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Packages that use Pdb | |
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RdcPanda |
Uses of Pdb in RdcPanda |
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Fields in RdcPanda declared as Pdb | |
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Pdb |
Goal.TreePdb.pdb
|
Fields in RdcPanda with type parameters of type Pdb | |
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java.util.Vector<Pdb> |
Goal.vecPdbSSE
|
Methods in RdcPanda that return Pdb | |
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Pdb |
ModelRdc.coordByBackward(double phi,
double psi,
double[] n1,
double[] nh1,
double[] ca1,
int residueNo,
java.lang.String resid1)
A method for computing coordinates of backbone atoms backward: with direasing residue no. |
Pdb |
ModelRdc.coordByResidue(double phi,
double psi,
double[] n1,
double[] nh1,
double[] ca1,
int residueNo,
java.lang.String resid1,
boolean first)
A method for computing coordinates of backbone atoms. |
Pdb |
ModelRdc.coordByResidueFull(double phi,
double psi,
double[] n1,
double[] nh1,
double[] ca1,
int residueNo,
java.lang.String resid1,
boolean first)
*A method for computing coordinates of backbone atoms, including all backbone atoms, ha, ca, n, hn, cb,c o. |
Pdb |
RotaPattern.getPdb()
Gets the pdb. |
Pdb |
PdbRdc.getPdb()
Gets the pdb. |
Pdb |
GraphCut.RotScore.getRotPdb()
|
Methods in RdcPanda that return types with arguments of type Pdb | |
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java.util.Vector<Pdb> |
ModelRdc.minHelix(java.util.Vector<Dipolar> rdcVec1,
java.util.Vector<Dipolar> rdcVec2,
double[] rdc1Cal,
double[] rdc2Cal,
java.util.Vector<Pdb> pdbVec,
double Syy,
double Szz,
double rmsd1,
double rmsd2,
int nCycle,
double weightAngles,
boolean debugDFS,
boolean printResults,
boolean isHelix)
A recusive function to compute all the backbone Phi/Psi for an n-residue helix or the first strand. |
java.util.Vector<Pdb> |
ModelRdc.minHelix(java.util.Vector<Dipolar> rdcVec1,
java.util.Vector<Dipolar> rdcVec2,
double[] rdc1Cal,
double[] rdc2Cal,
java.util.Vector<Pdb> pdbVec,
double Syy,
double Szz,
double rmsd1,
double rmsd2,
int nCycle,
double weightAngles,
boolean debugDFS,
boolean printResults,
boolean isHelix,
double[] NhRdcRmsd,
double[] ChRdcRmsd)
A recusive function to compute all the backbone Phi/Psi for an n-residue helix or the first strand. |
java.util.Vector<Pdb> |
ModelRdc.minHelix(java.util.Vector<Dipolar> rdcVec1,
java.util.Vector<Dipolar> rdcVec2,
double[] rdc1Cal,
double[] rdc2Cal,
java.util.Vector<Pdb> pdbVec,
double Syy,
double Szz,
double rmsd1,
double rmsd2,
int nCycle,
double weightAngles,
boolean debugDFS,
boolean printResults,
boolean isHelix,
java.util.Vector vecTalos)
A recusive function to compute all the backbone Phi/Psi for an n-residue helix or the first strand. |
java.util.Vector<Pdb> |
ModelRdc.minHelix4RDCs(java.util.Vector<Dipolar> rdcVec1,
java.util.Vector<Dipolar> rdcVec2,
java.util.Vector<Dipolar> helixRdcCaCoVec,
java.util.Vector<Dipolar> helixRdcCoNVec,
double[] rdc1Cal,
double[] rdc2Cal,
java.util.Vector<Pdb> pdbVec,
double Syy,
double Szz,
double rmsd1,
double rmsd2,
int nCycle,
double weightAngles,
