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D
D
- Variable in class Jampack.
Eig
The diagonal matrix of eigenvalues
D
- Variable in class Jampack.
Zspec
The matrix of eigenvalues
danSeq(double[], double[], double)
- Method in class RdcPanda.
PhiPsi
A method for computing the distance dN(i, i+1), between the NH(i) and NH(i+1) begin with an frame defined in the peptide plane i.
dCaCa(double, double)
- Method in class RdcPanda.
PhiPsi
A method for computing the distance Ca(i, i+1), between the CA(i) and CA(i+1) begin with an frame defined in the peptide plane i.
DEECut(Vector)
- Method in class RdcPanda.
GraphCut
DEE-Cut step in the graph cut algorithm
DelAdj(int)
- Method in class RdcPanda.
Nasca.Node
deleteDir(File)
- Static method in class RdcPanda.
RdcPanda
Delete a directory.
deleteRepeat(Vector, double, double, double)
- Method in class RdcPanda.
Assign
Delete repeated chemical shifts.
DeleteRepeat(Vector)
- Method in class RdcPanda.
BackNoe
delete repeated back-computed NOEs.
deleteRepeat(Vector, double, double, double)
- Method in class RdcPanda.
HcchTocsy
Delete repeat.
DeleteRepeatAsg(Vector)
- Method in class RdcPanda.
H1CS
delete repeated resonance assignments.
DeleteRepeatedNoesy3D(Vector)
- Method in class RdcPanda.
Noesy
delete repeated NOE peaks.
DeleteRepeatNOEs(Vector)
- Method in class RdcPanda.
Noe
delete repeated NOEs.
det(double[][])
- Static method in class RdcPanda.
Matrix
Generate identity matrix.
dihedralAngle(double[], double[], double[])
- Method in class RdcPanda.
Pdb
Method for computing dihedral angles between two planes defined by three vectors.
Dipolar
- Class in
RdcPanda
This class provides data structures processing experimental RDC data.
Dipolar()
- Constructor for class RdcPanda.
Dipolar
Instantiates a new dipolar.
Dipolar(int)
- Constructor for class RdcPanda.
Dipolar
Instantiates a new dipolar.
Dipolar(int, String, double, double)
- Constructor for class RdcPanda.
Dipolar
Instantiates a new dipolar.
Dipolar.rdcComparator
- Class in
RdcPanda
The Class rdcComparator.
Dipolar.rdcComparator()
- Constructor for class RdcPanda.
Dipolar.rdcComparator
dirCaCa(double[], double[], double, double[][])
- 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.
dirCos(double[])
- Method in class RdcPanda.
ModelRdc
cal the directioal cosines of the vector vec.
dirCos(double[])
- Method in class RdcPanda.
Pdb
cal the directioal cosines of the vector vec.
dirCos(double[])
- Method in class RdcPanda.
PdbRdc
cal the directioal cosines of the vector vec.
dirCos(double[])
- Method in class RdcPanda.
PdbRmsd
cal the directioal cosines of the vector vec.
dirCos(double[])
- Method in class RdcPanda.
PhiPsi
cal the directioal cosines of the vector vec.
dirCos(double[])
- Method in class RdcPanda.
ppGlobal
cal the directioal cosines of the vector vec.
Div(Z, Z)
- Method in class Jampack.
Z
Computes the quotient of two Z's.
Div(Z, double)
- Method in class Jampack.
Z
Computes the quotient of a Z and a double.
dnaIntra(double)
- Method in class RdcPanda.
PhiPsi
A method for computing the distance dN(i, i+1), between the NH(i) and NH(i+1) begin with an frame defined in the peptide plane i.
dNNseq(double, double)
- Method in class RdcPanda.
PhiPsi
A method for computing the distance dN(i, i+1), between the NH(i) and NH(i+1) begin with an frame defined in the peptide plane i.
dNNtest()
- Method in class RdcPanda.
PhiPsi
There is another method for computing these angles, see the backup file.
doAddRandomLoops(String, String, String)
- Method in class RdcPanda.
RdcPanda
add random loops to an ensemble of packed SSE structures (i.e.
doAddSideChains(String, String, String)
- Method in class RdcPanda.
