#include <FullAtomRNA_Fragments.hh>

Inheritance diagram for protocols::farna::FullAtomRNA_Fragments:

Public Member Functions
	FullAtomRNA_Fragments (std::string const &filename)

	~FullAtomRNA_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 ()

void	read_vall_torsions (std::string const filename)

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

Public Member Functions inherited from protocols::farna::RNA_Fragments
	RNA_Fragments ()

virtual	~RNA_Fragments ()

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)

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)

void	insert_fragment (core::pose::Pose &pose, Size const position, protocols::farna::TorsionSet const &torsion_set, toolbox::AllowInsertOP allow_insert)

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::farna::FullAtomRNA_Fragments::FullAtomRNA_Fragments ( std::string const & filename )

References read_vall_torsions().

protocols::farna::FullAtomRNA_Fragments::~FullAtomRNA_Fragments ( )

inline

Member Function Documentation

void protocols::farna::FullAtomRNA_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 from protocols::farna::RNA_Fragments.

References insert_fragment(), and pick_random_fragment().

void protocols::farna::FullAtomRNA_Fragments::insert_fragment	(	core::pose::Pose &	pose,
		Size const	position,
		protocols::farna::TorsionSet const &	torsion_set,
		toolbox::AllowInsertOP	allow_insert
	)

private

References core::pose::rna::apply_non_main_chain_sugar_coords(), core::id::BB, core::chemical::rna::CHI, core::pose::Pose::conformation(), protocols::farna::TorsionSet::get_size(), core::conformation::named_atom_id_to_atom_id(), core::chemical::rna::non_main_chain_sugar_atoms, protocols::farna::TorsionSet::non_main_chain_sugar_coords, protocols::farna::TorsionSet::non_main_chain_sugar_coords_defined, core::chemical::rna::NUM_RNA_MAINCHAIN_TORSIONS(), core::chemical::rna::NUM_RNA_TORSIONS(), core::pose::Pose::residue(), protocols::farna::TorsionSet::secstruct, core::pose::Pose::set_secstruct(), core::pose::Pose::set_torsion(), core::io::serialization::size(), protocols::farna::TorsionSet::torsions, and core::conformation::Residue::xyz().

Referenced by apply_random_fragment().

bool protocols::farna::FullAtomRNA_Fragments::is_fullatom ( )

virtual

Reimplemented from protocols::farna::RNA_Fragments.

std::string protocols::farna::FullAtomRNA_Fragments::name ( core::Size const & i ) const

inline

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

core::Real protocols::farna::FullAtomRNA_Fragments::non_main_chain_sugar_coords	(	core::Size const &	i,
		core::Size const &	j,
		core::Size const &	k
	)		const

inline

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

bool protocols::farna::FullAtomRNA_Fragments::non_main_chain_sugar_coords_defined ( ) const

inline

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

void protocols::farna::FullAtomRNA_Fragments::pick_fragment_library ( SequenceSecStructPair const & key )

private

References protocols::farna::compare_RNA_char(), protocols::farna::compare_RNA_secstruct(), fragment_library_pointer_map, core::io::serialization::size(), vall_secstruct_, vall_sequence_, and vall_size_.

Referenced by pick_random_fragment().

void protocols::farna::FullAtomRNA_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::farna::convert_based_on_match_type(), fragment_library_pointer_map, and pick_fragment_library().

Referenced by apply_random_fragment(), and pick_random_fragment().

void protocols::farna::FullAtomRNA_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`
	)

private

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

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

private

void protocols::farna::FullAtomRNA_Fragments::read_vall_torsions ( std::string const filename )

References core::chemical::element::I, core::init::init(), core::chemical::rna::NUM_EDGES(), core::chemical::rna::NUM_RNA_TORSIONS(), vall_edge_is_base_pairing_, vall_is_chainbreak_, vall_name_, vall_non_main_chain_sugar_coords_, vall_non_main_chain_sugar_coords_defined_, vall_secstruct_, vall_sequence_, vall_size_, and vall_torsions_.

Referenced by FullAtomRNA_Fragments().

char protocols::farna::FullAtomRNA_Fragments::secstruct ( core::Size const & i ) const

inline

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

core::Real protocols::farna::FullAtomRNA_Fragments::torsions	(	core::Size const &	i,
		core::Size const &	j
	)		const

inline

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

Member Data Documentation

FragmentLibraryPointerMap protocols::farna::FullAtomRNA_Fragments::fragment_library_pointer_map

private

Referenced by pick_fragment_library(), and pick_random_fragment().

FArray2D<bool> protocols::farna::FullAtomRNA_Fragments::vall_edge_is_base_pairing_

private

Referenced by read_vall_torsions().

FArray1D<bool> protocols::farna::FullAtomRNA_Fragments::vall_is_chainbreak_

private

Referenced by read_vall_torsions().

FArray1D<bool> protocols::farna::FullAtomRNA_Fragments::vall_makes_canonical_base_pair_

private

FArray1D<std::string> protocols::farna::FullAtomRNA_Fragments::vall_name_

private

Referenced by read_vall_torsions().

FArray3D<core::Real> protocols::farna::FullAtomRNA_Fragments::vall_non_main_chain_sugar_coords_

private

Referenced by read_vall_torsions().

bool protocols::farna::FullAtomRNA_Fragments::vall_non_main_chain_sugar_coords_defined_

private

Referenced by read_vall_torsions().

FArray1D<char> protocols::farna::FullAtomRNA_Fragments::vall_secstruct_

private

Referenced by pick_fragment_library(), and read_vall_torsions().

FArray1D<char> protocols::farna::FullAtomRNA_Fragments::vall_sequence_

private

Referenced by pick_fragment_library(), and read_vall_torsions().

core::Size protocols::farna::FullAtomRNA_Fragments::vall_size_

private

Referenced by pick_fragment_library(), and read_vall_torsions().

FArray2D<core::Real> protocols::farna::FullAtomRNA_Fragments::vall_torsions_

private

Referenced by read_vall_torsions().

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

src/protocols/farna/FullAtomRNA_Fragments.hh
src/protocols/farna/FullAtomRNA_Fragments.cc

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation