Uses of Class
RdcPanda.Pdb

Packages that use Pdb
RdcPanda   
 

Uses of Pdb in RdcPanda
 

Fields in RdcPanda declared as Pdb
 Pdb Goal.TreePdb.pdb
           
 

Fields in RdcPanda with type parameters of type Pdb
 java.util.Vector<Pdb> Goal.vecPdbSSE
           
 

Methods in RdcPanda that return Pdb
 Pdb ModelRdc.coordByBackward(double phi, double psi, double[] n1, double[] nh1, double[] ca1, int residueNo, java.lang.String resid1)
          A method for computing coordinates of backbone atoms backward: with direasing residue no.
 Pdb ModelRdc.coordByResidue(double phi, double psi, double[] n1, double[] nh1, double[] ca1, int residueNo, java.lang.String resid1, boolean first)
          A method for computing coordinates of backbone atoms.
 Pdb ModelRdc.coordByResidueFull(double phi, double psi, double[] n1, double[] nh1, double[] ca1, int residueNo, java.lang.String resid1, boolean first)
          *A method for computing coordinates of backbone atoms, including all backbone atoms, ha, ca, n, hn, cb,c o.
 Pdb RotaPattern.getPdb()
          Gets the pdb.
 Pdb PdbRdc.getPdb()
          Gets the pdb.
 Pdb GraphCut.RotScore.getRotPdb()
           
 

Methods in RdcPanda that return types with arguments of type Pdb
 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, 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<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.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 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> Goal.SearchSSEAnchors(int topK, int resNoLoop)
          find the SSE anchors (ca atoms) that can possibly interact with loops
 java.util.Vector<Pdb> Goal.SearchSSEAnchorsTop(int topK, int resNoLoop)
          find the top set of SSE anchors (ca atoms) that can possibly interact with loops
 

Methods in RdcPanda with parameters of type Pdb
 boolean Goal.CheckFirstResidue(Pdb preHalfPdb, int fixNo, double error, double[] dist)
          check whether the end residue closes the gap.
 boolean Goal.CheckFirstResidue(Pdb preHalfPdb, int fixNo, double error, double[] dist, double[] caDist)
          check whether the end residue closes the gap.
 boolean Goal.CheckFirstResidueOld(Pdb preHalfPdb, int fixNo, double error, double[] dist)
          check whether the end residue closes the gap.
 boolean Goal.CheckFirstResidueOld(Pdb preHalfPdb, int fixNo, double error, double[] dist, double[] caDist)
          check whether the end residue closes the gap.
 boolean Goal.CheckKinChainRestraint(Pdb nextHalfPdb, int endResNo, double error)
          check whether kinematic chain restraint is satisfied
 boolean Goal.CheckKinChainRestraintBackward(Pdb nextHalfPdb, int startResNo, double error)
          check whether kinematic chain restraint is satisfied
 boolean Goal.CheckLastResidue(Pdb nextHalfPdb, int endResNo, double error, double[] dist)
          check whether the end residue closes the gap
 boolean Goal.CheckLastResidue(Pdb nextHalfPdb, int endResNo, double error, double[] dist, double[] distCa)
          check whether the end residue closes the gap
 boolean Goal.CheckLastResidueOld(Pdb nextHalfPdb, int endResNo, double error, double[] dist)
          check whether the end residue closes the gap
 boolean Goal.CheckLastResidueOld(Pdb nextHalfPdb, int endResNo, double error, double[] dist, double[] distCa)
          check whether the end residue closes the gap
 boolean Goal.CheckNOEBtwCaNSSEs(Pdb curPdb, java.util.Vector vecSSEAnchors, double distUpCa)
          check whether the distance satisfies the NOE restraint from ca to anchors in SSEs
 java.util.Vector Pdb.compDistPatternFromPairRotams(int resNoA, int resNoB, Pdb pdbA, Pdb pdbB, double DistBound)
          Compute all distance patterns for a pair of rotamers, distances are from each proton in the rotamer to backbone protons including HA,HN, HB rotamers are in the same coordinate system,includes both from A->B and from B->A.
 double Pdb.compResRmsd(Pdb pdb1, Pdb pdb2)
          Compute rmsd between two rotamers only for non-proton atoms, assume they are in the same coordinate system.
 double Pdb.compResRmsdPairWise(Pdb pdb1, Pdb pdb2)
          Compute rmsd between two rotamers (for all atoms), assume they are in the same coordinate system.
 java.util.Vector vdw.convert2VDW(Pdb[] pdbVec)
          To convert the PDB coordinates into a flat structure for speed.
 void Goal.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
 void Goal.TreePdb.SetPdb(Pdb pp)
           
 

Method parameters in RdcPanda with type arguments of type Pdb
 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.
 double Goal.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.
 double Goal.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.
 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.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<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, 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<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.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.
 double Goal.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
 

Constructors in RdcPanda with parameters of type Pdb
Goal.TreePdb(Pdb pp)
           
Goal.TreePdb(Pdb pp, java.util.Vector pare, Goal.TreePdb child)
           
GraphCut.RotScore(int ID, Pdb pdb, double sc)
           
GraphCut.RotScore(Pdb pdb, double sc)
           
Pdb(Pdb pp)
          Instantiates a new pdb.
PdbRdc(Pdb pp, double rdc)
          Instantiates a new pdb rdc.
RotaPattern(Pdb pdbRot, double dbSc)
          Instantiates a new rota pattern.