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Class Summary | |
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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. |
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