protocols::frag_picker Namespace Reference

Namespaces
	nonlocal
	quota
	scores

Classes
class	BestTotalScoreSelector
	selects a given number of fragments using a quota scheme More...
class	BoundedPriorityQueue
class	BoundedCollector
	Keeps the N best fragments candidates for the final selection. More...
class	BoundedCollector_CompareTotalScore
class	CandidatesCollector
	A base class for collecting fragments. More...
class	CompareQueryPosition
	comparator based on a sequence position in a query More...
class	CompareTotalScore
	comparator based on the total score of fragments More...
class	CompareByScoreCombination
	comparator based on the linear combination of some score components More...
class	CompareScoreComponent
	comparator based on one of the score components calculated for fragments More...
class	CompositeFragmentSelector
	selects fragments by running several selectors More...
class	Contact
class	ContactCounts
class	CS2ndShift
class	CSTalosIO
class	CustomScoreSelector
	selects a given number of fragments using a quota scheme More...
class	DiversifyCrmsdByClustering
	selects fragments by running several selectors More...
class	DiversifyCrmsdSelector
	selects fragments by running several selectors More...
class	DiversifyDihedralsSelector
	selects fragments by running several selectors More...
class	FragmentCandidate
	Vector candidate says which X-mer from vall fits to a query sequence. More...
class	FragmentComparatorBase
class	QuotaDebug
class	FragmentPicker
	The core of the fragment picking machinery. More...
class	FragmentSelectingRule
	selects a given number of fragments just by selecting the best ones More...
class	GrabAllCollector
	Keeps all fragments candidates for the final selection. More...
class	JCouplingIO
class	LAMBEGO_IO
class	LazySortedVector1
class	PdbIdChunkFilter
class	AllowPdbIdFilter
	Accepts a chunk based on the pdb id of the source protein. More...
class	DenyPdbIdFilter
	Denies a chunk based on the pdb id of the source protein. More...
class	PhiPsiTalosIO
class	SidechainContactDistCutoff
	defines sidechain contact distance cutoffs. More...
class	TorsionBinIO
class	VallChunk
	represents a chunk of residues extracted from a vall. More...
class	VallChunkFilter
	a base class for a chunk filtering mechanism More...
class	VallProvider
	a vector of vall chunks More...
class	VallResidue
	class for managing a line of the Vall fragment library More...

