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PREV NEXT | FRAMES NO FRAMES |
Packages that use JampackException | |
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Jampack | |
RdcPanda |
Uses of JampackException in Jampack |
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Methods in Jampack that throw JampackException | |
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static Zmat |
Solve.ahib(Zltmat L,
Zmat B)
Solves LHX = B, where L is a Zltmat and B is a Zmat. |
static Zmat |
Solve.ahib(Zmat A,
Zmat B)
Solve AHX = B, where A is a Zmat and B is a Zmat. |
static Zmat |
Solve.ahib(Zutmat U,
Zmat B)
Solves UHX = B, where U is a Zutmat and B is a Zmat. |
static Zmat |
Solve.aib(Zltmat L,
Zmat B)
Solves LX = B, where L is a Zltmat and B is a Zmat. |
static Zmat |
Solve.aib(Zmat A,
Zmat B)
Solves AX = B, where A is a Zmat and B is a Zmat. |
static Zmat |
Solve.aib(Zpsdmat A,
Zmat B)
Solves AX = B, where A is a Zpsdmat and B is a Zmat. |
static Zmat |
Solve.aib(Zutmat U,
Zmat B)
Solves UX = B, where U is a Zutmat and B is a Zmat. |
static Zmat |
House.au(Zmat A,
Z1 u,
int r1,
int r2,
int c1,
int c2)
Postmultiplies the Householder transformation contained in a Z1 into a Zmat A[r1:r2,c1:c2] and overwrites Zmat A[r1:r2,c1:c2] with the results. |
static Zmat |
House.au(Zmat A,
Z1 u,
int r1,
int r2,
int c1,
int c2,
Z1 v)
Postmultiplies the Householder transformation contained in a Z1 into a Zmat A[r1:r2,c1:c2] and overwrites Zmat A[r1:r2,c1:c2] with the results. |
static Zmat |
Solve.bahi(Zmat B,
Zltmat L)
Solves XLH = B, where L is a Zltmat and B is a Zmat. |
static Zmat |
Solve.bahi(Zmat B,
Zmat A)
Solve XA^H = B, where A is a Zmat and B is a Zmat. |
static Zmat |
Solve.bahi(Zmat B,
Zutmat U)
Solves XUH = B, where U is a Zutmat and B is a Zmat. |
static Zmat |
Solve.bai(Zmat B,
Zltmat L)
Solves XL = B, where L is a Zltmat and B is a Zmat. |
static Zmat |
Solve.bai(Zmat B,
Zmat A)
Solve XA = B, where A is a Zmat and B is a Zmat. |
static Zmat |
Solve.bai(Zmat B,
Zpsdmat A)
Solves XA = B, where A is a Zpsdmat and B is a Zmat. |
static Zmat |
Solve.bai(Zmat B,
Zutmat U)
Solves XU = B, where U is a Zutmat and B is a Zmat. |
Zmat |
Zhqrd.bq(Zmat B)
Computes the product BQ. |
Zmat |
Zhqrd.bqh(Zmat A,
Zmat B)
Computes the product BQH. |
static void |
Swap.cols(Zmat A,
int c1,
int c2)
Interchances two columns of a Zmat (altered). |
Z |
Z.Div(Z a,
double b)
Computes the quotient of a Z and a double. |
Z |
Z.Div(Z a,
Z b)
Computes the quotient of two Z's. |
static Z1 |
House.genc(Zmat A,
int r1,
int r2,
int c)
Generates a Householder transformation from within the part of column c of a Zmat (altered) extending from rows r1 to r2. |
static Z1 |
House.genr(Zmat A,
int r,
int c1,
int c2)
Generates a Householder transformation from within the part of row r of a Zmat (altered) extending from columns c1 to c2. |
static Z1 |
Rand.nz1(int n)
Generates a normal random Z1. |
static Zmat |
Rand.nzmat(int m,
int n)
Generates a normal random Zmat. |
static Zdiagmat |
Inv.o(Zdiagmat D)
Computes the inverse of a Zdiagmat. |
static Zdiagmat |
Times.o(Zdiagmat D1,
Zdiagmat D2)
Computes the product of two Zdiagmats. |
static Zdiagmat |
Plus.o(Zdiagmat D1,
Zdiagmat D2)
Computes the sum of a Zdiagmat and a Zdiagmat. |
static Zdiagmat |
Minus.o(Zdiagmat D1,
Zdiagmat D2)
Computes the difference of a two Zdiagmats. |
static Zmat |
Times.o(Zdiagmat D,
Zmat A)
Computes the product of a Zdiagmat and a Zmat. |
static Zmat |
Plus.o(Zdiagmat D,
Zmat A)
Computes the sum of a Zdiagmat and a Zmat. |
static Zmat |
Minus.o(Zdiagmat D,
Zmat A)
Computes the difference of a Zdiagmat and a Zmat. |
static Zltmat |
Inv.o(Zltmat L)
Computes the inverse of a Zltmat. |
static Zmat |
Inv.o(Zmat A)
Computes the inverse of a square Zmat |
static Zmat |
Merge.o(Zmat[][] B)
Merges the matrices in an array of Zmats |
static Zmat[][] |
Block.o(Zmat A,
int[] ii,
int[] jj)
This method takes a Zmat A and two arrays ii and jj of length m and n and produces an (m-1)x(n-1) block matrix Zmat[m-1][n-1], whose (i,j)-element is A.get(ii[i], ii[i+1]-1, jj[j], jj[j+1]-1). |
static Zmat |
Times.o(Zmat A,
Zdiagmat D)
Computes the product of a Zmat and a Zdiagmat. |
static Zmat |
Plus.o(Zmat A,
Zdiagmat D)
Computes the sum of a Zmat and a Zdiagmat. |
static Zmat |
Minus.o(Zmat A,
Zdiagmat D)
Computes the difference of a Zmat and a Zdiagmat. |
static Zmat |
Times.o(Zmat A,
Zmat B)
Computes the product of two Zmats. |
static Zmat |
Plus.o(Zmat A,
Zmat B)
Computes the sum of two Zmats |
static Zmat |
Minus.o(Zmat A,
Zmat B)
Computes the difference of two Zmats. |
static Zpsdmat |
Inv.o(Zpsdmat A)
Computes the inverse of a Zpsdmat. |
static Zutmat |
Inv.o(Zutmat U)
Computes the inverse of a Zutmat. |
static Zmat |
Merge.o12(Zmat B00,
Zmat B01)
Merges its arguments to create the Zmat |
static Zmat |
Merge.o13(Zmat B00,
Zmat B01,
Zmat B02)
Merges its arguments to create the Zmat |
static Zmat |
Merge.o21(Zmat B00,
Zmat B10)
Merges its arguments to create the Zmat |
static Zmat |
Merge.o22(Zmat B00,
Zmat B01,
Zmat B10,
Zmat B11)
Merges its arguments to create the matrix |
static Zmat |
Merge.o23(Zmat B00,
Zmat B01,
Zmat B02,
Zmat B10,
Zmat B11,
Zmat B12)
Merges its arguments to create the Zmat |
static Zmat |
Merge.o31(Zmat B00,
Zmat B10,
Zmat B20)
Merges its arguments to create the Zmat |
static Zmat |
Merge.o32(Zmat B00,
Zmat B01,
Zmat B10,
Zmat B11,
Zmat B20,
Zmat B21)
Merges its arguments to create the Zmat |
static Zmat |
Merge.o33(Zmat B00,
Zmat B01,
Zmat B02,
Zmat B10,
Zmat B11,
Zmat B12,
Zmat B20,
Zmat B21,
Zmat B22)
Merges its arguments to create the Zmat |
Zmat |
Zhqrd.qb(Zmat B)
Computes the product QB. |
Zmat |
Zhqrd.qhb(Zmat B)
Computes the product QHB. |
static Zmat |
Pivot.row(Zmat A,
int[] pvt)
Pivots the rows of a Zmat (altered) as specified by a pivot array. |
static Zmat |
Pivot.rowi(Zmat A,
int[] pvt)
Pivots the rows of a Zmat (altered) as in the inverse order specified by a pivot array. |
static void |
Swap.rows(Zmat A,
int r1,
int r2)
Interchances two rows of a Zmat (altered). |
static void |
Parameters.setBaseIndex(int bx)
Resets the default base index. |
static Zmat |
House.ua(Z1 u,
Zmat A,
int r1,
int r2,
int c1,
int c2)
Premultiplies the Householder transformation contained in a Z1 into a Zmat A[r1:r2,c1:c2] and overwrites Zmat A[r1:r2,c1:c2] with the results. |
static Zmat |
House.ua(Z1 u,
Zmat A,
int r1,
int r2,
int c1,
int c2,
Z1 v)
Premultiplies the Householder transformation contained in a Z1 into a Zmat A[r1:r2,c1:c2] and overwrites Zmat A[r1:r2,c1:c2] with the results. |
static Z1 |
Rand.uz1(int n)
Generates a uniform random Z1. |
static Zmat |
Rand.uzmat(int m,
int n)
Generates a uniform random Zmat. |
Constructors in Jampack that throw JampackException | |
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Eig(Zmat A)
Creates an eigenvalue-vector decomposition of a square matrix A. |
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Schur(Zmat A)
Creats a Schur decomposition from a square Zmat. |
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Z1(int n)
Creates a Z1 initializes to zero. |
|
Zchol(Zmat A)
Constructs a Zchol from a Zmat A. |
|
Zdiagmat(Zmat A)
Constructs a Zdiagmat and initializes it to the principal diagonal of a Zmat. |
|
Zdiagmat(Zmat A,
int k)
Constructs a Zdiagmat and initializes it to the diagonal of a Zmat. |
|
Zhess(Zmat A)
Creates a Zhess from a square Zmat. |
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Zhqrd(Zmat A)
Computes a Householder QR decomposition of a Zmat |
|
Zltmat(double[][] re,
double[][] im)
|
|
Zludpp(Zmat A)
Computes the partially pivoted LU decompostion. |
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Zmat(double[][] re,
double[][] im)
Creates a Zmat and initializes its real and imaginary parts to a pair of arrays. |
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Zpsdmat(double[][] re,
double[][] im)
|
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Zqrd(Zmat A)
Constructs a Zqrd from a Zmat. |
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Zspec(Zmat AA)
Creates a Zspec from Zmat. |
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Zsvd(Zmat XX)
Computes the SVD of a Zmat XX. |
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Zutmat(double[][] re,
double[][] im)
|
Uses of JampackException in RdcPanda |
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Methods in RdcPanda that throw JampackException | |
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java.util.Vector |
Pdb.AlaninizeStructure(java.util.Vector vecPdb,
boolean[] resIndex,
java.lang.String rotSrc)
replace all non-NOE residues in pdb with alaline. |
java.util.Vector |
Pdb.AlaninizeStructureResName(java.util.Vector vecPdb,
java.lang.String rotSrc)
replace all non-NOE residues in pdb with alaline, according to the residue names. |
java.util.Vector |
Pdb.AssembleTwoSSEs(java.util.Vector vecSSEPdb1,
java.util.Vector vecSSEPdb2,
int brkResNo,
java.util.Vector<Dipolar> rdcVecNh,
java.util.Vector<Dipolar> rdcVecCh,
double Syy,
double Szz)
assemble two sses with some phi psi deviations in the break point, the assembled structure has minimum rdc rmsd and vdw energy. |
java.util.Vector |
Model.BackonbeRotation(java.util.Vector pdbAll,
java.util.Vector pdbBB)
rotate the whole protein according to the reference backbone such that the backbone coordinates are the same (both should have the same residues). |
java.util.Vector |
Model.BackonbeRotationAtResidue(java.util.Vector pdbAll,
java.util.Vector pdbBB,
int resNo)
rotate the whole protein according to the reference backbone at specific residue, such that the backbone coordinates are the same (both should have the same residues). |
java.util.Vector |
Loops.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 |
PdbRmsd.calcMinPackingRms(java.util.Vector noeVec,
java.util.Vector pdbVecA,
java.util.Vector pdbVecB,
double[] noeRms,
boolean debugNOE)
calculate the minimum rms between two sses, for checking packing symmetry In both SSEs, all rotamers are places. |
void |
RdcPanda.doAddRandomLoops(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
add random loops to an ensemble of packed SSE structures (i.e. |
void |
RdcPanda.doAddSideChains(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
* add the side chains and prune steic clahes. |
void |
RdcPanda.doCalAlignmentTensor(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
calculate the alignment tensor. |
void |
Loops.doCalLoops(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
compute the loop using a gradient search approach (like ccd.) |
void |
Pdb.doCalNOEScores(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
* compute the NOE satisfaction scores for all structure in an ensemble. |
void |
Noe.doCheckNoeByEnsemble(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