boolean debugDFS,
boolean printResults,
boolean isHelix,
java.util.Vector vecTalos,
double wtCoCa,
double wtCoN)
A recusive function to compute all the backbone Phi/Psi for an n-residue helix or the first strand. |
java.util.Vector<Pdb> |
ModelRdc.minHelix4RDCs(java.util.Vector<Pdb> vecPrePdb,
java.util.Vector<Dipolar> rdcVec1,
java.util.Vector<Dipolar> rdcVec2,
java.util.Vector<Dipolar> helixRdcCaCoVec,
java.util.Vector<Dipolar> helixRdcCoNVec,
double[] rdc1Cal,
double[] rdc2Cal,
java.util.Vector<Pdb> pdbVec,
double Syy,
double Szz,
double rmsd1,
double rmsd2,
int nCycle,
double weightAngles,
boolean debugDFS,
boolean printResults,
boolean isHelix,
java.util.Vector vecTalos,
double wtCoCa,
double wtCoN,
int startNo,
int endNo,
java.util.Vector vecSeq)
A recusive function to compute all the backbone Phi/Psi for an n-residue helix or the first strand. |
java.util.Vector<Pdb> |
ModelRdc.refineHelix22(java.util.Vector vecBB,
java.util.Vector<Dipolar> rdc1Vec,
java.util.Vector<Dipolar> rdc2Vec,
double Syy,
double Szz,
double[] ramaFilter,
double phiAve,
double psiAve,
int refineCycle,
int initialCycle,
double w4Angles,
double resolution,
boolean debugDFS,
boolean printResults,
double[] nhRdcRmsd,
double[] chRdcRmsd)
Refine helix22. |
java.util.Vector<Pdb> |
ModelRdc.refineHelix22(java.util.Vector vecBB,
java.util.Vector<Dipolar> rdc1Vec,
java.util.Vector<Dipolar> rdc2Vec,
double Syy,
double Szz,
double[] ramaFilter,
double phiAve,
double psiAve,
int refineCycle,
int initialCycle,
double w4Angles,
double resolution,
boolean debugDFS,
boolean printResults,
java.util.Vector vecTalos)
Refine helix22. |
java.util.Vector<Pdb> |
ModelRdc.refineHelix22NoGridSearch(java.util.Vector vecBB,
java.util.Vector<Dipolar> rdc1Vec,
java.util.Vector<Dipolar> rdc2Vec,
double Syy,
double Szz,
double[] ramaFilter,
double phiAve,
double psiAve,
int refineCycle,
int initialCycle,
double w4Angles,
double resolution,
boolean debugDFS,
boolean printResults,
double[] nhRdcRmsd,
double[] chRdcRmsd)
Refine helix22 no grid search. |
java.util.Vector<Pdb> |
ModelRdc.refineHelixW4RDCs(java.util.Vector vecBB,
java.util.Vector<Dipolar> rdc1Vec,
java.util.Vector<Dipolar> rdc2Vec,
java.util.Vector<Dipolar> helixRdcCaCoVec,
java.util.Vector<Dipolar> helixRdcCoNVec,
double Syy,
double Szz,
double[] ramaFilter,
double phiAve,
double psiAve,
int refineCycle,
int initialCycle,
double w4Angles,
double resolution,
boolean debugDFS,
boolean printResults,
java.util.Vector vecTalos)
Refine helix w4 rd cs. |
java.util.Vector<Pdb> |
ModelRdc.refineHelixW4RDCs(java.util.Vector vecPreBB,
java.util.Vector vecBB,
java.util.Vector<Dipolar> rdc1Vec,
java.util.Vector<Dipolar> rdc2Vec,
java.util.Vector<Dipolar> helixRdcCaCoVec,
java.util.Vector<Dipolar> helixRdcCoNVec,
double Syy,
double Szz,
double[] ramaFilter,
double phiAve,
double psiAve,
int refineCycle,
int initialCycle,
double w4Angles,
double resolution,
boolean debugDFS,
boolean printResults,
java.util.Vector vecTalos,
double wtCoCa,
double wtCoN,
int starNo,
int endNo,
java.util.Vector vecSeq)
refine the Helix with the weights for CaCo NCO RDCs. |
java.util.Vector<Pdb> |
ModelRdc.refineSaupe3(java.util.Vector<Pdb> pdbVec,
java.util.Vector<Dipolar> nhRdc,
