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Threader Class Reference

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#include "cn3d_threader.hpp"
(Private to src/app/cn3d.)

+ Collaboration diagram for Threader:

Classes

struct  Contact
 
struct  VirtualCoordinate
 

Public Types

enum  { MISSING_COORDINATE = 0 , VIRTUAL_RESIDUE , VIRTUAL_PEPTIDE }
 
typedef std::list< BlockMultipleAlignment * > AlignmentList
 
typedef std::list< std::pair< unsigned int, unsigned int > > IntervalList
 
typedef std::vector< IntervalList > GeometryViolationsForRow
 
typedef std::vector< VirtualCoordinate > VirtualCoordinateList
 
typedef std::list< Contact > ContactList
 

Public Member Functions

 Threader (AlignmentManager *parentAlnMgr)
 
 ~Threader (void)
 
bool Realign (const ThreaderOptions &options, BlockMultipleAlignment *masterMultiple, const AlignmentList *originalAlignments, AlignmentList *newAlignments, unsigned int *nRowsAddedToMultiple, SequenceViewer *sequenceViewer)
 
bool CalculateScores (const BlockMultipleAlignment *multiple, double weightPSSM)
 
unsigned int GetGeometryViolations (const BlockMultipleAlignment *multiple, GeometryViolationsForRow *violations)
 

Static Public Member Functions

static unsigned int EstimateNRandomStarts (const BlockMultipleAlignment *coreAlignment, const BlockMultipleAlignment *toBeThreaded)
 

Static Public Attributes

static const unsigned int SCALING_FACTOR = 1000000
 
static const std::string ThreaderResidues = "ARNDCQEGHILKMFPSTWYV"
 

Private Types

typedef std::map< const StructureBase *, Fld_Mtf * > ContactMap
 

Private Member Functions

Cor_Def * CreateCorDef (const BlockMultipleAlignment *multiple, double loopLengthMultiplier)
 
Qry_Seq * CreateQrySeq (const BlockMultipleAlignment *multiple, const BlockMultipleAlignment *pairwise, int terminalCutoff)
 
Rcx_Ptl * CreateRcxPtl (double weightContacts)
 
Gib_Scd * CreateGibScd (bool fast, unsigned int nRandomStarts)
 
Fld_Mtf * CreateFldMtf (const Sequence *masterSequence)
 
Seq_Mtf * CreateSeqMtf (const BlockMultipleAlignment *multiple, double weightPSSM)
 

Private Attributes

AlignmentManager * alignmentManager
 
ContactMap contacts
 

Detailed Description

Definition at line 74 of file cn3d_threader.hpp.

Member Typedef Documentation

◆ AlignmentList

typedef std::list< BlockMultipleAlignment * > Threader::AlignmentList

Definition at line 86 of file cn3d_threader.hpp.

◆ ContactList

typedef std::list< Contact > Threader::ContactList

Definition at line 121 of file cn3d_threader.hpp.

◆ ContactMap

typedef std::map< const StructureBase *, Fld_Mtf * > Threader::ContactMap
private

Definition at line 127 of file cn3d_threader.hpp.

◆ GeometryViolationsForRow

typedef std::vector< IntervalList > Threader::GeometryViolationsForRow

Definition at line 97 of file cn3d_threader.hpp.

◆ IntervalList

typedef std::list< std::pair < unsigned int, unsigned int > > Threader::IntervalList

Definition at line 96 of file cn3d_threader.hpp.

◆ VirtualCoordinateList

typedef std::vector< VirtualCoordinate > Threader::VirtualCoordinateList

Definition at line 113 of file cn3d_threader.hpp.

Member Enumeration Documentation

◆ anonymous enum

anonymous enum
Enumerator
MISSING_COORDINATE 
VIRTUAL_RESIDUE 
VIRTUAL_PEPTIDE 

Definition at line 107 of file cn3d_threader.hpp.

Constructor & Destructor Documentation

◆ Threader()

Threader::Threader ( AlignmentManager *  parentAlnMgr)

Definition at line 115 of file cn3d_threader.cpp.

◆ ~Threader()

Threader::~Threader ( void  )

Definition at line 120 of file cn3d_threader.cpp.

References contacts, and FreeFldMtf().

Member Function Documentation

◆ CalculateScores()

bool Threader::CalculateScores ( const BlockMultipleAlignment *  multiple,
double  weightPSSM 
)

Definition at line 1066 of file cn3d_threader.cpp.

References CalculateContactScore(), CalculatePSSMScore(), cleanup(), CreateFldMtf(), CreateRcxPtl(), CreateSeqMtf(), ERRORMSG, FreeRcxPtl(), FreeSeqMtf(), BlockMultipleAlignment::GetMaster(), BlockMultipleAlignment::GetSequenceOfRow(), BlockMultipleAlignment::GetUngappedAlignedBlocks(), i, StructureSet::isAlphaOnly, Sequence::Length(), LookupThreaderResidueNumberFromCharacterAbbrev(), Sequence::molecule, BlockMultipleAlignment::NRows(), NULL, StructureBase::parentSet, row, SCALING_FACTOR, Sequence::sequenceString, BlockMultipleAlignment::SetRowDouble(), and BlockMultipleAlignment::SetRowStatusLine().

