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

N

n - Variable in class Jampack.Zchol
The order of A and R
n - Variable in class Jampack.Zdiagmat
The order of the matrix (public)
nameConvert(Vector) - Method in class RdcPanda.Pdb
Lincong's original function: Convert the old PDB namaclature to new one bugs fixed...
nameConvert22(Vector) - Method in class RdcPanda.Pdb
Convert the old PDB namaclature to new one.
nameConvert2PDBNew(Vector) - Method in class RdcPanda.Pdb
Convert the old PDB namaclature to new one zeng changed the code,.
nameConvert4SmallRotLibCS(Vector) - Method in class RdcPanda.Pdb
Convert the old PDB namaclature to new one zeng changed the code, such that all methel group protons become one proxy proton.
nameConvert4SmallRotLibStr(Vector) - Method in class RdcPanda.Pdb
Convert the old PDB namaclature to new one for computing the structure rmsd.
nameConvertCS(Vector) - Method in class RdcPanda.Pdb
Convert the old PDB namaclature to new one zeng changed the code, such that all methel group protons become one proxy proton.
NameConvertFromBMRBNewToPDBNew(Vector) - Method in class RdcPanda.Noe
Convert naming scheme From BMRBNew To PDBNew, including pseudo protons of methyl groups.
NameConvertFromPDBNewToPDBNew(Vector) - Method in class RdcPanda.Noe
Convert naming scheme From PDBNew To PDBNew, just do the changes of pseudo protons of methyl groups (eg.HB#)
nameConvertOrder(Vector) - Method in class RdcPanda.Pdb
In this function, only the order of atom name is changed, and H-> HN eg 2HB=>HB2, 3HB=>HB3.
nameConvertStr(Vector) - Method in class RdcPanda.Pdb
Convert the old PDB namaclature to new one zeng changed the code, such that all methel group protons become one proxy proton.
NameFromBMRBToPDB(String, String) - Method in class RdcPanda.Pdb
Convert the BMRB-NEW namaclature to PDB-NEW namaclature return new atom name.
NameFromPdbToBMRB(String, String) - Method in class RdcPanda.Pdb
Convert the PDB-NEW namaclature to BMRB-NEW namaclature: e.g.
NameFromPDBToPDB(String, String) - Method in class RdcPanda.Pdb
Convert the PDB-NEW namaclature to PDB-NEW namaclature change the methel groups return new atom name.
Nasca - Class in RdcPanda
 
Nasca() - Constructor for class RdcPanda.Nasca
 
Nasca.Node - Class in RdcPanda
 
Nasca.Node(Nasca.Node) - Constructor for class RdcPanda.Nasca.Node
 
Nasca.Node() - Constructor for class RdcPanda.Nasca.Node
 
Nasca.Node(int) - Constructor for class RdcPanda.Nasca.Node
 
Nasca.Node(int, int, String, String, Vector) - Constructor for class RdcPanda.Nasca.Node
 
Nasca.Node(int, double, double, boolean) - Constructor for class RdcPanda.Nasca.Node
 
nc - Variable in class Jampack.Zmat
The number of columns
ncl - Variable in class Jampack.Zludpp
The number of columns in L
ncol - Variable in class Jampack.Zhqrd
The number of columns in A
nd() - Static method in class Jampack.Rand
Generates a normal random double.
ndary(int) - Static method in class Jampack.Rand
Generates a one-dimensional array of normal random doubles.
ndary(int, int) - Static method in class Jampack.Rand
Generates a two-dimensional array of normal random doubles.
newNCA(double, double, Matrix) - Method in class RdcPanda.PhiPsi
Method for the computation of new N->CA vector for residue $i+1$ from the computed \Phi and Psi angles.
newPdb(Vector, Matrix) - Method in class RdcPanda.Pdb
compute new PDB coordinates after the rotation by matrix R.
newPdbByTranslation(Vector, double[]) - Method in class RdcPanda.Pdb
compute new PDB coordinates after the translation.
newRG(double, double, Matrix) - Method in class RdcPanda.PhiPsi
Method for the computation of new N->CA vector for residue $i+1$ from the computed \Phi and Psi angles of residue $i$.
newRG(double, double, Matrix, boolean) - Method in class RdcPanda.PhiPsi
Method for the computation of new N->CA vector for residue $i+1$ from the computed \Phi and Psi angles of residue $i$.
newVecByTranslation(double[], double[]) - Method in class RdcPanda.PdbRdc
Compute the new vector after translation.
nh2ca2Cal() - Method in class RdcPanda.PhiPsi
Test the computation of psi1, phi2, psi2 given the peptide plane for residue 1 an d3 and phi1 without knowing the relative position between two planes.
nhRdcDif - Variable in class RdcPanda.Goal.TreePdb
 
nNhCaCal(double, double, double[], double[], double[]) - Method in class RdcPanda.ModelRdc
A method for computing coordinates of backbone atoms.
nNhCaCal(double, double, double[], double[], double[], boolean) - Method in class RdcPanda.ModelRdc
A method for computing coordinates of backbone atoms.
nNhCaHaByBackward(double, double, double[], double[], double[]) - Method in class RdcPanda.ModelRdc
A method for computing coordinates of backbone atoms backward: with direasing residue no.
Noe - Class in RdcPanda
This class provides data structures and functions for processing NOE assignment.
Noe() - Constructor for class RdcPanda.Noe
Constructors.
Noe(int, int) - Constructor for class RdcPanda.Noe
Instantiates a new noe.
Noe(int, int, String, String, String, String, double, double) - Constructor for class RdcPanda.Noe
Instantiates a new noe.
Noe(int, int, int, String, String, String, String, double, double) - Constructor for class RdcPanda.Noe
Instantiates a new noe.
Noe(int, int, int, String, String, String, String, double, double, double) - Constructor for class RdcPanda.Noe
Instantiates a new noe.
Noe(int, String, int, String, double, double) - Constructor for class RdcPanda.Noe
Instantiates a new noe.
Noe(int, Vector, Vector, double, double) - Constructor for class RdcPanda.Noe
Instantiates a new noe.
Noe(int, Vector, Vector, Noe) - Constructor for class RdcPanda.Noe
Instantiates a new noe.
Noe.NoeComparator - Class in RdcPanda
The Class NoeComparator.
Noe.NoeComparator() - Constructor for class RdcPanda.Noe.NoeComparator
 
Noe.noeComparatorA - Class in RdcPanda
The Class noeComparatorA.
Noe.noeComparatorA() - Constructor for class RdcPanda.Noe.noeComparatorA
 
Noe.noeComparatorB - Class in RdcPanda
The Class noeComparatorB.
Noe.noeComparatorB() - Constructor for class RdcPanda.Noe.noeComparatorB
 
Noe.noeComparatorC - Class in RdcPanda
The Class noeComparatorC.
Noe.noeComparatorC() - Constructor for class RdcPanda.Noe.noeComparatorC
 
NOEAsgFromCS(String, String, String) - Method in class RdcPanda.Assign
NOE assignment only based on the chemical shift information, and output the NOE table.
noeAssign1st(Vector, Vector) - Method in class RdcPanda.Peak
This is an earlier version of NOE assignment method, not filtered by Structure.
noeAssign2nd(Vector, Vector, Vector, Vector, Vector, Vector) - Method in class RdcPanda.Peak
an NOE assignment method, filtered by Structure.
noeAssign2ndLW(Vector, Vector, Vector, Vector) - Method in class RdcPanda.Peak
Lw's original + rotamer library an NOE assignment method, filtered by Structure.
noeAssign3rd(Vector, Vector, Vector, Vector, Vector, Vector) - Method in class RdcPanda.Peak
an NOE assignment method, filtered by Structure.
noeAssign3rdLW(Vector, Vector, Vector, Vector, Vector, Vector) - Method in class RdcPanda.Peak
Lincong's original + rotamer library an NOE assignment method, filtered by Structure.
noeAssignMat(Vector, Vector) - Method in class RdcPanda.Peak
Compute the possbile NOE assignment matrix, an idea not further pursued.
noeBackCompute(Vector, Vector) - Method in class RdcPanda.Peak
A method for back-computing NOEs, in the current implementation only compute the NOEs from amide protons ("H" in the Pdb file).
noeDisVsPhi() - Method in class RdcPanda.PhiPsi
Noe dis vs phi.
noeDisVsPsi() - Method in class RdcPanda.PhiPsi
Noe dis vs psi.
noeLimit(double) - Method in class RdcPanda.Peak
Noe limit.
NoeMethylCorrection(Vector, double) - Method in class RdcPanda.Noe
correct the NOE upper distance for an methyl NOE we assume that the pseudo methyl atoms of all old NOEs are labeled with "#" or "##".
NoePatternMatchScore(double, double, double, Vector, Vector, int[], boolean) - Method in class RdcPanda.Assign
Refined function for the general case: Compute the matching score between back-computed NOE pattern and original NOE list.
NoePatternMatchScore(Vector, Vector, Vector, int[]) - Method in class RdcPanda.Assign
Compute the matching score between backcomputed NOE pattern and original NOE list.
NoePatternMatchScore_old2(double, double, double, Vector, Vector, int[]) - Method in class RdcPanda.Assign
This is an old function, and can be deleted.
NoePatternMatchScoreWCali(double, double, double, Vector, Vector, int[], boolean, double) - Method in class RdcPanda.Assign
This is an old function with adding the calibration lines in the code.
NoePatternMatchScoreWCaliHdphic(double, double, double, Vector, Vector, int[], boolean, double) - Method in class RdcPanda.Assign
This is an old function, for hydrophilic residues.
NoePatternMatchScoreWCaliTestJBNMR1(double, double, double, Vector, Vector, int[], boolean, double) - Method in class RdcPanda.Assign
This is a test in order to address the comments from the second reviewer (point 4) from the JBNMR09 submission.
NoePatternMatchScoreWCaliTestJBNMR2(double, double, double, Vector, Vector, int[], boolean, double) - Method in class RdcPanda.Assign
This is a test in order to address the comments from the second reviewer (point 4) from the JBNMR09 submission.
noeReader(String, double) - Method in class RdcPanda.Noe
A very simple reader for NOE data, see the file format.
noeReader(String, double, Vector) - Method in class RdcPanda.Noe
A very simple reader for NOE data, see the file format.
noeReader2(String, double) - Method in class RdcPanda.Noe
A very simple reader for NOE data, see the file format.
noeReader_old_fromLW(String) - Method in class RdcPanda.Noe
A very simple reader for NOE data, see the file format.
noeReaderMultiAsg(String, Vector) - Method in class RdcPanda.Noe
read the NOE assignment in mutiple format.
noeSatisfiedScore(Vector, Vector, double[], double[], int[]) - Method in class RdcPanda.Noe
calculate the NOE satisfiation score.
noeSatisfiedScoreFF2(Vector, Vector, double[], double[], int[]) - Method in class RdcPanda.Noe
Special for ff2 // only consider noes in between two SSEs calculate the NOE satisfiation score.
noeScore - Variable in class RdcPanda.Goal.TreePdb
 
