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java.lang.ObjectRdcPanda.PdbRdc
public class 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. Written by Lincong Wang (2001-2005)
Constructor Summary | |
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PdbRdc()
Instantiates a new pdb rdc. |
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PdbRdc(Pdb pp,
double rdc)
Instantiates a new pdb rdc. |
Method Summary | |
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double |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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. |
double[] |
BackCalRdcs(java.util.Vector pdbVec,
java.util.Vector rdcVec,
java.lang.String atom1,
java.lang.String atom2,
Matrix mm,
double Sxx,
double Syy,
double Szz)
For back-computing RDCs. |
Matrix |
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. |
boolean |
bestFit(java.util.Vector pdbVec,
java.util.Vector rdcVec,
java.lang.String atom1,
java.lang.String atom2,
double[] rmsdArr,
boolean printResults)
Computing the Saupe matrix by SVD method and then diagonalizing it for computing the diagonalized elements and rotation matrix to one of POF. |
boolean |
bestFit(java.util.Vector pdbVec,
java.util.Vector rdcVec,
java.lang.String atom1,
java.lang.String atom2,
double[] rmsdArr,
double[] rdcArrN,
boolean printResults)
Computing the Saupe matrix by SVD method and then diagonalizing it for computing the diagonalized elements and rotation matrix to one of POF. |
Matrix |
bestFit4RDCs(java.util.Vector pdbVec,
java.util.Vector nhRdc,
java.util.Vector cahaRdc,
java.util.Vector cacoRdc,
java.util.Vector conRdc,
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 only the righ handedone are returned. |
double[] |
dirCos(double[] vec)
cal the directioal cosines of the vector vec. |
double[][] |
equGenerate(java.util.Vector pdbVec,
java.util.Vector rdcVec,
java.lang.String atom1,
java.lang.String atom2,
double rdcRatio)
A method to generate an equation consisting all the different internuclear vectors whose RDC are measured. |
Matrix |
eulerFit_old(java.util.Vector pdbVec,
java.util.Vector rdcVec1,
java.util.Vector rdcVec2,
double Syy,
double Szz,
double[] rmsds,
double resolution,
boolean debug)
Compute three Euler angles using two sets of RDC data and the corresponding Saupe elements Basic steps: extract the NH vectors with the corresponding RDC data as an array (for efficiency) For all the values of three Euler angles first compute the new NH directions after the rotation then compute the RDCs and RMSD from the new NH directions. |
Matrix |
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 |
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 |
eulerFitHB(java.util.Vector pdbVec,
java.util.Vector rdcVec1,
java.util.Vector rdcVec2,
double[] saupe,
Matrix rot,
double[] rmsds,
double resolution,
double weight4HB,
java.util.Vector pdbVecS1,
java.util.Vector hbVec,
Matrix mat4Dirs,
boolean debug)
Compute three Euler angles using two sets of RDC data and the corresponding Saupe elements Basic steps: extract the NH vectors with the corresponding RDC data as an array (for efficiency) For all the values of three Euler angles first compute the new NH directions after the rotation then compute the RDCs and RMSD from the new NH directions. |
Matrix |
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. |
Matrix |
fit4MissingRdc(java.util.Vector pdbVec,
java.util.Vector rdcVec1,
java.util.Vector rdcVec2,
double Syy,
double Szz,
double[] rmsds,
double resolution,
boolean debug)
Compute three Euler angles using two sets of RDC data (pissbile missing) and the corresponding Saupe elements Basic steps: extract the NH vectors with the corresponding RDC data as an array (for efficiency) For all the values of three Euler angles first compute the new NH directions after the rotation then compute the RDCs and RMSD from the new NH directions. |
Matrix |
fit4MissingRdcHB(java.util.Vector pdbVec,
java.util.Vector rdcVec1,
