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

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

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