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 THREAD_LOCAL 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 THREAD_LOCAL 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

Definition at line 72 of file util.hh.

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

Definition at line 85 of file util.hh.

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]	begin	Iterator pointing the beginning of the VallResidue extent.
[in]	end	Iterator pointing just past the end of the VallResidue extent.
[in]	srfd_type	The type of BBTorsionSRFD to use.

Definition at line 38 of file util.hh.

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

Definition at line 59 of file util.hh.

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]	ss	secondary structure string of desired frag length
[in]	aa	amino acid string of same length as ss string
[in]	abego	vector of string of desired frag length
[in]	top_n	return the top 'n' fragments, default 200
[in]	randomize	add random noise within [0, 0.001) to score to break up equivalent scores
[in]	srfd_type	The BBTorsionSRFD type to use.
[in]	ss	secondary structure string of desired frag length
[in]	aa	amino acid string of same length as ss string
[in]	abego	vector of string of desired frag length
[in]	top_n	return the top 'n' fragments, default 200
[in]	randomize	add random noise within [0, 0.001) to
[in]	srfd_type	The BBTorsionSRFD type to use. score to break up equivalent scores

Definition at line 117 of file util.cc.

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::jd2::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]	ss	secondary structure string of desired frag length
[in]	top_n	return the top 'n' fragments, default 200
[in]	randomize	add random noise within [0, 0.001) to score to break up equivalent scores
[in]	srfd_type	The BBTorsionSRFD type to use.
[in]	ss	secondary structure string of desired frag length
[in]	top_n	return the top 'n' fragments, default 200
[in]	randomize	add random noise within [0, 0.001) to
[in]	srfd_type	The BBTorsionSRFD type to use. score to break up equivalent scores

Definition at line 43 of file util.cc.

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::jd2::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]	ss	secondary structure string of desired frag length
[in]	aa	amino acid string of same length as ss string
[in]	top_n	return the top 'n' fragments, default 200
[in]	randomize	add random noise within [0, 0.001) to score to break up equivalent scores
[in]	srfd_type	The BBTorsionSRFD type to use.
[in]	ss	secondary structure string of desired frag length
[in]	aa	amino acid string of same length as ss string
[in]	top_n	return the top 'n' fragments, default 200
[in]	randomize	add random noise within [0, 0.001) to
[in]	srfd_type	The BBTorsionSRFD type to use. score to break up equivalent scores

Definition at line 79 of file util.cc.

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::jd2::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 THREAD_LOCAL basic::Tracer core::fragment::picking_old::vall::TR ( "core.fragment.picking_old.vall.VallLibrarian"  )

static

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

static

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

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

load standard Vall library from file

Parameters

[in]	filename
[out]	vall

Remarks

Currently a difference in id (pdb name) or resi (residue sequence id) will start a new stretch of lines defining a VallSection

Parameters

[in]	filename
[out]	vall

Definition at line 57 of file vall_io.cc.

References core::fragment::picking_old::vall::VallLibrary::add_section(), core::fragment::picking_old::vall::VallSection::append_residue(), core::fragment::picking_old::concepts::Book< Pages >::clear(), core::fragment::picking_old::vall::VallResidue::fill_from_string(), core::fragment::picking_old::vall::VallResidue::id(), core::fragment::picking_old::vall::VallLibrary::n_residues(), core::fragment::picking_old::vall::VallLibrary::reserve(), core::fragment::picking_old::vall::VallResidue::resi(), protocols::sparta::section(), core::fragment::picking_old::concepts::Book< Pages >::size(), core::fragment::picking_old::concepts::Library< Books >::size(), core::fragment::picking_old::vall::VallLibrary::tighten_memory(), and TR().

Referenced by core::fragment::picking_old::FragmentLibraryManager::get_Vall().