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

R

R - Variable in class Jampack.Zchol
The Cholesky factor
R - Variable in class Jampack.Zhqrd
The R factor.
R - Variable in class Jampack.Zqrd
The R factor.
radiiFromCb(Vector, String, String) - Method in class RdcPanda.Pdb
We can also derived the minimum and maximam using analytic expression but using rotamer as appeared in PDB may have certain advantage.
radiiFromNH(Vector, String, String) - Method in class RdcPanda.Pdb
Compute the distance from the nucleu NH to other nucleu.
ramaScore - Variable in class RdcPanda.Goal.TreePdb
 
Rand - Class in Jampack
The rand suite generates random objects with elements distributed randomly on [0,1] or normally with mean zero and standard deviation one.
Rand() - Constructor for class Jampack.Rand
 
RandomGraphMatching(Vector, Vector, int[][], double[][], Vector, Vector) - Method in class RdcPanda.Nasca
random graph matching algorithm.
RandomSelectRot(Vector) - Method in class RdcPanda.GraphCut
randomly select a rotamer proportial to its score
RandomVotingUpdate(Vector) - Method in class RdcPanda.GraphCut
update the match score using random voting scheme
rangeSearch(String, double, double, Vector) - Method in class RdcPanda.HcchTocsy
Range search.
rangeSearch(String, double, double, Vector) - Method in class RdcPanda.Hncacb
Range search.
rangeSearch(String, double, double, Vector) - Method in class RdcPanda.HnNoe
Extract all the HnNoe objects with proton CS or N15 CS in the range of [a, b] from an array of NOE peaks.
rangeSearch(String, double, double, Vector) - Method in class RdcPanda.Hsqc
Range search.
rangeSearch(String, double, double, Vector) - Method in class RdcPanda.Noesy
Extract all the HnNoe objects with proton CS or N15 CS in the range of [a, b] from an array of NOE peaks.
rangeSearch(Vector, double, double) - Method in class RdcPanda.Peak
Range Search: search all the protons with in the range [CS-h1Err, CS + h1Err].
rangeSearchScNoeCS1(Vector, double, double) - Method in class RdcPanda.Peak
Range Search: search all the protons with in the range [CS-h1Err, CS + h1Err].
rangeSearchScNoeCS2(Vector, double, double) - Method in class RdcPanda.Peak
Range Search: search all the protons with in the range [CS-h1Err, CS + h1Err].
rank() - Method in class RdcPanda.SingularValueDecomposition
Effective numerical matrix rank.
RdcPanda - package RdcPanda
 
RdcPanda - Class in RdcPanda
This class implements the main function of RDC-Panda.
RdcPanda() - Constructor for class RdcPanda.RdcPanda
 
rdcRead(String) - Method in class RdcPanda.Dipolar
A method for reading files with RDC restraints.
rdcRead(String, double) - Method in class RdcPanda.Dipolar
A method for reading files with RDC restraints.
rdcReader(String, Vector<IDof2aryStructure>, String) - Method in class RdcPanda.Dipolar
read RDC data file for a fragment as defined by secondary structure identification.
rdcReader(String, Vector<IDof2aryStructure>, String, double) - Method in class RdcPanda.Dipolar
read RDC data file for a fragment as defined by secondary structure identification.
rdcReader4CNS(String, String, double) - Method in class RdcPanda.Dipolar
A method for extracting RDC restraints from CNS format The required file format is: residue No.
rdcReader_old(String, Vector, String) - Method in class RdcPanda.Dipolar
This is an old function.
rdcThreshold - Variable in class RdcPanda.Goal
 
re - Variable in class Jampack.Z
The real part of Z.
ReadBMRBSatistics(String) - Method in class RdcPanda.H1CS
read BMRB statistical information.
ReaderSeq(String) - Method in class RdcPanda.Assign
Read protein sequence.
readPdb(String) - Method in class RdcPanda.Pdb
Reading PDB file in PDB Format!!! the magic number for substring is based on format for pdb file.
readPdbAndNoeHarmFromEnsemble(String) - Method in class RdcPanda.Pdb
Reading PDB file and other parameters in PDB Format from ensemble!!!.
readPdbAndNoeRmsdFromEnsemble(String) - Method in class RdcPanda.Pdb
Reading PDB file and other parameters in PDB Format from ensemble!!!.
readPdbAndParametersFromEnsemble(String) - Method in class RdcPanda.Pdb
Reading PDB file and other parameters in PDB Format from ensemble!!!.
readPdbAndParaXplor(String, double[], double[]) - Method in class RdcPanda.Pdb
Read pdb and para xplor.
readPdbEnergy(String, double[], int, int) - Method in class RdcPanda.Pdb
Read pdb energy.
readPdbFromEnsemble(String) - Method in class RdcPanda.Pdb
Reading PDB file in PDB Format from ensemble!!! the magic number for substring is based on format for pdb file.
ReadRamachandranFile(String) - Method in class RdcPanda.Loops
Read the Ramachandran probability score based on Richardsons' top500 structures.
readRotamer(String) - Method in class RdcPanda.Rotamer
Read rotamer.
readRotamerPdb(String) - Method in class RdcPanda.Pdb
Reading Rotamer file in PDB Format!!!.
refineHelix(Vector, Vector, double[], double, double, Map) - Method in class RdcPanda.ModelRdc
For computing the Helix.
refineHelix22(Vector, Vector<Dipolar>, Vector<Dipolar>, double, double, double[], double, double, int, int, double, double, boolean, boolean, Vector) - Method in class RdcPanda.ModelRdc
Refine helix22.
refineHelix22(Vector, Vector<Dipolar>, Vector<Dipolar>, double, double, double[], double, double, int, int, double, double, boolean, boolean, double[], double[]) - Method in class RdcPanda.ModelRdc
Refine helix22.
refineHelix22NoGridSearch(Vector, Vector<Dipolar>, Vector<Dipolar>, double, double, double[], double, double, int, int, double, double, boolean, boolean, double[], double[]) - Method in class RdcPanda.ModelRdc
Refine helix22 no grid search.
refineHelixW4RDCs(Vector, Vector<Dipolar>, Vector<Dipolar>, Vector<Dipolar>, Vector<Dipolar>, double, double, double[], double, double, int, int, double, double, boolean, boolean, Vector) - Method in class RdcPanda.ModelRdc
Refine helix w4 rd cs.
refineHelixW4RDCs(Vector, Vector, Vector<Dipolar>, Vector<Dipolar>, Vector<Dipolar>, Vector<Dipolar>, double, double, double[], double, double, int, int, double, double, boolean, boolean, Vector, double, double, int, int, Vector) - Method in class RdcPanda.ModelRdc
refine the Helix with the weights for CaCo NCO RDCs.
RefineMappingBasedAsg(Vector, Vector, int[][], double[][], Vector, Vector) - Method in class RdcPanda.Nasca
refine mapping based on backbone assignment
RefineMappingBasedBMRBOutliers(Vector, Vector, int[][], Vector) - Method in class RdcPanda.Nasca
refine mapping based on BMRB outliers
RefineMappingBasedNeighbor(Vector, Vector, int[][]) - Method in class RdcPanda.Nasca
refine mapping based on neighboring information
RefineMappingBasedRestrained(Vector, Vector, int[][], double[][], Vector, Vector) - Method in class RdcPanda.Nasca
refine mapping based on previous restrained mapping sets, modified from "RefineMappingBasedAsg"
RefineMappingBasedRotPattern(Vector, Vector, int[][]) - Method in class RdcPanda.Nasca
refine mapping based on intra NOE patterns Note: Sysmetry-only when distance<3.0A, and sidechain protons
RefineMappingDeeCut(Vector, Vector, int[][], double[][], Vector, Vector) - Method in class RdcPanda.Nasca
Use the DEE algorithm to prune possible side-chain resonance assignments.
RefineMappingDeeCutGoldstein(Vector, Vector, int[][], double[][], Vector, Vector) - Method in class RdcPanda.Nasca
Use the DEE algorithm to prune possible mapping.
RefineMappingForHG(Vector, Vector, int[][], double[][], Vector, Vector) - Method in class RdcPanda.Nasca
refine mapping for HG protons modified from "RefineMappingBasedAsg"
RefineResonGraph(Vector, Vector, int[][]) - Method in class RdcPanda.Nasca
refine resonance graph based currrent possible mapping set
RefineRotamerSelection(Vector, Vector, int[]) - Method in class RdcPanda.Pdb
refine the rotamer selection until no steric clash happens.
RefineRotamerSelectionRandom(Vector, Vector, int[]) - Method in class RdcPanda.Pdb
