Package rosetta :: Package protocols :: Package frag_picker :: Module _protocols_frag_picker_

Module _protocols_frag_picker_

Classes

AllowPdbIdFilter
Accepts a chunk based on the pdb id of the source protein If a given chunk comes from a registered pdb file then it will PASS the test.

AllowPdbIdFilterAP

AllowPdbIdFilterCAP

BestTotalScoreSelector
selects a given number of fragments using a quota scheme

BestTotalScoreSelectorAP

BestTotalScoreSelectorCAP

BoundedCollector_CompareTotalScore
protocols/frag_picker/BoundedCollector.hh:163

BoundedCollector_CompareTotalScoreAP

BoundedCollector_CompareTotalScoreCAP

BoundedCollector_T_protocols_frag_picker_CompareTotalScore_T
Keeps the N best fragments candidates for the final selection The purpose of a collector is to keep the best fragment candidates to the end of vall processing.

BoundedCollector_T_protocols_frag_picker_CompareTotalScore_TAP

BoundedCollector_T_protocols_frag_picker_CompareTotalScore_TCAP

CS2ndShift
protocols/frag_picker/CS2ndShift.hh:32

CS2ndShiftAP

CS2ndShiftCAP

CSTalosIO
protocols/frag_picker/CSTalosIO.hh:32

CSTalosIOAP

CSTalosIOCAP

CandidatesCollector
TODO write collector for mixed fragment lengths A base class for collecting fragments.

CandidatesCollectorAP

CandidatesCollectorCAP

CompareByScoreCombination
comparator based on the linear combination of some score components returns true if first pair has lower weighted score than the second one

CompareByScoreCombinationAP

CompareByScoreCombinationCAP

CompareQueryPosition
comparator based on a sequence position in a query

CompareQueryPositionAP

CompareQueryPositionCAP

CompareScoreComponent
comparator based on one of the score components calculated for fragments returns true if first pair has lower score component than the second one

CompareScoreComponentAP

CompareScoreComponentCAP

CompareTotalScore
comparator based on the total score of fragments returns true if first pair has lower total score than the second one

CompareTotalScoreAP

CompareTotalScoreCAP

CompositeFragmentSelector
selects fragments by running several selectors

CompositeFragmentSelectorAP

CompositeFragmentSelectorCAP

Contact
protocols/frag_picker/Contact.hh:36

ContactAP

ContactCAP

ContactCounts
protocols/frag_picker/ContactCounts.hh:32

ContactCountsAP

ContactCountsCAP

ContactType
protocols/frag_picker/ContactTypes.hh:23

CustomScoreSelector
selects a given number of fragments using a quota scheme

CustomScoreSelectorAP

CustomScoreSelectorCAP

DenyPdbIdFilter
Denies a chunk based on the pdb id of the source protein If a given chunk comes from a registered pdb file then it will FAIL the test.

DenyPdbIdFilterAP

DenyPdbIdFilterCAP

DiversifyCrmsdByClustering
selects fragments by running several selectors

DiversifyCrmsdByClusteringAP

DiversifyCrmsdByClusteringCAP

DiversifyCrmsdSelector
selects fragments by running several selectors

DiversifyCrmsdSelectorAP

DiversifyCrmsdSelectorCAP

DiversifyDihedralsSelector
selects fragments by running several selectors

DiversifyDihedralsSelectorAP

DiversifyDihedralsSelectorCAP

FragmentCandidate
Vector candidate says which X-mer from vall fits to a query sequence Scores for a given fragment are stored separately in a FragmentScoreMap object Therefore fragment containers hold std::pair<FragmentCandidateOP,FragmentScoreMapOP>

FragmentCandidateAP

FragmentCandidateCAP

FragmentComparatorBase
protocols/frag_picker/FragmentComparatorBase.hh:30

FragmentComparatorBaseAP

FragmentComparatorBaseCAP

FragmentPicker
The core of the fragment picking machinery FragmentPicker class does:\n

FragmentPickerAP

FragmentPickerCAP

FragmentSelectingRule
selects a given number of fragments just by selecting the best ones

FragmentSelectingRuleAP

FragmentSelectingRuleCAP

GrabAllCollector
Keeps all fragments candidates for the final selection The purpose of a collector is to keep fragment candidates to the end of vall processing.

GrabAllCollectorAP

GrabAllCollectorCAP

JCouplingIO
protocols/frag_picker/JCouplingIO.hh:32

JCouplingIOAP

JCouplingIOCAP

LAMBEGO_IO
protocols/frag_picker/LAMBEGO_IO.hh:27

LAMBEGO_IOAP

LAMBEGO_IOCAP

PdbIdChunkFilter
protocols/frag_picker/PdbIdChunkFilter.hh:32

PdbIdChunkFilterAP

PdbIdChunkFilterCAP

PhiPsiTalosIO
protocols/frag_picker/PhiPsiTalosIO.hh:35

PhiPsiTalosIOAP

PhiPsiTalosIOCAP

QuotaDebug
protocols/frag_picker/FragmentPicker.hh:62

QuotaDebugAP

QuotaDebugCAP

SidechainContactDistCutoff
defines sidechain contact distance cutoffs.