check the NOE table by an ensemble of structures, and output the statistical information. |
void |
RdcPanda.doCheckPackingSym(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
check the packing symmetry that best fit the noe restraints (namely with minimum NOE RMSD). |
void |
Goal.doGoalCalLoops(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
compute the loop using a gradient search approach (like ccd.) |
void |
Assign.doHANANOEAsg(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
HANA algorithm for the NOE assignment and output the NOE table. |
void |
RdcPanda.doMergeNCluster(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
* merge all structures in previous ensemble into one enemble (with the same pdb name) and cluster them according to given resolution. |
void |
RdcPanda.doMergeNClusterAll(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
* merge all structures in previous ensemble into one enemble (with the same pdb name) and cluster them according to given resolution. |
void |
Nasca.doNasca(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
Implement the NOE assignment (NASCA) algorithm without using the side-chain resonance infomration. |
void |
Noe.doNoeStatistics(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
output the NOE statistics. |
void |
RdcPanda.doRdcExactHelix(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
RDC-EXACT for two RDCs (CH and NH RDCs), and for long helix Co-Ca and Co-N RDCs are optional. |
void |
RdcPanda.doRdcExactHelixWOAT(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
RDC-EXACT without alignment tensor for two RDCs (CH and NH RDCs), and for long helix. |
void |
Model.doRdcExactSheet(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
compute the beta sheet using RDC-EXACT. |
void |
RdcPanda.doReadPDBEnergy(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
Read the engergy value from xplor PDB, and output the top structures with lowest energies. |
void |
Pdb.doReadPdbFragments(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
HANA algorithm for the NOE assignment and output the NOE table. |
void |
RdcPanda.doRefineRdcExact(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
refine the half start and end residues of pdb backbone solved from RDC-EXACT. |
void |
RdcPanda.doRefineRdcExactMiddle(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
refine the middle residues of pdb backbone solved from RDC-EXACT. |
void |
RdcPanda.doRunXplor(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
call Xplor as a subroutine given a script file. |
void |
RdcPanda.doSSEPacking(java.lang.String src,
java.lang.String strOut,
java.lang.String strInput)
Pack SSEs using sparse inter-SSE NOE restraints. |
java.util.Vector |
GraphCut.GraphConstruction(java.util.Vector vecPdbBB,
java.lang.String srcRotFile,
double noeLimit)
Construct the residue interation graph |
static void |
vdw.main(java.lang.String[] argv)
The main method. |
static void |
Rotamer.main(java.lang.String[] argv)
The main method. |
static void |
RdcPanda.main(java.lang.String[] args)
The main method. |
static void |
Model.main(java.lang.String[] argv)
The main method for testing. |
static void |
Dipolar.main(java.lang.String[] argv)
The main method for testing. |
static void |
SSEPacking.main1(java.lang.String[] argv)
Main function for testing. |
static void |
Model.main1(java.lang.String[] argv)
Main function for testing. |
void |
vdw.mergeAndCluster(java.lang.String src,
java.lang.String srcOut,
java.lang.String strPreEnsemb,
int maxStr,
int maxEnsemSize,
double resolution,
java.lang.String strNewEnsemb,
java.lang.String strDelimit)
