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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::Sizeanalyze_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

typedef utility::pointer::shared_ptr< const FragmentLibrary > core::fragment::rna::FragmentLibraryCOP
typedef utility::pointer::shared_ptr< FragmentLibrary > core::fragment::rna::FragmentLibraryOP
typedef std::tuple< std::string, std::string, RNA_FragmentHomologyExclusion, utility::vector1< SYN_ANTI_RESTRICTION > > core::fragment::rna::FragmentLibraryPointerKey
typedef utility::pointer::shared_ptr< RNA_Fragments const > core::fragment::rna::RNA_FragmentsCOP
typedef utility::pointer::shared_ptr< RNA_Fragments > core::fragment::rna::RNA_FragmentsOP

Enumeration Type Documentation

Enumerator
MATCH_ALL 
MATCH_YR 
MATCH_EXACT 
Enumerator
SYN 
ANTI 
ANY 

Function Documentation

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" 
)
std::string core::fragment::rna::figure_out_secstruct ( pose::Pose pose)
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().

bool core::fragment::rna::operator< ( RNA_FragmentHomologyExclusion const &  lhs,
RNA_FragmentHomologyExclusion const &  rhs 
)
inline
bool core::fragment::rna::satisfies_restriction ( Real const  torsion,
SYN_ANTI_RESTRICTION const  restriction 
)
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().

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