#include <FullAtomRNA_Fragments.hh>

Inheritance diagram for core::fragment::rna::FullAtomRNA_Fragments:

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

	~FullAtomRNA_Fragments () override

void	apply_random_fragment (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) const override

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 override

bool	is_fullatom () override

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

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

FragmentLibraryOP	get_fragment_library_pointer (std::string const &RNA_string, std::string const &RNA_secstruct_string, RNA_FragmentHomologyExclusionCOP const &homology_exclusion, utility::vector1< SYN_ANTI_RESTRICTION > const &restriction=utility::vector1< SYN_ANTI_RESTRICTION >(), Size const type=MATCH_YR) const override

void	insert_fragment (core::pose::Pose &pose, Size const position, TorsionSet const &torsion_set, core::pose::toolbox::AtomLevelDomainMapCOP atom_level_domain_map) const override

Public Member Functions inherited from core::fragment::rna::RNA_Fragments
	RNA_Fragments ()

	~RNA_Fragments () override

Private Member Functions
void	read_vall_torsions (std::string const &filename)

void	pick_random_fragment (TorsionSet &torsion_set, std::string const &RNA_string, std::string const &RNA_secstruct_string, RNA_FragmentHomologyExclusionCOP const &homology_exclusion, utility::vector1< SYN_ANTI_RESTRICTION > const &restriction=utility::vector1< SYN_ANTI_RESTRICTION >(), core::Size const type=MATCH_YR) const

void	pick_random_fragment (TorsionSet &torsion_set, core::pose::Pose &pose, core::Size const position, core::Size const size, RNA_FragmentHomologyExclusionCOP const &homology_exclusion, core::Size const type=MATCH_YR) const

void	pick_fragment_library (FragmentLibraryPointerKey const &key) const

Private Attributes
ObjexxFCL::FArray2D< core::Real >	vall_torsions_

ObjexxFCL::FArray3D< core::Real >	vall_non_main_chain_sugar_coords_

ObjexxFCL::FArray1D< char >	vall_sequence_

ObjexxFCL::FArray1D< bool >	vall_is_chainbreak_

ObjexxFCL::FArray2D< bool >	vall_edge_is_base_pairing_

ObjexxFCL::FArray1D< bool >	vall_makes_canonical_base_pair_

ObjexxFCL::FArray1D< char >	vall_secstruct_

ObjexxFCL::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

core::fragment::rna::FullAtomRNA_Fragments::FullAtomRNA_Fragments ( std::string const & filename )

References read_vall_torsions().

core::fragment::rna::FullAtomRNA_Fragments::~FullAtomRNA_Fragments ( )

inlineoverride

Member Function Documentation

void core::fragment::rna::FullAtomRNA_Fragments::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

overridevirtual

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

References core::fragment::rna::ANTI, core::fragment::rna::ANY, core::pose::full_model_info::const_full_model_info(), core::pose::full_model_info::full_model_info_defined(), get_fragment_library_pointer(), core::pose::rna::secstruct_legacy::get_rna_secstruct_legacy(), insert_fragment(), core::chemical::ResidueTypeBase::na_analogue(), core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, core::chemical::na_ura, core::pose::Pose::residue_type(), core::pose::Pose::sequence(), core::pose::Pose::size(), core::fragment::rna::SYN, and core::fragment::rna::TR().

void core::fragment::rna::FullAtomRNA_Fragments::apply_random_fragment	(	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
	)		const

overridevirtual

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

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

FragmentLibraryOP core::fragment::rna::FullAtomRNA_Fragments::get_fragment_library_pointer	(	std::string const &	RNA_string,
		std::string const &	RNA_secstruct_string,
		RNA_FragmentHomologyExclusionCOP const &	homology_exclusion,
		utility::vector1< SYN_ANTI_RESTRICTION > const &	restriction = `utility::vector1< SYN_ANTI_RESTRICTION >()`,
		Size const	type = `MATCH_YR`
	)		const

overridevirtual

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

References core::import_pose::convert_based_on_match_type(), fragment_library_pointer_map, and pick_fragment_library().

Referenced by apply_best_fragment(), and pick_random_fragment().

void core::fragment::rna::FullAtomRNA_Fragments::insert_fragment	(	core::pose::Pose &	pose,
		Size const	position,
		TorsionSet const &	torsion_set,
		core::pose::toolbox::AtomLevelDomainMapCOP	atom_level_domain_map
	)		const

overridevirtual

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

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

Referenced by apply_best_fragment(), and apply_random_fragment().

bool core::fragment::rna::FullAtomRNA_Fragments::is_fullatom ( )

overridevirtual

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

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

inline

References vall_name_.

Referenced by core::fragment::rna::FragmentLibrary::add_torsion().

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

inline

References vall_non_main_chain_sugar_coords_.

Referenced by core::fragment::rna::FragmentLibrary::add_torsion().

bool core::fragment::rna::FullAtomRNA_Fragments::non_main_chain_sugar_coords_defined ( ) const

inline

References vall_non_main_chain_sugar_coords_defined_.

