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O

o(Zmat, int[], int[]) - Static method in class Jampack.Block
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).
o(int) - Static method in class Jampack.Eye
Generates an identity matrix of order n.
o(int, int) - Static method in class Jampack.Eye
Generates an mxn matrix whose diagonal elements are one and whose off diagonal elements are zero.
o(Zmat) - Static method in class Jampack.H
Returns the conjugate transpose of a Zmat.
o(Zdiagmat) - Static method in class Jampack.H
Returns the conjugate transpose of a Zdiagmat.
o(Zltmat) - Static method in class Jampack.Inv
Computes the inverse of a Zltmat.
o(Zutmat) - Static method in class Jampack.Inv
Computes the inverse of a Zutmat.
o(Zmat) - Static method in class Jampack.Inv
Computes the inverse of a square Zmat
o(Zpsdmat) - Static method in class Jampack.Inv
Computes the inverse of a Zpsdmat.
o(Zdiagmat) - Static method in class Jampack.Inv
Computes the inverse of a Zdiagmat.
o(Zmat[][]) - Static method in class Jampack.Merge
Merges the matrices in an array of Zmats
o(Zmat, Zmat) - Static method in class Jampack.Minus
Computes the difference of two Zmats.
o(Zmat) - Static method in class Jampack.Minus
Negates a Zmat
o(Zmat, Zdiagmat) - Static method in class Jampack.Minus
Computes the difference of a Zmat and a Zdiagmat.
o(Zdiagmat, Zmat) - Static method in class Jampack.Minus
Computes the difference of a Zdiagmat and a Zmat.
o(Zdiagmat, Zdiagmat) - Static method in class Jampack.Minus
Computes the difference of a two Zdiagmats.
o(Zdiagmat) - Static method in class Jampack.Minus
Negates a Zdiagmat.
o(Zmat, Zmat) - Static method in class Jampack.Plus
Computes the sum of two Zmats
o(Zmat, Zdiagmat) - Static method in class Jampack.Plus
Computes the sum of a Zmat and a Zdiagmat.
o(Zdiagmat, Zmat) - Static method in class Jampack.Plus
Computes the sum of a Zdiagmat and a Zmat.
o(Zdiagmat, Zdiagmat) - Static method in class Jampack.Plus
Computes the sum of a Zdiagmat and a Zdiagmat.
o(int) - Static method in class Jampack.Print
Prints an int in default format.
o(int, int) - Static method in class Jampack.Print
Prints and int in a field of width w.
o(int[]) - Static method in class Jampack.Print
Prints an integer array in default format.
o(int[], int) - Static method in class Jampack.Print
Prints an integer array in fields of width w.
o(double) - Static method in class Jampack.Print
Prints a double in default e format.
o(double, int, int) - Static method in class Jampack.Print
Prints a double in w.d e format.
o(double[]) - Static method in class Jampack.Print
Prints an array of doubles in default e format.
o(double[], int, int) - Static method in class Jampack.Print
Prints an array of doubles in w.d e format.
o(double[][]) - Static method in class Jampack.Print
Prints a 2-dimensional array of doubles in default e format.
o(double[][], int, int) - Static method in class Jampack.Print
Prints a 2-dimensional array of doubles in w.d e format.
o(Z) - Static method in class Jampack.Print
Prints a Z in default e format.
o(Z, int, int) - Static method in class Jampack.Print
Prints a Z in w.d e format.
o(Z[]) - Static method in class Jampack.Print
Prints an array of Z's in default e format.
o(Z[], int, int) - Static method in class Jampack.Print
Prints an array of Z's in w.d e format.
o(Z[][]) - Static method in class Jampack.Print
Prints a 2-dimensional array of Z in default e format.
o(Z[][], int, int) - Static method in class Jampack.Print
Prints a 2-dimensional array of Z in w.d e format.
o(Z1) - Static method in class Jampack.Print
Prints a Z1 in default format.
o(Z1, int, int) - Static method in class Jampack.Print
Prints a Z1 in w.d e format
o(Zmat) - Static method in class Jampack.Print
Prints a Zmat in default e format.
o(Zmat, int, int) - Static method in class Jampack.Print
Prints a Zmat in w.d e format.
o(Zdiagmat) - Static method in class Jampack.Print
Prints a Zdiagmat in default format.
o(Zdiagmat, int, int) - Static method in class Jampack.Print
Prints a Zdiagmat in w.d e format.
o(Z, Zmat) - Static method in class Jampack.Times
Computes the product of a Z and a Zmat.
o(Zmat, Zmat) - Static method in class Jampack.Times
Computes the product of two Zmats.
o(Z, Zdiagmat) - Static method in class Jampack.Times
Computes the product of a Z and a Zdiagmat.
o(Zdiagmat, Zdiagmat) - Static method in class Jampack.Times
Computes the product of two Zdiagmats.
o(Zdiagmat, Zmat) - Static method in class Jampack.Times
Computes the product of a Zdiagmat and a Zmat.
o(Zmat, Zdiagmat) - Static method in class Jampack.Times
Computes the product of a Zmat and a Zdiagmat.
o12(Zmat, Zmat) - Static method in class Jampack.Merge
Merges its arguments to create the Zmat
o13(Zmat, Zmat, Zmat) - Static method in class Jampack.Merge
Merges its arguments to create the Zmat
o21(Zmat, Zmat) - Static method in class Jampack.Merge
Merges its arguments to create the Zmat
o22(Zmat, Zmat, Zmat, Zmat) - Static method in class Jampack.Merge
Merges its arguments to create the matrix
o23(Zmat, Zmat, Zmat, Zmat, Zmat, Zmat) - Static method in class Jampack.Merge
Merges its arguments to create the Zmat
o31(Zmat, Zmat, Zmat) - Static method in class Jampack.Merge
Merges its arguments to create the Zmat
o32(Zmat, Zmat, Zmat, Zmat, Zmat, Zmat) - Static method in class Jampack.Merge
Merges its arguments to create the Zmat
o33(Zmat, Zmat, Zmat, Zmat, Zmat, Zmat, Zmat, Zmat, Zmat) - Static method in class Jampack.Merge
Merges its arguments to create the Zmat
ONE - Static variable in class Jampack.Z
Complex 1.
OutputBackbone(Vector) - Method in class RdcPanda.Pdb
output the backbone of a pdb structure.
OutputBackboneNoCB(Vector) - Method in class RdcPanda.Pdb
output the backbone of a pdb structure.
OutputEnsemblePdbs(Vector, int, int, double) - Method in class RdcPanda.Goal
compute the structure fragment that best fits the NOE restraints.
OutputEnsemblePdbsBackward(Vector, int, int, double) - Method in class RdcPanda.Goal
compute the structure fragment that best fits the NOE restraints.
OutputMultiNOEAsg(Vector, String) - Method in class RdcPanda.Noe
output the noe assignment in multple format.
outputProgInfo() - Method in class RdcPanda.RdcPanda
Output prog info.
outPutRDCXplorFormat(Vector, String, String) - Method in class RdcPanda.Dipolar
output the RDCs in the xplor format.
OutputStericClashResidues(Vector, double[], double, boolean, boolean, double, int, boolean[], boolean) - Method in class RdcPanda.vdw
check the steric clashes, if the number of steric clashes is larger than some threshold, ruturn true, else return false.

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