NCBI C++ ToolKit
Classes | Public Types | Public Member Functions | Static Public Member Functions | Static Public Attributes | Private Types | Private Member Functions | Private Attributes | List of all members
Threader Class Reference

Search Toolkit Book for Threader

#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< IntervalListGeometryViolationsForRow
 
typedef std::vector< VirtualCoordinateVirtualCoordinateList
 
typedef std::list< ContactContactList
 

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_DefCreateCorDef (const BlockMultipleAlignment *multiple, double loopLengthMultiplier)
 
Qry_SeqCreateQrySeq (const BlockMultipleAlignment *multiple, const BlockMultipleAlignment *pairwise, int terminalCutoff)
 
Rcx_PtlCreateRcxPtl (double weightContacts)
 
Gib_ScdCreateGibScd (bool fast, unsigned int nRandomStarts)
 
Fld_MtfCreateFldMtf (const Sequence *masterSequence)
 
Seq_MtfCreateSeqMtf (const BlockMultipleAlignment *multiple, double weightPSSM)
 

Private Attributes

AlignmentManageralignmentManager
 
ContactMap contacts
 

Detailed Description

Definition at line 74 of file cn3d_threader.hpp.

Member Typedef Documentation

◆ 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

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

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 
)

◆ CreateCorDef()

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

◆ CreateFldMtf()

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

◆ CreateGibScd()

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

◆ CreateQrySeq()

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

◆ CreateRcxPtl()

Rcx_Ptl * Threader::CreateRcxPtl ( double  weightContacts)
private

◆ CreateSeqMtf()

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

◆ EstimateNRandomStarts()

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

◆ GetGeometryViolations()

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

◆ Realign()

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

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

The documentation for this class was generated from the following files:
Modified on Wed Apr 17 13:10:43 2024 by modify_doxy.py rev. 669887