core::fragment::rna Namespace Reference

Classes
class	FragmentLibrary
class	FullAtomRNA_Fragments
class	RNA_FragmentHomologyExclusion
class	RNA_Fragments
class	TorsionSet

Typedefs
typedef utility::pointer::shared_ptr< FragmentLibrary >	FragmentLibraryOP
typedef utility::pointer::shared_ptr< const FragmentLibrary >	FragmentLibraryCOP
typedef std::tuple< std::string, std::string, RNA_FragmentHomologyExclusion, utility::vector1< SYN_ANTI_RESTRICTION > >	FragmentLibraryPointerKey
typedef std::map< FragmentLibraryPointerKey, FragmentLibraryOP >	FragmentLibraryPointerMap
typedef utility::pointer::shared_ptr< RNA_FragmentHomologyExclusion >	RNA_FragmentHomologyExclusionOP
typedef utility::pointer::shared_ptr< const RNA_FragmentHomologyExclusion >	RNA_FragmentHomologyExclusionCOP
typedef utility::pointer::shared_ptr< RNA_Fragments >	RNA_FragmentsOP
typedef utility::pointer::shared_ptr< RNA_Fragments const >	RNA_FragmentsCOP

Enumerations
enum	SYN_ANTI_RESTRICTION { SYN , ANTI , ANY }
enum	_RNA_MatchType_ { MATCH_ALL , MATCH_YR , MATCH_EXACT }

Functions
static basic::Tracer	TR ("protocols.rna.denovo.fragments.FullAtomRNA_Fragments")
bool	satisfies_restriction (Real const torsion, SYN_ANTI_RESTRICTION const restriction)
utility::vector1< std::pair< Size, std::string > >	split_segments_longer_than_6mers (utility::vector1< std::pair< Size, std::string > > const &secstruct_segments)
void	obtain_secstruct_segments (utility::vector1< std::pair< Size, std::string > > &secstruct_segments, std::string const &secstruct)
std::string	figure_out_secstruct (pose::Pose &pose)
utility::vector1< core::Size >	analyze_for_homology (std::string const &in_file, RNA_Fragments const &fragments, std::string const &exclusion_match_type="MATCH_EXACT")
bool	operator< (RNA_FragmentHomologyExclusion const &lhs, RNA_FragmentHomologyExclusion const &rhs)

Typedef Documentation

FragmentLibraryCOP

typedef utility::pointer::shared_ptr< const FragmentLibrary > core::fragment::rna::FragmentLibraryCOP

FragmentLibraryOP

typedef utility::pointer::shared_ptr< FragmentLibrary > core::fragment::rna::FragmentLibraryOP

FragmentLibraryPointerKey

typedef std::tuple< std::string, std::string, RNA_FragmentHomologyExclusion, utility::vector1< SYN_ANTI_RESTRICTION > > core::fragment::rna::FragmentLibraryPointerKey

FragmentLibraryPointerMap

typedef std::map< FragmentLibraryPointerKey, FragmentLibraryOP > core::fragment::rna::FragmentLibraryPointerMap

RNA_FragmentHomologyExclusionCOP

typedef utility::pointer::shared_ptr< const RNA_FragmentHomologyExclusion > core::fragment::rna::RNA_FragmentHomologyExclusionCOP

RNA_FragmentHomologyExclusionOP

typedef utility::pointer::shared_ptr< RNA_FragmentHomologyExclusion > core::fragment::rna::RNA_FragmentHomologyExclusionOP

RNA_FragmentsCOP

typedef utility::pointer::shared_ptr< RNA_Fragments const > core::fragment::rna::RNA_FragmentsCOP

RNA_FragmentsOP

typedef utility::pointer::shared_ptr< RNA_Fragments > core::fragment::rna::RNA_FragmentsOP

Enumeration Type Documentation

_RNA_MatchType_

enum core::fragment::rna::_RNA_MatchType_

Enumerator
MATCH_ALL
MATCH_YR
MATCH_EXACT

SYN_ANTI_RESTRICTION

enum core::fragment::rna::SYN_ANTI_RESTRICTION

Enumerator
SYN
ANTI
ANY

Function Documentation

analyze_for_homology()

utility::vector1< core::Size > core::fragment::rna::analyze_for_homology	(	std::string const &	in_file,
		RNA_Fragments const &	fragments,
		std::string const &	exclusion_match_type = "MATCH_EXACT"
	)

References core::import_pose::cleanup(), core::chemical::FA_STANDARD, figure_out_secstruct(), core::fragment::rna::FragmentLibrary::get_align_depth(), core::fragment::rna::RNA_Fragments::get_fragment_library_pointer(), core::fragment::rna::FragmentLibrary::get_fragment_torsion_set(), core::fragment::rna::TorsionSet::get_index_in_vall(), core::import_pose::get_pdb_and_cleanup(), core::fragment::rna::RNA_Fragments::insert_fragment(), core::pose::make_pose_from_sequence(), MATCH_ALL, MATCH_EXACT, MATCH_YR, core::chemical::ResidueTypeBase::na_analogue(), core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, core::chemical::na_ura, obtain_secstruct_segments(), core::pose::Pose::residue_type(), core::pose::Pose::sequence(), core::pose::copydofs::setup_atom_id_map_match_atom_names(), split_segments_longer_than_6mers(), and core::scoring::superimpose_pose().

Referenced by core::fragment::rna::RNA_FragmentHomologyExclusion::RNA_FragmentHomologyExclusion().

figure_out_secstruct()

std::string core::fragment::rna::figure_out_secstruct

(

pose::Pose &

pose

)

References core::pose::rna::get_base_pairing_info(), core::scoring::rna_base_pair, and core::pose::Pose::size().

Referenced by analyze_for_homology().

obtain_secstruct_segments()

void core::fragment::rna::obtain_secstruct_segments	(	utility::vector1< std::pair< Size, std::string > > &	secstruct_segments,
		std::string const &	secstruct
	)

Referenced by analyze_for_homology().

operator<()

bool core::fragment::rna::operator< ( RNA_FragmentHomologyExclusion const &  lhs, RNA_FragmentHomologyExclusion const &  rhs  )

inline

References core::fragment::rna::RNA_FragmentHomologyExclusion::get_fragment_lines().

satisfies_restriction()

bool core::fragment::rna::satisfies_restriction	(	Real const	torsion,
		SYN_ANTI_RESTRICTION const	restriction
	)

References ANY, core::chemical::rna::RNA_FittedTorsionInfo::chi_north_anti(), core::chemical::rna::RNA_FittedTorsionInfo::chi_north_syn(), and core::chemical::rna::SYN.

Referenced by core::fragment::rna::FullAtomRNA_Fragments::pick_fragment_library().

split_segments_longer_than_6mers()

utility::vector1< std::pair< Size, std::string > > core::fragment::rna::split_segments_longer_than_6mers

(

utility::vector1< std::pair< Size, std::string > > const &

secstruct_segments

)

Referenced by analyze_for_homology().

TR()

static basic::Tracer core::fragment::rna::TR ( "protocols.rna.denovo.fragments.FullAtomRNA_Fragments"  )

static

Referenced by core::fragment::rna::FullAtomRNA_Fragments::apply_best_fragment(), core::fragment::rna::FullAtomRNA_Fragments::pick_fragment_library(), core::fragment::rna::FullAtomRNA_Fragments::pick_random_fragment(), and core::fragment::rna::FullAtomRNA_Fragments::read_vall_torsions().