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P

pa(Rot, Zmat, int, int, int, int) - Static method in class Jampack.Rot
Multiplies rows (ii1,jj1:jj2) and (ii2,jj1:jj2) of a Zmat (altered) by a plane rotation.
PackingHelicesBasedOnNOEPatterns(String[]) - Static method in class RdcPanda.SSEPacking
Packing helices based on noe patterns.
parameterReader(String) - Method in class RdcPanda.Model
Parameter reader.
Parameters - Class in Jampack
Parameter is a class containing global parameters for Jampack.
Parameters() - Constructor for class Jampack.Parameters
 
ParamReader(String) - Method in class RdcPanda.Assign
Read the parameters such as the number of refinement cycle etc for running the program.
parenPdb - Variable in class RdcPanda.Goal.TreePdb
 
parse(String[]) - Method in class RdcPanda.RdcPanda
Parses the.
pdb - Variable in class RdcPanda.Goal.TreePdb
 
Pdb - Class in RdcPanda
This class provides data structures and functions for processing and generating PDB files and extracting backbone angles etc.
Pdb() - Constructor for class RdcPanda.Pdb
Instantiates a new pdb.
Pdb(int) - Constructor for class RdcPanda.Pdb
Instantiates a new pdb.
Pdb(int, String, Vector) - Constructor for class RdcPanda.Pdb
Instantiates a new pdb.
Pdb(int, String, Vector, double) - Constructor for class RdcPanda.Pdb
Instantiates a new pdb.
Pdb(Pdb) - Constructor for class RdcPanda.Pdb
Instantiates a new pdb.
Pdb.PdbComparator - Class in RdcPanda
The Class PdbComparator.
Pdb.PdbComparator() - Constructor for class RdcPanda.Pdb.PdbComparator
 
PdbGenerateFromTree(Vector) - Method in class RdcPanda.Goal
 
PdbRdc - Class in RdcPanda
This class provides various SVD methods for best fitting RDCs and a structural fragment, and grid search method for computing the three Euler angles.
PdbRdc() - Constructor for class RdcPanda.PdbRdc
Instantiates a new pdb rdc.
PdbRdc(Pdb, double) - Constructor for class RdcPanda.PdbRdc
Instantiates a new pdb rdc.
PdbRmsd - Class in RdcPanda
A program for determining the relative positions of a helix and a beta sheet based on the NOE distances between them.
PdbRmsd() - Constructor for class RdcPanda.PdbRmsd
Instantiates a new pdb rmsd.
Peak - Class in RdcPanda
This class is modified from LW's original one, and some functions might be redundant with other classes.
Peak() - Constructor for class RdcPanda.Peak
Instantiates a new peak.
Peak(double) - Constructor for class RdcPanda.Peak
A constructor designed specifically for the Comparator class used for the Sort and BinarySearch.
Peak(String, double) - Constructor for class RdcPanda.Peak
Instantiates a new peak.
Peak(String, double, boolean) - Constructor for class RdcPanda.Peak
Instantiates a new peak.
Peak(String, double, double) - Constructor for class RdcPanda.Peak
Instantiates a new peak.
Peak(String, double, double, boolean) - Constructor for class RdcPanda.Peak
Instantiates a new peak.
Peak.csComparator - Class in RdcPanda
The Class csComparator.
Peak.csComparator() - Constructor for class RdcPanda.Peak.csComparator
 
pha(Rot, Zmat, int, int, int, int) - Static method in class Jampack.Rot
Multiplies rows (ii1,jj1:jj2) and (ii2,jj1:jj2) of a Zmat (altered) by the conjugate transpose of a plane rotation.
phi(double) - Static method in class RdcPanda.Gaussian
 
