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protocols::frag_picker Namespace Reference

Namespaces

 nonlocal
 
 quota
 
 scores
 

Classes

class  AllowPdbIdFilter
 Accepts a chunk based on the pdb id of the source protein. More...
 
class  BestTotalScoreSelector
 selects a given number of fragments using a quota scheme More...
 
class  BoundedCollector
 Keeps the N best fragments candidates for the final selection. More...
 
class  BoundedCollector_CompareTotalScore
 
class  BoundedPriorityQueue
 
class  CandidatesCollector
 A base class for collecting fragments. More...
 
class  CompareByScoreCombination
 comparator based on the linear combination of some score components More...
 
class  CompareQueryPosition
 comparator based on a sequence position in a query More...
 
class  CompareScoreComponent
 comparator based on one of the score components calculated for fragments More...
 
class  CompareTotalScore
 comparator based on the total score of 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  DenyPdbIdFilter
 Denies a chunk based on the pdb id of the source protein. 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  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  PhiPsiTalosIO
 
class  QuotaDebug
 
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::Realsetup_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

typedef utility::pointer::shared_ptr<AllowPdbIdFilter const> protocols::frag_picker::AllowPdbIdFilterCOP
typedef utility::pointer::shared_ptr<AllowPdbIdFilter> protocols::frag_picker::AllowPdbIdFilterOP
typedef utility::vector1<Candidate> protocols::frag_picker::Candidates
typedef utility::pointer::shared_ptr<CandidatesCollector const> protocols::frag_picker::CandidatesCollectorCOP
typedef utility::pointer::shared_ptr<CompareQueryPosition const> protocols::frag_picker::CompareQueryPositionCOP
typedef utility::pointer::shared_ptr<CompareScoreComponent const> protocols::frag_picker::CompareScoreComponentCOP
typedef utility::pointer::shared_ptr<CompareTotalScore const> protocols::frag_picker::CompareTotalScoreCOP
typedef utility::pointer::shared_ptr<CompareTotalScore> protocols::frag_picker::CompareTotalScoreOP
typedef utility::pointer::shared_ptr<Contact const> protocols::frag_picker::ContactCOP
typedef utility::pointer::shared_ptr<ContactCounts const> protocols::frag_picker::ContactCountsCOP
typedef utility::pointer::shared_ptr<ContactCounts> protocols::frag_picker::ContactCountsOP
typedef utility::pointer::shared_ptr<Contact> protocols::frag_picker::ContactOP
typedef utility::pointer::shared_ptr<CustomScoreSelector const> protocols::frag_picker::CustomScoreSelectorCOP
typedef utility::pointer::shared_ptr<DenyPdbIdFilter const> protocols::frag_picker::DenyPdbIdFilterCOP
typedef utility::pointer::shared_ptr<DenyPdbIdFilter> protocols::frag_picker::DenyPdbIdFilterOP
typedef utility::vector1<std::pair< ScoredCandidate, core::Real> > protocols::frag_picker::ExtraScoreVector
typedef utility::pointer::shared_ptr<FragmentCandidate const> protocols::frag_picker::FragmentCandidateCOP
typedef utility::pointer::shared_ptr<FragmentCandidate> protocols::frag_picker::FragmentCandidateOP
typedef utility::pointer::weak_ptr<FragmentPicker> protocols::frag_picker::FragmentPickerAP
typedef utility::pointer::weak_ptr<FragmentPicker const> protocols::frag_picker::FragmentPickerCAP
typedef utility::pointer::shared_ptr<FragmentPicker const> protocols::frag_picker::FragmentPickerCOP
typedef utility::pointer::shared_ptr<FragmentPicker> protocols::frag_picker::FragmentPickerOP
typedef utility::pointer::shared_ptr< FragmentScoreFilter const > protocols::frag_picker::FragmentScoreFilterCOP
typedef utility::pointer::shared_ptr< FragmentScoreFilter > protocols::frag_picker::FragmentScoreFilterOP
typedef utility::pointer::shared_ptr<FragmentSelectingRule const> protocols::frag_picker::FragmentSelectingRuleCOP
typedef utility::pointer::shared_ptr< GrabAllCollector const > protocols::frag_picker::GrabAllCollectorCOP
typedef utility::pointer::shared_ptr< GrabAllCollector > protocols::frag_picker::GrabAllCollectorOP
typedef utility::pointer::shared_ptr<PdbIdChunkFilter const> protocols::frag_picker::PdbIdChunkFilterCOP
typedef utility::pointer::shared_ptr<PdbIdChunkFilter> protocols::frag_picker::PdbIdChunkFilterOP
typedef utility::pointer::weak_ptr<VallChunk> protocols::frag_picker::VallChunkAP
typedef utility::pointer::weak_ptr<VallChunk const> protocols::frag_picker::VallChunkCAP
typedef utility::pointer::shared_ptr<VallChunk const> protocols::frag_picker::VallChunkCOP
typedef utility::pointer::shared_ptr<VallChunkFilter const> protocols::frag_picker::VallChunkFilterCOP
typedef utility::pointer::shared_ptr<VallChunkFilter> protocols::frag_picker::VallChunkFilterOP
typedef utility::pointer::shared_ptr<VallChunk> protocols::frag_picker::VallChunkOP
typedef utility::pointer::weak_ptr<VallProvider> protocols::frag_picker::VallProviderAP
typedef utility::pointer::weak_ptr<VallProvider const> protocols::frag_picker::VallProviderCAP
typedef utility::pointer::shared_ptr<VallProvider const> protocols::frag_picker::VallProviderCOP
typedef utility::pointer::shared_ptr<VallProvider> protocols::frag_picker::VallProviderOP
typedef utility::pointer::shared_ptr<VallResidue const> protocols::frag_picker::VallResidueCOP
typedef utility::pointer::shared_ptr<VallResidue> protocols::frag_picker::VallResidueOP

Enumeration Type Documentation

Enumerator
CA 
CB 
CEN 
UNK 
num_contact_types 

Function Documentation

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

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

std::ostream& protocols::frag_picker::operator<< ( std::ostream &  out,
FragmentCandidate const &  fr 
)
inline
std::ostream& protocols::frag_picker::operator<< ( std::ostream &  out,
std::pair< FragmentCandidateOP, scores::FragmentScoreMapOP > const &  pair 
)
inline
utility::vector1< FragmentCandidateOP > protocols::frag_picker::read_fragment_candidates ( std::string  file_name,
VallProviderOP  chunk_owner,
core::Size  max_nfrags_per_pos 
)
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().

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

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().

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().

bool protocols::frag_picker::sort_function ( ExtraScoreVector::value_type  p1,
ExtraScoreVector::value_type  p2 
)
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
static basic::Tracer protocols::frag_picker::tr ( "protocols.frag_picker.SecondaryShiftCalculator"  )
static
static basic::Tracer protocols::frag_picker::tr ( "protocols.frag_picker.FragmentPicker"  )
static
static basic::Tracer protocols::frag_picker::tracer ( "protocols.frag_picker.TorsionBinIO"  )
static
static basic::Tracer protocols::frag_picker::tracer ( "protocols.frag_picker.LAMBEGO_IO"  )
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
static basic::Tracer protocols::frag_picker::trDiversifyCrmsdByClustering ( "protocols.frag_picker.DiversifyCrmsdByClustering"  )
static
static basic::Tracer protocols::frag_picker::trDiversifyCrmsdSelector ( "protocols.frag_picker.DiversifyCrmsdSelector"  )
static
static basic::Tracer protocols::frag_picker::trDiversifyDihedralsSelector ( "protocols.frag_picker.DiversifyDihedralsSelector"  )
static
static basic::Tracer protocols::frag_picker::trFragmentCandidate ( "protocols.frag_picker.FragmentCandidate"  )
static
static basic::Tracer protocols::frag_picker::trJCouplingIO ( "protocols.frag_picker.TalosReader"  )
static
static basic::Tracer protocols::frag_picker::trPdbFilter ( "protocols.frag_picker.PdbIdChunkFilter"  )
static
utility::vector1< std::string >& protocols::frag_picker::type2name ( )
inline

vector that maps enum to string name

References setup_type2name().

Referenced by contact_name().