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SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.ObjectRdcPanda.Goal
public class Goal
Nested Class Summary | |
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class |
Goal.TreePdb
|
static class |
Goal.TreePdbAllComparator
|
static class |
Goal.TreePdbIDComparator
|
static class |
Goal.TreePdbNOEComparator
|
static class |
Goal.TreePdbRamaComparator
|
static class |
Goal.TreePdbRDCComparator
|
static class |
Goal.TreePdbSumRDCComparator
|
Field Summary | |
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double |
caliConstant
|
double |
gapThreshold
|
boolean |
isAllGridSearch
|
boolean |
isForward
|
int |
maxLeafNodes
|
double |
rdcThreshold
|
java.lang.String |
rotSrc
|
double |
Syy
|
double |
Szz
|
java.util.Vector<Noe> |
vecAmbNOEs
|
java.util.Vector<Assign> |
vecAsg
|
java.util.Vector<Dipolar> |
vecChRDC
|
java.util.Vector<Dipolar> |
vecNhRDC
|
java.util.Vector<Noesy> |
vecNOESY
|
java.util.Vector<Pdb> |
vecPdbSSE
|
java.util.Vector |
vecRamaAla
|
java.util.Vector |
vecRamaGeneral
|
java.util.Vector |
vecRamaGly
|
java.util.Vector |
vecRamaPrePro
|
java.util.Vector |
vecRamaPro
|
java.util.Vector<Assign> |
vecSeq
|
Constructor Summary | |
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Goal()
|
Method Summary | |
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double |
CaDistCorrection(java.lang.String res,
java.lang.String atom)
simple steric clash checking, used for checking steric clash between ca atom in rotamers and SSEs |
boolean |
CheckClashBtwCaNPdb(java.util.Vector vecPdb,
int curNo,
double[] caPos,
int numClashThreshold)
simple steric clash checking, used for checking steric clash between ca atom in rotamers and SSEs. |
boolean |
CheckClashBtwRotCaNSSEs(double[] caPos)
simple steric clash checking, used for checking steric clash between ca atom in rotamers and SSEs |
boolean |
CheckClashBtwRotCaNSSEsNew(double[] caPos,
int numClashThreshold)
simple steric clash checking, used for checking steric clash between ca atom in rotamers and SSEs. |
boolean |
CheckFirstResidue(Pdb preHalfPdb,
int fixNo,
double error,
double[] dist)
check whether the end residue closes the gap. |
boolean |
CheckFirstResidue(Pdb preHalfPdb,
int fixNo,
double error,
double[] dist,
double[] caDist)
check whether the end residue closes the gap. |
boolean |
CheckFirstResidueOld(Pdb preHalfPdb,
int fixNo,
double error,
double[] dist)
check whether the end residue closes the gap. |
boolean |
CheckFirstResidueOld(Pdb preHalfPdb,
int fixNo,
double error,
double[] dist,
double[] caDist)
check whether the end residue closes the gap. |
boolean |
CheckKinChainRestraint(Pdb nextHalfPdb,
int endResNo,
double error)
check whether kinematic chain restraint is satisfied |
boolean |
CheckKinChainRestraintBackward(Pdb nextHalfPdb,
int startResNo,
double error)
check whether kinematic chain restraint is satisfied |
boolean |
CheckKinConstraint(double[] caPos,
int noStart,
int noEnd,
int noCur)
check the kinematic restraint |
boolean |
CheckLastResidue(Pdb nextHalfPdb,
int endResNo,
double error,
double[] dist)
check whether the end residue closes the gap |
boolean |
CheckLastResidue(Pdb nextHalfPdb,
int endResNo,
double error,
double[] dist,
double[] distCa)
check whether the end residue closes the gap |
boolean |
CheckLastResidueOld(Pdb nextHalfPdb,
int endResNo,
double error,
double[] dist)
check whether the end residue closes the gap |
boolean |
CheckLastResidueOld(Pdb nextHalfPdb,
int endResNo,
double error,
double[] dist,
double[] distCa)
check whether the end residue closes the gap |
boolean |
CheckNOEBtwCaNSSEs(Pdb curPdb,
