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NCBI C++ ToolKit: src/app/cn3d/cn3d_threader.hpp Source File

*nRowsAddedToMultiple,

*sequenceViewer);

std::list < std::pair < unsigned int, unsigned int > >

;

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

;

bool mergeAfterEachSequence

int terminalResidueCutoff

bool freezeIsolatedBlocks

double loopLengthMultiplier

std::vector< VirtualCoordinate > VirtualCoordinateList

std::list< BlockMultipleAlignment * > AlignmentList

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

Cor_Def * CreateCorDef(const BlockMultipleAlignment *multiple, double loopLengthMultiplier)

std::vector< IntervalList > GeometryViolationsForRow

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

AlignmentManager * alignmentManager

Threader(AlignmentManager *parentAlnMgr)

static const unsigned int SCALING_FACTOR

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

static const std::string ThreaderResidues

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

Gib_Scd * CreateGibScd(bool fast, unsigned int nRandomStarts)

Seq_Mtf * CreateSeqMtf(const BlockMultipleAlignment *multiple, double weightPSSM)

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

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

bool CalculateScores(const BlockMultipleAlignment *multiple, double weightPSSM)

Fld_Mtf * CreateFldMtf(const Sequence *masterSequence)

Rcx_Ptl * CreateRcxPtl(double weightContacts)

std::list< Contact > ContactList

ThreaderOptions globalThreaderOptions

Include a standard set of the NCBI C++ Toolkit most basic headers.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

The NCBI C++/STL use hints.

static Threader::GeometryViolationsForRow violations

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