Referenced by AlignmentManager::CalculateRowScoresWithThreader().

◆ CreateCorDef()

Cor_Def * Threader::CreateCorDef ( const BlockMultipleAlignment *  multiple,
double  loopLengthMultiplier 
)
private

Definition at line 157 of file cn3d_threader.cpp.

References b, _Cor_Def::comn, _Cor_Def::comx, _Cor_Def::fll, BlockMultipleAlignment::GetMaster(), BlockMultipleAlignment::GetUnalignedBlockBefore(), BlockMultipleAlignment::GetUngappedAlignedBlocks(), int, Sequence::Length(), _Cor_Def::lll, _Cor_Def::llmn, _Cor_Def::llmx, _Cor_Def::lrfs, max(), _Cor_Def::n, n, NewCorDef(), _Cor_Def::nomn, _Cor_Def::nomx, NULL, compile_time_bits::range(), _Cor_Def::rfpt, _Cor_Def::sll, Block::Range::to, and Block::width.

Referenced by Realign().

◆ CreateFldMtf()

Fld_Mtf * Threader::CreateFldMtf ( const Sequence *  masterSequence)
private

Definition at line 710 of file cn3d_threader.cpp.

References contacts, GetContacts(), GetMinimumLoopLengths(), StructureBase::GetParentOfType(), GetVirtualCoordinates(), Molecule::identifier, StructureSet::isAlphaOnly, Sequence::Length(), Sequence::molecule, NewFldMtf(), NULL, StructureBase::parentSet, MoleculeIdentifier::pdbChain, MoleculeIdentifier::pdbID, Molecule::residues, TRACEMSG, and TranslateContacts().

Referenced by CalculateScores(), GetGeometryViolations(), and Realign().

◆ CreateGibScd()

Gib_Scd * Threader::CreateGibScd ( bool  fast,
unsigned int  nRandomStarts 
)
private

Definition at line 398 of file cn3d_threader.cpp.

References _Gib_Scd::als, _Gib_Scd::cef, _Gib_Scd::cet, _Gib_Scd::cfm, _Gib_Scd::crs, _Gib_Scd::csm, i, _Gib_Scd::isl, _Gib_Scd::iso, _Gib_Scd::ito, _Gib_Scd::lmf, _Gib_Scd::lms, _Gib_Scd::lmw, _Gib_Scd::nac, NewGibScd(), _Gib_Scd::nlc, _Gib_Scd::nrs, _Gib_Scd::nti, _Gib_Scd::ntp, _Gib_Scd::nts, _Gib_Scd::rsd, SCALING_FACTOR, _Gib_Scd::tma, _Gib_Scd::tml, and _Gib_Scd::trg.

Referenced by Realign().

◆ CreateQrySeq()

Qry_Seq * Threader::CreateQrySeq ( const BlockMultipleAlignment *  multiple,
const BlockMultipleAlignment *  pairwise,
int  terminalCutoff 
)
private

Definition at line 230 of file cn3d_threader.cpp.

References BlockMultipleAlignment::alignDependentFrom, BlockMultipleAlignment::alignDependentTo, Block::Range::from, BlockMultipleAlignment::GetSequenceOfRow(), BlockMultipleAlignment::GetUngappedAlignedBlocks(), i, INFOMSG, Sequence::Length(), LookupThreaderResidueNumberFromCharacterAbbrev(), _Qry_Seq::mn, _Qry_Seq::mx, _Qry_Seq::n, NewQrySeq(), offset, _Qry_Seq::sac, Sequence::sequenceString, _Qry_Seq::sq, and Block::Range::to.

Referenced by Realign().

◆ CreateRcxPtl()

Rcx_Ptl * Threader::CreateRcxPtl ( double  weightContacts)
private

Definition at line 329 of file cn3d_threader.cpp.

References ERRORMSG, FreeRcxPtl(), GetDataDir(), i, in(), NewRcxPtl(), NULL, NUM_RES_TYPES, Path(), _Rcx_Ptl::re, ReadToRowOfEnergies(), _Rcx_Ptl::rre, _Rcx_Ptl::rrt, SCALING_FACTOR, and ThrdRound().

Referenced by CalculateScores(), and Realign().

◆ CreateSeqMtf()

Seq_Mtf * Threader::CreateSeqMtf ( const BlockMultipleAlignment *  multiple,
double  weightPSSM 
)
private

Definition at line 126 of file cn3d_threader.cpp.