java.util.Vector vecSSEAnchors,
double distUpCa)
check whether the distance satisfies the NOE restraint from ca to anchors in SSEs |
boolean |
CheckStericClashBtwTwoFragments(java.util.Vector vecPdbA,
java.util.Vector vecPdbB)
simple steric clash checking, only using 1.8 as lower bound. |
double |
CompNoePatternScoreBetwSSEAndLoop(double errH,
double errHeavy,
java.util.Vector<Pdb> vecSSEPdb,
java.util.Vector<Pdb> vecPdbLoop,
double distBound,
java.util.Vector asgVec,
java.util.Vector vecNOESY)
compute NOE pattern between SSE and loops. |
int |
ComputeNoeSatisfaction(double[] caPos,
int noCur)
simple steric clash checking, used for checking steric clash between ca atom in rotamers and SSEs |
boolean |
CurPhiPsiGridBackwardMinRdcRmsd(java.util.Vector vecCurHalfPdb,
int curNo,
int startNo,
int lastNo,
double chRdc,
double nhRdc,
java.util.Vector vecCurFullPdb,
java.util.Vector vecPreHalfPdb,
boolean isFirst,
int topNodes)
compute possible phi/psi angles with min RDC RMSD similar to LoopCurResPhiPsiGridSearch function. |
boolean |
CurPhiPsiGridForwardMinRdcRmsd(java.util.Vector vecCurHalfPdb,
int curNo,
int startResNo,
int endResNo,
double chRdc,
double nhNextRdc,
java.util.Vector vecCurFullPdb,
java.util.Vector vecNextHalfPdb,
boolean isLast,
int topNodes)
compute possible phi/psi angles with min RDC RMSD similar to LoopCurResPhiPsiGridSearch function. |
void |
doGoalCalLoops(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
compute the loop using a gradient search approach (like ccd.) |
void |
EvaluateCandPositions(int noStart,
int noEnd,
java.util.Vector vecCandPosAll,
java.util.Vector vecPdbRef)
evaluate the set of candidate positions based on the known reference structure |
void |
KinNeighborSearch(Pdb PrePdb,
int curResNo,
int noStart,
int noEnd)
get the candidate positions for each ca atom using kinematic constraints and rotamer replacement find current ca atom candidate positions |
java.util.Vector |
LoopAllComputation(int noStart,
int noEnd)
compute the loop structures |
java.util.Vector |
LoopAllComputationBackward(int noStart,
int noEnd)
compute the loop structures from backward direction |
java.util.Vector |
LoopAllComputationBiDirection(int noStart,
int noEnd)
compute the loop structures from both direction |
boolean |
LoopCurResPhiPsiExactSearch(java.util.Vector vecCurHalfPdb,
int curNo,
int startResNo,
int endResNo,
double chRdc,
double nhNextRdc,
java.util.Vector vecCurFullPdb,
java.util.Vector vecNextHalfPdb,
boolean isLast)
compute possible phi/psi angles for current residue using RDC-EXACT algorithm. |
boolean |
LoopCurResPhiPsiExactSearchBackward(java.util.Vector vecCurHalfPdb,
int curNo,
int startNo,
int endResNo,
double chRdc,
double nhRdc,
java.util.Vector vecCurFullPdb,
java.util.Vector vecPreHalfPdb,
boolean isFirst)
compute possible phi/psi angles for current residue using RDC-EXACT algorithm. |
boolean |
LoopCurResPhiPsiGridSearch(java.util.Vector vecCurHalfPdb,
int curNo,
int startResNo,
int endResNo,
double chRdc,
double nhNextRdc,
java.util.Vector vecCurFullPdb,
java.util.Vector vecNextHalfPdb,
boolean isLast)
compute possible phi/psi angles for current residue when the RDCs are missing. |
boolean |
LoopCurResPhiPsiGridSearchBackward(java.util.Vector vecCurHalfPdb,
int curNo,
int startNo,
int lastNo,
double chRdc,
double nhRdc,
java.util.Vector vecCurFullPdb,
java.util.Vector vecPreHalfPdb,
boolean isFirst)
compute possible phi/psi angles for current residue when the RDCs are missing. |
boolean |
LoopFirstHalfResPsiGridSearch(int startNo,
int endResNo,
double nhNextRdc,
java.util.Vector vecCurFullPdb,
java.util.Vector vecNextHalfPdb)
compute possible psi angles for the first half residue. |
boolean |
LoopLastHalfResPsiGridSearch(int startNo,
int endResNo,
double nhRdc,
double chRdc,
java.util.Vector vecCurFullPdb,
java.util.Vector vecPreHalfPdb)
compute possible psi angles for the last half residue, which will be used to compute the second half fragment in a backward way. |
java.util.Vector |
LoopLocalGapClosure(java.util.Vector vecLoopOldPdb,
int noStart,
int noEnd)
use the gradient search to close the gap, while statisfying the NOE restraints |
java.util.Vector |
LoopLocalGapClosureBackward(java.util.Vector vecLoopOldPdb,
int noStart,
int noEnd)
use the gradient search to close the gap, for backward computation |
static void |
main(java.lang.String[] args)
|
java.util.Vector |
MergeTwoFragmentIntoOne(java.util.Vector vecPdbEnsemb1,
java.util.Vector vecPdbEnsemb2,
double error,
int noStart,
int noEnd,
int noMiddle,
boolean isFirstHalf)
Merge two framgements computed using backward and forward ways into one fragment |
java.util.Vector |
myPdbVectorCopy(java.util.Vector vecSrc)
|
java.util.Vector |
OutputEnsemblePdbs(java.util.Vector vecFinalTreePdb,
int noStart,
int noEnd,
double distUpCa)
compute the structure fragment that best fits the NOE restraints. |
java.util.Vector |
OutputEnsemblePdbsBackward(java.util.Vector vecFinalTreePdb,
int noStart,
int noEnd,
double distUpCa)
compute the structure fragment that best fits the NOE restraints. |
void |
PdbGenerateFromTree(java.util.Vector vecAllPdbTree)
|
void |
PlaneClustering(double resol,
java.util.Vector<Goal.TreePdb> vecCurTreePdb,
java.util.Vector<Goal.TreePdb> vecNextTreePdb)
clustering the first peptide plane, including ca, n, hn atoms. |
void |
PlaneClusteringAndTopSelection(double resol,
java.util.Vector<Goal.TreePdb> vecCurTreePdb,
java.util.Vector<Goal.TreePdb> vecNextTreePdb,
int topNum)
clustering the first peptide plane, including ca, n, hn atoms, and selecting the top planes. |
void |
PlaneClusteringAndTopSelectionNOEs(double resol,
java.util.Vector<Goal.TreePdb> vecCurTreePdb,
java.util.Vector<Goal.TreePdb> vecNextTreePdb,
int topNum,
int noStart,
boolean isForward)
clustering the first peptide plane, including ca, n, hn atoms, and selecting the top planes. |
void |
PlaneClusteringBackward(double resol,
java.util.Vector<Goal.TreePdb> vecCurTreePdb,
java.util.Vector<Goal.TreePdb> vecPreTreePdb)
clustering the first peptide plane, including ca, n, hn atoms. |
java.util.Vector |
RotamerReplacement(int noStart,
int noEnd)
Compute a structure, given the backbone and rotamers at all residue positions |
void |
RotamerReplacementKin(int noStart,
int noEnd)
get the candidate positions for each ca atom using kinematic constraints and rotamer replacement |
java.util.Vector |
RotamerReplacementOld(int noStart,
int noEnd)
Compute a structure, given the backbone and rotamers at all residue positions |
java.util.Vector |
SampleFirstHalfPlanes(int resNoFix,
boolean isSampleInitPlane)
use the grid search to find the set of variated peptide planes of the first residue |
java.util.Vector<Pdb> |
SearchSSEAnchors(int topK,
int resNoLoop)
find the SSE anchors (ca atoms) that can possibly interact with loops |
java.util.Vector<Pdb> |
SearchSSEAnchorsTop(int topK,
int resNoLoop)
find the top set of SSE anchors (ca atoms) that can possibly interact with loops |
double |
TranRotGridSearch(double[] tranX0,
double[] tranXn,
double[] rotX0,
double[] rotXn,
java.util.Vector<Pdb> vecRotPdb,
double tranResol,
double rotResol,
boolean isCheckClash,
double[] translation,
double[] rotation)
search T(3)*S(3) space to find the optimal solution that best fits the NOESY data |
