Rosetta 3.4
Namespaces | Classes | Typedefs | Enumerations | Functions
protocols::frag_picker Namespace Reference

Namespaces

namespace  nonlocal
namespace  quota
namespace  scores

Classes

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  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
< 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, SizePosPair
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
< 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.
std::map< std::string,
ContactType > & 
name2type ()
 map that converts string name to enum
utility::vector1< std::string > setup_type2name ()
 setup the vector that maps enum to string name
utility::vector1< std::string > & type2name ()
 vector that maps enum to string name
ContactType contact_type (std::string const &name)
 END: local functions.
std::string contact_name (ContactType type)
 give an enum type and return the string name
static basic::Tracer trCS2ndShift ("protocols.frag_picker.SecondaryShiftCalculator")
static basic::Tracer trCSTalosIO ("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
std::map< char, core::Real > & sa_faraggi_max ()
 faraggi SA max map
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)
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 trPicker ("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 trPhiPsiTalosIO ("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


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::parse_command_line().

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 
)
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 make_table_of_pilot_apps::begin, 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.SidechainContactDistCutoff"  ) [static]
static basic::Tracer protocols::frag_picker::TR ( "protocols.frag_picker.VallResidue"  ) [static]
static basic::Tracer protocols::frag_picker::tracer ( "protocols.frag_picker.LAMBEGO_IO"  ) [static]
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::trCS2ndShift ( "protocols.frag_picker.SecondaryShiftCalculator"  ) [static]
static basic::Tracer protocols::frag_picker::trCSTalosIO ( "protocols.frag_picker.TalosReader"  ) [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]
static basic::Tracer protocols::frag_picker::trPhiPsiTalosIO ( "protocols.frag_picker.PhiPsiTalosIO"  ) [static]
static basic::Tracer protocols::frag_picker::trPicker ( "protocols.frag_picker.FragmentPicker"  ) [static]
utility::vector1< std::string >& protocols::frag_picker::type2name ( ) [inline]

vector that maps enum to string name

References setup_type2name().

Referenced by contact_name().

 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines