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core::fragment::picking_old::vall Namespace Reference

Namespaces

 eval
 
 gen
 
 scores
 

Classes

class  VallLibrarian
 Librarian that picks fragments from the Vall. More...
 
class  VallLibrary
 Vall fragment library. More...
 
class  VallResidue
 class for managing a line of the Vall fragment library More...
 
class  VallResidues
 wrapper for a collection of VallResidue More...
 
class  VallSection
 class implementing the Book concept for a continuous section of lines in the Vall library More...
 
class  VallSections
 wrapper for a collection of VallSection More...
 

Functions

core::fragment::FragDataOPs pick_fragments_by_ss (std::string const &ss, core::Size const top_n, bool const randomize, BBTorsionSRFD const &srfd_type)
 pick fragments by default sec.struct IdentityScore More...
 
core::fragment::FragDataOPs pick_fragments_by_ss_plus_aa (std::string const &ss, std::string const &aa, core::Size const top_n, bool const randomize, BBTorsionSRFD const &srfd_type)
 pick fragments by default sec.struct IdentityScore More...
 
core::fragment::FragDataOPs pick_fragments (std::string const &ss, std::string const &aa, utility::vector1< std::string > const &abego, core::Size const top_n, bool const randomize, BBTorsionSRFD const &srfd_type)
 pick fragments by default sec.struct IdentityScore More...
 
template<typename VallResidueIterator >
AnnotatedFragDataOP extent_to_fragdata (VallResidueIterator begin, VallResidueIterator end, BBTorsionSRFD const &srfd_type=BBTorsionSRFD())
 convert a fragment extent to a FragData instance More...
 
template<typename VallResidueIterator >
AnnotatedFragDataOP extent_to_fragdata (VallResidueIterator begin, VallResidueIterator end, core::Real score, BBTorsionSRFD const &srfd_type=BBTorsionSRFD())
 adds score to fragdata object More...
 
template<typename VallResidueIterator >
std::string extent_aa_str (VallResidueIterator begin, VallResidueIterator end)
 extract amino acid sequence from a fragment extent into a string More...
 
template<typename VallResidueIterator >
std::string extent_ss_str (VallResidueIterator begin, VallResidueIterator end)
 extract secondary structure from a fragment extent into a string More...
 
static basic::Tracer TR ("core.fragment.picking_old.vall.vall_io")
 
void vall_library_from_file (std::string const &filename, VallLibrary &library, core::Size const preallocate)
 load standard Vall library from file More...
 
static basic::Tracer TR ("core.fragment.picking_old.vall.VallLibrarian")
 

Function Documentation

template<typename VallResidueIterator >
std::string core::fragment::picking_old::vall::extent_aa_str ( VallResidueIterator  begin,
VallResidueIterator  end 
)

extract amino acid sequence from a fragment extent into a string

References core::sequence::end.

template<typename VallResidueIterator >
std::string core::fragment::picking_old::vall::extent_ss_str ( VallResidueIterator  begin,
VallResidueIterator  end 
)

extract secondary structure from a fragment extent into a string

References core::sequence::end.

template<typename VallResidueIterator >
AnnotatedFragDataOP core::fragment::picking_old::vall::extent_to_fragdata ( VallResidueIterator  begin,
VallResidueIterator  end,
BBTorsionSRFD const &  srfd_type = BBTorsionSRFD() 
)

convert a fragment extent to a FragData instance

Parameters
[in]beginIterator pointing the beginning of the VallResidue extent.
[in]endIterator pointing just past the end of the VallResidue extent.
[in]srfd_typeThe type of BBTorsionSRFD to use.

References core::sequence::end.

Referenced by extent_to_fragdata(), and core::fragment::picking_old::vall::VallLibrarian::fragments().

template<typename VallResidueIterator >
AnnotatedFragDataOP core::fragment::picking_old::vall::extent_to_fragdata ( VallResidueIterator  begin,
VallResidueIterator  end,
core::Real  score,
BBTorsionSRFD const &  srfd_type = BBTorsionSRFD() 
)

adds score to fragdata object

References extent_to_fragdata().

core::fragment::FragDataOPs core::fragment::picking_old::vall::pick_fragments ( std::string const &  ss,
std::string const &  aa,
utility::vector1< std::string > const &  abego,
core::Size const  top_n,
bool const  randomize,
BBTorsionSRFD const &  srfd_type 
)

pick fragments by default sec.struct IdentityScore

Parameters
[in]sssecondary structure string of desired frag length
[in]aaamino acid string of same length as ss string
[in]abegovector of string of desired frag length
[in]top_nreturn the top 'n' fragments, default 200
[in]randomizeadd random noise within [0, 0.001) to score to break up equivalent scores
[in]srfd_typeThe BBTorsionSRFD type to use.
[in]sssecondary structure string of desired frag length
[in]aaamino acid string of same length as ss string
[in]abegovector of string of desired frag length
[in]top_nreturn the top 'n' fragments, default 200
[in]randomizeadd random noise within [0, 0.001) to
[in]srfd_typeThe BBTorsionSRFD type to use. score to break up equivalent scores