double |
TranRotGridSearchNew(double[] caSSE,
double[] tranX0,
double[] tranXn,
double[] tranResol,
double[] translation,
int noStart,
int noEnd,
int noCur,
java.util.Vector<RotaPattern> vecCandPos)
search T(3)*S(3) space to find the optimal solution that best fits the NOESY data Use euler angle rather than grid points. |
Methods inherited from class java.lang.Object |
---|
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public java.util.Vector<Assign> vecSeq
public java.util.Vector<Pdb> vecPdbSSE
public java.lang.String rotSrc
public java.util.Vector<Assign> vecAsg
public java.util.Vector<Noesy> vecNOESY
public double caliConstant
public java.util.Vector<Noe> vecAmbNOEs
public double Syy
public double Szz
public boolean isForward
public boolean isAllGridSearch
public double gapThreshold
public double rdcThreshold
public java.util.Vector<Dipolar> vecNhRDC
public java.util.Vector<Dipolar> vecChRDC
public java.util.Vector vecRamaAla
public java.util.Vector vecRamaGeneral
public java.util.Vector vecRamaPrePro
public java.util.Vector vecRamaPro
public java.util.Vector vecRamaGly
public int maxLeafNodes
Constructor Detail |
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public Goal()
Method Detail |
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public java.util.Vector<Pdb> SearchSSEAnchors(int topK, int resNoLoop)
topK
- the top number of ca atoms based on the number of ambiguous NOE assignments.resNoLoop
- the index of the loop residue
public java.util.Vector<Pdb> SearchSSEAnchorsTop(int topK, int resNoLoop)
topK
- the top number of ca atoms based on the number of ambiguous NOE assignments.resNoLoop
- the index of the loop residue
public double TranRotGridSearchNew(double[] caSSE, double[] tranX0, double[] tranXn, double[] tranResol, double[] translation, int noStart, int noEnd, int noCur, java.util.Vector<RotaPattern> vecCandPos)
tranX0,tranXn,
- coordinate boundary for translationrotX0,
- rotXn coordinate boundary for rotation (unit: degree)rotPdb
- original rotamer pdbtranResol
- grid resolution of translationrotResol
- grid resolution of rotationisCheckClash
- whether check the steric clash,not used so far
-
public double TranRotGridSearch(double[] tranX0, double[] tranXn, double[] rotX0, double[] rotXn, java.util.Vector<Pdb> vecRotPdb, double tranResol, double rotResol, boolean isCheckClash, double[] translation, double[] rotation)
tranX0,tranXn,
- coordinate boundary for translationrotX0,
- rotXn coordinate boundary for rotation (unit: degree)rotPdb
- original rotamer pdbtranResol
- grid resolution of translationrotResol
- grid resolution of rotationisCheckClash
- whether check the steric clash,not used so far
-
public double CompNoePatternScoreBetwSSEAndLoop(double errH, double errHeavy, java.util.Vector<Pdb> vecSSEPdb, java.util.Vector<Pdb> vecPdbLoop, double distBound, java.util.Vector asgVec, java.util.Vector vecNOESY)
errH,
- errHeavy: error windows.vecPdbLoop
- loop PdbvecPdbSSE
- SSE PdbdistBound
- upper bound limit for back-computed NOEsasgVec
- resonance assigment listvecNOESY
- NOESY cross peak list
public boolean CheckStericClashBtwTwoFragments(java.util.Vector vecPdbA, java.util.Vector vecPdbB)
-
-
-
-
public boolean CheckKinConstraint(double[] caPos, int noStart, int noEnd, int noCur)
caPos
- current ca atom coordinatesnoStart,noEnd
- staring and end residue numbers of the loop (fixed endpoints)noCur
- current residue number
-
public double CaDistCorrection(java.lang.String res, java.lang.String atom)
caPos
- expected ca atom position of the rotamernoCur
- current residue number
-
-
