Rosetta 3.4
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core::fragment::picking_old::vall Namespace Reference

Namespaces

namespace  eval
namespace  gen
namespace  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::FragDataList 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
core::fragment::FragDataList 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
core::fragment::FragDataList 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
template<typename VallResidueIterator >
FragDataOP extent_to_fragdata (VallResidueIterator begin, VallResidueIterator end, BBTorsionSRFD const &srfd_type=BBTorsionSRFD())
 convert a fragment extent to a FragData instance
template<typename VallResidueIterator >
std::string extent_aa_str (VallResidueIterator begin, VallResidueIterator end)
 extract amino acid sequence from a fragment extent into a string
template<typename VallResidueIterator >
std::string extent_ss_str (VallResidueIterator begin, VallResidueIterator end)
 extract secondary structure from a fragment extent into a string
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

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 >
FragDataOP 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::fragment::FragData::add_residue(), core::sequence::end, core::fragment::FragData::set_valid(), and core::fragment::FragData::size().

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

core::fragment::FragDataList 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(), core::fragment::picking_old::FragmentLibraryManager::get_instance(), core::fragment::picking_old::FragmentLibraryManager::get_Vall(), and core::fragment::picking_old::vall::VallLibrarian::top_fragments().

Referenced by protocols::jd2::parser::FragmentReader::apply().

core::fragment::FragDataList 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(), core::fragment::picking_old::FragmentLibraryManager::get_instance(), core::fragment::picking_old::FragmentLibraryManager::get_Vall(), and core::fragment::picking_old::vall::VallLibrarian::top_fragments().

Referenced by protocols::jd2::parser::FragmentReader::apply(), protocols::anchored_design::AnchorMoversData::autogenerate_design_frags(), and protocols::forge::components::VarLengthBuild::pick_fragments().

core::fragment::FragDataList 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(), core::fragment::picking_old::FragmentLibraryManager::get_instance(), core::fragment::picking_old::FragmentLibraryManager::get_Vall(), and core::fragment::picking_old::vall::VallLibrarian::top_fragments().

Referenced by protocols::jd2::parser::FragmentReader::apply(), protocols::anchored_design::AnchorMoversData::autogenerate_constseq_frags(), and protocols::forge::components::VarLengthBuild::pick_fragments().

static basic::Tracer core::fragment::picking_old::vall::TR ( "core.fragment.picking_old.vall.vall_io"  ) [static]

Referenced by vall_library_from_file().

void core::fragment::picking_old::vall::vall_library_from_file ( std::string const &  filename,
VallLibrary &  library,
core::Size const  preallocate 
)
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