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

I

I - Static variable in class Jampack.Z
Imaginary unit.
id - Variable in class RdcPanda.Goal.TreePdb
 
identifyNoeResidues(Vector, Vector, int) - Method in class RdcPanda.Noe
identify NOE residues for a sse.
identity(int, int) - Static method in class RdcPanda.Matrix
Generate identity matrix.
IDof2aryStructure - Class in RdcPanda
This class provides functions for processing files with secondary structure element information.
IDof2aryStructure() - Constructor for class RdcPanda.IDof2aryStructure
Constructors.
IDof2aryStructure(int, int, String) - Constructor for class RdcPanda.IDof2aryStructure
Instantiates a new i dof2ary structure.
IDof2aryStructureReader(String) - Method in class RdcPanda.IDof2aryStructure
A very simple reader for secondary structure identification file.
im - Variable in class Jampack.Z
The imaginary part of Z.
InitAmbiAssignment(double, double, double, double, double, Vector, Vector, Vector) - Method in class RdcPanda.Assign
Compute the intiial NOE assignments using only chemcial shift information.
InitAmbiAssignment4D(double, double, double, double, double, Vector, Vector, Vector) - Method in class RdcPanda.Assign
Initial NOE assignment for 4D NOESY.
InitAmbiAssignmentUnique(double, double, double, double, double, Vector, Vector, Vector) - Method in class RdcPanda.Assign
The same as InitAmbiAssignment, but only output those unique noe assignments.
Initialization(Vector, Vector, int[][], double[][], Vector) - Method in class RdcPanda.Nasca
Initialization.
intensityVsDistance(Vector, Vector, Vector) - Method in class RdcPanda.Peak
A temporary method to relate NOE intensity with distance,.
interAngle(double[], double[]) - Method in class RdcPanda.ModelRdc
calculate the angles between two vectors v1 and v2 The returned angle is in the [0,Pi] range.
interAngle(double[], double[]) - Method in class RdcPanda.Pdb
calculate the angles between two vectors v1 and v2 The returned angle is the [0,Pi] region.
interAngle(double[], double[]) - Method in class RdcPanda.PdbRmsd
calculate the angles between two vectors v1 and v2 The returned angle is in the [0,Pi] range or the cosine itself.
interAngle(double[], double[]) - Method in class RdcPanda.PhiPsi
calculate the angles between two vectors v1 and v2 The returned angle is in the [0,Pi] range.
interAngle(double[], double[]) - Method in class RdcPanda.ppGlobal
calculate the angles between two vectors v1 and v2 The returned angle is in the [0,Pi] range.
internuclearDistance(double[], double[]) - Method in class RdcPanda.PhiPsi
Compute the internuclear vector between two atoms.
internuclearVec(double[], double[]) - Method in class RdcPanda.ModelRdc
Compute the internuclear vector between two atoms.
internuclearVec(double[], double[]) - Method in class RdcPanda.Pdb
Compute the internuclear vector between two atoms.
internuclearVec(double[], double[]) - Method in class RdcPanda.PdbRdc
Compute the internuclear vector between two atoms.
internuclearVec(double[], double[]) - Method in class RdcPanda.Peak
Compute the internuclear vector between two atoms.
internuclearVec(double[], double[]) - Method in class RdcPanda.PhiPsi
Compute the internuclear vector between two atoms.
internuclearVec(double[], double[]) - Method in class RdcPanda.vdw
Internuclear vec.
Inv - Class in Jampack
Inv computes the inverse of a matrix.
Inv() - Constructor for class Jampack.Inv
 
isAllGridSearch - Variable in class RdcPanda.Goal
 
isBonded(int, int, String, String) - Method in class RdcPanda.vdw
Only for polyalanine.
isBonded(String, int, int, String, String) - Method in class RdcPanda.vdw
Checks if is bonded.
isCharged(String) - Method in class RdcPanda.Peak
check whether a residue is a charged amino acid.
IsEqual(Z, Z) - Method in class Jampack.Z
Tests two Z'z for equality.
isForward - Variable in class RdcPanda.Goal
 
isHydrophobic(String) - Method in class RdcPanda.Peak
check whether a residue is a hydrophobic amino acid.
isInAtomVec(Vector, String) - Method in class RdcPanda.Pdb
Checks if is in atom vec.
isInCloseAdj(Nasca.Node, Nasca.Node) - Method in class RdcPanda.Nasca
check whether one node is in another node's close neighbors
isInPdbClusters(Vector, Vector, double) - Method in class RdcPanda.Pdb
tell whether a structure is within the clusters of previous ensemble.
isInPhiPsiClusters(Vector, PhiPsi, double) - Method in class RdcPanda.Loops
tell whether a point is within the clusters of previous ensemble
isInPointClusters(Vector, Cartesian, double) - Method in class RdcPanda.Pdb
tell whether a point is within the clusters of previous ensemble.
isInStereoSet(Nasca.Node, Nasca.Node) - Method in class RdcPanda.Nasca
check whether one node is in another node's stereo set
isMappedBetwTwoSets(Vector, Vector, int[][], boolean, int, double[]) - Method in class RdcPanda.Nasca
check whether there exists at least one mapping between two node sets
isMappedBetwTwoSetsCalScore(Nasca.Node, Nasca.Node, Vector, Vector, int[][], boolean, int, double[], Vector) - Method in class RdcPanda.Nasca
check whether there exists at least one mapping between two node sets
isSkipOutEnsembe - Variable in class RdcPanda.PdbRmsd
The is skip out ensembe.
isTerminal() - Method in class RdcPanda.sp3Carbon
Checks if is terminal.
IterativeGradientSearch(Vector, double, double, Vector<Dipolar>, Vector<Dipolar>, int, int, Vector, Vector, double, double, boolean) - Method in class RdcPanda.Loops
 

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