public int ComputeNoeSatisfaction(double[] caPos, int noCur)
caPos
- expected ca atom position of the rotamernoCur
- current residue number
-
-
public boolean CheckNOEBtwCaNSSEs(Pdb curPdb, java.util.Vector vecSSEAnchors, double distUpCa)
curPdb
- current residuevecSSEAnchors
- list of anchored residues in SSEsdistUpCa
- distance upper bound for checking the NOE distance between Ca atoms
-
public boolean CheckClashBtwRotCaNSSEs(double[] caPos)
-
-
-
-
public boolean CheckClashBtwRotCaNSSEsNew(double[] caPos, int numClashThreshold)
-
-
-
-
public boolean CheckClashBtwCaNPdb(java.util.Vector vecPdb, int curNo, double[] caPos, int numClashThreshold)
-
-
-
-
public void KinNeighborSearch(Pdb PrePdb, int curResNo, int noStart, int noEnd)
vecPrePdb
- the whole structure computed in previous roundcurResNo
- current residue numbernoStart
- the first residue number in the loop fragmentnoEnd
- the end residue number in the loop fragmentpublic void RotamerReplacementKin(int noStart, int noEnd)
noStart
- starting residue number of the loopnoEnd
- last residue number of the looppublic java.util.Vector LoopLocalGapClosure(java.util.Vector vecLoopOldPdb, int noStart, int noEnd)
vecCurHalfPdb
- the set of all possible half planes for current residuecurNo
- current residue numberchRdc,nhNextRdc:
- at least one is missing (with the value -99999.9)isLast
- whether this is the last residue in the loop.
public java.util.Vector LoopLocalGapClosureBackward(java.util.Vector vecLoopOldPdb, int noStart, int noEnd)
vecCurHalfPdb
- the set of all possible half planes for current residuecurNo
- current residue numberchRdc,nhNextRdc:
- at least one is missing (with the value -99999.9)isLast
- whether this is the last residue in the loop.
public boolean LoopCurResPhiPsiGridSearch(java.util.Vector vecCurHalfPdb, int curNo, int startResNo, int endResNo, double chRdc, double nhNextRdc, java.util.Vector vecCurFullPdb, java.util.Vector vecNextHalfPdb, boolean isLast)
vecCurHalfPdb
- the set of all possible half planes for current residuecurNo
- current residue numberchRdc,nhNextRdc:
- at least one is missing (with the value -99999.9)isLast
- whether this is the last residue in the loop.
public boolean CurPhiPsiGridForwardMinRdcRmsd(java.util.Vector vecCurHalfPdb, int curNo, int startResNo, int endResNo, double chRdc, double nhNextRdc, java.util.Vector vecCurFullPdb, java.util.Vector vecNextHalfPdb, boolean isLast, int topNodes)
vecCurHalfPdb
- the set of all possible half planes for current residuecurNo
- current residue numberchRdc,nhNextRdc:
- at least one is missing (with the value -99999.9)isLast
- whether this is the last residue in the loop.topNodes
- top number of leaf nodes
public boolean CurPhiPsiGridBackwardMinRdcRmsd(java.util.Vector vecCurHalfPdb, int curNo, int startNo, int lastNo, double chRdc, double nhRdc, java.util.Vector vecCurFullPdb, java.util.Vector vecPreHalfPdb, boolean isFirst, int topNodes)
vecCurHalfPdb
- the set of all possible half planes for current residuecurNo
- current residue numberchRdc,nhNextRdc:
- at least one is missing (with the value -99999.9)isFirst
- whether this is the first residue in the loop.topNodes
- top number of leaf nodes
public boolean LoopCurResPhiPsiGridSearchBackward(java.util.Vector vecCurHalfPdb, int curNo, int startNo, int lastNo, double chRdc, double nhRdc, java.util.Vector vecCurFullPdb, java.util.Vector vecPreHalfPdb, boolean isFirst)
vecCurHalfPdb
- the set of all possible half planes for current residuecurNo
- current residue numberchRdc,nhRdc:
- at least one is missing (with the value -99999.9)isLast
- whether this is the last residue in the loop.
