Uses of Class
RdcPanda.Dipolar

Packages that use Dipolar
RdcPanda   
 

Uses of Dipolar in RdcPanda
 

Fields in RdcPanda with type parameters of type Dipolar
 java.util.Vector<Dipolar> Goal.vecChRDC
           
 java.util.Vector<Dipolar> Goal.vecNhRDC
           
 

Methods in RdcPanda that return types with arguments of type Dipolar
 java.util.Vector<java.util.Vector<Dipolar>> Dipolar.rdcReader(java.lang.String filename, java.util.Vector<IDof2aryStructure> idVec, java.lang.String idType)
          read RDC data file for a fragment as defined by secondary structure identification.
 java.util.Vector<java.util.Vector<Dipolar>> Dipolar.rdcReader(java.lang.String filename, java.util.Vector<IDof2aryStructure> idVec, java.lang.String idType, double dbSc)
          read RDC data file for a fragment as defined by secondary structure identification.
 

Method parameters in RdcPanda with type arguments of type Dipolar
 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 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.
 double PdbRdc.BackCal(java.util.Vector<Pdb> pdbVec, java.util.Vector<Dipolar> rdcVec, java.lang.String atom1, java.lang.String atom2, Matrix mm, double Sxx, double Syy, double Szz, double rdcRatio, double[] rdcBc)
          For back-computing RDCs.
 double PdbRdc.BackCal(java.util.Vector<Pdb> pdbVec, java.util.Vector<Dipolar> rdcVec, java.lang.String atom1, java.lang.String atom2, Matrix mm, double Sxx, double Syy, double Szz, double rdcRatio, double[] rdcBc, double[] squareRmsd, int[] size)
          For back-computing RDCs.
 double PdbRdc.BackCalCACO(java.util.Vector<Pdb> pdbVec, java.util.Vector<Dipolar> rdcVec, java.lang.String atom1, java.lang.String atom2, Matrix mm, double Sxx, double Syy, double Szz, double rdcRatio, double[] rdcBc, double[] squareRmsd, int[] size, boolean isPrint)
          For back-computing RDCs.
 double PdbRdc.BackCalCACOOnePdb(java.util.Vector<Pdb> pdbVec, java.util.Vector<Dipolar> rdcVec, java.lang.String atom1, java.lang.String atom2, Matrix mm, double Sxx, double Syy, double Szz, double rdcRatio)
          compute rdc rmsd for only one pdb.
 double PdbRdc.BackCalCON(java.util.Vector<Pdb> pdbVec, java.util.Vector<Dipolar> rdcVec, java.lang.String atom1, java.lang.String atom2, Matrix mm, double Sxx, double Syy, double Szz, double rdcRatio, double[] rdcBc, double[] squareRmsd, int[] size, boolean isPrint)
          For back-computing RDCs from Co at residue i to N at residue i+1.
 double PdbRdc.BackCalCONOnePdb(java.util.Vector<Pdb> pdbVec, java.util.Vector<Dipolar> rdcVec, java.lang.String atom1, java.lang.String atom2, Matrix mm, double Sxx, double Syy, double Szz, double rdcRatio)
          compute rdc rmsd for only one pdb from Co at residue i to N at residue i+1.
 double PdbRdc.BackCalNH(java.util.Vector<Pdb> pdbVec, java.util.Vector<Dipolar> rdcVec, java.lang.String atom1, java.lang.String atom2, Matrix mm, double Sxx, double Syy, double Szz, double rdcRatio, double[] rdcBc)
          For back-computing NH RDCs since the NH RDC of the fiest residue is NOT used in the DFS-based refinement.
 double PdbRdc.BackCalNH(java.util.Vector<Pdb> pdbVec, java.util.Vector<Dipolar> rdcVec, java.lang.String atom1, java.lang.String atom2, Matrix mm, double Sxx, double Syy, double Szz, double rdcRatio, double[] rdcBc, double[] squareRmsd, int[] size)
          For back-computing NH RDCs since the NH RDC of the fiest residue is NOT used in the DFS-based refinement.
 double PdbRdc.BackCalNHOne(java.util.Vector<Pdb> pdbVec, java.util.Vector<Dipolar> rdcVec, java.lang.String atom1, java.lang.String atom2, Matrix mm, double Sxx, double Syy, double Szz, double rdcRatio, double[] rdcBc, double[] squareRmsd, int[] size)
          compute the RDC deviation for one residue.
 double PdbRdc.BackCalOne(java.util.Vector<Pdb> pdbVec, java.util.Vector<Dipolar> rdcVec, java.lang.String atom1, java.lang.String atom2, Matrix mm, double Sxx, double Syy, double Szz, double rdcRatio, double[] rdcBc, double[] squareRmsd, int[] size)
          compute rdc deviation for one residue For back-computing RDCs.
 double PdbRdc.BackCalOnePdb(java.util.Vector<Pdb> pdbVec, java.util.Vector<Dipolar> rdcVec, java.lang.String atom1, java.lang.String atom2, Matrix mm, double Sxx, double Syy, double Szz, double rdcRatio)
          compute rdc rmsd for only one pdb.
 Matrix PdbRdc.bestFit(java.util.Vector<Pdb> pdbVec, java.util.Vector nhRdc, java.util.Vector<Dipolar> cahaRdc, double[] rdc1Cal, double[] rdc2Cal, double[] eigenValues)
          Best fit Two sets of RDC data from one medium such as NH and CH please note that the rotation matrix returned by the eigenValueDecomposition method is rather arbitrary so we need to make sure that only the righ handedone are returned.
 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 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.
 Matrix PdbRdc.eulerFit(java.util.Vector<Pdb> pdbVec, java.util.Vector<Dipolar> rdcVec1, java.util.Vector<Dipolar> rdcVec2, double Syy, double Szz, double[] rmsds, double resolution, boolean debug)
          Note: Lincong's has a serious bug.
 Matrix PdbRdc.eulerFit(java.util.Vector<Pdb> pdbVec, java.util.Vector<Dipolar> rdcVec1, java.util.Vector<Dipolar> rdcVec2, double Syy, double Szz, double[] rmsds, double resolution, boolean debug)
          Note: Lincong's has a serious bug.
 Matrix PdbRdc.eulerFit4RDCs(java.util.Vector<Pdb> pdbVec, java.util.Vector<Dipolar> rdcVec1, java.util.Vector<Dipolar> rdcVec2, java.util.Vector<Dipolar> rdcVecCaCo, java.util.Vector<Dipolar> rdcVecCoN, double Syy, double Szz, double[] rmsds, double resolution, boolean debug)
          Note: Lincong's has a serious bug.
 Matrix PdbRdc.eulerFit4RDCs(java.util.Vector<Pdb> pdbVec, java.util.Vector<Dipolar> rdcVec1, java.util.Vector<Dipolar> rdcVec2, java.util.Vector<Dipolar> rdcVecCaCo, java.util.Vector<Dipolar> rdcVecCoN, double Syy, double Szz, double[] rmsds, double resolution, boolean debug)
          Note: Lincong's has a serious bug.
 Matrix PdbRdc.eulerFit4RDCs(java.util.Vector<Pdb> pdbVec, java.util.Vector<Dipolar> rdcVec1, java.util.Vector<Dipolar> rdcVec2, java.util.Vector<Dipolar> rdcVecCaCo, java.util.Vector<Dipolar> rdcVecCoN, double Syy, double Szz, double[] rmsds, double resolution, boolean debug)
          Note: Lincong's has a serious bug.
 Matrix PdbRdc.eulerFit4RDCs(java.util.Vector<Pdb> pdbVec, java.util.Vector<Dipolar> rdcVec1, java.util.Vector<Dipolar> rdcVec2, java.util.Vector<Dipolar> rdcVecCaCo, java.util.Vector<Dipolar> rdcVecCoN, double Syy, double Szz, double[] rmsds, double resolution, boolean debug)
          Note: Lincong's has a serious bug.
 Matrix PdbRdc.eulerFitPrintEnsemble(java.util.Vector<Pdb> pdbVec, java.util.Vector<Dipolar> rdcVec1, java.util.Vector<Dipolar> rdcVec2, double Syy, double Szz, double[] rmsds, double resolution, boolean debug, double RdcRmsdThreshold)
          print out all pdb orientations in which rdc rmsd is smaler than some threshold, in grid search.
 Matrix PdbRdc.eulerFitPrintEnsemble(java.util.Vector<Pdb> pdbVec, java.util.Vector<Dipolar> rdcVec1, java.util.Vector<Dipolar> rdcVec2, double Syy, double Szz, double[] rmsds, double resolution, boolean debug, double RdcRmsdThreshold)
          print out all pdb orientations in which rdc rmsd is smaler than some threshold, in grid search.
 java.util.Vector Loops.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)
           
 java.util.Vector Loops.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)
           
 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)
          A recusive function to compute all the backbone Phi/Psi for an n-residue helix or the first strand.
 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)
          A recusive function to compute all the backbone Phi/Psi for an n-residue helix or the first strand.
 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, double[] NhRdcRmsd, double[] ChRdcRmsd)
          A recusive function to compute all the backbone Phi/Psi for an n-residue helix or the first strand.
 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, double[] NhRdcRmsd, double[] ChRdcRmsd)
          A recusive function to compute all the backbone Phi/Psi for an n-residue helix or the first strand.
 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.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<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<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<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<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<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<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.
 void ModelRdc.PrintAllByGridSearch(java.util.Vector vecHelixBB, java.util.Vector<Dipolar> rdc1Vec, java.util.Vector<Dipolar> rdc2Vec, double Syy, double Szz, double resolution, double rdcRmsdThreshold)
          Prints the all by grid search.
 void ModelRdc.PrintAllByGridSearch(java.util.Vector vecHelixBB, java.util.Vector<Dipolar> rdc1Vec, java.util.Vector<Dipolar> rdc2Vec, double Syy, double Szz, double resolution, double rdcRmsdThreshold)
          Prints the all by grid search.
 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, double[] nhRdcRmsd, double[] chRdcRmsd)
          Refine helix22.
 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, double[] nhRdcRmsd, double[] chRdcRmsd)
          Refine helix22.
 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.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.refineHelix22NoGridSearch(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, double[] nhRdcRmsd, double[] chRdcRmsd)
          Refine helix22 no grid search.
 java.util.Vector<Pdb> ModelRdc.refineHelix22NoGridSearch(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, double[] nhRdcRmsd, double[] chRdcRmsd)
          Refine helix22 no grid search.
 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 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 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 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<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<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<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<Pdb> ModelRdc.refineSaupe3(java.util.Vector<Pdb> pdbVec, java.util.Vector<Dipolar> nhRdc, java.util.Vector<Dipolar> cahaRdc, double[] saupeSave)
          Modified by zeng for computing the alignment tensor based on structure and RDCs Update the Saupe elements for the second time.
 java.util.Vector<Pdb> ModelRdc.refineSaupe3(java.util.Vector<Pdb> pdbVec, java.util.Vector<Dipolar> nhRdc, java.util.Vector<Dipolar> cahaRdc, double[] saupeSave)
          Modified by zeng for computing the alignment tensor based on structure and RDCs Update the Saupe elements for the second time.
 java.util.Vector Loops.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)
           
 java.util.Vector Loops.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)