merge all structures in previous ensemble into one enemble (with the same pdb name) and cluster them according to given resolution. |
void |
vdw.mergeAndClusterAll(java.lang.String src,
java.lang.String srcOut,
double resolution,
java.lang.String strNewEnsemb)
similar to "mergeAndCluster", but cluster all structures in one directory as an ensemble merge all structures in previous ensemble into one enemble (with the same pdb name) and cluster them according to given resolution. |
java.util.Vector<Pdb> |
ModelRdc.minHelix(java.util.Vector<Dipolar> rdcVec1,
java.util.Vector<Dipolar> rdcVec2,
double[] rdc1Cal,
double[] rdc2Cal,
java.util.Vector<Pdb> pdbVec,
double Syy,
double Szz,
double rmsd1,
double rmsd2,
int nCycle,
double weightAngles,
boolean debugDFS,
boolean printResults,
boolean isHelix,
java.util.Vector vecTalos)
A recusive function to compute all the backbone Phi/Psi for an n-residue helix or the first strand. |
java.util.Vector<Pdb> |
ModelRdc.minHelix4RDCs(java.util.Vector<Dipolar> rdcVec1,
java.util.Vector<Dipolar> rdcVec2,
java.util.Vector<Dipolar> helixRdcCaCoVec,
java.util.Vector<Dipolar> helixRdcCoNVec,
double[] rdc1Cal,
double[] rdc2Cal,
java.util.Vector<Pdb> pdbVec,
double Syy,
double Szz,
double rmsd1,
double rmsd2,
int nCycle,
double weightAngles,
boolean debugDFS,
boolean printResults,
boolean isHelix,
java.util.Vector vecTalos,
double wtCoCa,
double wtCoN)
A recusive function to compute all the backbone Phi/Psi for an n-residue helix or the first strand. |
java.util.Vector<Pdb> |
ModelRdc.minHelix4RDCs(java.util.Vector<Pdb> vecPrePdb,
java.util.Vector<Dipolar> rdcVec1,
java.util.Vector<Dipolar> rdcVec2,
java.util.Vector<Dipolar> helixRdcCaCoVec,
java.util.Vector<Dipolar> helixRdcCoNVec,
double[] rdc1Cal,
double[] rdc2Cal,
java.util.Vector<Pdb> pdbVec,
double Syy,
double Szz,
double rmsd1,
double rmsd2,
int nCycle,
double weightAngles,
boolean debugDFS,
boolean printResults,
boolean isHelix,
java.util.Vector vecTalos,
double wtCoCa,
double wtCoN,
int startNo,
int endNo,
java.util.Vector vecSeq)
A recusive function to compute all the backbone Phi/Psi for an n-residue helix or the first strand. |
java.util.Vector |
Noe.NoeMethylCorrection(java.util.Vector vecNoeOld,
double metCorrection)
correct the NOE upper distance for an methyl NOE we assume that the pseudo methyl atoms of all old NOEs are labeled with "#" or "##". |
static void |
SSEPacking.PackingHelicesBasedOnNOEPatterns(java.lang.String[] argv)
Packing helices based on noe patterns. |
void |
RdcPanda.parse(java.lang.String[] args)
Parses the. |
java.util.Vector |
PdbRmsd.positionByAmbiNOEAllRotamers(java.util.Vector noeVec,
java.util.Vector pdbVecA,
java.util.Vector pdbVecB,
double[] noeRms,
boolean debugNOE,
java.util.Vector vecUpdateNOE,
java.lang.String strPass,
java.util.Vector vecSeq,
double resol_cluster)
pack two SSEs based on Amgibuous NOE restratints. |
java.util.Vector |
PdbRmsd.positionByNOEAllRotamers(java.util.Vector noeVec,
java.util.Vector pdbVecA,
java.util.Vector pdbVecB,
double[] noeRms,
boolean debugNOE,
java.util.Vector vecUpdateNOE,
java.lang.String strPass,
java.util.Vector vecSeq,
double resol_cluster)
pack two SSEs based on NOE restratints In both SSEs, all rotamers are placed. |
java.util.Vector |
PdbRmsd.positionByNOEAllRotamersGrid(java.util.Vector noeVec,
java.util.Vector pdbVecA,
java.util.Vector pdbVecB,
double[] noeRms,
boolean debugNOE,
java.util.Vector vecUpdateNOE)
pack two SSEs based on NOE restratints In both SSEs, all rotamers are places. |
java.util.Vector |
PdbRmsd.positionByNOEAllRotamersSaved(java.util.Vector noeVec,
java.util.Vector pdbVecA,
