Uses of Class
Jampack.JampackException

Packages that use JampackException
Jampack   
RdcPanda   
 

Uses of JampackException in Jampack
 

Methods in Jampack that throw JampackException
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
Eig(Zmat A)
          Creates an eigenvalue-vector decomposition of a square matrix A.
Schur(Zmat A)
          Creats a Schur decomposition from a square Zmat.
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.
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.
Zmat(double[][] re, double[][] im)
          Creates a Zmat and initializes its real and imaginary parts to a pair of arrays.
Zpsdmat(double[][] re, double[][] im)
           
Zqrd(Zmat A)
          Constructs a Zqrd from a Zmat.
Zspec(Zmat AA)
          Creates a Zspec from Zmat.
Zsvd(Zmat XX)
          Computes the SVD of a Zmat XX.
Zutmat(double[][] re, double[][] im)
           
 

Uses of JampackException in RdcPanda
 

Methods in RdcPanda that throw JampackException
 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.