#include <FullAtomRNA_Fragments.hh>

Inheritance diagram for protocols::rna::FullAtomRNA_Fragments:

Collaboration diagram for protocols::rna::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::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	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::rna::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

Detailed Description

Definition at line 125 of file FullAtomRNA_Fragments.hh.

Constructor & Destructor Documentation

protocols::rna::FullAtomRNA_Fragments::FullAtomRNA_Fragments ( std::string const & filename)

Definition at line 176 of file FullAtomRNA_Fragments.cc.

References read_vall_torsions().

protocols::rna::FullAtomRNA_Fragments::~FullAtomRNA_Fragments ( )

inline

Definition at line 131 of file FullAtomRNA_Fragments.hh.

Member Function Documentation

void protocols::rna::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::rna::RNA_Fragments.

Definition at line 313 of file FullAtomRNA_Fragments.cc.

References insert_fragment(), and pick_random_fragment().

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

private

Definition at line 327 of file FullAtomRNA_Fragments.cc.

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

Referenced by apply_random_fragment().

bool protocols::rna::FullAtomRNA_Fragments::is_fullatom ( )

virtual

Reimplemented from protocols::rna::RNA_Fragments.

Definition at line 533 of file FullAtomRNA_Fragments.cc.

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

inline

Definition at line 152 of file FullAtomRNA_Fragments.hh.

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

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

inline

Definition at line 161 of file FullAtomRNA_Fragments.hh.

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

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

inline

Definition at line 158 of file FullAtomRNA_Fragments.hh.

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

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

private

Definition at line 184 of file FullAtomRNA_Fragments.cc.

References protocols::rna::RNA_Fragments::compare_RNA_char(), protocols::rna::RNA_Fragments::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::rna::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

Definition at line 257 of file FullAtomRNA_Fragments.cc.

References protocols::rna::RNA_Fragments::convert_based_on_match_type(), fragment_library_pointer_map, and pick_fragment_library().

Referenced by apply_random_fragment(), and pick_random_fragment().

void protocols::rna::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`
	)