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

mergeAfterEachSequence(

),

freezeIsolatedBlocks(

),

loopLengthMultiplier(1.5),

terminalResidueCutoff(-1)

Char2Int charMap;

(charMap.size() == 0) {

Char2Int::const_iterator c = charMap.find((

)

(

));

((c != charMap.end()) ? c->second : -1);

alignmentManager(parentAlnMgr)

ContactMap::iterator c, ce =

.end();

(multiple->

() == 1) {

(

res=0; res<multiple->

()->Length(); ++res)

(

);

(

);

(

);

(

c=0; c<multiple->

()->Length(); ++c)

MIN_LOOP_MAX = 2;

EXTENSION_MAX = 10;

corDef->

.

[0] = corDef->

.

[alignedBlocks.size()] =

corDef->

.

[0] = corDef->

.

[alignedBlocks.size()] =

corDef->

.

[0] = corDef->

.

[alignedBlocks.size()] = 0;

BlockMultipleAlignment::UngappedAlignedBlockList::const_iterator

= alignedBlocks.begin(), be = alignedBlocks.end();

,

;

(

=1, ++

;

!=be; ++

, ++

) {

= (

) (loopLengthMultiplier * uaBlock->

);

(

< MIN_LOOP_MAX)

= MIN_LOOP_MAX;

(

=0,

=alignedBlocks.begin();

!=be; ++

, ++

) {

range = (*b)->GetRangeOfRow(0);

mid = (range->

+ range->

) / 2;

corDef->

.

[0] = corDef->

.

[0] + EXTENSION_MAX;

corDef->

.

[alignedBlocks.size() - 1] = corDef->

.

[alignedBlocks.size() - 1] + EXTENSION_MAX;

(corDef->

.

[alignedBlocks.size() - 1] + corDef->

.

[alignedBlocks.size() - 1] >=

corDef->

.

[alignedBlocks.size() - 1] =

nUnaligned, extN;

(

=0,

=alignedBlocks.begin();

!=be; ++

, ++

) {

range = (*b)->GetRangeOfRow(0);

nUnaligned = range->

- prevRange->

- 1;

extN = nUnaligned / 2;

corDef->

.

[

- 1] = corDef->

.

[

- 1] + nUnaligned - extN;

corDef->

.

= 0;

(

=0;

<dependentSeq->

(); ++

)

BlockMultipleAlignment::UngappedAlignedBlockList::const_iterator

m, me = multipleABlocks.end(), p, pe = pairwiseABlocks.end();

(

=0, m=multipleABlocks.begin(); m!=me; ++

, ++m) {

multipleRange = (*m)->GetRangeOfRow(0);

(p=pairwiseABlocks.begin(); p!=pe; ++p) {

pairwiseRange = (*p)->GetRangeOfRow(0);

(pairwiseRange->

<= multipleRange->

&& pairwiseRange->

>= multipleRange->

) {

masterCenter = (multipleRange->

+ multipleRange->

) / 2;

= masterCenter - pairwiseRange->

;

pairwiseRange = (*p)->GetRangeOfRow(1);

(terminalCutoff >= 0) {

(qrySeq->

.

[0] == -1) {

}

(pairwiseABlocks.size() > 0) {

*nextQryBlock = pairwiseABlocks.front()->GetRangeOfRow(1);

qrySeq->

.

[0] = nextQryBlock->

- 1 - terminalCutoff;

(qrySeq->

.

[0] < 0) qrySeq->

.

[0] = 0;

(

<< qrySeq->

.

[0] + 1);

(qrySeq->

.

[multipleABlocks.size() - 1] == -1) {

}

(pairwiseABlocks.size() > 0) {

*prevQryBlock = pairwiseABlocks.back()->GetRangeOfRow(1);

qrySeq->

.

[multipleABlocks.size() - 1] = prevQryBlock->

+ 1 + terminalCutoff;

(qrySeq->

.

[multipleABlocks.size() - 1] >= qrySeq->

||

qrySeq->

.

[multipleABlocks.size() - 1] < 0)

qrySeq->

.

[multipleABlocks.size() - 1] = qrySeq->

- 1;

(

<< qrySeq->

.

