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java.lang.ObjectRdcPanda.Loops
public class Loops
Field Summary | |
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double |
caliConstant
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java.util.Random |
generator
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java.util.Vector |
vecPdbSSE
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java.util.Vector |
vecRamaAla
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java.util.Vector |
vecRamaGeneral
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java.util.Vector |
vecRamaGly
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java.util.Vector |
vecRamaPrePro
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java.util.Vector |
vecRamaPro
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java.util.Vector |
vecSeq
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Constructor Summary | |
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Loops()
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Method Summary | |
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java.util.Vector |
calcFragment(double Syy,
double Szz,
java.util.Vector<Dipolar> vecChRdc,
java.util.Vector<Dipolar> vecNhRdc,
double[] n1,
double[] nh1,
double[] ca1,
int noStart,
int noEnd,
java.util.Vector vecNoesy,
java.util.Vector asgVec,
double csErrH,
double csErrHeavy,
boolean isSkipNOE)
Compute the structure fragment that best fits the RDC and NOESY data. |
java.util.Vector |
CombineSSEandLoop(java.util.Vector vecSSEPdb,
java.util.Vector vecLoopPdb)
combine the sse pdb with the loop pdb. |
double |
CompNoePatternScoreBetwSSEAndLoop(double errH,
double errHeavy,
java.util.Vector vecPdbCombin,
double distBound,
java.util.Vector asgVec,
java.util.Vector vecNOESY)
compute NOE pattern between SSE and loops. |
double |
CompRamachandranScore(double phi,
double psi,
java.util.Vector vecRamachandran)
Compute the Ramachandran probability score based on Richardsons' top500 structures. |
void |
doCalLoops(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
compute the loop using a gradient search approach (like ccd.) |
java.lang.String |
GetResNameFromSequence(java.util.Vector vecSequence,
int res_no)
get the residue name from the sequence information, given the residue number. |
boolean |
isInPhiPsiClusters(java.util.Vector vecPhiPsi,
PhiPsi ff,
double resolution)
tell whether a point is within the clusters of previous ensemble |
java.util.Vector |
IterativeGradientSearch(java.util.Vector vecPrePdb,
double Syy,
double Szz,
java.util.Vector<Dipolar> vecChRdc,
java.util.Vector<Dipolar> vecNhRdc,
int noStart,
int noEnd,
java.util.Vector vecNoesy,
java.util.Vector asgVec,
double csErrH,
double csErrHeavy,
boolean isSkipNOE)
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java.util.Vector |
phiCalAll(double Syy,
double Szz,
double rdc,
Matrix Rg)
Compute the Phi angles from RDC equations. |
boolean |
phiPsiChainAll(double[] rdcArrCH,
double[] rdcArrNH,
int[] isChRDC,
int[] isNhRDC,
Matrix rg,
double Syy,
double Szz,
int i,
int resNo,
int N,
double[] ppS,
java.util.Vector ppVec,
boolean rightHand,
int resNoStart)
A recusive function to compute all the backbone (phi, psi) angles for a fragment. |
PhiPsi |
PhiPsiRandomFromRamachandran(java.util.Vector vecSeq,
int resNo)
Randomly sample the (Phi, Psi) angles according to distribution from Ramachandran. |
java.util.Vector |
psiCalAll(double Syy,
double Szz,
double rdc,
double phi,
Matrix rg)
Compute the Psi angles. |
java.util.Vector |
ReadRamachandranFile(java.lang.String ssePdbFile)
Read the Ramachandran probability score based on Richardsons' top500 structures. |
java.util.Vector |
ResidueGradientSearch(java.util.Vector vecPrePdb,
int curResNo,
double Syy,
double Szz,
java.util.Vector<Dipolar> vecChRdc,
java.util.Vector<Dipolar> vecNhRdc,
int noStart,
int noEnd,
java.util.Vector vecNoesy,
java.util.Vector asgVec,
double csErrH,
double csErrHeavy,
double[] endDist,
boolean isSkipNOE)
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Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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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 java.util.Random generator
public java.util.Vector vecSeq
public java.util.Vector vecPdbSSE
public double caliConstant
Constructor Detail |
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public Loops()
Method Detail |
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public void doCalLoops(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
public java.util.Vector IterativeGradientSearch(java.util.Vector vecPrePdb, double Syy, double Szz, java.util.Vector<Dipolar> vecChRdc, java.util.Vector<Dipolar> vecNhRdc, int noStart, int noEnd, java.util.Vector vecNoesy, java.util.Vector asgVec, double csErrH, double csErrHeavy, boolean isSkipNOE)