noeSearch(Vector, Vector, int, String, int, String, double[]) - Method in class RdcPanda.Peak
return NOEs between the two nuclei specified in the input if exists.
Noesy - Class in RdcPanda
This class provides data structures and functions for processing NOESY spectra.
Noesy() - Constructor for class RdcPanda.Noesy
Instantiates a new noesy.
Noesy(int) - Constructor for class RdcPanda.Noesy
Instantiates a new noesy.
Noesy(int, String, double, double, double, double) - Constructor for class RdcPanda.Noesy
Instantiates a new noesy.
Noesy(int, String, double, double, double, double, double) - Constructor for class RdcPanda.Noesy
Instantiates a new noesy.
Noesy(int, String, double, double, double, double, double, double) - Constructor for class RdcPanda.Noesy
Instantiates a new noesy.
Noesy.h1Comparator - Class in RdcPanda
The Class h1Comparator.
Noesy.h1Comparator() - Constructor for class RdcPanda.Noesy.h1Comparator
 
Noesy.h2Comparator - Class in RdcPanda
The Class h2Comparator.
Noesy.h2Comparator() - Constructor for class RdcPanda.Noesy.h2Comparator
 
Noesy.heavyComparator - Class in RdcPanda
The Class heavyComparator.
Noesy.heavyComparator() - Constructor for class RdcPanda.Noesy.heavyComparator
 
Noesy.IntensityComparator - Class in RdcPanda
The Class IntensityComparator.
Noesy.IntensityComparator() - Constructor for class RdcPanda.Noesy.IntensityComparator
 
Noesy.resNoComparator - Class in RdcPanda
The Class resNoComparator.
Noesy.resNoComparator() - Constructor for class RdcPanda.Noesy.resNoComparator
 
NoesyReader(String) - Method in class RdcPanda.HcchTocsy
Read NOESY peaks in xeasy format The required file format is:.
NoesyReader(String) - Method in class RdcPanda.HnNoe
Read NOESY peaks in xeasy format The required file format is:.
NoesyReader(String) - Method in class RdcPanda.Noesy
Read NOESY peaks in xeasy format The required file format is:.
NoesyReaderNMRView(String) - Method in class RdcPanda.Noesy
Read NOESY peaks in NMRView format The required file format is:.
NoesyReaderNMRView4D(String) - Method in class RdcPanda.Noesy
Read 4D NOESY peaks in NMRView format The required file format is:.
Norm - Class in Jampack
Norm computes norms of matrices.
Norm() - Constructor for class Jampack.Norm
 
norm1() - Method in class RdcPanda.Matrix
One norm.
norm2() - Method in class RdcPanda.SingularValueDecomposition
Two norm.
nr - Variable in class Jampack.Zmat
The number of rows
nrl - Variable in class Jampack.Zludpp
The number of rows in L
nrow - Variable in class Jampack.Zhqrd
The number of rows in A
ntran - Variable in class Jampack.Zhqrd
The number of Householder transformations
nucluesByAA(String) - Method in class RdcPanda.Residue
The atom identifiers are based on the IUPAC-IUB and X-plor For different nomenclature this functions should modified correspondingly input: residue type output: all atoms belong to one amino acid.
nz() - Static method in class Jampack.Rand
Generates a normal random complex number, i.e., a complex number whose real and imaginary parts are random.
nz1(int) - Static method in class Jampack.Rand
Generates a normal random Z1.
nzmat(int, int) - Static method in class Jampack.Rand
Generates a normal random Zmat.

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