refine the rotamer selection until no steric clash happens, using Gaussian random sampling at each rotamer position.
RefineRotamerSelectionRecur(Vector, Vector, int, Vector, boolean[]) - Method in class RdcPanda.Pdb
refine the rotamer selection until no steric clash happens, by enumerating all possible rotamers in the order of NOE matching scores.
RefineRotamerSelectionSearch(Vector, int, String, int) - Method in class RdcPanda.Pdb
wait...
RefineRotLib(Vector, Vector, Vector, Vector, Vector, int, double, int, int[], Vector) - Method in class RdcPanda.RotaPattern
calculate the score of each rotamer, and choose rotamers with highest scores.
RefineRotLib(double, double, double, Vector, Vector, Vector, Vector, int, double, int, int[]) - Method in class RdcPanda.RotaPattern
Refined function for general case: calculate the score of each rotamer, and choose rotamers with highest scores.
RefineRotLib(double, double, double, Vector, Vector, Vector, Vector, int, double, int, double[]) - Method in class RdcPanda.RotaPattern
Refined function for general case: calculate the score of each rotamer, and choose rotamers with highest scores.
RefineRotLibNew(double, double, double, Vector, Vector, Vector, Vector, int, double, int, Vector, double) - Method in class RdcPanda.RotaPattern
Refined function for general case: calculate the score of each rotamer, and return ensemble of rotamers with highest scores.
RefineRotLibNewUsingBins(double, double, double, Vector, Vector, Vector, Vector, int, double, int, Vector) - Method in class RdcPanda.RotaPattern
calibration scheme: using bin scheme.
RefineRotLibWOSCAsg(double, double, double, Vector, Vector, Vector, Vector, int, double, int, Vector, Vector, Vector, int[][], Vector) - Method in class RdcPanda.Nasca
rotamer selection without sidechain resonance assignment: calculate the score of each rotamer, and return ensemble of rotamers with highest scores
refineSaupe(Vector, Vector, double[], double[], double, double, int, int, boolean, boolean, Vector) - Method in class RdcPanda.ModelRdc
Refine Saupe elements from an initial model.
refineSaupe2(Vector, Vector, Vector, Vector, Vector, Vector, double[]) - Method in class RdcPanda.ModelRdc
This is an old function.
refineSaupe3(Vector<Pdb>, Vector<Dipolar>, Vector<Dipolar>, double[]) - Method in class RdcPanda.ModelRdc
Modified by zeng for computing the alignment tensor based on structure and RDCs Update the Saupe elements for the second time.
refineSaupe4RDCsWOAT(Vector, Vector, Vector, Vector, double[], double[], double, double, int, int, boolean, boolean, Vector) - Method in class RdcPanda.ModelRdc
Refine Saupe elements from an initial model.
refineSaupe4RDCsWOAT(Vector, Vector, Vector, Vector, Vector, Vector, double[], double[], double, double, int, int, boolean, boolean, Vector, double, double, int, int, Vector) - Method in class RdcPanda.ModelRdc
Refine Saupe elements from an initial model.
refineStrand(Vector, Vector, double, double, double[], double, double, int, int, double, double, boolean, boolean) - Method in class RdcPanda.ModelRdc
For computing the first Strand which is NOT H-bonded to others.
refineStrand(Vector, Vector, double, double, double, double, int, int, double, double, double, Vector, Vector, boolean, boolean, boolean) - Method in class RdcPanda.ModelRdc
For computing the others Strands which IS H-bonded to others.
refineStrand2(Vector, Vector, double, double, double, double, int, int, double, double, double, Vector, Vector, boolean, boolean, boolean) - Method in class RdcPanda.ModelRdc
For computing the others Strands which IS H-bonded to others.
Residue - Class in RdcPanda
A very simple Residue class with the Notation like Val1, Ala25.
Residue() - Constructor for class RdcPanda.Residue
Instantiates a new residue.
Residue(int) - Constructor for class RdcPanda.Residue
A constructor designed specifically for the Comparator class used for the Sort and BinarySearch.
Residue(int, String) - Constructor for class RdcPanda.Residue
Instantiates a new residue.
Residue(int, String, Vector) - Constructor for class RdcPanda.Residue
Instantiates a new residue.
Residue(int, String, Vector, Vector) - Constructor for class RdcPanda.Residue
Instantiates a new residue.
Residue(int, String, Vector, Map) - Constructor for class RdcPanda.Residue
Instantiates a new residue.
Residue.caComparator - Class in RdcPanda
The Class caComparator.
Residue.caComparator() - Constructor for class RdcPanda.Residue.caComparator
 