Typedefs
typedef utility::pointer::owning_ptr < BestTotalScoreSelector >	BestTotalScoreSelectorOP
typedef utility::pointer::owning_ptr < BestTotalScoreSelector const >	BestTotalScoreSelectorCOP
typedef utility::pointer::owning_ptr < CandidatesCollector >	CandidatesCollectorOP
typedef utility::pointer::owning_ptr < CandidatesCollector const >	CandidatesCollectorCOP
typedef utility::pointer::owning_ptr < CompareQueryPosition >	CompareQueryPositionOP
typedef utility::pointer::owning_ptr < CompareQueryPosition const >	CompareQueryPositionCOP
typedef utility::pointer::owning_ptr < CompareTotalScore >	CompareTotalScoreOP
typedef utility::pointer::owning_ptr < CompareTotalScore const >	CompareTotalScoreCOP
typedef utility::pointer::owning_ptr < CompareScoreComponent >	CompareScoreComponentOP
typedef utility::pointer::owning_ptr < CompareScoreComponent const >	CompareScoreComponentCOP
typedef utility::pointer::owning_ptr < Contact >	ContactOP
typedef utility::pointer::owning_ptr < Contact const >	ContactCOP
typedef utility::pointer::owning_ptr < ContactCounts >	ContactCountsOP
typedef utility::pointer::owning_ptr < ContactCounts const >	ContactCountsCOP
typedef utility::vector1 < std::pair< ScoredCandidate, core::Real > >	ExtraScoreVector
typedef utility::pointer::owning_ptr < CustomScoreSelector >	CustomScoreSelectorOP
typedef utility::pointer::owning_ptr < CustomScoreSelector const >	CustomScoreSelectorCOP
typedef utility::pointer::owning_ptr < FragmentCandidate >	FragmentCandidateOP
typedef utility::pointer::owning_ptr < FragmentCandidate const >	FragmentCandidateCOP
typedef std::pair < FragmentCandidateOP, scores::FragmentScoreMapOP >	ScoredCandidate
typedef utility::vector1 < ScoredCandidate >	ScoredCandidatesVector1
typedef utility::pointer::owning_ptr < FragmentComparatorBase >	FragmentComparatorBaseOP
typedef utility::pointer::owning_ptr < FragmentComparatorBase const >	FragmentComparatorBaseCOP
typedef utility::pointer::owning_ptr < FragmentPicker >	FragmentPickerOP
typedef utility::pointer::owning_ptr < FragmentPicker const >	FragmentPickerCOP
typedef std::pair< Size, Size >	PosPair
typedef std::pair < FragmentCandidateOP, scores::FragmentScoreMapOP >	Candidate
typedef utility::vector1 < Candidate >	Candidates
typedef std::map< Size, CandidatesCollectorOP >	CandidatesSink
typedef utility::pointer::owning_ptr < FragmentSelectingRule >	FragmentSelectingRuleOP
typedef utility::pointer::owning_ptr < FragmentSelectingRule const >	FragmentSelectingRuleCOP
typedef utility::pointer::owning_ptr < GrabAllCollector >	GrabAllCollectorOP
typedef utility::pointer::owning_ptr < GrabAllCollector const >	GrabAllCollectorCOP
typedef utility::pointer::owning_ptr < PdbIdChunkFilter >	PdbIdChunkFilterOP
typedef utility::pointer::owning_ptr < PdbIdChunkFilter const >	PdbIdChunkFilterCOP
typedef utility::pointer::owning_ptr < AllowPdbIdFilter >	AllowPdbIdFilterOP
typedef utility::pointer::owning_ptr < AllowPdbIdFilter const >	AllowPdbIdFilterCOP
typedef utility::pointer::owning_ptr < DenyPdbIdFilter >	DenyPdbIdFilterOP
typedef utility::pointer::owning_ptr < DenyPdbIdFilter const >	DenyPdbIdFilterCOP
typedef utility::pointer::owning_ptr < SidechainContactDistCutoff >	SidechainContactDistCutoffOP
typedef utility::pointer::owning_ptr < SidechainContactDistCutoff const >	SidechainContactDistCutoffCOP
typedef utility::pointer::owning_ptr < VallChunk >	VallChunkOP
typedef utility::pointer::owning_ptr < VallChunk const >	VallChunkCOP
typedef utility::pointer::owning_ptr < VallChunkFilter >	VallChunkFilterOP
typedef utility::pointer::owning_ptr < VallChunkFilter const >	VallChunkFilterCOP
typedef utility::pointer::owning_ptr < VallProvider >	VallProviderOP
typedef utility::pointer::owning_ptr < VallProvider const >	VallProviderCOP
typedef utility::pointer::access_ptr < VallProvider >	VallProviderAP
typedef utility::pointer::access_ptr < VallProvider const >	VallProviderCAP
typedef utility::pointer::owning_ptr < VallResidue >	VallResidueOP
typedef utility::pointer::owning_ptr < VallResidue const >	VallResidueCOP

Enumerations
enum	ContactType {   CA =1, CB, CEN, UNK,   num_contact_types = UNK }

Functions
static basic::Tracer	trBestTotalScoreSelector ("protocols.frag_picker.BestTotalScoreSelector")
std::map< std::string, ContactType >	setup_name2type ()
	BEGIN: local functions. More...
std::map< std::string, ContactType > &	name2type ()
	map that converts string name to enum More...
utility::vector1< std::string >	setup_type2name ()
	setup the vector that maps enum to string name More...
utility::vector1< std::string > &	type2name ()
	vector that maps enum to string name More...
ContactType	contact_type (std::string const &name)
	END: local functions. More...
std::string	contact_name (ContactType type)
	give an enum type and return the string name More...
static basic::Tracer	tr ("protocols.frag_picker.SecondaryShiftCalculator")
static basic::Tracer	tr ("protocols.frag_picker.TalosReader")
static basic::Tracer	trCustomScoreSelector ("protocols.frag_picker.CustomScoreSelector")
bool	sort_function (ExtraScoreVector::value_type p1, ExtraScoreVector::value_type p2)
static basic::Tracer	trDiversifyCrmsdByClustering ("protocols.frag_picker.DiversifyCrmsdByClustering")
static basic::Tracer	trDiversifyCrmsdSelector ("protocols.frag_picker.DiversifyCrmsdSelector")
static basic::Tracer	trDiversifyDihedralsSelector ("protocols.frag_picker.DiversifyDihedralsSelector")
std::map< char, core::Real >	setup_faraggi_map ()
	setup the faraggi SA max map, see Faraggi et al. Proteins 2008 More...
std::map< char, core::Real > &	sa_faraggi_max ()
	faraggi SA max map More...
core::Real	sa_faraggi_max (char aa)
static basic::Tracer	trFragmentCandidate ("protocols.frag_picker.FragmentCandidate")
utility::vector1 < FragmentCandidateOP >	read_fragment_candidates (std::string file_name, VallProviderOP chunk_owner, Size max_nfrags_per_pos)
std::ostream &	operator<< (std::ostream &out, FragmentCandidate const &fr)
std::ostream &	operator<< (std::ostream &out, std::pair< FragmentCandidateOP, scores::FragmentScoreMapOP > const &pair)
static basic::Tracer	tr ("protocols.frag_picker.FragmentPicker")
static basic::Tracer	trJCouplingIO ("protocols.frag_picker.TalosReader")
static basic::Tracer	tracer ("protocols.frag_picker.LAMBEGO_IO")
static basic::Tracer	trPdbFilter ("protocols.frag_picker.PdbIdChunkFilter")
static basic::Tracer	tr ("protocols.frag_picker.PhiPsiTalosIO")
static basic::Tracer	TR ("protocols.frag_picker.SidechainContactDistCutoff")
static basic::Tracer	tracer ("protocols.frag_picker.TorsionBinIO")
static basic::Tracer	TR ("protocols.frag_picker.VallResidue")

Typedef Documentation

typedef utility::pointer::owning_ptr<AllowPdbIdFilter const> protocols::frag_picker::AllowPdbIdFilterCOP

Definition at line 35 of file PdbIdChunkFilter.fwd.hh.

typedef utility::pointer::owning_ptr<AllowPdbIdFilter> protocols::frag_picker::AllowPdbIdFilterOP

Definition at line 33 of file PdbIdChunkFilter.fwd.hh.

typedef utility::pointer::owning_ptr<BestTotalScoreSelector const> protocols::frag_picker::BestTotalScoreSelectorCOP

Definition at line 29 of file BestTotalScoreSelector.fwd.hh.

typedef utility::pointer::owning_ptr<BestTotalScoreSelector> protocols::frag_picker::BestTotalScoreSelectorOP

Definition at line 24 of file BestTotalScoreSelector.fwd.hh.

typedef std::pair<FragmentCandidateOP, scores::FragmentScoreMapOP> protocols::frag_picker::Candidate

Definition at line 58 of file FragmentPicker.hh.

typedef utility::vector1<Candidate> protocols::frag_picker::Candidates

Definition at line 59 of file FragmentPicker.hh.

typedef utility::pointer::owning_ptr<CandidatesCollector const> protocols::frag_picker::CandidatesCollectorCOP

Definition at line 29 of file CandidatesCollector.fwd.hh.

typedef utility::pointer::owning_ptr<CandidatesCollector> protocols::frag_picker::CandidatesCollectorOP

Definition at line 25 of file CandidatesCollector.fwd.hh.

typedef std::map<Size, CandidatesCollectorOP> protocols::frag_picker::CandidatesSink

Definition at line 60 of file FragmentPicker.hh.

typedef utility::pointer::owning_ptr<CompareQueryPosition const> protocols::frag_picker::CompareQueryPositionCOP

Definition at line 29 of file CommonFragmentComparators.fwd.hh.

typedef utility::pointer::owning_ptr<CompareQueryPosition> protocols::frag_picker::CompareQueryPositionOP

Definition at line 26 of file CommonFragmentComparators.fwd.hh.