References core::fragment::picking_old::vall::VallLibrarian::add_fragment_eval(), core::fragment::picking_old::vall::VallLibrarian::add_fragment_gen(), core::fragment::picking_old::vall::VallLibrarian::catalog(), and core::fragment::picking_old::vall::VallLibrarian::top_fragments().

Referenced by protocols::parser::FragmentReader::apply(), and protocols::forge::components::VarLengthBuild::pick_fragments().

core::fragment::FragDataOPs core::fragment::picking_old::vall::pick_fragments_by_ss ( std::string const &  ss,
core::Size const  top_n,
bool const  randomize,
BBTorsionSRFD const &  srfd_type 
)

pick fragments by default sec.struct IdentityScore

Parameters
[in]sssecondary structure string of desired frag length
[in]top_nreturn the top 'n' fragments, default 200
[in]randomizeadd random noise within [0, 0.001) to score to break up equivalent scores
[in]srfd_typeThe BBTorsionSRFD type to use.
[in]sssecondary structure string of desired frag length
[in]top_nreturn the top 'n' fragments, default 200
[in]randomizeadd random noise within [0, 0.001) to
[in]srfd_typeThe BBTorsionSRFD type to use. score to break up equivalent scores

References core::fragment::picking_old::vall::VallLibrarian::add_fragment_eval(), core::fragment::picking_old::vall::VallLibrarian::add_fragment_gen(), core::fragment::picking_old::vall::VallLibrarian::catalog(), and core::fragment::picking_old::vall::VallLibrarian::top_fragments().

Referenced by protocols::parser::FragmentReader::apply(), protocols::anchored_design::AnchorMoversData::autogenerate_design_frags(), protocols::seeded_abinitio::SegmentHybridizer::check_and_create_fragments(), protocols::forge::components::VarLengthBuild::pick_fragments(), and protocols::protein_interface_design::movers::LoopRemodel::pick_loop_frags().

core::fragment::FragDataOPs core::fragment::picking_old::vall::pick_fragments_by_ss_plus_aa ( std::string const &  ss,
std::string const &  aa,
core::Size const  top_n,
bool const  randomize,
BBTorsionSRFD const &  srfd_type 
)

pick fragments by default sec.struct IdentityScore

Parameters
[in]sssecondary structure string of desired frag length
[in]aaamino acid string of same length as ss string
[in]top_nreturn the top 'n' fragments, default 200
[in]randomizeadd random noise within [0, 0.001) to score to break up equivalent scores
[in]srfd_typeThe BBTorsionSRFD type to use.
[in]sssecondary structure string of desired frag length
[in]aaamino acid string of same length as ss string
[in]top_nreturn the top 'n' fragments, default 200
[in]randomizeadd random noise within [0, 0.001) to
[in]srfd_typeThe BBTorsionSRFD type to use. score to break up equivalent scores

References core::fragment::picking_old::vall::VallLibrarian::add_fragment_eval(), core::fragment::picking_old::vall::VallLibrarian::add_fragment_gen(), core::fragment::picking_old::vall::VallLibrarian::catalog(), and core::fragment::picking_old::vall::VallLibrarian::top_fragments().

Referenced by protocols::parser::FragmentReader::apply(), protocols::anchored_design::AnchorMoversData::autogenerate_constseq_frags(), protocols::seeded_abinitio::SegmentHybridizer::check_and_create_fragments(), protocols::hybridization::HybridizeProtocol::check_and_create_fragments(), protocols::hybridization::create_fragment_set(), protocols::hybridization::create_fragment_set_no_ssbias(), protocols::forge::components::VarLengthBuild::pick_fragments(), protocols::protein_interface_design::movers::LoopRemodel::pick_loop_frags(), and protocols::rbsegment_relax::OptimizeThreadingMover::rebuild_unaligned().

static basic::Tracer core::fragment::picking_old::vall::TR ( "core.fragment.picking_old.vall.VallLibrarian"  )
static
static basic::Tracer core::fragment::picking_old::vall::TR ( "core.fragment.picking_old.vall.vall_io"  )
static
void core::fragment::picking_old::vall::vall_library_from_file ( std::string const &  filename,
VallLibrary &  library,
core::Size const  preallocate 
)