Residue.cbComparator - Class in RdcPanda
The Class cbComparator.
Residue.cbComparator() - Constructor for class RdcPanda.Residue.cbComparator
 
ResidueGradientSearch(Vector, int, double, double, Vector<Dipolar>, Vector<Dipolar>, int, int, Vector, Vector, double, double, double[], boolean) - Method in class RdcPanda.Loops
 
residueNameFromSeq(Vector, int) - Method in class RdcPanda.Pdb
get the residue name from protein sequence.
residueNameUpdate(Vector, Vector) - Method in class RdcPanda.Pdb
work for bb only? A temporary method for converting the residue name in the RDC-derived PDB file, which are "ALA", to real Residue name, also to build the conformation of proline and glycine residue.
residueNameUpdate_from_structure(Vector, Vector) - Method in class RdcPanda.Pdb
A temporary method for converting the residue name in the RDC-derived PDB file, which are "ALA", to real Residue name, also to build the conformation of proline and glycine residue.
residueNameUpdateNoStr(Vector, Vector) - Method in class RdcPanda.Pdb
change residue name according to sequnce, without changing structure.
resonID - Variable in class RdcPanda.H1CS
The reson id.
restraintsBackward(int, int, Vector, Vector, Vector, Vector, double, double) - Method in class RdcPanda.PhiPsi
To extract all the sequential restraints (both RDCs and NOEs) involving the backbone nuclei (HA and NH) located in the turn or the loop.
RgCal(double[], double[]) - Method in class RdcPanda.PhiPsi
Compute the global rotation matrix for rotating a coordinate frame such as the PDB frame where the two vectors NH(i)->N(i) (nToh) and N(i)->CA(i) (nToca) defined into the following frame: +Z-axis along the bond NH(i)->N(i), "->" means from nuclear NH(i) to nuclear N(i).
RgCal(double[], double[], boolean) - Method in class RdcPanda.PhiPsi
Rg cal.
RgCal(double[], double[]) - Method in class RdcPanda.ppGlobal
compute global rotation (Rg) with two noncolinear vectors, Rg is the rotation matrix for rotating the PDB coordinate system into the following system: +z-axis along the bond NH(i)->N(i), "->" means from atom N(i) to atom NH(i).
RgCal(double[], double[], boolean) - Method in class RdcPanda.ppGlobal
Rg cal.
RgCal(double[], double) - Method in class RdcPanda.ppGlobal
compute global rotation (Rg) with two no colinear vectors Rg is the same as the last method Here the input are the NH vector and one Euler angle gamma for the N(i)->CA(i) vector accounting the rotation of the peptide plane along the NH vector.
ringResonanceAsg(double, double) - Method in class RdcPanda.Peak
ringResonaceAsg: search all the protons with in the range [CS-Err, CS + Err] and assign the H resonance.
Rot - Class in Jampack
Rot generates and manipulates plane rotations.
Rot() - Constructor for class Jampack.Rot
 
