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

S

S - Variable in class Jampack.Zsvd
The diagonal matrix of singular values
SampleFirstHalfPlanes(int, boolean) - Method in class RdcPanda.Goal
use the grid search to find the set of variated peptide planes of the first residue
Schur - Class in Jampack
Schur implements the Schur decomposition of a matrix.
Schur(Zmat) - Constructor for class Jampack.Schur
Creats a Schur decomposition from a square Zmat.
ScNoe - Class in RdcPanda
This class is no longer used and replaced by H1CS.
ScNoe() - Constructor for class RdcPanda.ScNoe
Instantiates a new sc noe.
ScNoe(double) - Constructor for class RdcPanda.ScNoe
Instantiates a new sc noe.
ScNoe(double, double) - Constructor for class RdcPanda.ScNoe
Instantiates a new sc noe.
ScNoe(double, double, double) - Constructor for class RdcPanda.ScNoe
Instantiates a new sc noe.
ScNoe.cs1Comparator - Class in RdcPanda
The Class cs1Comparator.
ScNoe.cs1Comparator() - Constructor for class RdcPanda.ScNoe.cs1Comparator
 
ScNoe.cs2Comparator - Class in RdcPanda
The Class cs2Comparator.
ScNoe.cs2Comparator() - Constructor for class RdcPanda.ScNoe.cs2Comparator
 
ScNoe.intensityComparator - Class in RdcPanda
The Class intensityComparator.
ScNoe.intensityComparator() - Constructor for class RdcPanda.ScNoe.intensityComparator
 
scNoeGenerate(Vector, int, String, double, Vector) - Method in class RdcPanda.Peak
A function to generate NOEs from side-chains to HN or HA, //no longer used.
SearchSSEAnchors(int, int) - Method in class RdcPanda.Goal
find the SSE anchors (ca atoms) that can possibly interact with loops
SearchSSEAnchorsTop(int, int) - Method in class RdcPanda.Goal
find the top set of SSE anchors (ca atoms) that can possibly interact with loops
set(int, int, double) - Method in class RdcPanda.Matrix
Set a single element.
setAAName(String) - Method in class RdcPanda.Rotamer
Sets the aA name.
setAssignedID(int) - Method in class RdcPanda.Nasca.Node
 
setAssignMap(Map) - Method in class RdcPanda.HcchTocsy
Sets the assign map.
setAssignMap(Map) - Method in class RdcPanda.HnNoe
Sets the assign map.
setAtom(String) - Method in class RdcPanda.Cartesian
Sets the atom name.
setAtom1Name(String) - Method in class RdcPanda.Noe
Sets the atom1 name.
setAtom2Name(String) - Method in class RdcPanda.Noe
Sets the atom2 name.
setAtomName(String) - Method in class RdcPanda.H1CS
Sets the atom name.
setAtomName(String) - Method in class RdcPanda.Nasca.Node
 
setAtomVec(Vector) - Method in class RdcPanda.Pdb
Sets the atom vec.
setAtomVec(Vector) - Method in class RdcPanda.Rotamer
Sets the atom vec.
setBaseIndex(int) - Static method in class Jampack.Parameters
Resets the default base index.
setBinIndex(int) - Method in class RdcPanda.Noesy
Sets the bin index.
SetCalibration(Vector) - Method in class RdcPanda.Noesy
calibration of intensity: using xplor-NIH method The required file format is:.
SetCalibration2(Vector) - Method in class RdcPanda.Noesy
calibration of intensity: using -3 The required file format is:.
SetCalibrationC13(Vector, Vector) - Method in class RdcPanda.Noesy
the following rules are used to calibrate the constant k 1.
SetCalibrationC13Sec(Vector, Vector, Vector) - Method in class RdcPanda.Noesy
incompleted..., this function can be delested...
SetCalibrationCyana(Vector, Vector, double) - Method in class RdcPanda.Noesy
calibrate one NOE peak, using a calibration strategy similar to CYANA.
SetCalibrationN15(Vector, Vector, Vector, double[]) - Method in class RdcPanda.Noesy
we use the HN(i)-HA(i-1) in SSE regions to calibrate distance from peak intensity (dist<2.5A).
SetCalibrationOneCyana(BackNoe, Noesy, double) - Method in class RdcPanda.Noesy
calibrate one NOE peak, using a calibration strategy similar to CYANA.
SetChRdcDif(double) - Method in class RdcPanda.Goal.TreePdb
 
setCoord(double[]) - Method in class RdcPanda.vdw
Sets the coord.
setCS(double) - Method in class RdcPanda.H1CS
Sets the cS.
setCS(double) - Method in class RdcPanda.Peak
Sets the cS.
setCSLower(double) - Method in class RdcPanda.Nasca.Node
 
setCSUpper(double) - Method in class RdcPanda.Nasca.Node
 
setDistLower(double) - Method in class RdcPanda.Noe
Sets the dist lower.
setDistUpper(double) - Method in class RdcPanda.Noe
Sets the dist upper.
SetEndDist(double) - Method in class RdcPanda.Goal.TreePdb
 
setErr(double) - Method in class RdcPanda.Dipolar
Sets the err.
setHcchVec(Vector) - Method in class RdcPanda.Residue
Sets the hcch vec.
setHCS1(double) - Method in class RdcPanda.ScNoe
Sets the hC s1.
setHCS2(double) - Method in class RdcPanda.ScNoe
Sets the hC s2.
setHeavyCS(double) - Method in class RdcPanda.Nasca.Node
 
setHistory() - Static method in class Jampack.Parameters
Sets the history flag.
setHomoScore(double, int) - Method in class RdcPanda.GraphCut
 
SetID(int) - Method in class RdcPanda.Goal.TreePdb
 
setID(String) - Method in class RdcPanda.vdw
Sets the iD.
setInitialRotScore() - Method in class RdcPanda.GraphCut
 
setIntensity(double) - Method in class RdcPanda.ScNoe
Sets the intensity.
setIsAssigned(boolean) - Method in class RdcPanda.Nasca.Node
 
setIsMissing(boolean) - Method in class RdcPanda.BackNoe
Sets the checks if is missing.
setIsRestrained(boolean) - Method in class RdcPanda.Nasca.Node
 
setMaxValue(double) - Method in class RdcPanda.Assign
Sets the max value.
setMissingIndex(int[]) - Method in class RdcPanda.Assign
Sets the missing index.
setMissingPenalty(double, double, double) - Method in class RdcPanda.BackNoe
Sets the missing penalty.
setMissingProb(double) - Method in class RdcPanda.BackNoe
Sets the missing prob.
setNeighbors(Vector) - Method in class RdcPanda.GraphCut
 
SetNhRdcDif(double) - Method in class RdcPanda.Goal.TreePdb
 
setNodeID(int) - Method in class RdcPanda.Nasca.Node
 
setNucleus(String) - Method in class RdcPanda.Peak
Sets the nucleus.
setOriginID(int) - Method in class RdcPanda.GraphCut.RotScore
 
setOutputParams(int, int, int) - Static method in class Jampack.Parameters
Changes the output parameters.
setPairScore(double, int, int, int) - Method in class RdcPanda.GraphCut
 
SetParenPdb(Goal.TreePdb) - Method in class RdcPanda.Goal.TreePdb
 
SetPdb(Pdb) - Method in class RdcPanda.Goal.TreePdb
 
setPeakID(int) - Method in class RdcPanda.Noe
Sets the peak id.
setPeakVec(Vector) - Method in class RdcPanda.Residue
Sets the peak vec.
setPhi(double) - Method in class RdcPanda.PhiPsi
Sets the phi.
setProtonCS(double) - Method in class RdcPanda.Nasca.Node
 
setPrunedLabel(int) - Method in class RdcPanda.GraphCut
 
setPsi(double) - Method in class RdcPanda.PhiPsi
Sets the psi.
SetRamaScore(double) - Method in class RdcPanda.Goal.TreePdb
 
setRatioEnsemb(double) - Method in class RdcPanda.Noe
Sets the ratio ensemb.
setRdc(double) - Method in class RdcPanda.Dipolar
Sets the rdc.
setResidue(String) - Method in class RdcPanda.Pdb
Sets the residue.
setResidueNo(int) - Method in class RdcPanda.Dipolar
Sets the residue no.
setResidueNo(int) - Method in class RdcPanda.H1CS
Sets the residue no.
setResidueNo(int) - Method in class RdcPanda.HcchTocsy
Sets the residue no.
setResidueNo(int) - Method in class RdcPanda.Hncacb
Sets the residue no.
setResidueNo(int) - Method in class RdcPanda.HnNoe
Sets the residue no.
setResidueNo(int) - Method in class RdcPanda.Hsqc
Sets the residue no.
setResidueNo(int) - Method in class RdcPanda.Noesy
Sets the residue no.
setResidueNo(int) - Method in class RdcPanda.Pdb
Sets the residue no.
setResidueNo(int) - Method in class RdcPanda.Residue
Sets the residue no.
setResidueType(String) - Method in class RdcPanda.H1CS
Sets the residue type.
setResidueType(String) - Method in class RdcPanda.HcchTocsy
Sets the residue type.
setResidueType(String) - Method in class RdcPanda.HnNoe
Sets the residue type.
setResidueType(String) - Method in class RdcPanda.Hsqc
Sets the residue type.
setResidueType(String) - Method in class RdcPanda.Noesy
Sets the residue type.
setResidueType(String) - Method in class RdcPanda.Residue
Sets the residue type.
setResName(String) - Method in class RdcPanda.Nasca.Node
 
setResNameA(String) - Method in class RdcPanda.Noe
Sets the res name a.
setResNameB(String) - Method in class RdcPanda.Noe
Sets the res name b.
setResNo(int) - Method in class RdcPanda.Nasca.Node
 
setResNoA(int) - Method in class RdcPanda.Noe
Sets the res no a.
setResNoB(int) - Method in class RdcPanda.Noe
Sets the res no b.
setRmsd(double) - Method in class RdcPanda.BackNoe
Sets the rmsd.
setRmsdAll(double, double, double) - Method in class RdcPanda.BackNoe
Sets the rmsd all.
setRotamerRatio(double) - Method in class RdcPanda.Pdb
Sets the rotamer ratio.
setRotlabel(int) - Method in class RdcPanda.GraphCut
 
setSameUpperBounds4All(Vector, double) - Method in class RdcPanda.Noe
set the same upper bound for all NOEs.
setScore(double) - Method in class RdcPanda.GraphCut.RotScore
 
setScore(double) - Method in class RdcPanda.RotaPattern
Sets the score.
setSeed(long) - Static method in class Jampack.Rand
Sets the seed for the random number generator.
SetSumRdcDif(double) - Method in class RdcPanda.Goal.TreePdb
 
setUpperDist(double) - Method in class RdcPanda.Noesy
Sets the upper dist.
setVecH_A(Vector) - Method in class RdcPanda.Noe
Sets the vec h_ a.
setVecH_B(Vector) - Method in class RdcPanda.Noe
Sets the vec h_ b.
sheetModel(Vector, Vector, double, double, Vector, Vector, Vector[], boolean) - Method in class RdcPanda.Model
Compute s beta-sheet with the order specified by orderVec.
sheetModel2(Vector, Vector, Vector, double, double, Vector, Vector, Vector[], boolean) - Method in class RdcPanda.Model
Compute s beta-sheet with the order specified by orderVec.
ShufflingCut(Vector) - Method in class RdcPanda.GraphCut
Shuffling step in the graph cut algorithm
si - Variable in class Jampack.Rot
The imaginary part of the sine of the rotation
SimulateBackCompNOEPeak(Vector, Hdist) - Method in class RdcPanda.RotaPattern
for simulate ca NOEs, Back compute an NOE peak from a given pair of NOE distance.
SimulatedCaNoe(Vector, Vector, double) - Method in class RdcPanda.Peak
generate the simulated ca noes from x-ray structure.
sinAngles(double, double, double, double[]) - Static method in class RdcPanda.Maths
solve the sin equation: a * sin(theta) + b * cos(theta) = c;.
SingularValueDecomposition - Class in RdcPanda
This class provides functions for SVD operations (from Jama package).
SingularValueDecomposition(Matrix) - Constructor for class RdcPanda.SingularValueDecomposition
Construct the singular value decomposition.
sixAngles(Vector) - Method in class RdcPanda.Pdb
pdbVec is a Vector of Pdb Objects e.g.
Solve - Class in Jampack
Solve solves linear systems of the form
Solve() - Constructor for class Jampack.Solve
 
sortAssign(Vector) - Method in class RdcPanda.Assign
Written by Lincong.
sortRotScore() - Method in class RdcPanda.GraphCut
 
sp3Carbon - Class in RdcPanda
represeting the tetrahedral of the sp3 Carbon configuration IN order to compute the coordinates we need only to know the coordinates of the top atom then using the information provided by the sp3Carbon object we should be able to compute all the coordinates of other atoms.
sp3Carbon() - Constructor for class RdcPanda.sp3Carbon
Instantiates a new sp3 carbon.
sp3Carbon(double, double, double, double, double, double, double, double, double, boolean) - Constructor for class RdcPanda.sp3Carbon
Instantiates a new sp3 carbon.
sp3Carbon(double[], boolean) - Constructor for class RdcPanda.sp3Carbon
The Constructor.
sp3Carbon(double[], double[], double[], double[], double[], double[], boolean) - Constructor for class RdcPanda.sp3Carbon
Instantiates a new sp3 carbon.
Sqrt(Z) - Method in class Jampack.Z
Computes the principal value of the square root of a Z.
sr - Variable in class Jampack.Rot
The real part of the sine of the rotation
SSEPacking - Class in RdcPanda
This class provides functions for packing SSE fragments.
SSEPacking() - Constructor for class RdcPanda.SSEPacking
Instantiates a new sSE packing.
SSEPacking(double, double, double, double) - Constructor for class RdcPanda.SSEPacking
Instantiates a new sSE packing.
SSEPacking.SSEPackingComparator - Class in RdcPanda
The Class SSEPackingComparator.
SSEPacking.SSEPackingComparator() - Constructor for class RdcPanda.SSEPacking.SSEPackingComparator
 
SSEsOneToOnePacking(String[]) - Static method in class RdcPanda.SSEPacking
packing two single SSEs using sparse NOE restraints.
StatisticsAllSCAssignment(Vector, Vector, int[][], Vector) - Method in class RdcPanda.Nasca
New: compute the statistical information of the sidechain assignment
StatisticsAllSCAssignmentOld(Vector, Vector, int[][], Vector) - Method in class RdcPanda.Nasca
This is an old function.
statsOfSixAngles(String) - Method in class RdcPanda.Pdb
A method to compute all the angles from ultrahigh resolution PDBs.
stereoID - Variable in class RdcPanda.Nasca.Node
 
StereospecificNoeAsg(Vector) - Method in class RdcPanda.Assign
consider the stereospecific assignments.
sumRdcDif - Variable in class RdcPanda.Goal.TreePdb
 
svd() - Method in class RdcPanda.Matrix
Singular Value Decomposition.
Swap - Class in Jampack
Swap interchanges rows and columns of a matrix.
Swap() - Constructor for class Jampack.Swap
 
SwapStereoAsg(Vector, int) - Method in class RdcPanda.Assign
swap the stereospecific assignment for a given residue we assume the atom naming scheme is PDB-New.
Syy - Variable in class RdcPanda.Goal
 
Szz - Variable in class RdcPanda.Goal
 

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