java.util.Vector pdbVecB,
double[] noeRms,
boolean debugNOE,
java.util.Vector vecUpdateNOE,
java.lang.String strPass,
java.util.Vector vecSeq)
Position by noe all rotamers saved. |
boolean |
Rotamer.pruneRotamers(java.util.Vector vecPdb,
java.lang.String rotSrc,
java.util.Vector noeVec,
int curNo,
int lastNo,
java.util.Vector vecEmsemblePdbSave)
prune rotamers based on: 1: collisions with backbone atoms; 2: collisions between pairwise rotamer atoms; 3: NOE constraints, including pairwise and local NOEs Note: a recurrsive approach is used. |
java.util.Vector<Pdb> |
ModelRdc.refineHelix22(java.util.Vector vecBB,
java.util.Vector<Dipolar> rdc1Vec,
java.util.Vector<Dipolar> rdc2Vec,
double Syy,
double Szz,
double[] ramaFilter,
double phiAve,
double psiAve,
int refineCycle,
int initialCycle,
double w4Angles,
double resolution,
boolean debugDFS,
boolean printResults,
java.util.Vector vecTalos)
Refine helix22. |
java.util.Vector<Pdb> |
ModelRdc.refineHelixW4RDCs(java.util.Vector vecBB,
java.util.Vector<Dipolar> rdc1Vec,
java.util.Vector<Dipolar> rdc2Vec,
java.util.Vector<Dipolar> helixRdcCaCoVec,
java.util.Vector<Dipolar> helixRdcCoNVec,
double Syy,
double Szz,
double[] ramaFilter,
double phiAve,
double psiAve,
int refineCycle,
int initialCycle,
double w4Angles,
double resolution,
boolean debugDFS,
boolean printResults,
java.util.Vector vecTalos)
Refine helix w4 rd cs. |
java.util.Vector<Pdb> |
ModelRdc.refineHelixW4RDCs(java.util.Vector vecPreBB,
java.util.Vector vecBB,
java.util.Vector<Dipolar> rdc1Vec,
java.util.Vector<Dipolar> rdc2Vec,
java.util.Vector<Dipolar> helixRdcCaCoVec,
java.util.Vector<Dipolar> helixRdcCoNVec,
double Syy,
double Szz,
double[] ramaFilter,
double phiAve,
double psiAve,
int refineCycle,
int initialCycle,
double w4Angles,
double resolution,
boolean debugDFS,
boolean printResults,
java.util.Vector vecTalos,
double wtCoCa,
double wtCoN,
int starNo,
int endNo,
java.util.Vector vecSeq)
refine the Helix with the weights for CaCo NCO RDCs. |
java.util.Vector |
ModelRdc.refineSaupe(java.util.Vector rdc1Vec,
java.util.Vector rdc2Vec,
double[] saupe,
double[] ramaFilter,
double phiAve,
double psiAve,
int refineCycle,
int nCycle,
boolean debugDFS,
boolean printResults,
java.util.Vector vecTalos)
Refine Saupe elements from an initial model. |
java.util.Vector |
ModelRdc.refineSaupe4RDCsWOAT(java.util.Vector rdc1Vec,
java.util.Vector rdc2Vec,
java.util.Vector rdcCaCoVec,
java.util.Vector rdcCoNVec,
double[] saupe,
double[] ramaFilter,
double phiAve,
double psiAve,
int refineCycle,
int nCycle,
boolean debugDFS,
boolean printResults,
java.util.Vector vecTalos)
Refine Saupe elements from an initial model. |
java.util.Vector |
ModelRdc.refineSaupe4RDCsWOAT(java.util.Vector vecPreBB,
java.util.Vector pdbVec,
java.util.Vector rdc1Vec,
java.util.Vector rdc2Vec,
java.util.Vector rdcCaCoVec,
java.util.Vector rdcCoNVec,
double[] saupe,
double[] ramaFilter,
double phiAve,
double psiAve,
int refineCycle,
int nCycle,
boolean debugDFS,
boolean printResults,
java.util.Vector vecTalos,
double wtCoCa,
double wtCoN,
int starNo,
int endNo,
java.util.Vector vecSeq)
Refine Saupe elements from an initial model. |
java.util.Vector |
Pdb.RotamSelectAndStructureNoClash(double csErrH,
double csErrN,
double csErrCA,
java.util.Vector pdbBBVec,
java.util.Vector asgVec,
java.lang.String rotSrc,
java.util.Vector NoesyVec,
double distBound,
int pickNum,
boolean[] resIndex)
Rotam select and structure no clash. |
static void |
SSEPacking.SSEsOneToOnePacking(java.lang.String[] argv)
packing two single SSEs using sparse NOE restraints. |
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