A B C D E F G H I J K L M N O P Q R S T U V X Z

M

main(String[]) - Static method in class RdcPanda.Dipolar
The main method for testing.
main(String[]) - Static method in class RdcPanda.Gaussian
 
main(String[]) - Static method in class RdcPanda.Goal
 
main(String[]) - Static method in class RdcPanda.H1CS
The main method for testing.
main(String[]) - Static method in class RdcPanda.Model
The main method for testing.
main(String[]) - Static method in class RdcPanda.Noe
The main method.
main(String[]) - Static method in class RdcPanda.Pdb
The main method.
main(String[]) - Static method in class RdcPanda.RdcPanda
The main method.
main(String[]) - Static method in class RdcPanda.Rotamer
The main method.
main(String[]) - Static method in class RdcPanda.vdw
The main method.
main0(String[]) - Static method in class RdcPanda.H1CS
Main0 for testing.
main0(String[]) - Static method in class RdcPanda.Pdb
Main0.
main00(String[]) - Static method in class RdcPanda.Pdb
Main00.
main1(String[]) - Static method in class RdcPanda.Model
Main function for testing.
main1(String[]) - Static method in class RdcPanda.Pdb
Main1.
main1(String[]) - Static method in class RdcPanda.SSEPacking
Main function for testing.
main2(String[]) - Static method in class RdcPanda.H1CS
Main2 for testing.
matchC13Hsqc(Vector, Vector) - Method in class RdcPanda.Assign
Written by Lincong, only used in his previous functions.
Maths - Class in RdcPanda
* This class is modified from the Jama numeric package.
Maths() - Constructor for class RdcPanda.Maths
 
Matrix - Class in RdcPanda
This class is modified from the Jama numeric package.
Matrix(int, int) - Constructor for class RdcPanda.Matrix
Construct an m-by-n matrix of zeros.
Matrix(int, int, double) - Constructor for class RdcPanda.Matrix
Construct an m-by-n constant matrix.
Matrix(double[][]) - Constructor for class RdcPanda.Matrix
Construct a matrix from a 2-D array.
Matrix(double[][], int, int) - Constructor for class RdcPanda.Matrix
Construct a matrix quickly without checking arguments.
Matrix(double[], int) - Constructor for class RdcPanda.Matrix
Construct a matrix from a one-dimensional packed array.
MAXITER - Static variable in class Jampack.Schur
Limits the number of interations in the QR algorithm
MAXITER - Static variable in class Jampack.Zsvd
Limits the number of iterations in the SVD algorithm
maxLeafNodes - Variable in class RdcPanda.Goal
 
maxMappedID - Variable in class RdcPanda.Nasca.Node
 
maxMapScore - Variable in class RdcPanda.Nasca.Node
 
measureDis(Vector, int, String, String, int, String, String, double[]) - Method in class RdcPanda.Pdb
Compute the NOE distance between two nuclei (A, B) in a structure specified by pdbVec There are two numbers: 15 Degree and 45 Degree for correct the most possible orientation changing.
measureDisFromRotam(Vector, Vector, Vector, int, String, String, int, String, String, double[]) - Method in class RdcPanda.Pdb
Compute the NOE distance between two nuclei (A, B) in a structure specified by pdbVec There are two numbers: 15 Degree and 45 Degree for correct the most possible orientation changing.
measureDist(Cartesian, Cartesian) - Method in class RdcPanda.Cartesian
Measure distance between points in 3D.
measureDisXray(Vector, int, String, String, int, String, String, double[]) - Method in class RdcPanda.Pdb
Compute the NOE distance between two nuclei (A, B) in a structure specified by pdbVec.
measurePackDisAllRotamers(Vector, Vector, int, String, int, String, double, double, double[], double[]) - Method in class RdcPanda.Pdb
measure the packing distances between two sses all rotamers are put into the sse backbones The number themselves are set rather arbitrariry.
measureVDW4Ensemble() - Method in class RdcPanda.vdw
Measure vd w4 ensemble.
Merge - Class in Jampack
Merge is a class containing programs to merge matrices into one big matrix.
Merge() - Constructor for class Jampack.Merge
 
mergeAll(Vector, Vector, double, double) - Method in class RdcPanda.Assign
Written by Lincong.
mergeAll3(Vector, Vector) - Method in class RdcPanda.Assign
written by LW.
mergeAll4(Vector) - Method in class RdcPanda.Assign
written by LW.
mergeAndCluster(String, String, String, int, int, double, String, String) - Method in class RdcPanda.vdw
merge all structures in previous ensemble into one enemble (with the same pdb name) and cluster them according to given resolution.
mergeAndClusterAll(String, String, double, String) - Method in class RdcPanda.vdw
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.
mergeAssignAndNoe(Vector, Vector, Vector, double, double, double, double) - Method in class RdcPanda.Assign
Written by Lincong, only used in his previous functions.
mergeC13Noe(Vector, Vector, double, double) - Method in class RdcPanda.Assign
Written by Lincong, only used in his previous functions.
mergeHcch(Vector, double, double) - Method in class RdcPanda.HcchTocsy
Merge hcch.
mergeHNCACB(Vector) - Method in class RdcPanda.Hncacb
Merge hncacb.
mergeHnNoe(Vector, double, double) - Method in class RdcPanda.HnNoe
a method to merge NOE peaks since some NOE peaks are picked with a lightly different CS more than once.
mergeHnNoe(Vector, double, double) - Method in class RdcPanda.Noesy
a method to merge NOE peaks since some NOE peaks are picked with a lightly different CS more than once.
mergeNoe(Vector, Vector, double, double) - Method in class RdcPanda.Assign
Written by Lincong, only used in his previous functions.
mergeNoeAndAssign(Vector, Vector, Vector, double, double) - Method in class RdcPanda.Assign
Written by Lincong, only used in his previous functions.
MergeTwoFragmentIntoOne(Vector, Vector, double, int, int, int, boolean) - Method in class RdcPanda.Goal
Merge two framgements computed using backward and forward ways into one fragment
minBeta(Vector, Vector, double[], double[], Vector, double, double, double, double, Vector, Vector, int, double, double, boolean, boolean) - Method in class RdcPanda.ModelRdc
A recusive function to compute all the backbone Phi/Psi for an n-residue fragment.
minBeta2(Vector, Vector, double[], double[], Vector, double, double, double, double, Vector, Vector, Vector, Vector, int, double, double, boolean, boolean) - Method in class RdcPanda.ModelRdc
A recusive function to compute all the backbone Phi/Psi for an n-residue fragment.
minHelix(Vector<Dipolar>, Vector<Dipolar>, double[], double[], Vector<Pdb>, double, double, double, double, int, double, boolean, boolean, boolean) - Method in class RdcPanda.ModelRdc
A recusive function to compute all the backbone Phi/Psi for an n-residue helix or the first strand.
minHelix(Vector<Dipolar>, Vector<Dipolar>, double[], double[], Vector<Pdb>, double, double, double, double, int, double, boolean, boolean, boolean, Vector) - Method in class RdcPanda.ModelRdc
A recusive function to compute all the backbone Phi/Psi for an n-residue helix or the first strand.
minHelix(Vector<Dipolar>, Vector<Dipolar>, double[], double[], Vector<Pdb>, double, double, double, double, int, double, boolean, boolean, boolean, double[], double[]) - Method in class RdcPanda.ModelRdc
A recusive function to compute all the backbone Phi/Psi for an n-residue helix or the first strand.
minHelix4RDCs(Vector<Dipolar>, Vector<Dipolar>, Vector<Dipolar>, Vector<Dipolar>, double[], double[], Vector<Pdb>, double, double, double, double, int, double, boolean, boolean, boolean, Vector, double, double) - Method in class RdcPanda.ModelRdc
A recusive function to compute all the backbone Phi/Psi for an n-residue helix or the first strand.
minHelix4RDCs(Vector<Pdb>, Vector<Dipolar>, Vector<Dipolar>, Vector<Dipolar>, Vector<Dipolar>, double[], double[], Vector<Pdb>, double, double, double, double, int, double, boolean, boolean, boolean, Vector, double, double, int, int, Vector) - Method in class RdcPanda.ModelRdc
A recusive function to compute all the backbone Phi/Psi for an n-residue helix or the first strand.
minHelix_old(Vector, Vector, double[], double[], Vector, double, double, double, double, int, double, boolean, boolean, boolean) - Method in class RdcPanda.ModelRdc
A recusive function to compute all the backbone Phi/Psi for an n-residue fragment.
minTurns(Vector, Vector, Vector, Vector, Vector, Vector, double, double, int, int, double, double) - Method in class RdcPanda.ModelRdc
Compute the turns based on NOEs and RDCs.
Minus - Class in Jampack
Minus negates a matrix or computes the difference of two matrices.
Minus() - Constructor for class Jampack.Minus
 
Minus(Z) - Method in class Jampack.Z
Computes unary minus of a Z.
Minus(Z, Z) - Method in class Jampack.Z
Computes the difference of two Z's.
minus(Matrix) - Method in class RdcPanda.Matrix
C = A - B.
Model - Class in RdcPanda
This class provides functions that compute backbone from RDC-EXACT algorithm.
Model() - Constructor for class RdcPanda.Model
Instantiates a new model.
modelBuild(Vector, double[], double[], double[]) - Method in class RdcPanda.ModelRdc
Build model (compute the coordinates of backbone atoms (N, NH, CA, CO, O and HA) from the standard geometry and Phi/Psi angle.
modelBuild(Vector, double[], double[], double[], boolean) - Method in class RdcPanda.ModelRdc
Model build.
modelBuild(double[], double[], double[], double[], double[], int, boolean) - Method in class RdcPanda.ModelRdc
Build model (compute the coordinates of backbone atoms (N, NH, CA, CO, O and HA) from the standard geometry and Phi/Psi angle.
modelBuildLoopBackward(Vector, double[], double[], double[], int, int) - Method in class RdcPanda.ModelRdc
By Michael Zeng.
ModelRdc - Class in RdcPanda
A program for computing all the backbond dihedral ($\phi$, $\psi$) angles of an $\alpha$-helix or a $\beta$-strand based on exact solution and a systematic search.
ModelRdc() - Constructor for class RdcPanda.ModelRdc
Instantiates a new model rdc.
ModelRdc(int) - Constructor for class RdcPanda.ModelRdc
Instantiates a new model rdc.
ModelRdc(int, String, double, double) - Constructor for class RdcPanda.ModelRdc
Instantiates a new model rdc.
ModelRdc.mdComparator - Class in RdcPanda
The Class mdComparator.
ModelRdc.mdComparator() - Constructor for class RdcPanda.ModelRdc.mdComparator
 
myPdbVectorCopy(Vector) - Method in class RdcPanda.Goal
 
myVectorCopy(Vector) - Method in class RdcPanda.Nasca
 
myVectorCopyOneLayer(Vector) - Method in class RdcPanda.Nasca
 

A B C D E F G H I J K L M N O P Q R S T U V X Z