public java.util.Vector SampleFirstHalfPlanes(int resNoFix, boolean isSampleInitPlane)
resNoFix
- the residue number of fixed residue of the loop.isSampleInitPlane
- whether sampling the init peptite plane positions
public boolean LoopFirstHalfResPsiGridSearch(int startNo, int endResNo, double nhNextRdc, java.util.Vector vecCurFullPdb, java.util.Vector vecNextHalfPdb)
curNo
- current residue numberchRdc,nhNextRdc:
- at least one is missing (with the value -99999.9)isLast
- whether this is the last residue in the loop.
public boolean LoopLastHalfResPsiGridSearch(int startNo, int endResNo, double nhRdc, double chRdc, java.util.Vector vecCurFullPdb, java.util.Vector vecPreHalfPdb)
curNo
- current residue numberchRdc,nhRdc:
- at least one is missing (with the value -99999.9)isLast
- whether this is the last residue in the loop.
public boolean CheckLastResidueOld(Pdb nextHalfPdb, int endResNo, double error, double[] dist)
- nextHalfPdb
- end residue computed from looperror
- threshold for checking whether the gap is closedendResNo
- end residue no in SSE.
public boolean CheckLastResidue(Pdb nextHalfPdb, int endResNo, double error, double[] dist)
- nextHalfPdb
- end residue computed from looperror
- threshold for checking whether the gap is closedendResNo
- end residue no in SSE.
public boolean CheckLastResidue(Pdb nextHalfPdb, int endResNo, double error, double[] dist, double[] distCa)
- nextHalfPdb
- end residue computed from looperror
- threshold for checking whether the gap is closedendResNo
- end residue no in SSE.
public boolean CheckLastResidueOld(Pdb nextHalfPdb, int endResNo, double error, double[] dist, double[] distCa)
- nextHalfPdb
- end residue computed from looperror
- threshold for checking whether the gap is closedendResNo
- end residue no in SSE.
public boolean CheckFirstResidue(Pdb preHalfPdb, int fixNo, double error, double[] dist, double[] caDist)
- nextHalfPdb
- end residue computed from looperror
- threshold for checking whether the gap is closedendResNo
- end residue no in SSE.
public boolean CheckFirstResidue(Pdb preHalfPdb, int fixNo, double error, double[] dist)
- nextHalfPdb
- end residue computed from looperror
- threshold for checking whether the gap is closedendResNo
- end residue no in SSE.
public boolean CheckFirstResidueOld(Pdb preHalfPdb, int fixNo, double error, double[] dist, double[] caDist)
- nextHalfPdb
- end residue computed from looperror
- threshold for checking whether the gap is closedendResNo
- end residue no in SSE.
public boolean CheckFirstResidueOld(Pdb preHalfPdb, int fixNo, double error, double[] dist)
- nextHalfPdb
- end residue computed from looperror
- threshold for checking whether the gap is closedendResNo
- end residue no in SSE.
public boolean CheckKinChainRestraint(Pdb nextHalfPdb, int endResNo, double error)
- nextHalfPdb
- end residue computed from looperror
- thresholdendResNo
- end residue no in SSE.
public boolean CheckKinChainRestraintBackward(Pdb nextHalfPdb, int startResNo, double error)
- nextHalfPdb
- end residue computed from looperror
- thresholdendResNo
- end residue no in SSE.