SidechainContactDistCutoffAP

SidechainContactDistCutoffCAP

SingletonBase_T_core_chemical_ChemicalManager_T
SingletonBase is meant to serve as a base class for singleton classes in Rosetta handling the initialization of the singleton in a thread-safe way.

SingletonBase_T_core_chemical_ChemicalManager_TAP

SingletonBase_T_core_chemical_ChemicalManager_TCAP

TorsionBinIO
protocols/frag_picker/TorsionBinIO.hh:27

TorsionBinIOAP

TorsionBinIOCAP

VallChunk
represents a chunk of residues extracted from a vall.

VallChunkAP

VallChunkCAP

VallChunkFilter
a base class for a chunk filtering mechanism Chunk filtering is used to screen chunks before any fragment is evaluated Therefore it is the fastest way to excluded unwanted proteins @see AllowPdbIdFilter and DenyPdbIdFilter for implementations

VallChunkFilterAP

VallChunkFilterCAP

VallProvider
a vector of vall chunks

VallProviderAP

VallProviderCAP

VallResidue
class for managing a line of the Vall fragment library

VallResidueAP

VallResidueCAP

__CPP_AllowPdbIdFilter__

__CPP_BestTotalScoreSelector__

__CPP_BoundedCollector<protocols::frag_picker::CompareTotalScore>__

__CPP_CandidatesCollector__

__CPP_CompareByScoreCombination__

__CPP_CompareQueryPosition__

__CPP_CompareScoreComponent__

__CPP_CompareTotalScore__

__CPP_CompositeFragmentSelector__

__CPP_CustomScoreSelector__

__CPP_DenyPdbIdFilter__

__CPP_DiversifyCrmsdByClustering__

__CPP_DiversifyCrmsdSelector__

__CPP_DiversifyDihedralsSelector__

__CPP_FragmentComparatorBase__

__CPP_FragmentSelectingRule__

__CPP_GrabAllCollector__

__CPP_VallChunkFilter__

Functions

[hide private]

contact_name(...)
contact_name( (ContactType)type) -> str : //////////////////////////////////////////////////// give an enum type and return the string name ////////////////////////////////////////////////////

contact_type(...)
contact_type( (str)name) -> ContactType : /////////////////////////////////////////////////////// give a string name and return its enum type ///////////////////////////////////////////////////////

read_fragment_candidates(...)
read_fragment_candidates( (str), (VallProvider) [, (int)max_nfrags_per_pos=900000000]) -> object : protocols/frag_picker/FragmentCandidate.hh:44

sa_faraggi_max(...)
sa_faraggi_max( (str)aa) -> float : protocols/frag_picker/Faraggi_SA.hh:30

Variables

[hide private]

CA = rosetta.protocols.frag_picker._protocols_frag_picker_.Con...

CB = rosetta.protocols.frag_picker._protocols_frag_picker_.Con...

CEN = rosetta.protocols.frag_picker._protocols_frag_picker_.Co...

UNK = rosetta.protocols.frag_picker._protocols_frag_picker_.Co...

__package__ = None

num_contact_types = rosetta.protocols.frag_picker._protocols_f...

Function Details

[hide private]

contact_name(...)


contact_name( (ContactType)type) -> str :
    ////////////////////////////////////////////////////
     give an enum type and return the string name
    ////////////////////////////////////////////////////
    

    C++ signature :
        std::string contact_name(protocols::frag_picker::ContactType)

contact_type(...)


contact_type( (str)name) -> ContactType :
    ///////////////////////////////////////////////////////
     give a string name and return its enum type
    ///////////////////////////////////////////////////////
    

    C++ signature :
        protocols::frag_picker::ContactType contact_type(std::string)

read_fragment_candidates(...)


read_fragment_candidates( (str), (VallProvider) [, (int)max_nfrags_per_pos=900000000]) -> object :
    protocols/frag_picker/FragmentCandidate.hh:44

    C++ signature :
        utility::vector1<boost::shared_ptr<protocols::frag_picker::FragmentCandidate>, std::allocator<boost::shared_ptr<protocols::frag_picker::FragmentCandidate> > > read_fragment_candidates(std::string,boost::shared_ptr<protocols::frag_picker::VallProvider> [,unsigned long=900000000])

sa_faraggi_max(...)


sa_faraggi_max( (str)aa) -> float :
    protocols/frag_picker/Faraggi_SA.hh:30

    C++ signature :
        double sa_faraggi_max(char)

Variables Details

[hide private]

CA

Value:

rosetta.protocols.frag_picker._protocols_frag_picker_.ContactType.CA

CB

Value:

rosetta.protocols.frag_picker._protocols_frag_picker_.ContactType.CB

CEN

Value:

rosetta.protocols.frag_picker._protocols_frag_picker_.ContactType.CEN

UNK

Value:

rosetta.protocols.frag_picker._protocols_frag_picker_.ContactType.UNK

num_contact_types

Value:

rosetta.protocols.frag_picker._protocols_frag_picker_.ContactType.num_
contact_types