RdcPanda
* add the side chains and prune steic clahes.
doCalAlignmentTensor(String, String, String)
- Method in class RdcPanda.
RdcPanda
calculate the alignment tensor.
doCalLoops(String, String, String)
- Method in class RdcPanda.
Loops
compute the loop using a gradient search approach (like ccd.)
doCalNOEScores(String, String, String)
- Method in class RdcPanda.
Pdb
* compute the NOE satisfaction scores for all structure in an ensemble.
doCheckNoeByEnsemble(String, String, String)
- Method in class RdcPanda.
Noe
check the NOE table by an ensemble of structures, and output the statistical information.
doCheckPackingSym(String, String, String)
- Method in class RdcPanda.
RdcPanda
check the packing symmetry that best fit the noe restraints (namely with minimum NOE RMSD).
doCompareTwoNOETables(String, String, String)
- Method in class RdcPanda.
Assign
compare two NOE table and output the summary.
doExtractNOEs(String, String, String)
- Method in class RdcPanda.
Assign
extract NOEs in certain regions.
doGoalCalLoops(String, String, String)
- Method in class RdcPanda.
Goal
compute the loop using a gradient search approach (like ccd.)
doHANANOEAsg(String, String, String)
- Method in class RdcPanda.
Assign
HANA algorithm for the NOE assignment and output the NOE table.
doLongNOEsAsgWOStructure(String, String, String)
- Method in class RdcPanda.
Assign
refine the long-range NOE assignment without structure information.
doLongNOEsAsgWOStructureNew(String, String, String)
- Method in class RdcPanda.
Assign
refine the long-range NOE assignment without structure information, better version of doLongNOEsAsgWOStructure.
doMergeNCluster(String, String, String)
- Method in class RdcPanda.
RdcPanda
* merge all structures in previous ensemble into one enemble (with the same pdb name) and cluster them according to given resolution.
doMergeNClusterAll(String, String, String)
- Method in class RdcPanda.
RdcPanda
* merge all structures in previous ensemble into one enemble (with the same pdb name) and cluster them according to given resolution.
doNasca(String, String, String)
- Method in class RdcPanda.
Nasca
Implement the NOE assignment (NASCA) algorithm without using the side-chain resonance infomration.
doNoeStatistics(String, String, String)
- Method in class RdcPanda.
Noe
output the NOE statistics.
doRdcExactHelix(String, String, String)
- Method in class RdcPanda.
RdcPanda
RDC-EXACT for two RDCs (CH and NH RDCs), and for long helix Co-Ca and Co-N RDCs are optional.
doRdcExactHelixWOAT(String, String, String)
- Method in class RdcPanda.
RdcPanda
RDC-EXACT without alignment tensor for two RDCs (CH and NH RDCs), and for long helix.
doRdcExactSheet(String, String, String)
- Method in class RdcPanda.
Model
compute the beta sheet using RDC-EXACT.
doReadPDBEnergy(String, String, String)
- Method in class RdcPanda.
RdcPanda
Read the engergy value from xplor PDB, and output the top structures with lowest energies.
doReadPdbFragments(String, String, String)
- Method in class RdcPanda.
Pdb
HANA algorithm for the NOE assignment and output the NOE table.
doRefineNOEsWBB(String, String, String)
- Method in class RdcPanda.
Assign
note: randomStructureSlect..need to be fixed, refine the NOE assignment using given the backbone and output the refine NOE table.
doRefineRdcExact(String, String, String)
- Method in class RdcPanda.
RdcPanda
refine the half start and end residues of pdb backbone solved from RDC-EXACT.
doRefineRdcExactMiddle(String, String, String)
- Method in class RdcPanda.
RdcPanda
refine the middle residues of pdb backbone solved from RDC-EXACT.
doRunXplor(String, String, String)
- Method in class RdcPanda.
RdcPanda
call Xplor as a subroutine given a script file.
doSSEPacking(String, String, String)
- Method in class RdcPanda.
RdcPanda
Pack SSEs using sparse inter-SSE NOE restraints.
DoubletoEstring(double, int, int)
- Static method in class Jampack.
Print
Converts a double to w.d e format.
dx
- Variable in class Jampack.
Zdiagmat
The index of the last diagonal (public)
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