References ERRORMSG, GetBLOSUM62Score(), BlockMultipleAlignment::GetMaster(), BlockMultipleAlignment::GetPSSM(), BlockMultipleAlignment::HasNoAlignedBlocks(), Sequence::Length(), LookupNCBIStdaaNumberFromCharacter(), NewSeqMtf(), BlockMultipleAlignment::NRows(), NULL, r(), SCALING_FACTOR, Sequence::sequenceString, ThrdRound(), ThreaderResidues, TRACEMSG, and _Seq_Mtf::ww.

Referenced by CalculateScores(), and Realign().

◆ EstimateNRandomStarts()

unsigned int Threader::EstimateNRandomStarts ( const BlockMultipleAlignment *  coreAlignment,
const BlockMultipleAlignment *  toBeThreaded 
)
static

Definition at line 1183 of file cn3d_threader.cpp.

References Block::Range::from, BlockMultipleAlignment::GetUngappedAlignedBlocks(), and Block::Range::to.

Referenced by SequenceDisplay::MouseDown(), and UpdateViewerWindow::OnRunThreader().

◆ GetGeometryViolations()

unsigned int Threader::GetGeometryViolations ( const BlockMultipleAlignment *  multiple,
GeometryViolationsForRow *  violations 
)

Definition at line 1124 of file cn3d_threader.cpp.

References b, CreateFldMtf(), ERRORMSG, Block::Range::from, BlockMultipleAlignment::GetMaster(), BlockMultipleAlignment::GetSequenceOfRow(), BlockMultipleAlignment::GetUngappedAlignedBlocks(), Sequence::identifier, StructureSet::isAlphaOnly, kMax_Int, _Fld_Mtf::mll, Sequence::molecule, n, BlockMultipleAlignment::NRows(), StructureBase::parentSet, row, Block::Range::to, MoleculeIdentifier::ToString(), and violations.

Referenced by BlockMultipleAlignment::ShowGeometryViolations().

◆ Realign()

bool Threader::Realign ( const ThreaderOptions &  options,
BlockMultipleAlignment *  masterMultiple,
const AlignmentList *  originalAlignments,
AlignmentList *  newAlignments,
unsigned int *  nRowsAddedToMultiple,
SequenceViewer *  sequenceViewer 
)

Definition at line 830 of file cn3d_threader.cpp.

References alignmentManager, atd(), cleanup(), BlockMultipleAlignment::Clone(), CreateAlignmentFromThdTbl(), CreateCorDef(), CreateFldMtf(), CreateGibScd(), CreateQrySeq(), CreateRcxPtl(), CreateSeqMtf(), NStr::DoubleToString(), ViewerBase::EditorIsOn(), ERRORMSG, FreeCorDef(), FreeGibScd(), FreeQrySeq(), FreeRcxPtl(), FreeSeqMtf(), FreeThdTbl(), FreezeIsolatedBlocks(), ThreaderOptions::freezeIsolatedBlocks, BlockMultipleAlignment::GetMaster(), i, INFOMSG, StructureSet::isAlphaOnly, ThreaderOptions::loopLengthMultiplier, ThreaderOptions::mergeAfterEachSequence, BlockMultipleAlignment::MergeAlignment(), Sequence::molecule, _Cor_Def::n, _Thd_Tbl::n, NewThdTbl(), ThreaderOptions::nRandomStarts, ThreaderOptions::nResultAlignments, _Gib_Scd::ntp, NULL, StructureBase::parentSet, PrintCorDef(), PrintFldMtf(), PrintQrySeq(), PrintSeqMtf(), PrintThdTbl(), SCALING_FACTOR, BlockMultipleAlignment::SetRowDouble(), BlockMultipleAlignment::SetRowStatusLine(), _Cor_Def::sll, string, ThreaderOptions::terminalResidueCutoff, _Thd_Tbl::tf, _Thd_Tbl::tg, TRACEMSG, SequenceViewer::TurnOnEditor(), and ThreaderOptions::weightPSSM.

Referenced by AlignmentManager::ThreadAllUpdates(), and AlignmentManager::ThreadUpdate().

Member Data Documentation

◆ alignmentManager

AlignmentManager* Threader::alignmentManager
private

Definition at line 124 of file cn3d_threader.hpp.

Referenced by Realign().

◆ contacts

ContactMap Threader::contacts
private

Definition at line 128 of file cn3d_threader.hpp.

Referenced by CreateFldMtf(), and ~Threader().

◆ SCALING_FACTOR

const unsigned int Threader::SCALING_FACTOR = 1000000
static

Definition at line 80 of file cn3d_threader.hpp.

Referenced by CalculateScores(), CreateGibScd(), CreateRcxPtl(), CreateSeqMtf(), and Realign().

◆ ThreaderResidues

const string Threader::ThreaderResidues = "ARNDCQEGHILKMFPSTWYV"
static

Definition at line 81 of file cn3d_threader.hpp.

Referenced by CreateSeqMtf(), LookupNCBIStdaaNumberFromThreaderResidueNumber(), and LookupThreaderResidueNumberFromCharacterAbbrev().

The documentation for this class was generated from the following files:
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