public java.util.Vector ResidueGradientSearch(java.util.Vector vecPrePdb, int curResNo, double Syy, double Szz, java.util.Vector<Dipolar> vecChRdc, java.util.Vector<Dipolar> vecNhRdc, int noStart, int noEnd, java.util.Vector vecNoesy, java.util.Vector asgVec, double csErrH, double csErrHeavy, double[] endDist, boolean isSkipNOE)
vecPrePdb
- the whole structure computed in previous roundcurResNo
- current residue numberSyy
- Alignment tensorSzz
- Alignment tensorvecChRdc
- ch rdcsvecNhRdc
- nh rdcsnoStart
- the first residue number in the loop fragmentnoEnd
- the end residue number in the loop fragmentvecNoesy
- NOESY cross peaksasgVec
- resonance assignment listcsErrH
- error for proton chemical shiftcsErrHeavy
- error for heavy atom chemical shiftendDist
- distance between ending pointsisSkipNOE
- whether skip the NOE matching score in the scoring function
public java.util.Vector calcFragment(double Syy, double Szz, java.util.Vector<Dipolar> vecChRdc, java.util.Vector<Dipolar> vecNhRdc, double[] n1, double[] nh1, double[] ca1, int noStart, int noEnd, java.util.Vector vecNoesy, java.util.Vector asgVec, double csErrH, double csErrHeavy, boolean isSkipNOE) throws JampackException
Syy,
- Szz: the Saupe elementvecChRdc
- an array of CH RDCs for the fragment.vecNhRdc
- an array of NH RDCs for the fragment.n1
- the direction cosine for amide nitrogen of the first residue.nh1
- the direction cosine for amide proton.ca1
- the direction cosine for Ca.noStart
- the residue number of the first residue of a fragment.noEnd
- the residue number of the end residue of a fragment.vecNoesy
- NOESY peak list.asgVec
- resonance listcsErrH,
- csErrHeavy error window for protons and heavy atoms (i.e. C13 or N15)isSkipNOE
- whether skip the NOE matching score in the scoring function
JampackException
public double CompNoePatternScoreBetwSSEAndLoop(double errH, double errHeavy, java.util.Vector vecPdbCombin, 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 java.util.Vector CombineSSEandLoop(java.util.Vector vecSSEPdb, java.util.Vector vecLoopPdb)
vecSSEPdb
- SSE pdbvecLoopPdb
- loop pdb
public PhiPsi PhiPsiRandomFromRamachandran(java.util.Vector vecSeq, int resNo)
resNo
- residue numbervecSeq
- sequence informationpublic boolean phiPsiChainAll(double[] rdcArrCH, double[] rdcArrNH, int[] isChRDC, int[] isNhRDC, Matrix rg, double Syy, double Szz, int i, int resNo, int N, double[] ppS, java.util.Vector ppVec, boolean rightHand, int resNoStart)
rdcArrCH
- an array of CH RDCs for the fragmentrdcArrNH
- an array of NH RDCs for the fragmentisChRDC,isNhRDC
- an array indicating whether RDC is available (i.e. not missing).rg
- a matrix to rotate the POF to a coodinate system defined in the first peptide plane.Syy
- Saupe elements computed from both NH and CH rdcsSzz
- Saupe elements computed from both NH and CH rdcsi
- the current depth of the depth-first search. Begin the call with i = 0;resNo
- residue number of current residue;N
- the total depth of the depth-first search.ppS
- a temporary array for saving intermediate (\phi, \psi) angles.ppVec
- an array for saving and returning final (\phi, \psi) angles.rightHand
- make sure the computed rg has the same handedness as the rotating matrix by the SVD methodresNoStart
- starting residue indexpublic java.util.Vector ReadRamachandranFile(java.lang.String ssePdbFile)
vecRamachandran
- vector of Ramachandran database informationphi
- input phi angle valuepsi
- input psi angle value
public double CompRamachandranScore(double phi, double psi, java.util.Vector vecRamachandran)
vecRamachandran
- vector of Ramachandran database informationphi
- input phi angle value, in radian unitpsi
- input psi angle value, in radian unit
public java.util.Vector phiCalAll(double Syy, double Szz, double rdc, Matrix Rg)
rdc
- Rdc data of CH vectorrg
- the rotation matrix rotate a POF to a frame defined in the peptine plane $i$Syy
- diagonilized Saupe elements computed by SVD with both CH and NH RDCs.Szz
- diagonilized Saupe elements
public java.lang.String GetResNameFromSequence(java.util.Vector vecSequence, int res_no)
vecSeqence
- sequence informationres_no
- residue number
public java.util.Vector psiCalAll(double Syy, double Szz, double rdc, double phi, Matrix rg)
rdc
- Rdc data of NH vectorphi
- the computed \phi value for the same residuerg
- the rotation matrix rotate a POF to a frame defined in the peptine plane $i$Syy
- diagonilized Saupe elements computed by SVD with both CH and NH RDCs.Szz
- diagonilized Saupe elements
public boolean isInPhiPsiClusters(java.util.Vector vecPhiPsi, PhiPsi ff, double resolution)
vecPoints
- ensemble of point tocc
- the obj pointresolution
- resolution of the clustering
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