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C
ca2caDirCal(double, double, double[], Matrix)
- Method in class RdcPanda.
PhiPsi
A method for computing the the Vector CA(i)-->CA(i+1), between the CA(i) and CA(i+1) begin with an frame defined in the peptide plane i.
caByNextPeptidePlane(double[], Matrix)
- Method in class RdcPanda.
PhiPsi
Ca by next peptide plane.
CaDistCorrection(String, String)
- Method in class RdcPanda.
Goal
simple steric clash checking, used for checking steric clash between ca atom in rotamers and SSEs
calcFragment(double, double, Vector<Dipolar>, Vector<Dipolar>, double[], double[], double[], int, int, Vector, Vector, double, double, boolean)
- Method in class RdcPanda.
Loops
Compute the structure fragment that best fits the RDC and NOESY data.
calcMinPackingRms(Vector, Vector, Vector, double[], boolean)
- Method in class RdcPanda.
PdbRmsd
calculate the minimum rms between two sses, for checking packing symmetry In both SSEs, all rotamers are places.
caliConstant
- Variable in class RdcPanda.
Goal
caliConstant
- Variable in class RdcPanda.
Loops
Cartesian
- Class in
RdcPanda
This class defines Cartesian coordinates for individual atom in protein structure.
Cartesian()
- Constructor for class RdcPanda.
Cartesian
Instantiates a new cartesian.
Cartesian(String, double, double, double)
- Constructor for class RdcPanda.
Cartesian
Instantiates a new cartesian.
Cartesian(String, double[])
- Constructor for class RdcPanda.
Cartesian
Instantiates a new cartesian.
centerCal(Vector)
- Method in class RdcPanda.
PdbRmsd
compute the center of a PDB object (the 3D coordinates).
centerCal(double[][])
- Method in class RdcPanda.
PdbRmsd
compute the center of a PDB coordinates when the coordinates are represented as an array of nx3.
centerCalNew(Vector)
- Method in class RdcPanda.
PdbRmsd
compute the center of a PDB coordinates when the coordinates are represented as an array of nx3.
centerFit(Vector, Vector, Vector, boolean)
- Method in class RdcPanda.
PdbRmsd
compute the H-bond energy term between the two paired strands.
centerFitVec(Vector, Vector, Vector, boolean)
- Method in class RdcPanda.
PdbRmsd
compute the H-bond energy term between the two paired strands.
CheckBackNOE(Vector, Vector, Vector, int, String, String, int, String, String, double)
- Method in class RdcPanda.
Peak
check whether there exists a back Noe from H2 to H1.
CheckClashBtwCaNPdb(Vector, int, double[], int)
- Method in class RdcPanda.
Goal
simple steric clash checking, used for checking steric clash between ca atom in rotamers and SSEs.
CheckClashBtwRotCaNSSEs(double[])
- Method in class RdcPanda.
Goal
simple steric clash checking, used for checking steric clash between ca atom in rotamers and SSEs
CheckClashBtwRotCaNSSEsNew(double[], int)
- Method in class RdcPanda.
Goal
simple steric clash checking, used for checking steric clash between ca atom in rotamers and SSEs.
checkCSBMRBOrder(Vector)
- Method in class RdcPanda.
H1CS
written by LW.
CheckFirstResidue(Pdb, int, double, double[], double[])
- Method in class RdcPanda.
Goal
check whether the end residue closes the gap.
CheckFirstResidue(Pdb, int, double, double[])
- Method in class RdcPanda.
Goal
check whether the end residue closes the gap.
CheckFirstResidueOld(Pdb, int, double, double[], double[])
- Method in class RdcPanda.
Goal
check whether the end residue closes the gap.
CheckFirstResidueOld(Pdb, int, double, double[])
- Method in class RdcPanda.
Goal
check whether the end residue closes the gap.
CheckKinChainRestraint(Pdb, int, double)
- Method in class RdcPanda.
Goal
check whether kinematic chain restraint is satisfied
CheckKinChainRestraintBackward(Pdb, int, double)
- Method in class RdcPanda.
Goal
check whether kinematic chain restraint is satisfied
CheckKinConstraint(double[], int, int, int)
- Method in class RdcPanda.
Goal
check the kinematic restraint
CheckLastResidue(Pdb, int, double, double[])
- Method in class RdcPanda.
Goal
check whether the end residue closes the gap
CheckLastResidue(Pdb, int, double, double[], double[])
- Method in class RdcPanda.
Goal
check whether the end residue closes the gap
CheckLastResidueOld(Pdb, int, double, double[])
- Method in class RdcPanda.
Goal
check whether the end residue closes the gap
CheckLastResidueOld(Pdb, int, double, double[], double[])
- Method in class RdcPanda.
Goal
check whether the end residue closes the gap
CheckLongRangNOE(Vector, int)
- Method in class RdcPanda.
Peak
for long-range noes, check whether number of neighboring noes is larger than some bound.
checkNoe(Vector, int, String, int, String, double, double, double[])
- Method in class RdcPanda.
Peak
Refined function: for the general case.
checkNoe2(Vector, int, String, int, String, double, double, double[])
- Method in class RdcPanda.
Peak
Compute all the possible NOE peaks from the nucleus with coordA to all other nuclei in a PDB structure, the.
checkNoe_old(Vector, Vector, int, String, int, String, double, double, double[])
- Method in class RdcPanda.
Peak
Compute all the possible NOE peaks from the nucleus with coordA to all other nuclei in a PDB structure, the.
CheckNOEBtwCaNSSEs(Pdb, Vector, double)
- Method in class RdcPanda.
Goal
check whether the distance satisfies the NOE restraint from ca to anchors in SSEs
CheckNoeHInPdb(Vector, Vector)
- Method in class RdcPanda.
Noe
check whether there is a atom name in noe talbe which is not in pdb.
checkNoeNew(Vector, int, String, int, String, double, double, double[])
- Method in class RdcPanda.
Peak
better version of "checkNoe" Refined function: for the general case.
checkNoeNew2(Vector, int, String, int, String, double, double, double[])
- Method in class RdcPanda.
Peak
similar to checkNoeNew, with additional0.5 A
CheckNoeSym(Vector)
- Method in class RdcPanda.
Peak
refine NOEs and only keep those NOE with symmetry property, for C13 NOESY and sidechain N15 NOESY.
checkStericClash(Vector, double[], double, boolean, boolean, double, int, int[])
- Method in class RdcPanda.
vdw
check the steric clashes, if the number of steric clashes is larger than some threshold, ruturn true, else return false.
CheckStericClashBtwTwoFragments(Vector, Vector)
- Method in class RdcPanda.
Goal
simple steric clash checking, only using 1.8 as lower bound.
checkSymmetry(Vector, double, double, double)
- Method in class RdcPanda.
Peak
check whether there exists a symmetric Noe from side-chains to other protons.
checkVDW(String, String, double, boolean)
- Method in class RdcPanda.
vdw
Check vdw.
chRdcDif
- Variable in class RdcPanda.
Goal.TreePdb
clone()
- Method in class RdcPanda.
Matrix
Clone the Matrix object.
coefPhiBackward(double, double, double, double[][], double[])
- Method in class RdcPanda.
PhiPsi
Method for generating coefs for the quartic equation for computing phi_i from NH RDCs for residue i by working backwards from the residue i+1.
coefPsiBackward(double, double, double, double[][], double[])
- Method in class RdcPanda.
PhiPsi
Method for generating coefs for the quartic equation.
cols(Zmat, int, int)
- Static method in class Jampack.
Swap
Interchances two columns of a Zmat (altered).
CombineSSEandLoop(Vector, Vector)
- Method in class RdcPanda.
Loops
combine the sse pdb with the loop pdb.
CombinRotBB(Vector, Vector, int)
- Method in class RdcPanda.
Pdb
plug rotamer into backbone.
compare(Object, Object)
- Method in class RdcPanda.
Assign.assignComparator
compare(Object, Object)
- Method in class RdcPanda.
Assign.caComparator
compare(Object, Object)
- Method in class RdcPanda.
Assign.haComparator
compare(Object, Object)
- Method in class RdcPanda.
Assign.hnComparator
compare(Object, Object)
- Method in class RdcPanda.
Dipolar.rdcComparator
compare(Object, Object)
- Method in class RdcPanda.
Goal.TreePdbAllComparator
compare(Object, Object)
- Method in class RdcPanda.
Goal.TreePdbIDComparator
compare(Object, Object)
- Method in class RdcPanda.
Goal.TreePdbNOEComparator
compare(Object, Object)
- Method in class RdcPanda.
Goal.TreePdbRamaComparator
compare(Object, Object)
- Method in class RdcPanda.
Goal.TreePdbRDCComparator
compare(Object, Object)
- Method in class RdcPanda.
Goal.TreePdbSumRDCComparator
compare(Object, Object)
- Method in class RdcPanda.
GraphCut.ResNoComparator
compare(Object, Object)
- Method in class RdcPanda.
GraphCut.RotScoreComparator
compare(Object, Object)
- Method in class RdcPanda.
H1CS.csComparator
compare(Object, Object)
- Method in class RdcPanda.
H1CS.resNoComparator
compare(Object, Object)
- Method in class RdcPanda.
Hbond.HbondComparatorA
compare(Object, Object)
- Method in class RdcPanda.
Hbond.HbondComparatorB
compare(Object, Object)
- Method in class RdcPanda.
HcchTocsy.c13Comparator
compare(Object, Object)
- Method in class RdcPanda.
HcchTocsy.h1Comparator
compare(Object, Object)
- Method in class RdcPanda.
HcchTocsy.haComparator
compare(Object, Object)
- Method in class RdcPanda.
HcchTocsy.resNoComparator
compare(Object, Object)
- Method in class RdcPanda.
Hncacb.c13Comparator
compare(Object, Object)
- Method in class RdcPanda.
Hncacb.hnComparator
compare(Object, Object)
- Method in class RdcPanda.
Hncacb.n15Comparator
compare(Object, Object)
- Method in class RdcPanda.
Hncacb.peakNoComparator
compare(Object, Object)
- Method in class RdcPanda.
Hncacb.resNoComparator
compare(Object, Object)
- Method in class RdcPanda.
HnNoe.h1Comparator
compare(Object, Object)
- Method in class RdcPanda.
HnNoe.hnComparator
compare(Object, Object)
- Method in class RdcPanda.
HnNoe.n15Comparator
compare(Object, Object)
- Method in class RdcPanda.
HnNoe.resNoComparator
compare(Object, Object)
- Method in class RdcPanda.
Hsqc.hnComparator
compare(Object, Object)
- Method in class RdcPanda.
Hsqc.n15Comparator
compare(Object, Object)
- Method in class RdcPanda.
Hsqc.peakNoComparator
compare(Object, Object)
- Method in class RdcPanda.
Hsqc.resNoComparator
compare(Object, Object)
- Method in class RdcPanda.
ModelRdc.mdComparator
compare(Object, Object)
- Method in class RdcPanda.
Noe.NoeComparator
compare(Object, Object)
- Method in class RdcPanda.
Noe.noeComparatorA
compare(Object, Object)
- Method in class RdcPanda.
Noe.noeComparatorB
compare(Object, Object)
- Method in class RdcPanda.
Noe.noeComparatorC
compare(Object, Object)
- Method in class RdcPanda.
Noesy.h1Comparator
compare(Object, Object)
- Method in class RdcPanda.
Noesy.h2Comparator
compare(Object, Object)
- Method in class RdcPanda.
Noesy.heavyComparator
compare(Object, Object)
- Method in class RdcPanda.
Noesy.IntensityComparator
compare(Object, Object)
- Method in class RdcPanda.
Noesy.resNoComparator
compare(Object, Object)
- Method in class RdcPanda.
Pdb.PdbComparator
compare(Object, Object)
- Method in class RdcPanda.
Peak.csComparator
compare(Object, Object)
- Method in class RdcPanda.
PhiPsi.PPComparator
compare(Object, Object)
- Method in class RdcPanda.
Residue.caComparator
compare(Object, Object)
- Method in class RdcPanda.
Residue.cbComparator
compare(Object, Object)
- Method in class RdcPanda.
RotaPattern.scoreComparator
compare(Object, Object)
- Method in class RdcPanda.
ScNoe.cs1Comparator
compare(Object, Object)
- Method in class RdcPanda.
ScNoe.cs2Comparator
compare(Object, Object)
- Method in class RdcPanda.
ScNoe.intensityComparator
compare(Object, Object)
- Method in class RdcPanda.
SSEPacking.SSEPackingComparator
compare(Object, Object)
- Method in class RdcPanda.
vdw.VdwComparator
compare(Object, Object)
- Method in class RdcPanda.
vdw.VdwNoeComparator
CompareAsgToManualAsg(Vector, Vector, double[])
- Method in class RdcPanda.
Noe
Compare assignment results with manual assignments.
CompareAsgToRefStr(Vector, Vector, double, double, double[])
- Method in class RdcPanda.
Noe
Compare assignment results with manual assignments.
CompareSCAsgsWRefAsgs(Vector, Vector, Vector)
- Method in class RdcPanda.
H1CS
compute the statistical information of the sidechain assignment, compared with the reference assignment list.
CompareSCAsgsWRefAsgsOld(Vector, Vector)
- Method in class RdcPanda.
H1CS
This is an old function.
compDistPatternForRotam(Vector, int, Vector, double)
- Method in class RdcPanda.
Pdb
Compute all distance patterns for a rotamer, distances are from each proton in the rotamer to backbone protons including HA,HN, HB.
compDistPatternForRotam_old(Vector, int, Vector, double)
- Method in class RdcPanda.
Pdb
Compute all distance patterns for a rotamer, distances are from each proton in the rotamer to backbone protons including HA,HN, HB.
compDistPatternForSSEPacking(Vector, Vector, double)
- Method in class RdcPanda.
Pdb
Compute all distance patterns for two secondary structure elements, whose coordinates are fixed.
compDistPatternFromPairRotams(int, int, Pdb, Pdb, double)
- Method in class RdcPanda.
Pdb
Compute all distance patterns for a pair of rotamers, distances are from each proton in the rotamer to backbone protons including HA,HN, HB rotamers are in the same coordinate system,includes both from A->B and from B->A.
CompMaxMatchScore_old(Vector, double, double, int, int, int[])
- Method in class RdcPanda.
Assign
recursively compute the max matching score.
CompNoePatternScoreBetwSSEAndLoop(double, double, Vector<Pdb>, Vector<Pdb>, double, Vector, Vector)
- Method in class RdcPanda.
Goal
compute NOE pattern between SSE and loops.
CompNoePatternScoreBetwSSEAndLoop(double, double, Vector, double, Vector, Vector)
- Method in class RdcPanda.
Loops
compute NOE pattern between SSE and loops.
CompOneToOneMapBtwInterval(Vector, Vector, int[][], double, double)
- Method in class RdcPanda.
Nasca
compute all possible one-to-one mapping for all resonances within an interval
compOverAllRmsdBetweenRotXray(Vector, Vector, String, Vector, Vector, Vector, double, int)
- Method in class RdcPanda.
Pdb
Compute a structure, given the backbone and rotamers at all residue positions.
CompRamachandranScore(double, double, Vector)
- Method in class RdcPanda.
Loops
Compute the Ramachandran probability score based on Richardsons' top500 structures.
compResRmsd(Pdb, Pdb)
- Method in class RdcPanda.
Pdb
Compute rmsd between two rotamers only for non-proton atoms, assume they are in the same coordinate system.
compResRmsdPairWise(Pdb, Pdb)
- Method in class RdcPanda.
Pdb
Compute rmsd between two rotamers (for all atoms), assume they are in the same coordinate system.
compRmsdBetwTwoPdbs(Vector, Vector, boolean)
- Method in class RdcPanda.
Pdb
Compute rmsd between two pdb structures with the same length and in the same coordinate system.
compRmsdRotXrayBB(Vector, Vector, int, double[], boolean)
- Method in class RdcPanda.
Pdb
Compute rmsd between a rotamer and corresponding side-chain in x-ray structure.
ComputeAStarEstimatedCost(Vector, Vector, Vector, int)
- Method in class RdcPanda.
Nasca
compute the estimated cost in A* search.
ComputeNoeSatisfaction(double[], int)
- Method in class RdcPanda.
Goal
simple steric clash checking, used for checking steric clash between ca atom in rotamers and SSEs
ComputeScoringFunction(Vector, Vector, Vector, Vector, double, double, double, double)
- Method in class RdcPanda.
GraphCut
calculate the scoring function based on NOE patterns
computeVDW(Vector, double[], boolean)
- Method in class RdcPanda.
vdw
Compute the vdw energy.
computeVDW(Vector, double[], double, boolean)
- Method in class RdcPanda.
vdw
Compute the vdw energy.
computeVDW(Vector, double[], double, boolean, boolean)
- Method in class RdcPanda.
vdw
Compute the vdw energy.
cond()
- Method in class RdcPanda.
SingularValueDecomposition
Two norm condition number.
Conj(Z)
- Method in class Jampack.
Z
Computes the conjugate of a Z.
Const
- Class in
RdcPanda
This class defines various global constants for the entire program.