[multipleABlocks.size() - 1] + 1);

, Count=0;

InsideStr =

;

(

=0;

<Str.size(); ++

) {

(!InsideStr && (Str[

] !=

)) {

(Str[

] ==

) {

(!InFile.eof()) {

InFile.getline(Str,

(Str));

*FileName =

;

, j, k;

kNumDistances = 6;

kPeptideIndex = 20;

(

<<

<<

);

(

=0;

<kNumDistances; ++

) {

(InFile->eof())

;

InFile->getline(ResName,

(ResName),

);

(InFile->eof())

;

(InFile->eof())

;

InFile->getline(ResName,

(ResName),

);

(InFile->eof())

;

(j=0; j<kNumDistances; ++j) {

(InFile->eof())

;

(

=0;

<kNumDistances; ++

) {

pmf->

[

][j][k] = pmf->

[

][j][k] + pmf->

[

][j] + pmf->

[

][k];

(

<< FileName);

NumTrajectoryPoints;

kNumTempSteps = 3;

gsp->

= nRandomStarts;

gsp->

= kNumTempSteps;

(gsp->

== 0) {

NumTrajectoryPoints = 1;

NumTrajectoryPoints = 0;

(

=0;

<kNumTempSteps; ++

) {

NumTrajectoryPoints += gsp->

[

] * (gsp->

[

] + gsp->

[

]);

NumTrajectoryPoints *= gsp->

;

NumTrajectoryPoints += gsp->

;

gsp->

= NumTrajectoryPoints;

Residue::AtomInfoMap::const_iterator

, ae = res->

().end();

(

->second->atomicNumber == 6) {

(

->second->code ==

)

= atomSet->

(ap,

,

);

(

->second->code ==

)

CA = atomSet->

(ap,

,

);

(

->second->code ==

)

= atomSet->

(ap,

,

);

}

(

->second->atomicNumber == 7 &&

->second->code ==

)

= atomSet->

(ap,

,

);

(

&& CA &&

&&

)

;

toCB =

->site - CA->site;

CaN, CaC, cross, bisect;

CaN =

->site - CA->site;

CaC =

->site - CA->site;

cross = vector_cross(CaN, CaC);

toCB = 0.816497 * cross - 0.57735 * bisect;

coord->

= CA->site + 2.4 * toCB;

Molecule::DisulfideMap::const_iterator ds = mol->

.find(res->

);

(ds->second - 1) * 2;

*atom1 = atomSet->

(ap1,

,

),

*atom2 = atomSet->

(ap2,

,

);

coord->

= (atom1->

+ atom2->site) / 2;

virtualCoordinates->resize(2 * mol->

.size() - 1);

Molecule::ResidueMap::const_iterator

, re = mol->

.end();

prevResidue,

->second, &((*virtualCoordinates)[

++]));

prevResidue =

->second;

->second, &((*virtualCoordinates)[

++]));

dist = (p2 - p1).length();

, j, bin;

(

=0;

<coords.size(); ++

) {

(

<< ((

%2 == 0) ?

:

) << (

/2));

(j=

+10; j<coords.size(); ++j) {

(coords[

].disulfideWith == (

)j || coords[j].disulfideWith == (

)

)

resResContacts->resize(resResContacts->size() + 1);

resResContacts->back().vc1 =

;

resResContacts->back().vc2 = j;

resResContacts->back().distanceBin = bin;

resPepContacts->resize(resPepContacts->size() + 1);

resPepContacts->back().distanceBin = bin;

resPepContacts->back().vc1 =

;

resPepContacts->back().vc2 = j;

resPepContacts->back().vc2 =

;

resPepContacts->back().vc1 = j;

Threader::ContactList::const_iterator c;

(

=0, c=resResContacts.begin();

<resResContacts.size(); ++

, ++c) {

fldMtf->

.

[

] = c->vc1 / 2;

fldMtf->

.

[

] = c->vc2 / 2;

fldMtf->

.

[

] = c->distanceBin;

(

=0, c=resPepContacts.begin();

<resPepContacts.size(); ++

, ++c) {

fldMtf->

.

[

] = c->vc1 / 2;

fldMtf->

.

[

] = c->vc2 / 2;

fldMtf->

.

[

] = c->distanceBin;

Molecule::ResidueMap::const_iterator

,

, re = mol->

.end();

a1 = atomSet->

(ap1,

,

);

(

=

, j=

;

!=re; ++

, ++j) {

fldMtf->

[

][j] = 0;

a2 = atomSet->

(ap2,

,

);

fldMtf->

[

][j] = fldMtf->

[j][

] =

(!a1 || !a2) ? 0 : (

) (((a2->

- a1->

).length() - 2.7) / 3.4);

(!masterSequence)

;

ContactMap::iterator c = mol ?