Rotamer - Class in RdcPanda
This class provides data structures and functions related to rotamers.
Rotamer() - Constructor for class RdcPanda.Rotamer
Instantiates a new rotamer.
Rotamer(String) - Constructor for class RdcPanda.Rotamer
Instantiates a new rotamer.
Rotamer(String, Vector) - Constructor for class RdcPanda.Rotamer
Instantiates a new rotamer.
RotamerReplacement(int, int) - Method in class RdcPanda.Goal
Compute a structure, given the backbone and rotamers at all residue positions
RotamerReplacementKin(int, int) - Method in class RdcPanda.Goal
get the candidate positions for each ca atom using kinematic constraints and rotamer replacement
RotamerReplacementOld(int, int) - Method in class RdcPanda.Goal
Compute a structure, given the backbone and rotamers at all residue positions
RotamerSelection(Vector, Vector, int) - Method in class RdcPanda.GraphCut
select top rotamers with highest scores
RotamSelectAndStructure(double, double, double, Vector, Vector, String, Vector, double, int, double) - Method in class RdcPanda.Pdb
Compute a structure, given the backbone and rotamers at all residue positions.
RotamSelectAndStructureNoClash(double, double, double, Vector, Vector, String, Vector, double, int, boolean[]) - Method in class RdcPanda.Pdb
Rotam select and structure no clash.
RotamSelectWOSCAsg(Vector, Vector, Vector, Vector, Vector, int[][], Vector) - Method in class RdcPanda.Nasca
Compute a structure without sidechain resonances, given the backbone and rotamers at all residue positions
RotaPattern - Class in RdcPanda
This class implements data structures and functions that deal with the rotamer properties.
RotaPattern(double[], double) - Constructor for class RdcPanda.RotaPattern
Instantiates a new rota pattern.
RotaPattern(Pdb, double) - Constructor for class RdcPanda.RotaPattern
Instantiates a new rota pattern.
RotaPattern(int, double) - Constructor for class RdcPanda.RotaPattern
Instantiates a new rota pattern.
RotaPattern() - Constructor for class RdcPanda.RotaPattern
Instantiates a new rota pattern.
RotaPattern(int, String, Vector, Vector) - Constructor for class RdcPanda.RotaPattern
Instantiates a new rota pattern.
RotaPattern(int, String, Vector, Vector, Vector) - Constructor for class RdcPanda.RotaPattern
Instantiates a new rota pattern.
RotaPattern.scoreComparator - Class in RdcPanda
The Class scoreComparator.
RotaPattern.scoreComparator() - Constructor for class RdcPanda.RotaPattern.scoreComparator
 
rotationMat(double, String) - Method in class RdcPanda.Matrix
make a 3x3 rotation matrix with a rotation angle theta and along an axis Please note that only axis only take +/-x, y, z A method by Lincong Wang.
rotLibName - Variable in class RdcPanda.RdcPanda
The path of rot lib location.
rotSrc - Variable in class RdcPanda.Goal
 
row(Zmat, int[]) - Static method in class Jampack.Pivot
Pivots the rows of a Zmat (altered) as specified by a pivot array.
rowi(Zmat, int[]) - Static method in class Jampack.Pivot
Pivots the rows of a Zmat (altered) as in the inverse order specified by a pivot array.
rows(Zmat, int, int) - Static method in class Jampack.Swap
Interchances two rows of a Zmat (altered).
rx - Variable in class Jampack.Zmat
The upper row index

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