typedef utility::pointer::owning_ptr<CompareScoreComponent const> protocols::frag_picker::CompareScoreComponentCOP

Definition at line 35 of file CommonFragmentComparators.fwd.hh.

typedef utility::pointer::owning_ptr<CompareScoreComponent> protocols::frag_picker::CompareScoreComponentOP

Definition at line 34 of file CommonFragmentComparators.fwd.hh.

typedef utility::pointer::owning_ptr<CompareTotalScore const> protocols::frag_picker::CompareTotalScoreCOP

Definition at line 32 of file CommonFragmentComparators.fwd.hh.

typedef utility::pointer::owning_ptr<CompareTotalScore> protocols::frag_picker::CompareTotalScoreOP

Definition at line 31 of file CommonFragmentComparators.fwd.hh.

typedef utility::pointer::owning_ptr<Contact const> protocols::frag_picker::ContactCOP

Definition at line 28 of file Contact.fwd.hh.

typedef utility::pointer::owning_ptr<ContactCounts const> protocols::frag_picker::ContactCountsCOP

Definition at line 28 of file ContactCounts.fwd.hh.

typedef utility::pointer::owning_ptr<ContactCounts> protocols::frag_picker::ContactCountsOP

Definition at line 25 of file ContactCounts.fwd.hh.

typedef utility::pointer::owning_ptr<Contact> protocols::frag_picker::ContactOP

Definition at line 25 of file Contact.fwd.hh.

typedef utility::pointer::owning_ptr<CustomScoreSelector const> protocols::frag_picker::CustomScoreSelectorCOP

Definition at line 29 of file CustomScoreSelector.fwd.hh.

typedef utility::pointer::owning_ptr<CustomScoreSelector> protocols::frag_picker::CustomScoreSelectorOP

Definition at line 24 of file CustomScoreSelector.fwd.hh.

typedef utility::pointer::owning_ptr<DenyPdbIdFilter const> protocols::frag_picker::DenyPdbIdFilterCOP

Definition at line 38 of file PdbIdChunkFilter.fwd.hh.

typedef utility::pointer::owning_ptr<DenyPdbIdFilter> protocols::frag_picker::DenyPdbIdFilterOP

Definition at line 37 of file PdbIdChunkFilter.fwd.hh.

typedef utility::vector1<std::pair< ScoredCandidate, core::Real> > protocols::frag_picker::ExtraScoreVector

Definition at line 32 of file CustomScoreSelector.cc.

typedef utility::pointer::owning_ptr<FragmentCandidate const> protocols::frag_picker::FragmentCandidateCOP

Definition at line 32 of file FragmentCandidate.fwd.hh.

typedef utility::pointer::owning_ptr<FragmentCandidate> protocols::frag_picker::FragmentCandidateOP

Definition at line 29 of file FragmentCandidate.fwd.hh.

typedef utility::pointer::owning_ptr<FragmentComparatorBase const> protocols::frag_picker::FragmentComparatorBaseCOP

Definition at line 27 of file FragmentComparatorBase.fwd.hh.

typedef utility::pointer::owning_ptr<FragmentComparatorBase> protocols::frag_picker::FragmentComparatorBaseOP

Definition at line 24 of file FragmentComparatorBase.fwd.hh.

typedef utility::pointer::owning_ptr<FragmentPicker const> protocols::frag_picker::FragmentPickerCOP

Definition at line 27 of file FragmentPicker.fwd.hh.

typedef utility::pointer::owning_ptr<FragmentPicker> protocols::frag_picker::FragmentPickerOP

Definition at line 24 of file FragmentPicker.fwd.hh.

typedef utility::pointer::owning_ptr<FragmentSelectingRule const> protocols::frag_picker::FragmentSelectingRuleCOP

Definition at line 29 of file FragmentSelectingRule.fwd.hh.

typedef utility::pointer::owning_ptr<FragmentSelectingRule> protocols::frag_picker::FragmentSelectingRuleOP

Definition at line 24 of file FragmentSelectingRule.fwd.hh.

typedef utility::pointer::owning_ptr< GrabAllCollector const > protocols::frag_picker::GrabAllCollectorCOP

Definition at line 39 of file GrabAllCollector.hh.

typedef utility::pointer::owning_ptr< GrabAllCollector > protocols::frag_picker::GrabAllCollectorOP

Definition at line 37 of file GrabAllCollector.hh.

typedef utility::pointer::owning_ptr<PdbIdChunkFilter const> protocols::frag_picker::PdbIdChunkFilterCOP

Definition at line 31 of file PdbIdChunkFilter.fwd.hh.

typedef utility::pointer::owning_ptr<PdbIdChunkFilter> protocols::frag_picker::PdbIdChunkFilterOP

Definition at line 27 of file PdbIdChunkFilter.fwd.hh.

typedef std::pair<Size,Size> protocols::frag_picker::PosPair

Definition at line 57 of file FragmentPicker.hh.

typedef std::pair<FragmentCandidateOP, scores::FragmentScoreMapOP> protocols::frag_picker::ScoredCandidate

Definition at line 33 of file FragmentCandidate.fwd.hh.

typedef utility::vector1<ScoredCandidate> protocols::frag_picker::ScoredCandidatesVector1

Definition at line 34 of file FragmentCandidate.fwd.hh.

typedef utility::pointer::owning_ptr<SidechainContactDistCutoff const> protocols::frag_picker::SidechainContactDistCutoffCOP

Definition at line 23 of file SidechainContactDistCutoff.fwd.hh.

typedef utility::pointer::owning_ptr<SidechainContactDistCutoff> protocols::frag_picker::SidechainContactDistCutoffOP

Definition at line 21 of file SidechainContactDistCutoff.fwd.hh.

typedef utility::pointer::owning_ptr<VallChunk const> protocols::frag_picker::VallChunkCOP

Definition at line 28 of file VallChunk.fwd.hh.

typedef utility::pointer::owning_ptr<VallChunkFilter const> protocols::frag_picker::VallChunkFilterCOP

Definition at line 28 of file VallChunkFilter.fwd.hh.

typedef utility::pointer::owning_ptr<VallChunkFilter> protocols::frag_picker::VallChunkFilterOP

Definition at line 25 of file VallChunkFilter.fwd.hh.

typedef utility::pointer::owning_ptr<VallChunk> protocols::frag_picker::VallChunkOP

Definition at line 25 of file VallChunk.fwd.hh.

typedef utility::pointer::access_ptr<VallProvider> protocols::frag_picker::VallProviderAP

Definition at line 30 of file VallProvider.fwd.hh.

typedef utility::pointer::access_ptr<VallProvider const> protocols::frag_picker::VallProviderCAP

Definition at line 31 of file VallProvider.fwd.hh.

typedef utility::pointer::owning_ptr<VallProvider const> protocols::frag_picker::VallProviderCOP

Definition at line 28 of file VallProvider.fwd.hh.

typedef utility::pointer::owning_ptr<VallProvider> protocols::frag_picker::VallProviderOP

Definition at line 25 of file VallProvider.fwd.hh.

typedef utility::pointer::owning_ptr<VallResidue const> protocols::frag_picker::VallResidueCOP

Definition at line 28 of file VallResidue.fwd.hh.

typedef utility::pointer::owning_ptr<VallResidue> protocols::frag_picker::VallResidueOP

Definition at line 25 of file VallResidue.fwd.hh.

Enumeration Type Documentation

enum protocols::frag_picker::ContactType

Enumerator
CA
CB
CEN
UNK
num_contact_types

Definition at line 23 of file ContactTypes.hh.

Function Documentation

std::string protocols::frag_picker::contact_name

(

ContactType

type)

give an enum type and return the string name

Definition at line 84 of file ContactTypes.cc.

References num_contact_types, and type2name().

Referenced by protocols::frag_picker::FragmentPicker::fragment_contacts(), protocols::frag_picker::FragmentPicker::nonlocal_pairs(), protocols::frag_picker::nonlocal::NonlocalPair::print(), and protocols::frag_picker::Contact::type_name().

ContactType protocols::frag_picker::contact_type

(

std::string const &

name)

END: local functions.

give a string name and return its enum type

Definition at line 72 of file ContactTypes.cc.

References core::sequence::end, and name2type().

Referenced by protocols::frag_picker::FragmentPicker::parse_command_line().

std::map< std::string, ContactType >& protocols::frag_picker::name2type ( )

inline

map that converts string name to enum

Definition at line 42 of file ContactTypes.cc.

References setup_name2type().

Referenced by contact_type(), and setup_type2name().

std::ostream& protocols::frag_picker::operator<< ( std::ostream &  out, FragmentCandidate const &  fr  )

inline

Definition at line 184 of file FragmentCandidate.hh.

References protocols::frag_picker::FragmentCandidate::get_first_index_in_query(), protocols::frag_picker::FragmentCandidate::get_first_index_in_vall(), and protocols::frag_picker::FragmentCandidate::get_pdb_id().

std::ostream& protocols::frag_picker::operator<< ( std::ostream &  out, std::pair< FragmentCandidateOP, scores::FragmentScoreMapOP > const &  pair  )

inline

Definition at line 190 of file FragmentCandidate.hh.

References core::pack::dunbrack::c, and core::scoring::pair.

utility::vector1< FragmentCandidateOP > protocols::frag_picker::read_fragment_candidates	(	std::string	file_name,
		VallProviderOP	chunk_owner,
		Size	max_nfrags_per_pos
	)

Definition at line 76 of file FragmentCandidate.cc.

References core::pack::dunbrack::c, and trFragmentCandidate().

std::map< char, core::Real >& protocols::frag_picker::sa_faraggi_max ( )

inline

faraggi SA max map

Definition at line 76 of file Faraggi_SA.cc.

References setup_faraggi_map().

Referenced by protocols::frag_picker::VallResidue::fill_from_string_version1(), sa_faraggi_max(), and protocols::frag_picker::scores::SolventAccessibility::SolventAccessibility().

core::Real protocols::frag_picker::sa_faraggi_max

(

char

aa)

Definition at line 84 of file Faraggi_SA.cc.

References core::sequence::end, and sa_faraggi_max().

std::map< char, core::Real > protocols::frag_picker::setup_faraggi_map

(

)

setup the faraggi SA max map, see Faraggi et al. Proteins 2008

Definition at line 30 of file Faraggi_SA.cc.

Referenced by sa_faraggi_max().

std::map< std::string, ContactType > protocols::frag_picker::setup_name2type

(

)

BEGIN: local functions.

setup the map that converts string name to enum

Definition at line 31 of file ContactTypes.cc.

References CA, CB, CEN, and UNK.

Referenced by name2type().

utility::vector1< std::string > protocols::frag_picker::setup_type2name

(

)

setup the vector that maps enum to string name

Definition at line 49 of file ContactTypes.cc.

References core::sequence::end, name2type(), and num_contact_types.

Referenced by type2name().

bool protocols::frag_picker::sort_function	(	ExtraScoreVector::value_type	p1,
		ExtraScoreVector::value_type	p2
	)

Definition at line 34 of file CustomScoreSelector.cc.

Referenced by protocols::frag_picker::CustomScoreSelector::select_fragments().

static basic::Tracer protocols::frag_picker::tr ( "protocols.frag_picker.TalosReader"  )

static

static basic::Tracer protocols::frag_picker::TR ( "protocols.frag_picker.VallResidue"  )

static

static basic::Tracer protocols::frag_picker::tr ( "protocols.frag_picker.PhiPsiTalosIO"  )

static

static basic::Tracer protocols::frag_picker::TR ( "protocols.frag_picker.SidechainContactDistCutoff"  )

static

Referenced by protocols::frag_picker::VallProvider::cache_pose(), protocols::frag_picker::VallProvider::cache_profile(), protocols::frag_picker::VallProvider::find_chunk(), protocols::frag_picker::VallResidue::format_string(), protocols::frag_picker::VallResidue::format_string_cs(), protocols::frag_picker::VallResidue::format_string_residue_depth_version1(), protocols::frag_picker::VallResidue::format_string_version1(), protocols::frag_picker::SidechainContactDistCutoff::initialize(), and protocols::frag_picker::VallProvider::vallChunksFromLibrary().