java.util.Vector<Dipolar> cahaRdc,
double[] saupeSave)
Modified by zeng for computing the alignment tensor based on structure and RDCs Update the Saupe elements for the second time. |
java.util.Vector<Pdb> |
Goal.SearchSSEAnchors(int topK,
int resNoLoop)
find the SSE anchors (ca atoms) that can possibly interact with loops |
java.util.Vector<Pdb> |
Goal.SearchSSEAnchorsTop(int topK,
int resNoLoop)
find the top set of SSE anchors (ca atoms) that can possibly interact with loops |
Methods in RdcPanda with parameters of type Pdb | |
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boolean |
Goal.CheckFirstResidue(Pdb preHalfPdb,
int fixNo,
double error,
double[] dist)
check whether the end residue closes the gap. |
boolean |
Goal.CheckFirstResidue(Pdb preHalfPdb,
int fixNo,
double error,
double[] dist,
double[] caDist)
check whether the end residue closes the gap. |
boolean |
Goal.CheckFirstResidueOld(Pdb preHalfPdb,
int fixNo,
double error,
double[] dist)
check whether the end residue closes the gap. |
boolean |
Goal.CheckFirstResidueOld(Pdb preHalfPdb,
int fixNo,
double error,
double[] dist,
double[] caDist)
check whether the end residue closes the gap. |
boolean |
Goal.CheckKinChainRestraint(Pdb nextHalfPdb,
int endResNo,
double error)
check whether kinematic chain restraint is satisfied |
boolean |
Goal.CheckKinChainRestraintBackward(Pdb nextHalfPdb,
int startResNo,
double error)
check whether kinematic chain restraint is satisfied |
boolean |
Goal.CheckLastResidue(Pdb nextHalfPdb,
int endResNo,
double error,
double[] dist)
check whether the end residue closes the gap |
boolean |
Goal.CheckLastResidue(Pdb nextHalfPdb,
int endResNo,
double error,
double[] dist,
double[] distCa)
check whether the end residue closes the gap |
boolean |
Goal.CheckLastResidueOld(Pdb nextHalfPdb,
int endResNo,
double error,
double[] dist)
check whether the end residue closes the gap |
boolean |
Goal.CheckLastResidueOld(Pdb nextHalfPdb,
int endResNo,
double error,
double[] dist,
double[] distCa)
check whether the end residue closes the gap |
boolean |
Goal.CheckNOEBtwCaNSSEs(Pdb curPdb,
java.util.Vector vecSSEAnchors,
double distUpCa)
check whether the distance satisfies the NOE restraint from ca to anchors in SSEs |
java.util.Vector |
Pdb.compDistPatternFromPairRotams(int resNoA,
int resNoB,
Pdb pdbA,
Pdb pdbB,
double DistBound)
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. |
double |
Pdb.compResRmsd(Pdb pdb1,
Pdb pdb2)
Compute rmsd between two rotamers only for non-proton atoms, assume they are in the same coordinate system. |
double |
Pdb.compResRmsdPairWise(Pdb pdb1,
Pdb pdb2)
Compute rmsd between two rotamers (for all atoms), assume they are in the same coordinate system. |
java.util.Vector |
vdw.convert2VDW(Pdb[] pdbVec)
To convert the PDB coordinates into a flat structure for speed. |
void |
Goal.KinNeighborSearch(Pdb PrePdb,
int curResNo,
int noStart,
int noEnd)
get the candidate positions for each ca atom using kinematic constraints and rotamer replacement find current ca atom candidate positions |
void |
Goal.TreePdb.SetPdb(Pdb pp)
|
Method parameters in RdcPanda with type arguments of type Pdb | |
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double |