phi(double, double, double) - Static method in class RdcPanda.Gaussian
 
Phi(double) - Static method in class RdcPanda.Gaussian
 
Phi(double, double, double) - Static method in class RdcPanda.Gaussian
 
phiCal(double, double, double, Matrix) - Method in class RdcPanda.PhiPsi
Compute the Phi angles.
phiCal(double, double, double, Matrix, boolean) - Method in class RdcPanda.PhiPsi
Compute the Phi angles.
phiCal(double, double, double, Matrix, boolean, int, Vector) - Method in class RdcPanda.PhiPsi
Compute the Phi angles.
phiCalAll(double, double, double, Matrix) - Method in class RdcPanda.Loops
Compute the Phi angles from RDC equations.
phiCalBackward(double, double, double, double, Matrix) - Method in class RdcPanda.PhiPsi
Compute the Psi angles.
phiCalLoop(double, double, double, Matrix) - Method in class RdcPanda.PhiPsi
Compute the Phi angles for loop fragment.
phiCalNoe(double) - Method in class RdcPanda.PhiPsi
Compute the Phi angles from the NOE distances, given the coordinates for ca and nh.
phiExtend(double, double, double) - Static method in class RdcPanda.Gaussian
 
PhiPsi - Class in RdcPanda
Various methods for exact solution and systematic search including the computation of rotation to the frist peptide plane the DFS-search and solver of the quartic equation and the computation of \phi and \psi angles from two vectors in consecutive planse etc.
PhiPsi(double, double, double) - Constructor for class RdcPanda.PhiPsi
Instantiates a new phi psi.
PhiPsi() - Constructor for class RdcPanda.PhiPsi
Instantiates a new phi psi.
PhiPsi(int) - Constructor for class RdcPanda.PhiPsi
Instantiates a new phi psi.
PhiPsi(int, String, double, double) - Constructor for class RdcPanda.PhiPsi
Instantiates a new phi psi.
PhiPsi(int, String, double, double, double, double, double, double) - Constructor for class RdcPanda.PhiPsi
Instantiates a new phi psi.
PhiPsi.PPComparator - Class in RdcPanda
The Class PPComparator.
PhiPsi.PPComparator() - Constructor for class RdcPanda.PhiPsi.PPComparator
 
phiPsiBackwardTest(Vector, Vector) - Method in class RdcPanda.PhiPsi
Phi psi backward test.
phiPsiByCa(Matrix, double[], double[][]) - Method in class RdcPanda.PhiPsi
********************************************************************************* This method compute the \Phi and \Psi pair from the coordinates of CA(i) and CA(i+1) EXACTLY assuming the six angles are known.
phiPsiByPP13(double[], double[], double[], double[], double) - Method in class RdcPanda.PhiPsi
computation of psi1, phi2, psi2 given the peptide planes for residue 1 an d3 and phi1 without knowing the relative position between two planes.
phiPsiByPP14(double[], double[], double[], double[], Matrix, Matrix, Vector) - Method in class RdcPanda.PhiPsi
Compute the CA directions of residues 2 and 3 specified by polar angles (theta, phi), given the CA coordinates for residue 1 and 3 and the theta polar angle for residue 2.
phiPsiByRdcNoe(Vector, double[][], double, double, double[], double[], double[], Matrix, int, int, double[], Vector, double[], double[], double[]) - Method in class RdcPanda.PhiPsi
A recusive function to compute all the backbone (phi, psi) angles for an $m$-residue fragment This is a version for real computation, NOT for collecting running statistics.
PhiPsiCalPDB(double[], double[], double[]) - Method in class RdcPanda.Pdb
Compute Phi and Psi directly from three backbone vectors (not NH vector).
phiPsiChain(double[], double[], Matrix, double, double, int, int, double[], Vector, boolean, boolean) - Method in class RdcPanda.PhiPsi
A recusive function to compute all the backbone (phi, psi) angles for an $N$-residue fragment This is a version for real computation, NOT for collecting running statistics.
phiPsiChainAll(double[], double[], int[], int[], Matrix, double, double, int, int, int, double[], Vector, boolean, int) - Method in class RdcPanda.Loops
A recusive function to compute all the backbone (phi, psi) angles for a fragment.
phiPsiChainTalos(double[], double[], Matrix, double, double, int, int, double[], Vector, boolean, boolean, int, Vector) - Method in class RdcPanda.PhiPsi
A recusive function to compute all the backbone (phi, psi) angles for an $N$-residue fragment This is a version for real computation, NOT for collecting running statistics.
PhiPsiRandomFromRamachandran(Vector, int) - Method in class RdcPanda.Loops
Randomly sample the (Phi, Psi) angles according to distribution from Ramachandran.
PhiPsiTotalPdb(Vector) - Method in class RdcPanda.Pdb
Compute all the backbone Phi and Psi angles from PDB from the backbone backbone bond vectors between heavy atoms.
Pivot - Class in Jampack
Pivot applys a sequence of pivot operations to the rows of a matrix.
Pivot() - Constructor for class Jampack.Pivot
 
PlaneClustering(double, Vector<Goal.TreePdb>, Vector<Goal.TreePdb>) - Method in class RdcPanda.Goal
clustering the first peptide plane, including ca, n, hn atoms.
PlaneClusteringAndTopSelection(double, Vector<Goal.TreePdb>, Vector<Goal.TreePdb>, int) - Method in class RdcPanda.Goal
clustering the first peptide plane, including ca, n, hn atoms, and selecting the top planes.
PlaneClusteringAndTopSelectionNOEs(double, Vector<Goal.TreePdb>, Vector<Goal.TreePdb>, int, int, boolean) - Method in class RdcPanda.Goal
clustering the first peptide plane, including ca, n, hn atoms, and selecting the top planes.
PlaneClusteringBackward(double, Vector<Goal.TreePdb>, Vector<Goal.TreePdb>) - Method in class RdcPanda.Goal
clustering the first peptide plane, including ca, n, hn atoms.
Plus - Class in Jampack
Plus Computes the sum of two matrices.
Plus() - Constructor for class Jampack.Plus
 
Plus(Z, Z) - Method in class Jampack.Z
Computes the sum of two Z's.
plus(Matrix) - Method in class RdcPanda.Matrix
C = A + B.
positionByAmbiNOEAllRotamers(Vector, Vector, Vector, double[], boolean, Vector, String, Vector, double) - Method in class RdcPanda.PdbRmsd
pack two SSEs based on Amgibuous NOE restratints.
positionByNOE(Vector, Vector, Vector, double[], boolean, Vector) - Method in class RdcPanda.PdbRmsd
use exact name for pseduo protons Compute the new center of atoms involved in NOE distances.
positionByNOE_old(Vector, Vector, Vector, double[], boolean, Vector) - Method in class RdcPanda.PdbRmsd
use heavy atom to replace pseduo protons Compute the new center of atoms involved in NOE distances.
positionByNOEAllRotamers(Vector, Vector, Vector, double[], boolean, Vector, String, Vector, double) - Method in class RdcPanda.PdbRmsd
pack two SSEs based on NOE restratints In both SSEs, all rotamers are placed.
positionByNOEAllRotamersGrid(Vector, Vector, Vector, double[], boolean, Vector) - Method in class RdcPanda.PdbRmsd
pack two SSEs based on NOE restratints In both SSEs, all rotamers are places.
positionByNOEAllRotamersSaved(Vector, Vector, Vector, double[], boolean, Vector, String, Vector) - Method in class RdcPanda.PdbRmsd
Position by noe all rotamers saved.
positionByNOENew(Vector, Vector, Vector, double[], boolean, Vector) - Method in class RdcPanda.PdbRmsd
Note: all rotamers are put in both structures.
positionByNOEPatterns(Vector, Vector, Vector, Vector, double, double, double, double, int, double[]) - Method in class RdcPanda.PdbRmsd
pack two sses based on back-computed NOE patterns.
ppGlobal - Class in RdcPanda
A class for computing the first peptide plane from an NCA and NH vector.
ppGlobal() - Constructor for class RdcPanda.ppGlobal
Instantiates a new pp global.
Print - Class in Jampack
Print prints numbers, matrices, and arrays.
Print() - Constructor for class Jampack.Print
 
print(int, int) - Method in class RdcPanda.Matrix
Print the matrix to stdout.
print(PrintWriter, int, int) - Method in class RdcPanda.Matrix
Print the matrix to the output stream.
print(NumberFormat, int) - Method in class RdcPanda.Matrix
Prints the.
print(PrintWriter, NumberFormat, int) - Method in class RdcPanda.Matrix
Print the matrix to the output stream.
print(Vector) - Method in class RdcPanda.Pdb
A method for printing the coordinates in PDB format the magic Number comes from PDB file format.
PrintAllAssignment(Vector) - Method in class RdcPanda.H1CS
print all resonance assignments.
PrintAllAssignmentCyana(Vector) - Method in class RdcPanda.H1CS
print all resonance assignments in CYANA format.
PrintAllAssignmentToFileBMRB(Vector, PrintWriter) - Method in class RdcPanda.H1CS
print all resonance assignments to file, in BMRB format.
PrintAllAssignmentToFileCyana(Vector, PrintWriter) - Method in class RdcPanda.H1CS
print all resonance assignments to file, in CYANA format.
PrintAllByGridSearch(Vector, Vector<Dipolar>, Vector<Dipolar>, double, double, double, double) - Method in class RdcPanda.ModelRdc
Prints the all by grid search.
PrintAllPossibleMappings(Vector, Vector, int[][]) - Method in class RdcPanda.Nasca
print out all possible for proton nodes
printArray(double[]) - Method in class RdcPanda.Pdb
Prints the array.
printArray(double[]) - Method in class RdcPanda.PhiPsi
Prints the array.
printArray(double[]) - Method in class RdcPanda.sp3Carbon
Prints the array.
PrintNOE(Vector) - Method in class RdcPanda.Noe
print noe.
printToFile(Vector, String, PrintWriter) - Method in class RdcPanda.Pdb
A method for printing the coordinates in PDB format the magic Number comes from PDB file format.
protonID - Variable in class RdcPanda.H1CS
The proton id.
PrunAmbgNoeAsg(Vector, Vector, double, double, int) - Method in class RdcPanda.Assign
Prune ambiguous NOE assignment using given structural information.
pruneRotamers(Vector, String, Vector, int, int, Vector) - Method in class RdcPanda.Rotamer
prune rotamers based on: 1: collisions with backbone atoms; 2: collisions between pairwise rotamer atoms; 3: NOE constraints, including pairwise and local NOEs Note: a recurrsive approach is used.
psiCal(double, double, double, double, Matrix) - Method in class RdcPanda.PhiPsi
Compute the Psi angles.
psiCal(double, double, double, double, Matrix, boolean) - Method in class RdcPanda.PhiPsi
Compute the Psi angles.
psiCal(double, double, double, double, Matrix, boolean, int, Vector) - Method in class RdcPanda.PhiPsi
Compute the Psi angles.
psiCalAll(double, double, double, double, Matrix) - Method in class RdcPanda.Loops
Compute the Psi angles.
psiCalBackward(double, double, double, Matrix) - Method in class RdcPanda.PhiPsi
Compute the Phi angles.
psiCalLoop(double, double, double, double, Matrix) - Method in class RdcPanda.PhiPsi
Compute the Psi angles for loops.
psiCalNoe(double) - Method in class RdcPanda.PhiPsi
Compute the Phi angles from the NOE distances, given the coordinates for ca and nh.
put(int, Z) - Method in class Jampack.Z1
Sets the ith element of a Z1 to a Z.
put(int, double, double) - Method in class Jampack.Z1
Sets the real and imaginary parts of the ith element of a Z1.
put(int, Z) - Method in class Jampack.Zdiagmat
Writes the ii-th diagonal element of a Zdiagmat.
put(int, int, Z) - Method in class Jampack.Zmat
Writes the (ii,jj) element of a Zmat.
put(int, int, int, int, Zmat) - Method in class Jampack.Zmat
Overwrites the submatrix (ii1:ii2, jj1:jj2) with a Zmat.
put(int[], int, int, Zmat) - Method in class Jampack.Zmat
Overwrites the submatrix (ii[], jj1:jj2) with a Zmat.
put(int, int, int[], Zmat) - Method in class Jampack.Zmat
Overwrites the submatrix (ii1:ii2, jj[]) with a Zmat.
put(int[], int[], Zmat) - Method in class Jampack.Zmat
Overwrites the submatrix (ii[], jj[]) with a Zmat.
put0(int, Z) - Method in class Jampack.Zdiagmat
Writes the ith diagonal element of a Zdiagmat (0-based).
put0(int, int, Z) - Method in class Jampack.Zmat
Writes the zero-based (i,j)-element of a Zmat.
pvt - Variable in class Jampack.Zludpp
The pivot array (see Pivot.java )

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