Const()
- Constructor for class RdcPanda.
Const
ConstructProtonPositions(Vector, String, double)
- Method in class RdcPanda.
Nasca
put all rotamers at each redidue, and construct the label set (i.e.
ConstructResonGraph(Vector, Vector, double, double, double, double)
- Method in class RdcPanda.
Nasca
add the reosnance node into the graph from given assigned resonance list
ConstructResonGraphFromAsgedList(Vector, Vector)
- Method in class RdcPanda.
Nasca
add the reosnance node into the graph from given assigned resonance list
ConstructResonGraphSymmetry(Vector, Vector, double, double, double, double)
- Method in class RdcPanda.
Nasca
add the reosnance node into the graph from given assigned resonance list
convert2VDW(Vector)
- Method in class RdcPanda.
vdw
To convert the PDB coordinates into a flat structure for speed.
convert2VDW(Pdb[])
- Method in class RdcPanda.
vdw
To convert the PDB coordinates into a flat structure for speed.
ConvertAllNoeToBBNoe(Vector, Vector)
- Method in class RdcPanda.
Noe
convert genaral noe into noes between backbones.
ConvertCyanNoeAsgToXplor(String, PrintWriter)
- Method in class RdcPanda.
Noe
long reange noe read from cyana format.
ConvertMultiToSingleAsg(Vector)
- Method in class RdcPanda.
Noe
convert all multiple NOE assignments into single assignment format.
ConvertNoeFromBMRMToPDB(Vector)
- Method in class RdcPanda.
Noe
convert an NOE set from BMRB-NEW to PDB-NEW format.
ConvertSingleToMultiAsg(Vector)
- Method in class RdcPanda.
Noe
convert all NOE assignments into multiple assignment format.
ConvertXplorAsgToUplFormat(Vector, Vector, String)
- Method in class RdcPanda.
Noe
convert from the xplor noe format to cyna upl format.
ConvertXplorAsgToUplFormatFF2(Vector, Vector)
- Method in class RdcPanda.
Noe
convert from the xplor noe format to cyna upl format.
coordByBackward(double, double, double[], double[], double[], int, String)
- Method in class RdcPanda.
ModelRdc
A method for computing coordinates of backbone atoms backward: with direasing residue no.
coordByBackwardNew(double, double, double[], double[], double[], int)
- Method in class RdcPanda.
ModelRdc
By Michael Zeng.
coordByResidue(double, double, double[], double[], double[], int, String, boolean)
- Method in class RdcPanda.
ModelRdc
A method for computing coordinates of backbone atoms.
coordByResidueFull(double, double, double[], double[], double[], int, String, boolean)
- Method in class RdcPanda.
ModelRdc
*A method for computing coordinates of backbone atoms, including all backbone atoms, ha, ca, n, hn, cb,c o.
copy()
- Method in class RdcPanda.
Matrix
Make a deep copy of a matrix.
copyfile(String, String)
- Static method in class RdcPanda.
Nasca
countStericClash(Vector, double[], double, boolean, boolean, double)
- Method in class RdcPanda.
vdw
count the number of steric clash, given the threshold of penetration, ruturn true, else return false.
countStericClashBetweenTwo(Vector, Vector, double[], double, boolean, boolean, double)
- Method in class RdcPanda.
vdw
count the number of steric clash between two structures, given the threshold of penetration, ruturn true, else return false.
CSNameConvertFromBMRBNewToPDBNew(Vector)
- Method in class RdcPanda.
H1CS
Convert naming scheme From BMRBNew To PDBNew, including pseudo protons of methyl groups.
CSNameConvertFromPDBNewToBMRBNew(Vector)
- Method in class RdcPanda.
H1CS
Convert naming scheme From PDBNew To BMRBNew, including pseudo protons of methyl groups.
CurPhiPsiGridBackwardMinRdcRmsd(Vector, int, int, int, double, double, Vector, Vector, boolean, int)
- Method in class RdcPanda.
Goal
compute possible phi/psi angles with min RDC RMSD similar to LoopCurResPhiPsiGridSearch function.
CurPhiPsiGridForwardMinRdcRmsd(Vector, int, int, int, double, double, Vector, Vector, boolean, int)
- Method in class RdcPanda.
Goal
compute possible phi/psi angles with min RDC RMSD similar to LoopCurResPhiPsiGridSearch function.
cx
- Variable in class Jampack.
Zmat
The upper column index
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