Referenced by core::fragment::rna::FragmentLibrary::add_torsion().

void core::fragment::rna::FullAtomRNA_Fragments::pick_fragment_library ( FragmentLibraryPointerKey const & key ) const

private

References core::fragment::rna::ANTI, core::fragment::rna::ANY, core::import_pose::compare_RNA_char(), core::import_pose::compare_RNA_secstruct(), fragment_library_pointer_map, core::fragment::rna::RNA_FragmentHomologyExclusion::get_fragment_lines(), core::fragment::rna::satisfies_restriction(), core::fragment::rna::SYN, core::fragment::rna::TR(), vall_secstruct_, vall_sequence_, vall_size_, and vall_torsions_.

Referenced by get_fragment_library_pointer().

void core::fragment::rna::FullAtomRNA_Fragments::pick_random_fragment	(	TorsionSet &	torsion_set,
		std::string const &	RNA_string,
		std::string const &	RNA_secstruct_string,
		RNA_FragmentHomologyExclusionCOP const &	homology_exclusion,
		utility::vector1< SYN_ANTI_RESTRICTION > const &	restriction = `utility::vector1< SYN_ANTI_RESTRICTION >()`,
		core::Size const	type = `MATCH_YR`
	)		const

private

References get_fragment_library_pointer(), and core::fragment::rna::TR().

Referenced by apply_random_fragment(), and pick_random_fragment().

void core::fragment::rna::FullAtomRNA_Fragments::pick_random_fragment	(	TorsionSet &	torsion_set,
		core::pose::Pose &	pose,
		core::Size const	position,
		core::Size const	size,
		RNA_FragmentHomologyExclusionCOP const &	homology_exclusion,
		core::Size const	type = `MATCH_YR`
	)		const

private

References core::fragment::rna::ANTI, core::fragment::rna::ANY, core::pose::full_model_info::const_full_model_info(), core::pose::full_model_info::full_model_info_defined(), core::pose::rna::secstruct_legacy::get_rna_secstruct_legacy(), core::chemical::ResidueTypeBase::na_analogue(), core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, core::chemical::na_ura, pick_random_fragment(), core::pose::Pose::residue_type(), core::pose::Pose::sequence(), and core::fragment::rna::SYN.

void core::fragment::rna::FullAtomRNA_Fragments::read_vall_torsions ( std::string const & filename )

private

References core::chemical::element::I, core::init::init(), core::chemical::rna::NUM_EDGES(), core::chemical::rna::NUM_RNA_TORSIONS(), core::fragment::rna::TR(), 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 core::fragment::rna::FullAtomRNA_Fragments::secstruct ( core::Size const & i ) const

inline

References vall_secstruct_.

Referenced by core::fragment::rna::FragmentLibrary::add_torsion().

core::Real core::fragment::rna::FullAtomRNA_Fragments::torsions	(	core::Size const &	i,
		core::Size const &	j
	)		const

inline

References vall_torsions_.

Referenced by core::fragment::rna::FragmentLibrary::add_torsion().

Member Data Documentation

FragmentLibraryPointerMap core::fragment::rna::FullAtomRNA_Fragments::fragment_library_pointer_map

mutableprivate

Referenced by get_fragment_library_pointer(), and pick_fragment_library().

ObjexxFCL::FArray2D<bool> core::fragment::rna::FullAtomRNA_Fragments::vall_edge_is_base_pairing_

private

Referenced by read_vall_torsions().

ObjexxFCL::FArray1D<bool> core::fragment::rna::FullAtomRNA_Fragments::vall_is_chainbreak_

private

Referenced by read_vall_torsions().

ObjexxFCL::FArray1D<bool> core::fragment::rna::FullAtomRNA_Fragments::vall_makes_canonical_base_pair_

private

ObjexxFCL::FArray1D<std::string> core::fragment::rna::FullAtomRNA_Fragments::vall_name_

private

Referenced by name(), and read_vall_torsions().

ObjexxFCL::FArray3D<core::Real> core::fragment::rna::FullAtomRNA_Fragments::vall_non_main_chain_sugar_coords_

private

Referenced by non_main_chain_sugar_coords(), and read_vall_torsions().

bool core::fragment::rna::FullAtomRNA_Fragments::vall_non_main_chain_sugar_coords_defined_

private

Referenced by non_main_chain_sugar_coords_defined(), and read_vall_torsions().

ObjexxFCL::FArray1D<char> core::fragment::rna::FullAtomRNA_Fragments::vall_secstruct_

private

Referenced by pick_fragment_library(), read_vall_torsions(), and secstruct().

ObjexxFCL::FArray1D<char> core::fragment::rna::FullAtomRNA_Fragments::vall_sequence_

private

Referenced by pick_fragment_library(), and read_vall_torsions().

core::Size core::fragment::rna::FullAtomRNA_Fragments::vall_size_

private

Referenced by pick_fragment_library(), and read_vall_torsions().

ObjexxFCL::FArray2D<core::Real> core::fragment::rna::FullAtomRNA_Fragments::vall_torsions_

private

Referenced by pick_fragment_library(), read_vall_torsions(), and torsions().

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

src/core/fragment/rna/FullAtomRNA_Fragments.hh
src/core/fragment/rna/FullAtomRNA_Fragments.cc

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation