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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  FragmentScoreFilter
 –brief– More...
 
class  FragmentScoreFilterCreator
 
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::shared_ptr< BestTotalScoreSelector > BestTotalScoreSelectorOP
 
typedef utility::pointer::shared_ptr< BestTotalScoreSelector const > BestTotalScoreSelectorCOP
 
typedef utility::pointer::shared_ptr< CandidatesCollector > CandidatesCollectorOP
 
typedef utility::pointer::shared_ptr< CandidatesCollector const > CandidatesCollectorCOP
 
typedef utility::pointer::shared_ptr< CompareQueryPosition > CompareQueryPositionOP
 
typedef utility::pointer::shared_ptr< CompareQueryPosition const > CompareQueryPositionCOP
 
typedef utility::pointer::shared_ptr< CompareTotalScore > CompareTotalScoreOP
 
typedef utility::pointer::shared_ptr< CompareTotalScore const > CompareTotalScoreCOP
 
typedef utility::pointer::shared_ptr< CompareScoreComponent > CompareScoreComponentOP
 
typedef utility::pointer::shared_ptr< CompareScoreComponent const > CompareScoreComponentCOP
 
typedef utility::pointer::shared_ptr< Contact > ContactOP
 
typedef utility::pointer::shared_ptr< Contact const > ContactCOP
 
typedef utility::pointer::shared_ptr< ContactCounts > ContactCountsOP
 
typedef utility::pointer::shared_ptr< ContactCounts const > ContactCountsCOP
 
typedef utility::vector1< std::pair< ScoredCandidate, core::Real > > ExtraScoreVector
 
typedef utility::pointer::shared_ptr< CustomScoreSelector > CustomScoreSelectorOP
 
typedef utility::pointer::shared_ptr< CustomScoreSelector const > CustomScoreSelectorCOP
 
typedef utility::pointer::shared_ptr< FragmentCandidate > FragmentCandidateOP
 
typedef utility::pointer::shared_ptr< FragmentCandidate const > FragmentCandidateCOP
 
typedef std::pair< FragmentCandidateOP, scores::FragmentScoreMapOP > ScoredCandidate
 
typedef utility::vector1< ScoredCandidate > ScoredCandidatesVector1
 
typedef utility::pointer::shared_ptr< FragmentComparatorBase > FragmentComparatorBaseOP
 
typedef utility::pointer::shared_ptr< FragmentComparatorBase const > FragmentComparatorBaseCOP
 
typedef utility::pointer::shared_ptr< FragmentPicker > FragmentPickerOP
 
typedef utility::pointer::shared_ptr< FragmentPicker const > FragmentPickerCOP
 
typedef utility::pointer::weak_ptr< FragmentPicker > FragmentPickerAP
 
typedef utility::pointer::weak_ptr< FragmentPicker const > FragmentPickerCAP
 
typedef std::pair< core::Size, core::Size > PosPair
 
typedef std::pair< FragmentCandidateOP, scores::FragmentScoreMapOP > Candidate
 
typedef utility::vector1< Candidate > Candidates
 
typedef std::map< core::Size, CandidatesCollectorOP > CandidatesSink
 
typedef utility::pointer::shared_ptr< FragmentScoreFilter > FragmentScoreFilterOP
 
typedef utility::pointer::shared_ptr< FragmentScoreFilter const > FragmentScoreFilterCOP
 
typedef utility::pointer::shared_ptr< FragmentSelectingRule > FragmentSelectingRuleOP
 
typedef utility::pointer::shared_ptr< FragmentSelectingRule const > FragmentSelectingRuleCOP
 
typedef utility::pointer::shared_ptr< GrabAllCollector > GrabAllCollectorOP
 
typedef utility::pointer::shared_ptr< GrabAllCollector const > GrabAllCollectorCOP
 
typedef utility::pointer::shared_ptr< PdbIdChunkFilter > PdbIdChunkFilterOP
 
typedef utility::pointer::shared_ptr< PdbIdChunkFilter const > PdbIdChunkFilterCOP
 
typedef utility::pointer::shared_ptr< AllowPdbIdFilter > AllowPdbIdFilterOP
 
typedef utility::pointer::shared_ptr< AllowPdbIdFilter const > AllowPdbIdFilterCOP
 
typedef utility::pointer::shared_ptr< DenyPdbIdFilter > DenyPdbIdFilterOP
 
typedef utility::pointer::shared_ptr< DenyPdbIdFilter const > DenyPdbIdFilterCOP
 
typedef utility::pointer::shared_ptr< SidechainContactDistCutoff > SidechainContactDistCutoffOP
 
typedef utility::pointer::shared_ptr< SidechainContactDistCutoff const > SidechainContactDistCutoffCOP
 
typedef utility::pointer::shared_ptr< VallChunk > VallChunkOP
 
typedef utility::pointer::shared_ptr< VallChunk const > VallChunkCOP
 
typedef utility::pointer::weak_ptr< VallChunk > VallChunkAP
 
typedef utility::pointer::weak_ptr< VallChunk const > VallChunkCAP
 
typedef utility::pointer::shared_ptr< VallChunkFilter > VallChunkFilterOP
 
typedef utility::pointer::shared_ptr< VallChunkFilter const > VallChunkFilterCOP
 
typedef utility::pointer::shared_ptr< VallProvider > VallProviderOP
 
typedef utility::pointer::shared_ptr< VallProvider const > VallProviderCOP
 
typedef utility::pointer::weak_ptr< VallProvider > VallProviderAP
 
typedef utility::pointer::weak_ptr< VallProvider const > VallProviderCAP
 
typedef utility::pointer::shared_ptr< VallResidue > VallResidueOP
 
typedef utility::pointer::shared_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, core::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")
 
void convert_binary_checkpoint (std::string const &check_filename)
 
void run_command (std::string const &cmd)
 Run a command in a terminal. More...
 
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

◆ AllowPdbIdFilterCOP

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

◆ AllowPdbIdFilterOP

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

◆ BestTotalScoreSelectorCOP

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

◆ BestTotalScoreSelectorOP

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

◆ Candidate

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

◆ Candidates

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

◆ CandidatesCollectorCOP

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

◆ CandidatesCollectorOP

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

◆ CandidatesSink

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

◆ CompareQueryPositionCOP

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

◆ CompareQueryPositionOP

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

◆ CompareScoreComponentCOP

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

◆ CompareScoreComponentOP

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

◆ CompareTotalScoreCOP

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

◆ CompareTotalScoreOP

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

◆ ContactCOP

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

◆ ContactCountsCOP

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

◆ ContactCountsOP

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

◆ ContactOP

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

◆ CustomScoreSelectorCOP

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

◆ CustomScoreSelectorOP

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

◆ DenyPdbIdFilterCOP

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

◆ DenyPdbIdFilterOP

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

◆ ExtraScoreVector

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

◆ FragmentCandidateCOP

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

◆ FragmentCandidateOP

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

◆ FragmentComparatorBaseCOP

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

◆ FragmentComparatorBaseOP

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

◆ FragmentPickerAP

typedef utility::pointer::weak_ptr<FragmentPicker> protocols::frag_picker::FragmentPickerAP

◆ FragmentPickerCAP

typedef utility::pointer::weak_ptr<FragmentPicker const> protocols::frag_picker::FragmentPickerCAP

◆ FragmentPickerCOP

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

◆ FragmentPickerOP

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

◆ FragmentScoreFilterCOP

typedef utility::pointer::shared_ptr< FragmentScoreFilter const > protocols::frag_picker::FragmentScoreFilterCOP

◆ FragmentScoreFilterOP

typedef utility::pointer::shared_ptr< FragmentScoreFilter > protocols::frag_picker::FragmentScoreFilterOP

◆ FragmentSelectingRuleCOP

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

◆ FragmentSelectingRuleOP

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

◆ GrabAllCollectorCOP

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

◆ GrabAllCollectorOP

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

◆ PdbIdChunkFilterCOP

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

◆ PdbIdChunkFilterOP

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

◆ PosPair

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

◆ ScoredCandidate

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

◆ ScoredCandidatesVector1

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

◆ SidechainContactDistCutoffCOP

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

◆ SidechainContactDistCutoffOP

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

◆ VallChunkAP

typedef utility::pointer::weak_ptr<VallChunk> protocols::frag_picker::VallChunkAP

◆ VallChunkCAP

typedef utility::pointer::weak_ptr<VallChunk const> protocols::frag_picker::VallChunkCAP

◆ VallChunkCOP

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

◆ VallChunkFilterCOP

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

◆ VallChunkFilterOP

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

◆ VallChunkOP

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

◆ VallProviderAP

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

◆ VallProviderCAP

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

◆ VallProviderCOP

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

◆ VallProviderOP

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

◆ VallResidueCOP

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

◆ VallResidueOP

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

Enumeration Type Documentation

◆ ContactType

enum protocols::frag_picker::ContactType
Enumerator
CA 
CB 
CEN 
UNK 
num_contact_types 

Function Documentation

◆ contact_name()

std::string protocols::frag_picker::contact_name ( ContactType  type)

give an enum type and return the string name

References num_contact_types, and type2name().

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

◆ contact_type()

ContactType protocols::frag_picker::contact_type ( std::string const &  name)

END: local functions.

give a string name and return its enum type

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

Referenced by protocols::frag_picker::FragmentPicker::output_pair_counts(), and protocols::frag_picker::FragmentPicker::parse_command_line().

◆ convert_binary_checkpoint()

void protocols::frag_picker::convert_binary_checkpoint ( std::string const &  check_filename)

References core::conformation::membrane::in, core::id::to_string(), and TR().

Referenced by protocols::frag_picker::FragmentScoreFilter::setup_fragment_picker().

◆ name2type()

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

map that converts string name to enum

References setup_name2type().

Referenced by contact_type(), and setup_type2name().

◆ operator<<() [1/2]

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

References protocols::frag_picker::FragmentCandidate::get_first_index_in_query(), protocols::frag_picker::FragmentCandidate::get_first_index_in_vall(), protocols::frag_picker::FragmentCandidate::get_pdb_id(), and core::conformation::membrane::out.

◆ operator<<() [2/2]

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

References core::conformation::membrane::out, and core::scoring::pair.

◆ read_fragment_candidates()

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

References trFragmentCandidate().

◆ run_command()

void protocols::frag_picker::run_command ( std::string const &  cmd)

Run a command in a terminal.

References core::id::to_string(), and TR().

Referenced by protocols::frag_picker::FragmentScoreFilter::setup_fragment_picker().

◆ sa_faraggi_max() [1/2]

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

faraggi SA max map

References setup_faraggi_map().

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

◆ sa_faraggi_max() [2/2]

core::Real protocols::frag_picker::sa_faraggi_max ( char  aa)

References protocols::cluster::calibur::aa, core::sequence::end, and sa_faraggi_max().

◆ setup_faraggi_map()

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

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

Referenced by sa_faraggi_max().

◆ setup_name2type()

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

BEGIN: local functions.

setup the map that converts string name to enum

References CA, CB, CEN, and UNK.

Referenced by name2type().

◆ setup_type2name()

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

setup the vector that maps enum to string name

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

Referenced by type2name().

◆ sort_function()

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

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

◆ tr() [1/4]

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

◆ tr() [2/4]

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

◆ tr() [3/4]

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_max_threads(), protocols::frag_picker::FragmentPicker::set_query_seq(), 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().

◆ TR() [1/2]

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

Referenced by protocols::frag_picker::FragmentScoreFilter::apply(), protocols::frag_picker::VallProvider::cache_pose(), protocols::frag_picker::VallProvider::cache_profile(), protocols::frag_picker::FragmentScoreFilter::compute(), convert_binary_checkpoint(), 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(), protocols::frag_picker::FragmentScoreFilter::rescore_fragment_crmsd(), run_command(), protocols::frag_picker::FragmentScoreFilter::setup_fragment_picker(), and protocols::frag_picker::VallProvider::vallChunksFromLibrary().

◆ tr() [4/4]

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

◆ TR() [2/2]

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

◆ tracer() [1/2]

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

Referenced by protocols::evaluation::dump_matrix_no(), protocols::toolbox::dump_matrix_no(), protocols::frag_picker::LAMBEGO_IO::read(), protocols::frag_picker::TorsionBinIO::read(), protocols::analysis::InterfaceAnalyzerMover::set_use_tracer(), protocols::loops::filters::LoopAnalyzerFilter::set_use_tracer(), protocols::analysis::LoopAnalyzerMover::set_use_tracer(), core::scoring::nmr::NMRSpinlabel::show(), core::scoring::nmr::pcs::PCSData::show(), core::scoring::nmr::pcs::PCSMultiSet::show(), core::scoring::nmr::pcs::PCSSingle::show(), core::scoring::nmr::pcs::PCSSingleSet::show(), core::scoring::nmr::pre::PREData::show(), core::scoring::nmr::pre::PREMultiSet::show(), core::scoring::nmr::pre::PRESingle::show(), core::scoring::nmr::pre::PRESingleSet::show(), core::scoring::nmr::rdc::RDCData::show(), core::scoring::nmr::rdc::RDCMultiSet::show(), core::scoring::nmr::rdc::RDCSingle::show(), core::scoring::nmr::rdc::RDCSingleSet::show(), protocols::nmr::pre::PREMover::show(), protocols::nmr::pcs::PCSEnergy::show_additional_info(), protocols::nmr::pre::PREEnergy::show_additional_info(), protocols::nmr::rdc::RDCEnergy::show_additional_info(), core::scoring::nmr::pcs::PCSTensor::show_tensor_stats(), core::scoring::nmr::rdc::RDCTensor::show_tensor_stats(), which_ostream(), and protocols::analysis::which_ostream().

◆ tracer() [2/2]

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

◆ trBestTotalScoreSelector()

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

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

◆ trCustomScoreSelector()

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

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

◆ trDiversifyCrmsdByClustering()

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

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

◆ trDiversifyCrmsdSelector()

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

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

◆ trDiversifyDihedralsSelector()

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

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

◆ trFragmentCandidate()

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

Referenced by read_fragment_candidates().

◆ trJCouplingIO()

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

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

◆ trPdbFilter()

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().

◆ type2name()

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

vector that maps enum to string name

References setup_type2name().

Referenced by contact_name().

Generated on Sat Mar 2 2024 12:17:59 for Rosetta by doxygen 1.9.1