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NCBI C++ ToolKit: Threader Class Reference

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

Definition at line 74 of file cn3d_threader.hpp.

Definition at line 107 of file cn3d_threader.hpp.

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().

Definition at line 157 of file cn3d_threader.cpp.

References b, _Cor_Def::comn, _Cor_Def::comx, _Cor_Def::fll, Block::Range::from, 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, _Cor_Def::rfpt, _Cor_Def::sll, Block::Range::to, and Block::width.

Referenced by Realign().

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().

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().

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().

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().

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().

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().

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().

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

• src/app/cn3d/cn3d_threader.hpp
• src/app/cn3d/cn3d_threader.cpp

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