PdbRdc.BackCal(java.util.Vector<Pdb> pdbVec,
java.util.Vector<Dipolar> rdcVec,
java.lang.String atom1,
java.lang.String atom2,
Matrix mm,
double Sxx,
double Syy,
double Szz,
double rdcRatio,
double[] rdcBc)
For back-computing RDCs. |
double |
PdbRdc.BackCal(java.util.Vector<Pdb> pdbVec,
java.util.Vector<Dipolar> rdcVec,
java.lang.String atom1,
java.lang.String atom2,
Matrix mm,
double Sxx,
double Syy,
double Szz,
double rdcRatio,
double[] rdcBc,
double[] squareRmsd,
int[] size)
For back-computing RDCs. |
double |
PdbRdc.BackCalCACO(java.util.Vector<Pdb> pdbVec,
java.util.Vector<Dipolar> rdcVec,
java.lang.String atom1,
java.lang.String atom2,
Matrix mm,
double Sxx,
double Syy,
double Szz,
double rdcRatio,
double[] rdcBc,
double[] squareRmsd,
int[] size,
boolean isPrint)
For back-computing RDCs. |
double |
PdbRdc.BackCalCACOOnePdb(java.util.Vector<Pdb> pdbVec,
java.util.Vector<Dipolar> rdcVec,
java.lang.String atom1,
java.lang.String atom2,
Matrix mm,
double Sxx,
double Syy,
double Szz,
double rdcRatio)
compute rdc rmsd for only one pdb. |
double |
PdbRdc.BackCalCON(java.util.Vector<Pdb> pdbVec,
java.util.Vector<Dipolar> rdcVec,
java.lang.String atom1,
java.lang.String atom2,
Matrix mm,
double Sxx,
double Syy,
double Szz,
double rdcRatio,
double[] rdcBc,
double[] squareRmsd,
int[] size,
boolean isPrint)
For back-computing RDCs from Co at residue i to N at residue i+1. |
double |
PdbRdc.BackCalCONOnePdb(java.util.Vector<Pdb> pdbVec,
java.util.Vector<Dipolar> rdcVec,
java.lang.String atom1,
java.lang.String atom2,
Matrix mm,
double Sxx,
double Syy,
double Szz,
double rdcRatio)
compute rdc rmsd for only one pdb from Co at residue i to N at residue i+1. |
double |
PdbRdc.BackCalNH(java.util.Vector<Pdb> pdbVec,
java.util.Vector<Dipolar> rdcVec,
java.lang.String atom1,
java.lang.String atom2,
Matrix mm,
double Sxx,
double Syy,
double Szz,
double rdcRatio,
double[] rdcBc)
For back-computing NH RDCs since the NH RDC of the fiest residue is NOT used in the DFS-based refinement. |
double |
PdbRdc.BackCalNH(java.util.Vector<Pdb> pdbVec,
java.util.Vector<Dipolar> rdcVec,
java.lang.String atom1,
java.lang.String atom2,
Matrix mm,
double Sxx,
double Syy,
double Szz,
double rdcRatio,
double[] rdcBc,
double[] squareRmsd,
int[] size)
For back-computing NH RDCs since the NH RDC of the fiest residue is NOT used in the DFS-based refinement. |
double |
PdbRdc.BackCalNHOne(java.util.Vector<Pdb> pdbVec,
java.util.Vector<Dipolar> rdcVec,
java.lang.String atom1,
java.lang.String atom2,
Matrix mm,
double Sxx,
double Syy,
double Szz,
double rdcRatio,
double[] rdcBc,
double[] squareRmsd,
int[] size)
compute the RDC deviation for one residue. |
double |
PdbRdc.BackCalOne(java.util.Vector<Pdb> pdbVec,
java.util.Vector<Dipolar> rdcVec,
java.lang.String atom1,
java.lang.String atom2,
Matrix mm,
double Sxx,
double Syy,
double Szz,
double rdcRatio,
double[] rdcBc,
double[] squareRmsd,
int[] size)
compute rdc deviation for one residue For back-computing RDCs. |
double |
PdbRdc.BackCalOnePdb(java.util.Vector<Pdb> pdbVec,
java.util.Vector<Dipolar> rdcVec,
java.lang.String atom1,
java.lang.String atom2,
Matrix mm,
double Sxx,
double Syy,
double Szz,
double rdcRatio)