public java.util.Vector OutputEnsemblePdbs(java.util.Vector vecFinalTreePdb, int noStart, int noEnd, double distUpCa)
vecFinalTreePdb
- storing all possible pdbs for the final residuenoStart,
- noEnd, end residue numbersdistUpCa
- distance upper bound between ca atoms
public java.util.Vector OutputEnsemblePdbsBackward(java.util.Vector vecFinalTreePdb, int noStart, int noEnd, double distUpCa)
vecFinalTreePdb
- storing all possible pdbs for the final residuenoStart,
- noEnd, end residue numbersdistUpCa
- distance upper bound between ca atoms
public java.util.Vector LoopAllComputation(int noStart, int noEnd)
noStart
- starting residue, in SSEnoEnd
- last residue, in SSE
public java.util.Vector LoopAllComputationBiDirection(int noStart, int noEnd)
noStart
- starting residue, in SSEnoEnd
- last residue, in SSE
public java.util.Vector LoopAllComputationBackward(int noStart, int noEnd)
noStart
- starting residue, in SSEnoEnd
- last residue, in SSE
public java.util.Vector MergeTwoFragmentIntoOne(java.util.Vector vecPdbEnsemb1, java.util.Vector vecPdbEnsemb2, double error, int noStart, int noEnd, int noMiddle, boolean isFirstHalf)
vecPdbEnsemb1
- ensemble of the the first fragmentvecPdbEnsemb2
- ensemble of the the second fragmenterror
- error shreshold for connecting two ca atomsisFirstHalf
- whether the first half of the first fragment is aligned.
public void PdbGenerateFromTree(java.util.Vector vecAllPdbTree)
public boolean LoopCurResPhiPsiExactSearch(java.util.Vector vecCurHalfPdb, int curNo, int startResNo, int endResNo, double chRdc, double nhNextRdc, java.util.Vector vecCurFullPdb, java.util.Vector vecNextHalfPdb, boolean isLast)
vecPrePdb
- vector to store all possible current planes, given previous residueint
- curNo current residue numberchRdc
- ch rdc of current residuenhNextRDC
- nh rdc of the next residue
public boolean LoopCurResPhiPsiExactSearchBackward(java.util.Vector vecCurHalfPdb, int curNo, int startNo, int endResNo, double chRdc, double nhRdc, java.util.Vector vecCurFullPdb, java.util.Vector vecPreHalfPdb, boolean isFirst)
vecPrePdb
- vector to store all possible current planes, given previous residueint
- curNo current residue numberchRdc
- ch rdc of current residuenhNextRDC
- nh rdc of the next residue
public void PlaneClustering(double resol, java.util.Vector<Goal.TreePdb> vecCurTreePdb, java.util.Vector<Goal.TreePdb> vecNextTreePdb)
-
- public void PlaneClusteringBackward(double resol, java.util.Vector<Goal.TreePdb> vecCurTreePdb, java.util.Vector<Goal.TreePdb> vecPreTreePdb)
-
- public void PlaneClusteringAndTopSelection(double resol, java.util.Vector<Goal.TreePdb> vecCurTreePdb, java.util.Vector<Goal.TreePdb> vecNextTreePdb, int topNum)
resol
- vecCurTreePdb,vecNextTreePdb
- topNum
- number of top selected planes.public void PlaneClusteringAndTopSelectionNOEs(double resol, java.util.Vector<Goal.TreePdb> vecCurTreePdb, java.util.Vector<Goal.TreePdb> vecNextTreePdb, int topNum, int noStart, boolean isForward)
resol
- vecCurTreePdb,vecNextTreePdb
- topNum
- number of top selected planes.noStart
- residue num of endisForward
- whether is forward or backward, 1 if forward.public java.util.Vector RotamerReplacement(int noStart, int noEnd)
noStart
- starting residue number of the loopnoEnd
- last residue number of the loop
public java.util.Vector RotamerReplacementOld(int noStart, int noEnd)
noStart
- starting residue number of the loopnoEnd
- last residue number of the loop
public void EvaluateCandPositions(int noStart, int noEnd, java.util.Vector vecCandPosAll, java.util.Vector vecPdbRef)
noStart,noEnd
- endpoints of the loopvecCandPosAll
- the chain of all candidate positionsvecPdbRef
- reference structure pdb (under the same frame)public java.util.Vector myPdbVectorCopy(java.util.Vector vecSrc)
public static void main(java.lang.String[] args)
public void doGoalCalLoops(java.lang.String src, java.lang.String strOut, java.lang.String strInput) throws JampackException
src
- location of the input filestrOut
- location of the output filestrInput
- input file name
JampackException
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