.find(mol) :

.find(masterSequence);

(c !=

.end())

c->second;

*atomSet =

->coordSets.front()->atomSet;

(virtualCoordinates, &resResContacts, &resPepContacts);

fldMtf =

(mol->

.size(), resResContacts.size(), resPepContacts.size());

resPepContacts.sort();

(corDef->

.

!= thdTbl->

|| (

)nResult >= thdTbl->

) {

(

);

(

block=0; block<corDef->

.

; ++block) {

corDef->

.

[block] - thdTbl->

[block][nResult],

corDef->

.

[block] + thdTbl->

[block][nResult]);

thdTbl->

[block][nResult] - thdTbl->

[block][nResult],

thdTbl->

[block][nResult] + thdTbl->

[block][nResult]);

aBlock->

= thdTbl->

[block][nResult] + 1 + thdTbl->

[block][nResult];

(

);

(

);

(!corDef || !masterCorDef || !qrySeq ||

corDef->

.

!= masterCorDef->

.

|| corDef->

.

!= qrySeq->

.

) {

(

);

(

=0;

<corDef->

.

; ++

) {

(qrySeq->

.

[

] < 0 || qrySeq->

.

[

] < 0)

;

adjacentLeft = (

> 0 && (qrySeq->

.

[

- 1] < 0 || qrySeq->

.

[

- 1] < 0));

adjacentRight = (

< corDef->

.

- 1 &&

(qrySeq->

.

[

+ 1] < 0 || qrySeq->

.

[

+ 1] < 0));

(!adjacentRight) {

*nRowsAddedToMultiple,

*sequenceViewer)

*nRowsAddedToMultiple = 0;

(!masterMultiple || !originalAlignments || !newAlignments || originalAlignments->size() == 0)

zscs = 0;

*trajectory =

;

retval =

;

AlignmentList::const_iterator p, pe = originalAlignments->end();

(

);

trajectory =

[gibScd->

];

pFile = fopen(

,

);

pFile = fopen(

,

);

(p=originalAlignments->begin(); p!=pe; ) {

((*p)->NRows() != 2 || (*p)->GetMaster() != masterMultiple->

()) {

(

);

success = 0;

pFile = fopen(

,

);

pFile = fopen(

,

);

(

<< (*p)->GetSequenceOfRow(1)->identifier->ToString());

success =

(fldMtf, corDef, qrySeq, rcxPtl, gibScd, thdTbl, seqMtf,

pFile = fopen(

,

);

(

=0;

<thdTbl->

; ++

) {

(thdTbl->

[

] <= 0)

;

sequences->front() = (*p)->GetMaster();

sequences->back() = (*p)->GetSequenceOfRow(1);

(!newAlignment)

;

newAlignment =

;

++(*nRowsAddedToMultiple);

newAlignments->push_back(newAlignment);

newAlignment = (*p)->

();

newAlignments->push_back(newAlignment);

(trajectory)

[] trajectory;

,

vector < int >& residueNumbers,

*seqMtf)

BlockMultipleAlignment::UngappedAlignedBlockList::const_iterator

, be = aBlocks.end();

(

=aBlocks.begin();

!=be; ++

) {

masterRange = (*b)->GetRangeOfRow(0);

dependentRange = (*b)->GetRangeOfRow(

);

(

=0;

<(*b)->width; ++

)

(residueNumbers[dependentRange->

+

] >= 0)

score += seqMtf->

[masterRange->

+

][residueNumbers[dependentRange->

+

]];

,

vector < int >& residueNumbers,

*fldMtf,

*rcxPtl)

seqIndex1, seqIndex2, resNum1, resNum2, dist,

;

(

=0;

<fldMtf->

.

; ++

) {

(seqIndex1 < 0)

;

(seqIndex2 < 0)

;

resNum1 = residueNumbers[seqIndex1];

resNum2 = residueNumbers[seqIndex2];

(resNum1 < 0 || resNum2 < 0)

;

dist = fldMtf->

.

[

];

score += rcxPtl->

[dist][resNum1][resNum2] + rcxPtl->

[dist][resNum1] + rcxPtl->

[dist][resNum2];

(

=0;

<fldMtf->

.

; ++

) {

(seqIndex1 < 0)

;

resNum1 = residueNumbers[seqIndex1];

(resNum1 < 0)

;

dist = fldMtf->

.

[

];

score += rcxPtl->

[dist][resNum1][resNum2] + rcxPtl->

[dist][resNum1] + rcxPtl->

[dist][resNum2];

vector < int > residueNumbers;

retval =

;

(

);

residueNumbers.resize(seq->

());

(

=0;

<seq->

(); ++

)

scorePSSM = (weightPSSM > 0.0) ?

scoreContacts = (weightPSSM < 1.0) ?

oss <<

<< weightPSSM <<

<< score;

(

);

BlockMultipleAlignment::UngappedAlignedBlockList::const_iterator

, be = aBlocks.end(),

;

nViolations = 0,

;

(

=aBlocks.begin();

!=be; ++

) {

(

== be)

;

thisRange = (*b)->GetRangeOfRow(

);

nextRange = (*n)->GetRangeOfRow(

);

(fldMtf->

[thisRange->

][nextRange->

] < minimumLoop)

minimumLoop = fldMtf->

[thisRange->

][nextRange->

];

thisRange = (*b)->GetRangeOfRow(

);

nextRange = (*n)->GetRangeOfRow(

);

(nextRange->

- thisRange->

- 1 < minimumLoop) {

(*violations)[

].push_back(make_pair(thisRange->

, nextRange->

));

nBlocksToAlign = 0;

BlockMultipleAlignment::UngappedAlignedBlockList::const_iterator

m, me = multipleABlocks.end(), p, pe = pairwiseABlocks.end();

(m=multipleABlocks.begin(); m!=me; ++m) {

multipleRange = (*m)->GetRangeOfRow(0);

realignBlock =

;

(p=pairwiseABlocks.begin(); p!=pe; ++p) {

pairwiseRange = (*p)->GetRangeOfRow(0);

(pairwiseRange->

<= multipleRange->

&& pairwiseRange->

>= multipleRange->

) {

realignBlock =

;

(realignBlock) ++nBlocksToAlign;

(nBlocksToAlign <= 1)

(

) (exp(1.5 + 0.25432 * nBlocksToAlign) + 0.5);

const AtomCoord * GetAtom(const AtomPntr &atom, bool getAny=false, bool suppressWarning=false) const

BlockMultipleAlignment * Clone(void) const

std::vector< const Sequence * > SequenceList

const UnalignedBlock * GetUnalignedBlockBefore(const UngappedAlignedBlock *aBlock) const

void SetRowDouble(unsigned int row, double value) const

const BLAST_Matrix * GetPSSM(void) const

void SetRowStatusLine(unsigned int row, const std::string &value) const

const Sequence * GetMaster(void) const

std::vector< const UngappedAlignedBlock * > UngappedAlignedBlockList

const Sequence * GetSequenceOfRow(unsigned int row) const

void GetUngappedAlignedBlocks(UngappedAlignedBlockList *blocks) const

unsigned int NRows(void) const

bool HasNoAlignedBlocks(void) const

bool UpdateBlockMapAndColors(bool clearRowInfo=true)

int GetAlignedDependentIndex(unsigned int masterSeqIndex, unsigned int dependentRow) const

bool IsAligned(unsigned int row, unsigned int seqIndex) const

bool AddUnalignedBlocks(void)

bool AddAlignedBlockAtEnd(UngappedAlignedBlock *newBlock)

bool MergeAlignment(const BlockMultipleAlignment *newAlignment)

void SetRangeOfRow(unsigned int row, int from, int to)

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

std::string ToString(void) const

DisulfideMap disulfideMap

const MoleculeIdentifier * identifier

static const int NO_ALPHA_ID

const AtomInfoMap & GetAtomInfos(void) const

const Molecule * molecule

const MoleculeIdentifier * identifier

unsigned int Length(void) const

bool GetParentOfType(const T **ptr, bool warnIfNotFound=true) const

bool mergeAfterEachSequence

int terminalResidueCutoff

bool freezeIsolatedBlocks

double loopLengthMultiplier

std::vector< VirtualCoordinate > VirtualCoordinateList

std::list< BlockMultipleAlignment * > AlignmentList

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

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

bool EditorIsOn(void) const

static void ReadToRowOfEnergies(ifstream &InFile, unsigned int NumResTypes)