compute rdc rmsd for only one pdb. |
Matrix |
PdbRdc.bestFit(java.util.Vector<Pdb> pdbVec,
java.util.Vector nhRdc,
java.util.Vector<Dipolar> cahaRdc,
double[] rdc1Cal,
double[] rdc2Cal,
double[] eigenValues)
Best fit Two sets of RDC data from one medium such as NH and CH please note that the rotation matrix returned by the eigenValueDecomposition method is rather arbitrary so we need to make sure that only the righ handedone are returned. |
double |
Goal.CompNoePatternScoreBetwSSEAndLoop(double errH,
double errHeavy,
java.util.Vector<Pdb> vecSSEPdb,
java.util.Vector<Pdb> vecPdbLoop,
double distBound,
java.util.Vector asgVec,
java.util.Vector vecNOESY)
compute NOE pattern between SSE and loops. |
double |
Goal.CompNoePatternScoreBetwSSEAndLoop(double errH,
double errHeavy,
java.util.Vector<Pdb> vecSSEPdb,
java.util.Vector<Pdb> vecPdbLoop,
double distBound,
java.util.Vector asgVec,
java.util.Vector vecNOESY)
compute NOE pattern between SSE and loops. |
Matrix |
PdbRdc.eulerFit(java.util.Vector<Pdb> pdbVec,
java.util.Vector<Dipolar> rdcVec1,
java.util.Vector<Dipolar> rdcVec2,
double Syy,
double Szz,
double[] rmsds,
double resolution,
boolean debug)
Note: Lincong's has a serious bug. |
Matrix |
PdbRdc.eulerFit4RDCs(java.util.Vector<Pdb> pdbVec,
java.util.Vector<Dipolar> rdcVec1,
java.util.Vector<Dipolar> rdcVec2,
java.util.Vector<Dipolar> rdcVecCaCo,
java.util.Vector<Dipolar> rdcVecCoN,
double Syy,
double Szz,
double[] rmsds,
double resolution,
boolean debug)
Note: Lincong's has a serious bug. |
Matrix |
PdbRdc.eulerFitPrintEnsemble(java.util.Vector<Pdb> pdbVec,
java.util.Vector<Dipolar> rdcVec1,
java.util.Vector<Dipolar> rdcVec2,
double Syy,
double Szz,
double[] rmsds,
double resolution,
boolean debug,
double RdcRmsdThreshold)
print out all pdb orientations in which rdc rmsd is smaler than some threshold, in grid search. |
java.util.Vector<Pdb> |
ModelRdc.minHelix(java.util.Vector<Dipolar> rdcVec1,
java.util.Vector<Dipolar> rdcVec2,
double[] rdc1Cal,
double[] rdc2Cal,
java.util.Vector<Pdb> pdbVec,
double Syy,
double Szz,
double rmsd1,
double rmsd2,
int nCycle,
double weightAngles,
boolean debugDFS,
boolean printResults,
boolean isHelix)
A recusive function to compute all the backbone Phi/Psi for an n-residue helix or the first strand. |
java.util.Vector<Pdb> |
ModelRdc.minHelix(java.util.Vector<Dipolar> rdcVec1,
java.util.Vector<Dipolar> rdcVec2,
double[] rdc1Cal,
double[] rdc2Cal,
java.util.Vector<Pdb> pdbVec,
double Syy,
double Szz,
double rmsd1,
double rmsd2,
int nCycle,
double weightAngles,
boolean debugDFS,
boolean printResults,
boolean isHelix,
double[] NhRdcRmsd,
double[] ChRdcRmsd)
A recusive function to compute all the backbone Phi/Psi for an n-residue helix or the first strand. |
java.util.Vector<Pdb> |
ModelRdc.minHelix(java.util.Vector<Dipolar> rdcVec1,
java.util.Vector<Dipolar> rdcVec2,
double[] rdc1Cal,
double[] rdc2Cal,
java.util.Vector<Pdb> pdbVec,
double Syy,
double Szz,
double rmsd1,
double rmsd2,
int nCycle,
double weightAngles,
boolean debugDFS,
boolean printResults,
boolean isHelix,
java.util.Vector vecTalos)
A recusive function to compute all the backbone Phi/Psi for an n-residue helix or the first strand. |
java.util.Vector<Pdb> |
