Package RdcPanda

Class Summary
Assign This class provides functions that involves NOE assignment, such initial NOE assignment using only chemical shift information, pruning ambiguous NOE assignments using given structural information,etc.
Assign.assignComparator The Class assignComparator.
Assign.caComparator The Class caComparator.
Assign.haComparator The Class haComparator.
Assign.hnComparator The Class hnComparator.
BackNoe This class provides functions that involves back-computed NOEs.
Cartesian This class defines Cartesian coordinates for individual atom in protein structure.
Const This class defines various global constants for the entire program.
Dipolar This class provides data structures processing experimental RDC data.
Dipolar.rdcComparator The Class rdcComparator.
EigenvalueDecomposition Eigenvalues and eigenvectors of a real matrix.
Gaussian Compilation: javac Gaussian.java Execution: java Gaussian x mu sigma Function to compute the Gaussian pdf (probability density function) and the Gaussian cdf (cumulative density function) % java Gaussian 820 1019 209 0.17050966869132111 % java Gaussian 1500 1019 209 0.9893164837383883 % java Gaussian 1500 1025 231 0.9801220907365489 The approximation is accurate to absolute error less than 8 * 10^(-16).
Goal  
Goal.TreePdbAllComparator  
Goal.TreePdbIDComparator  
Goal.TreePdbNOEComparator  
Goal.TreePdbRamaComparator  
Goal.TreePdbRDCComparator  
Goal.TreePdbSumRDCComparator  
GraphCut  
GraphCut.ResNoComparator  
GraphCut.RotScoreComparator  
H1CS This class provides data structures that involve chemical shifts.
H1CS.csComparator The Class csComparator.
H1CS.resNoComparator The Class resNoComparator.
Hbond This class defines data structures related to h-bonds.
Hbond.HbondComparatorA The Class HbondComparatorA.
Hbond.HbondComparatorB The Class HbondComparatorB.
HcchTocsy This class defines data structures related to HcchTocsy.
HcchTocsy.c13Comparator The Class c13Comparator.
HcchTocsy.h1Comparator The Class h1Comparator.
HcchTocsy.haComparator The Class haComparator.
HcchTocsy.resNoComparator The Class resNoComparator.
Hdist This class provides data structures related to back-computed NOE distance restraints.
Hncacb This class defines data structures related to Hncacb.
Hncacb.c13Comparator The Class c13Comparator.
Hncacb.hnComparator The Class hnComparator.
Hncacb.n15Comparator The Class n15Comparator.
Hncacb.peakNoComparator The Class peakNoComparator.
Hncacb.resNoComparator The Class resNoComparator.
HnNoe This class defines data structures related to N-15 labeled NOEs.
HnNoe.h1Comparator The Class h1Comparator.
HnNoe.hnComparator The Class hnComparator.
HnNoe.n15Comparator The Class n15Comparator.
HnNoe.resNoComparator The Class resNoComparator.
Hsqc This class defines data structures related to HSQC peaks.
Hsqc.hnComparator The Class hnComparator.
Hsqc.n15Comparator The Class n15Comparator.
Hsqc.peakNoComparator The Class peakNoComparator.
Hsqc.resNoComparator The Class resNoComparator.
IDof2aryStructure This class provides functions for processing files with secondary structure element information.
Loops  
Maths * This class is modified from the Jama numeric package.
Matrix This class is modified from the Jama numeric package.
Model This class provides functions that compute backbone from RDC-EXACT algorithm.
ModelRdc A program for computing all the backbond dihedral ($\phi$, $\psi$) angles of an $\alpha$-helix or a $\beta$-strand based on exact solution and a systematic search.
ModelRdc.mdComparator The Class mdComparator.
Nasca  
Noe This class provides data structures and functions for processing NOE assignment.
Noe.NoeComparator The Class NoeComparator.
Noe.noeComparatorA The Class noeComparatorA.
Noe.noeComparatorB The Class noeComparatorB.
Noe.noeComparatorC The Class noeComparatorC.
Noesy This class provides data structures and functions for processing NOESY spectra.
Noesy.h1Comparator The Class h1Comparator.
Noesy.h2Comparator The Class h2Comparator.
Noesy.heavyComparator The Class heavyComparator.
Noesy.IntensityComparator The Class IntensityComparator.
Noesy.resNoComparator The Class resNoComparator.
Pdb This class provides data structures and functions for processing and generating PDB files and extracting backbone angles etc.
Pdb.PdbComparator The Class PdbComparator.
PdbRdc This class provides various SVD methods for best fitting RDCs and a structural fragment, and grid search method for computing the three Euler angles.
PdbRmsd A program for determining the relative positions of a helix and a beta sheet based on the NOE distances between them.
Peak This class is modified from LW's original one, and some functions might be redundant with other classes.
Peak.csComparator The Class csComparator.
PhiPsi 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.PPComparator The Class PPComparator.
ppGlobal A class for computing the first peptide plane from an NCA and NH vector.
RdcPanda This class implements the main function of RDC-Panda.
Residue A very simple Residue class with the Notation like Val1, Ala25.
Residue.caComparator The Class caComparator.
Residue.cbComparator The Class cbComparator.
Rotamer This class provides data structures and functions related to rotamers.
RotaPattern This class implements data structures and functions that deal with the rotamer properties.
RotaPattern.scoreComparator The Class scoreComparator.
ScNoe This class is no longer used and replaced by H1CS.
ScNoe.cs1Comparator The Class cs1Comparator.
ScNoe.cs2Comparator The Class cs2Comparator.
ScNoe.intensityComparator The Class intensityComparator.
SingularValueDecomposition This class provides functions for SVD operations (from Jama package).
sp3Carbon represeting the tetrahedral of the sp3 Carbon configuration IN order to compute the coordinates we need only to know the coordinates of the top atom then using the information provided by the sp3Carbon object we should be able to compute all the coordinates of other atoms.
SSEPacking This class provides functions for packing SSE fragments.
SSEPacking.SSEPackingComparator The Class SSEPackingComparator.
vdw A class for computing the vdw repellsion.
vdw.VdwComparator The Class VdwComparator.
vdw.VdwNoeComparator The Class VdwNoeComparator.