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

A

aah(Zmat) - Static method in class Jampack.Times
Computes AAH, where A is a Zmat.
abs(Z) - Static method in class Jampack.Z
Computes the absolute value of a Z.
abs1(Z) - Static method in class Jampack.Z
Computes the 1-norm of a Z
AddAdj(Nasca.Node) - Method in class RdcPanda.Nasca.Node
 
AddAdjNOESY(Noesy) - Method in class RdcPanda.Nasca.Node
 
addCaNoe(HcchTocsy) - Method in class RdcPanda.BackNoe
Adds the ca noe.
AddChildPdb(Goal.TreePdb) - Method in class RdcPanda.Goal.TreePdb
 
AddCloseAdj(Nasca.Node) - Method in class RdcPanda.Nasca.Node
 
AddCoord(Cartesian) - Method in class RdcPanda.Nasca.Node
 
addCoords(double[], double[]) - Method in class RdcPanda.ModelRdc
adding two vectors.
addCoords(double[], double[]) - Method in class RdcPanda.PhiPsi
adding two vectors.
addCoords(double[], double[]) - Method in class RdcPanda.sp3Carbon
Add two coordinates.
addH_A(H1CS) - Method in class RdcPanda.Noe
Adds the h_ a.
addH_B(H1CS) - Method in class RdcPanda.Noe
Adds the h_ b.
addHnNoe(HnNoe) - Method in class RdcPanda.BackNoe
Adds the hn noe.
addMappingNode(Nasca.Node) - Method in class RdcPanda.Nasca.Node
 
AddProtonCoordinates(int, String, String, Cartesian, Vector) - Method in class RdcPanda.Nasca
add the coordinates of a proton into the graph
addProtons(Noe) - Method in class RdcPanda.Noe
Adds the protons.
AddResonanceNode(Vector, double, double, double, double, double) - Method in class RdcPanda.Nasca
add the reosnance node into the graph
addRotScore(int, double) - Method in class RdcPanda.GraphCut
 
addScore(double) - Method in class RdcPanda.GraphCut.RotScore
 
adjustBaseIndex(Zmat) - Static method in class Jampack.Parameters
Adjust the base index of a Zmat to make it conform to the default.
adjustBaseIndex(Zdiagmat) - Static method in class Jampack.Parameters
Adjust the base index of a Zdiagmat to make it conform to the default.
aha(Zmat) - Static method in class Jampack.Times
Computes AHA, where A is a Zmat.
ahib(Zltmat, Zmat) - Static method in class Jampack.Solve
Solves LHX = B, where L is a Zltmat and B is a Zmat.
ahib(Zutmat, Zmat) - Static method in class Jampack.Solve
Solves UHX = B, where U is a Zutmat and B is a Zmat.
ahib(Zmat, Zmat) - Static method in class Jampack.Solve
Solve AHX = B, where A is a Zmat and B is a Zmat.
aib(Zltmat, Zmat) - Static method in class Jampack.Solve
Solves LX = B, where L is a Zltmat and B is a Zmat.
aib(Zutmat, Zmat) - Static method in class Jampack.Solve
Solves UX = B, where U is a Zutmat and B is a Zmat.
aib(Zmat, Zmat) - Static method in class Jampack.Solve
Solves AX = B, where A is a Zmat and B is a Zmat.
aib(Zpsdmat, Zmat) - Static method in class Jampack.Solve
Solves AX = B, where A is a Zpsdmat and B is a Zmat.
AlaninizeStructure(Vector, boolean[], String) - Method in class RdcPanda.Pdb
replace all non-NOE residues in pdb with alaline.
AlaninizeStructureResName(Vector, String) - Method in class RdcPanda.Pdb
replace all non-NOE residues in pdb with alaline, according to the residue names.
allNoes(Vector, Vector, double[], double, double) - Method in class RdcPanda.Peak
Compute all the possible NOE peaks from the nucleus with coordA to all other nuclei in a PDB structure, the.
allProtonSorted(Vector) - Method in class RdcPanda.Peak
A method to extract all the protons and convert the Assign object to Peak object Please note that the returned Peak has special identification for the nucleus element.
allProtonSorted_old(Vector) - Method in class RdcPanda.Peak
A method to extract all the protons and convert the Assign object to Peak object Please note that the returned Peak has special identification for the nucleus element.
AllRotamersStructure(Vector, String) - Method in class RdcPanda.Pdb
put all rotamers at each redidue.
anglesAndLenOfSp3(double[], double[], double[], double[], double[], double[]) - Method in class RdcPanda.sp3Carbon
Compute the side-chain angles as represented by SP3 object from the coordinates of 4 atoms.
ap(Zmat, Rot, int, int, int, int) - Static method in class Jampack.Rot
Multiplies columns (ii1:ii2,jj1) and A(ii2:ii2,jj1) of a Zmat (altered) by a plane rotation.
aph(Zmat, Rot, int, int, int, int) - Static method in class Jampack.Rot
Multiplies columns (ii1:ii2,jj1) and A(ii2:ii2,jj1) of a Zmat (altered) by the conjugate transpose of plane rotation.
asgedId - Variable in class RdcPanda.Nasca.Node
 
asgReader3(String) - Method in class RdcPanda.Assign
Written by Lincong, only used in his previous functions.
AssembleTwoSSEs(Vector, Vector, int, Vector<Dipolar>, Vector<Dipolar>, double, double) - Method in class RdcPanda.Pdb
assemble two sses with some phi psi deviations in the break point, the assembled structure has minimum rdc rmsd and vdw energy.
Assign - Class in RdcPanda
This class provides functions that involves NOE assignment, such initial NOE assignment using only chemical shift information, pruning ambiguous NOE assignments using given structural information,etc.
Assign() - Constructor for class RdcPanda.Assign
Instantiates a new assign.
Assign(int) - Constructor for class RdcPanda.Assign
Instantiates a new assign.
Assign(int, String) - Constructor for class RdcPanda.Assign
Instantiates a new assign.
Assign(int, String, Map) - Constructor for class RdcPanda.Assign
Instantiates a new assign.
Assign(int, String, Map, Vector, Vector) - Constructor for class RdcPanda.Assign
Instantiates a new assign.
Assign(int, String, Map, Vector, Vector, Vector) - Constructor for class RdcPanda.Assign
Instantiates a new assign.
Assign.assignComparator - Class in RdcPanda
The Class assignComparator.
Assign.assignComparator() - Constructor for class RdcPanda.Assign.assignComparator
 
Assign.caComparator - Class in RdcPanda
The Class caComparator.
Assign.caComparator() - Constructor for class RdcPanda.Assign.caComparator
 
Assign.haComparator - Class in RdcPanda
The Class haComparator.
Assign.haComparator() - Constructor for class RdcPanda.Assign.haComparator
 
Assign.hnComparator - Class in RdcPanda
The Class hnComparator.
Assign.hnComparator() - Constructor for class RdcPanda.Assign.hnComparator
 
assignHsqc(Vector, Vector) - Method in class RdcPanda.Assign
Written by Lincong, only used in his previous functions.
assignReader(String, double) - Method in class RdcPanda.Assign
Read the resonance assignment.
assignReader2(String, Vector, Vector) - Method in class RdcPanda.Assign
Read the resonance assignment, meanwhile update the residue name for each chemical shift.
AStarSearchForSCAsgs(Vector, Vector, int[][], double[][], Vector, Vector) - Method in class RdcPanda.Nasca
Apply the A* search algorithm to find the optimal side-chain resonances.
au(Zmat, Z1, int, int, int, int, Z1) - Static method in class Jampack.House
Postmultiplies the Householder transformation contained in a Z1 into a Zmat A[r1:r2,c1:c2] and overwrites Zmat A[r1:r2,c1:c2] with the results.
au(Zmat, Z1, int, int, int, int) - Static method in class Jampack.House
Postmultiplies the Householder transformation contained in a Z1 into a Zmat A[r1:r2,c1:c2] and overwrites Zmat A[r1:r2,c1:c2] with the results.

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