization::size().

Referenced by protocols::rna::FullAtomRNA_Fragments::pick_random_fragment().

bool protocols::rna::RNA_Fragments::is_fullatom ( )

virtual

Reimplemented in protocols::rna::FullAtomRNA_Fragments, and protocols::coarse_rna::CoarseRNA_Fragments.

std::string protocols::rna::RNA_Fragments::name ( core::Size const & i) const

inline

Referenced by protocols::rna::FragmentLibrary::add_torsion().

core::Real protocols::rna::RNA_Fragments::non_main_chain_sugar_coords	(	core::Size const &	i,
		core::Size const &	j,
		core::Size const &	k
	)		const

inline

Referenced by protocols::rna::FragmentLibrary::add_torsion().

bool protocols::rna::RNA_Fragments::non_main_chain_sugar_coords_defined ( ) const

inline

Referenced by protocols::rna::FragmentLibrary::add_torsion().

void protocols::rna::RNA_Fragments::pick_fragment_library ( SequenceSecStructPair const & key)

private

References protocols::rna::FragmentLibrary::add_torsion(), protocols::rna::compare_RNA_char(), protocols::rna::compare_RNA_secstruct(), protocols::rna::FragmentLibrary::get_align_depth(), and core::io::serialization::size().

void protocols::rna::RNA_Fragments::pick_random_fragment	(	TorsionSet &	torsion_set,
		core::pose::Pose &	pose,
		core::Size const	position,
		core::Size const	size,
		core::Size const	type = `MATCH_YR`
	)

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

void protocols::rna::RNA_Fragments::pick_random_fragment	(	TorsionSet &	torsion_set,
		std::string const	RNA_string,
		std::string const	RNA_secstruct_string,
		core::Size const	type = `MATCH_YR`
	)

private

References protocols::rna::convert_based_on_match_type().

void protocols::rna::RNA_Fragments::pick_random_fragment	(	FArray1D< core::Real > &	RNA_torsions,
		std::string const	RNA_string
	)

private

void protocols::rna::RNA_Fragments::read_vall_torsions ( std::string const filename)

References core::init(), core::scoring::rna::NUM_EDGES(), and core::scoring::rna::NUM_RNA_TORSIONS().

char protocols::rna::RNA_Fragments::secstruct ( core::Size const & i) const

inline

Referenced by protocols::rna::FragmentLibrary::add_torsion().

core::Real protocols::rna::RNA_Fragments::torsions	(	core::Size const &	i,
		core::Size const &	j
	)		const

inline

Referenced by protocols::rna::FragmentLibrary::add_torsion().

Member Data Documentation

FragmentLibraryPointerMap protocols::rna::RNA_Fragments::fragment_library_pointer_map

private

FArray2D<bool> protocols::rna::RNA_Fragments::vall_edge_is_base_pairing_

private

FArray1D<bool> protocols::rna::RNA_Fragments::vall_is_chainbreak_

private

FArray1D<bool> protocols::rna::RNA_Fragments::vall_makes_canonical_base_pair_

private

FArray1D<std::string> protocols::rna::RNA_Fragments::vall_name_

private

FArray3D<core::Real> protocols::rna::RNA_Fragments::vall_non_main_chain_sugar_coords_

private

bool protocols::rna::RNA_Fragments::vall_non_main_chain_sugar_coords_defined_

private

FArray1D<char> protocols::rna::RNA_Fragments::vall_secstruct_

private

FArray1D<char> protocols::rna::RNA_Fragments::vall_sequence_

private

core::Size protocols::rna::RNA_Fragments::vall_size_

private

FArray2D<core::Real> protocols::rna::RNA_Fragments::vall_torsions_

private

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

src/protocols/rna/RNA_Fragments.hh
src/protocols/rna/RNA_FragmentsClasses.hh
src/protocols/rna/RNA_Fragments.cc
src/protocols/rna/RNA_FragmentsClasses.cc

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation