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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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