ThreaderOptions globalThreaderOptions

static void GetVirtualResidue(const AtomSet *atomSet, const Molecule *mol, const Residue *res, Threader::VirtualCoordinate *coord)

static void GetVirtualPeptide(const AtomSet *atomSet, const Molecule *mol, const Residue *res1, const Residue *res2, Threader::VirtualCoordinate *coord)

static bool FreezeIsolatedBlocks(Cor_Def *corDef, const Cor_Def *masterCorDef, const Qry_Seq *qrySeq)

static const unsigned int NUM_RES_TYPES

static unsigned int CountWords(char *chs)

bool operator<(const Threader::Contact &c1, const Threader::Contact &c2)

static int LookupThreaderResidueNumberFromCharacterAbbrev(char r)

static double CalculatePSSMScore(const BlockMultipleAlignment::UngappedAlignedBlockList &aBlocks, unsigned int row, const vector< int > &residueNumbers, const Seq_Mtf *seqMtf)

unsigned int LookupNCBIStdaaNumberFromThreaderResidueNumber(char r)

static void TranslateContacts(const Threader::ContactList &resResContacts, const Threader::ContactList &resPepContacts, Fld_Mtf *fldMtf)

static void GetVirtualCoordinates(const Molecule *mol, const AtomSet *atomSet, Threader::VirtualCoordinateList *virtualCoordinates)

static void GetMinimumLoopLengths(const Molecule *mol, const AtomSet *atomSet, Fld_Mtf *fldMtf)

static const unsigned int MAX_DISTANCE_BIN

static BlockMultipleAlignment * CreateAlignmentFromThdTbl(const Thd_Tbl *thdTbl, unsigned int nResult, const Cor_Def *corDef, BlockMultipleAlignment::SequenceList *sequences, AlignmentManager *alignmentManager)

static double CalculateContactScore(const BlockMultipleAlignment *multiple, unsigned int row, const vector< int > &residueNumbers, const Fld_Mtf *fldMtf, const Rcx_Ptl *rcxPtl)

static void GetContacts(const Threader::VirtualCoordinateList &coords, Threader::ContactList *resResContacts, Threader::ContactList *resPepContacts)

static unsigned int BinDistance(const Vector &p1, const Vector &p2)

#define NO_VIRTUAL_COORDINATE(coord)

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

string Path(const string &dir, const string &file)

static void cleanup(void)

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

static string DoubleToString(double value, int precision=-1, TNumToStringFlags flags=0)

Convert double to string.

unsigned int

A callback function used to compare two keys in a database.

const struct ncbi::grid::netcache::search::fields::SIZE size

The NCBI C++/STL use hints.

std::istream & in(std::istream &in_, double &x_)

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

static Threader::GeometryViolationsForRow violations

static const sljit_gpr r1

static const sljit_gpr r2

#define row(bind, expected)

static int GetBLOSUM62Score(char a, char b)

unsigned char LookupNCBIStdaaNumberFromCharacter(char r)

Gib_Scd * NewGibScd(int NumTempSteps)

Fld_Mtf * FreeFldMtf(Fld_Mtf *mtf)

Thd_Tbl * NewThdTbl(int NumResults, int NumCoreElements)

Rcx_Ptl * NewRcxPtl(int NumResTypes, int NumDistances, int PeptideIndex)

Rcx_Ptl * FreeRcxPtl(Rcx_Ptl *pmf)

Cor_Def * FreeCorDef(Cor_Def *cdf)

Seq_Mtf * NewSeqMtf(int NumResidues, int AlphabetSize)

void PrintCorDef(Cor_Def *cdf, FILE *pFile)

int atd(Fld_Mtf *mtf, Cor_Def *cdf, Qry_Seq *qsq, Rcx_Ptl *pmf, Gib_Scd *gsp, Thd_Tbl *ttb, Seq_Mtf *psm, float *trg, int zscs, double ScalingFactor, float PSSM_Weight)

void PrintThdTbl(Thd_Tbl *ttb, FILE *pFile)

int ThrdRound(double Num)

Fld_Mtf * NewFldMtf(int NumResidues, int NumResResContacts, int NumResPepContacts)

void PrintFldMtf(Fld_Mtf *mtf, FILE *pFile)

Qry_Seq * FreeQrySeq(Qry_Seq *qsq)

Gib_Scd * FreeGibScd(Gib_Scd *gsp)

Thd_Tbl * FreeThdTbl(Thd_Tbl *ttb)

Seq_Mtf * FreeSeqMtf(Seq_Mtf *psm)

void PrintSeqMtf(Seq_Mtf *psm, FILE *pFile)

Cor_Def * NewCorDef(int NumBlocks)

Qry_Seq * NewQrySeq(int NumResidues, int NumBlocks)

void PrintQrySeq(Qry_Seq *qsq, FILE *pFile)

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