ModelRdc.minHelix4RDCs(java.util.Vector<Dipolar> rdcVec1,
java.util.Vector<Dipolar> rdcVec2,
java.util.Vector<Dipolar> helixRdcCaCoVec,
java.util.Vector<Dipolar> helixRdcCoNVec,
double[] rdc1Cal,
double[] rdc2Cal,
java.util.Vector<Pdb> pdbVec,
double Syy,
double Szz,
double rmsd1,
double rmsd2,
int nCycle,
double weightAngles,
boolean debugDFS,
boolean printResults,
boolean isHelix,
java.util.Vector vecTalos,
double wtCoCa,
double wtCoN)
A recusive function to compute all the backbone Phi/Psi for an n-residue helix or the first strand. |
java.util.Vector<Pdb> |
ModelRdc.minHelix4RDCs(java.util.Vector<Pdb> vecPrePdb,
java.util.Vector<Dipolar> rdcVec1,
java.util.Vector<Dipolar> rdcVec2,
java.util.Vector<Dipolar> helixRdcCaCoVec,
java.util.Vector<Dipolar> helixRdcCoNVec,
double[] rdc1Cal,
double[] rdc2Cal,
java.util.Vector<Pdb> pdbVec,
double Syy,
double Szz,
double rmsd1,
double rmsd2,
int nCycle,
double weightAngles,
boolean debugDFS,
boolean printResults,
boolean isHelix,
java.util.Vector vecTalos,
double wtCoCa,
double wtCoN,
int startNo,
int endNo,
java.util.Vector vecSeq)
A recusive function to compute all the backbone Phi/Psi for an n-residue helix or the first strand. |
java.util.Vector<Pdb> |
ModelRdc.minHelix4RDCs(java.util.Vector<Pdb> vecPrePdb,
java.util.Vector<Dipolar> rdcVec1,
java.util.Vector<Dipolar> rdcVec2,
java.util.Vector<Dipolar> helixRdcCaCoVec,
java.util.Vector<Dipolar> helixRdcCoNVec,
double[] rdc1Cal,
double[] rdc2Cal,
java.util.Vector<Pdb> pdbVec,
double Syy,
double Szz,
double rmsd1,
double rmsd2,
int nCycle,
double weightAngles,
boolean debugDFS,
boolean printResults,
boolean isHelix,
java.util.Vector vecTalos,
double wtCoCa,
double wtCoN,
int startNo,
int endNo,
java.util.Vector vecSeq)
A recusive function to compute all the backbone Phi/Psi for an n-residue helix or the first strand. |
java.util.Vector<Pdb> |
ModelRdc.refineSaupe3(java.util.Vector<Pdb> pdbVec,
java.util.Vector<Dipolar> nhRdc,
java.util.Vector<Dipolar> cahaRdc,
double[] saupeSave)
Modified by zeng for computing the alignment tensor based on structure and RDCs Update the Saupe elements for the second time. |
double |
Goal.TranRotGridSearch(double[] tranX0,
double[] tranXn,
double[] rotX0,
double[] rotXn,
java.util.Vector<Pdb> vecRotPdb,
double tranResol,
double rotResol,
boolean isCheckClash,
double[] translation,
double[] rotation)
search T(3)*S(3) space to find the optimal solution that best fits the NOESY data |
Constructors in RdcPanda with parameters of type Pdb | |
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Goal.TreePdb(Pdb pp)
|
|
Goal.TreePdb(Pdb pp,
java.util.Vector pare,
Goal.TreePdb child)
|
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GraphCut.RotScore(int ID,
Pdb pdb,
double sc)
|
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GraphCut.RotScore(Pdb pdb,
double sc)
|
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Pdb(Pdb pp)
Instantiates a new pdb. |
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PdbRdc(Pdb pp,
double rdc)
Instantiates a new pdb rdc. |
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RotaPattern(Pdb pdbRot,
double dbSc)
Instantiates a new rota pattern. |
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