static basic::Tracer protocols::frag_picker::tr ( "protocols.frag_picker.SecondaryShiftCalculator"  )

static

Referenced by protocols::frag_picker::FragmentPicker::bounded_protocol(), protocols::frag_picker::CS2ndShift::CS2ndShift(), protocols::frag_picker::FragmentPicker::is_valid_chunk(), protocols::frag_picker::FragmentPicker::keep_all_protocol(), protocols::frag_picker::FragmentPicker::nonlocal_pairs(), protocols::frag_picker::FragmentPicker::output_fragments(), protocols::frag_picker::FragmentPicker::parse_command_line(), protocols::frag_picker::FragmentPicker::pick_candidates(), protocols::frag_picker::FragmentPicker::quota_protocol(), protocols::frag_picker::CSTalosIO::read(), protocols::frag_picker::PhiPsiTalosIO::read(), protocols::frag_picker::CS2ndShift::read_adjust_table(), protocols::frag_picker::FragmentPicker::read_ss_files(), protocols::frag_picker::CS2ndShift::read_sslimit_table(), protocols::frag_picker::FragmentPicker::save_candidates(), protocols::frag_picker::FragmentPicker::save_fragments(), protocols::frag_picker::FragmentPicker::set_up_quota_nnmake_style(), protocols::frag_picker::FragmentPicker::set_up_ss_abego_quota(), and protocols::frag_picker::QuotaDebug::write_summary().

static basic::Tracer protocols::frag_picker::tr ( "protocols.frag_picker.FragmentPicker"  )

static

static basic::Tracer protocols::frag_picker::tracer ( "protocols.frag_picker.LAMBEGO_IO"  )

static

Referenced by protocols::frag_picker::LAMBEGO_IO::read(), protocols::frag_picker::TorsionBinIO::read(), protocols::analysis::InterfaceAnalyzerMover::set_tracer(), and protocols::analysis::InterfaceAnalyzerMover::use_tracer().

static basic::Tracer protocols::frag_picker::tracer ( "protocols.frag_picker.TorsionBinIO"  )

static

static basic::Tracer protocols::frag_picker::trBestTotalScoreSelector ( "protocols.frag_picker.BestTotalScoreSelector"  )

static

static basic::Tracer protocols::frag_picker::trCustomScoreSelector ( "protocols.frag_picker.CustomScoreSelector"  )

static

Referenced by protocols::frag_picker::CustomScoreSelector::select_fragments().

static basic::Tracer protocols::frag_picker::trDiversifyCrmsdByClustering ( "protocols.frag_picker.DiversifyCrmsdByClustering"  )

static

Referenced by protocols::frag_picker::DiversifyCrmsdByClustering::select_fragments().

static basic::Tracer protocols::frag_picker::trDiversifyCrmsdSelector ( "protocols.frag_picker.DiversifyCrmsdSelector"  )

static

Referenced by protocols::frag_picker::DiversifyCrmsdSelector::select_fragments().

static basic::Tracer protocols::frag_picker::trDiversifyDihedralsSelector ( "protocols.frag_picker.DiversifyDihedralsSelector"  )

static

Referenced by protocols::frag_picker::DiversifyDihedralsSelector::select_fragments().

static basic::Tracer protocols::frag_picker::trFragmentCandidate ( "protocols.frag_picker.FragmentCandidate"  )

static

Referenced by read_fragment_candidates().

static basic::Tracer protocols::frag_picker::trJCouplingIO ( "protocols.frag_picker.TalosReader"  )

static

Referenced by protocols::frag_picker::JCouplingIO::read().

static basic::Tracer protocols::frag_picker::trPdbFilter ( "protocols.frag_picker.PdbIdChunkFilter"  )

static

Referenced by protocols::frag_picker::PdbIdChunkFilter::load_pdb_id_from_file(), protocols::frag_picker::AllowPdbIdFilter::test_chunk(), and protocols::frag_picker::DenyPdbIdFilter::test_chunk().

utility::vector1< std::string >& protocols::frag_picker::type2name ( )

inline

vector that maps enum to string name

Definition at line 60 of file ContactTypes.cc.

References setup_type2name().

Referenced by contact_name().