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B

BackCal(Vector<Pdb>, Vector<Dipolar>, String, String, Matrix, double, double, double, double, double[], double[], int[]) - Method in class RdcPanda.PdbRdc
For back-computing RDCs.
BackCal(Vector<Pdb>, Vector<Dipolar>, String, String, Matrix, double, double, double, double, double[]) - Method in class RdcPanda.PdbRdc
For back-computing RDCs.
BackCalCACO(Vector<Pdb>, Vector<Dipolar>, String, String, Matrix, double, double, double, double, double[], double[], int[], boolean) - Method in class RdcPanda.PdbRdc
For back-computing RDCs.
BackCalCACOOnePdb(Vector<Pdb>, Vector<Dipolar>, String, String, Matrix, double, double, double, double) - Method in class RdcPanda.PdbRdc
compute rdc rmsd for only one pdb.
BackCalCON(Vector<Pdb>, Vector<Dipolar>, String, String, Matrix, double, double, double, double, double[], double[], int[], boolean) - Method in class RdcPanda.PdbRdc
For back-computing RDCs from Co at residue i to N at residue i+1.
BackCalCONOnePdb(Vector<Pdb>, Vector<Dipolar>, String, String, Matrix, double, double, double, double) - Method in class RdcPanda.PdbRdc
compute rdc rmsd for only one pdb from Co at residue i to N at residue i+1.
BackCalNH(Vector<Pdb>, Vector<Dipolar>, String, String, Matrix, double, double, double, double, double[], double[], int[]) - Method in class RdcPanda.PdbRdc
For back-computing NH RDCs since the NH RDC of the fiest residue is NOT used in the DFS-based refinement.
BackCalNH(Vector<Pdb>, Vector<Dipolar>, String, String, Matrix, double, double, double, double, double[]) - Method in class RdcPanda.PdbRdc
For back-computing NH RDCs since the NH RDC of the fiest residue is NOT used in the DFS-based refinement.
BackCalNHOne(Vector<Pdb>, Vector<Dipolar>, String, String, Matrix, double, double, double, double, double[], double[], int[]) - Method in class RdcPanda.PdbRdc
compute the RDC deviation for one residue.
BackCalOne(Vector<Pdb>, Vector<Dipolar>, String, String, Matrix, double, double, double, double, double[], double[], int[]) - Method in class RdcPanda.PdbRdc
compute rdc deviation for one residue For back-computing RDCs.
BackCalOnePdb(Vector<Pdb>, Vector<Dipolar>, String, String, Matrix, double, double, double, double) - Method in class RdcPanda.PdbRdc
compute rdc rmsd for only one pdb.
BackCalRdcs(Vector, Vector, String, String, Matrix, double, double, double) - Method in class RdcPanda.PdbRdc
For back-computing RDCs.
BackCompNoePattern(Vector, int, String, Vector) - Method in class RdcPanda.RotaPattern
Back compute all NOE peaks from given pairs of NOE distance patterns for a rotamer.
BackCompNOEPeak(Vector, Hdist) - Method in class RdcPanda.RotaPattern
Back compute an NOE peak from a given pair of NOE distance.
BackCSGenerate(Vector, int, String, String, int, String, String, String, double) - Method in class RdcPanda.Peak
A function to generate and check back NOE chemical shifts.
BackNoe - Class in RdcPanda
This class provides functions that involves back-computed NOEs.
BackNoe() - Constructor for class RdcPanda.BackNoe
Instantiates a new back noe.
BackNoe(double, double, double) - Constructor for class RdcPanda.BackNoe
Instantiates a new back noe.
BackNoe(double, double, double, double, double, int, int, String, String, String, String, String) - Constructor for class RdcPanda.BackNoe
Instantiates a new back noe.
BackNoeDeleteRepeat(Vector) - Method in class RdcPanda.Assign
delete repeated back noes, mainly from methyl groups.
BackNOEGenerate(Vector, Vector, Vector, Vector, Vector, Vector) - Method in class RdcPanda.Peak
generate the back noes from assignment based on x-ray structure.
BackonbeRotation(Vector, Vector) - Method in class RdcPanda.Model
rotate the whole protein according to the reference backbone such that the backbone coordinates are the same (both should have the same residues).
BackonbeRotationAtResidue(Vector, Vector, int) - Method in class RdcPanda.Model
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).
backwardCoords(Vector) - Method in class RdcPanda.PhiPsi
Testing the Computation of backbone structure backwards.
bahi(Zmat, Zltmat) - Static method in class Jampack.Solve
Solves XLH = B, where L is a Zltmat and B is a Zmat.
bahi(Zmat, Zutmat) - Static method in class Jampack.Solve
Solves XUH = B, where U is a Zutmat and B is a Zmat.
bahi(Zmat, Zmat) - Static method in class Jampack.Solve
Solve XA^H = B, where A is a Zmat and B is a Zmat.
bai(Zmat, Zltmat) - Static method in class Jampack.Solve
Solves XL = B, where L is a Zltmat and B is a Zmat.
bai(Zmat, Zutmat) - Static method in class Jampack.Solve
Solves XU = B, where U is a Zutmat and B is a Zmat.
bai(Zmat, Zmat) - Static method in class Jampack.Solve
Solve XA = B, where A is a Zmat and B is a Zmat.
bai(Zmat, Zpsdmat) - Static method in class Jampack.Solve
Solves XA = B, where A is a Zpsdmat and B is a Zmat.
bestFit(Vector, Vector, String, String, double[], boolean) - Method in class RdcPanda.PdbRdc
Computing the Saupe matrix by SVD method and then diagonalizing it for computing the diagonalized elements and rotation matrix to one of POF.
bestFit(Vector, Vector, String, String, double[], double[], boolean) - Method in class RdcPanda.PdbRdc
Computing the Saupe matrix by SVD method and then diagonalizing it for computing the diagonalized elements and rotation matrix to one of POF.
bestFit(Vector<Pdb>, Vector, Vector<Dipolar>, double[], double[], double[]) - Method in class RdcPanda.PdbRdc
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.
bestFit4RDCs(Vector, Vector, Vector, Vector, Vector, double[], double[], double[]) - Method in class RdcPanda.PdbRdc
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 only the righ handedone are returned.
Block - Class in Jampack
Block contains a static method for partitioning a matrix.
Block() - Constructor for class Jampack.Block
 
BMRBSatisticsScore(Vector, Vector) - Method in class RdcPanda.H1CS
compute the fitness score compared to BMRB statistical information.
bq(Zmat) - Method in class Jampack.Zhqrd
Computes the product BQ.
bqh(Zmat, Zmat) - Method in class Jampack.Zhqrd
Computes the product BQH.
bx - Variable in class Jampack.Zdiagmat
The base index (public)
bx - Variable in class Jampack.Zmat
The base index

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