java.util.Vector rdcVec2,
double Syy,
double Szz,
java.util.Vector pdbVecA,
double[] rmsds,
double resolution,
double weight4HB,
java.util.Vector hbVec,
boolean debug)
Compute three Euler angles using two sets of RDC data (pissbile missing) and the corresponding Saupe elements Basic steps: extract the NH vectors with the corresponding RDC data as an array (for efficiency) For all the values of three Euler angles first compute the new NH directions after the rotation then compute the RDCs and RMSD from the new NH directions. |
Matrix |
fit4MissingRdcHB2(java.util.Vector pdbVec,
java.util.Vector rdcVec1,
java.util.Vector rdcVec2,
double Syy,
double Szz,
java.util.Vector pdbVecA1,
java.util.Vector pdbVecA2,
double[] rmsds,
double resolution,
double weight4HB,
java.util.Vector hbVec1,
java.util.Vector hbVec2,
boolean debug)
Compute three Euler angles using two sets of RDC data (pissbile missing) and the corresponding Saupe elements Basic steps: extract the NH vectors with the corresponding RDC data as an array (for efficiency) For all the values of three Euler angles first compute the new NH directions after the rotation then compute the RDCs and RMSD from the new NH directions. |
Pdb |
getPdb()
Gets the pdb. |
double |
getRdc()
Gets the rdc. |
double[] |
internuclearVec(double[] n1,
double[] n2)
Compute the internuclear vector between two atoms. |
double[] |
newVecByTranslation(double[] n1,
double[] vT)
Compute the new vector after translation. |
Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public PdbRdc()
public PdbRdc(Pdb pp, double rdc)
pp
- the pprdc
- the rdcMethod Detail |
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public Pdb getPdb()
public double getRdc()
public double[] dirCos(double[] vec)
vec
- the vec
public double[] internuclearVec(double[] n1, double[] n2)
n1
- the coordinate for atom 1n2
- the coordinate for atom 2
public double[] newVecByTranslation(double[] n1, double[] vT)
n1
- the coordinate for atom 1vT
- the translation vector
public boolean bestFit(java.util.Vector pdbVec, java.util.Vector rdcVec, java.lang.String atom1, java.lang.String atom2, double[] rmsdArr, boolean printResults)
pdbVec
- a vector of PDB objects.rdcVec
- a corresponding RDC vector.rmsdArr
- for returning the five Saupe elements and the best-fitted RMSDatom1
- the nucleus type whose RDC for the internuclear vector are recordedatom2
- the nucleus type whose RDC for the internuclear vector are recordedprintResults
- if true, it prints the back-computed RDCs.
public boolean bestFit(java.util.Vector pdbVec, java.util.Vector rdcVec, java.lang.String atom1, java.lang.String atom2, double[] rmsdArr, double[] rdcArrN, boolean printResults)
pdbVec
- a vector of PDB objects.rdcVec
- a corresponding RDC vector.rmsdArr
- for returning the five Saupe elements and the best-fitted RMSDrdcArrN
- back-computed RDCsatom1
- the nucleus type whose RDC for the internuclear vector are recordedatom2
- the nucleus type whose RDC for the internuclear vector are recordedprintResults
- if true, it prints the back-computed RDCs.
public double[][] equGenerate(java.util.Vector pdbVec, java.util.Vector rdcVec, java.lang.String atom1, java.lang.String atom2, double rdcRatio)
pdbVec
- the PDB ccordinatesrdcVec
- used for extracting the PDB coordiantes with the RDC dataatom1
- the atom like N and H whose vector has RDC measured valuesatom2
- the atom like N and H whose vector has RDC measured valuesrdcRatio
- the theoretical value of RDC strength compared with CH (which is set as 1.00)
Real experimental value may differ due to Dynamics etc
public Matrix bestFit(java.util.Vector<Pdb> pdbVec, java.util.Vector nhRdc, java.util.Vector<Dipolar> cahaRdc, double[] rdc1Cal, double[] rdc2Cal, double[] eigenValues)
pdbVec
- CoordinatesnhRdc
- the measured NH rdcscahaRdc
- the measured CH rdcsrdc1Cal
- for saving back-computed NH Rdcs including those of missing experimental RDCsrdc2Cal
- for saving back-computed CH Rdcs including those of missing experimental RDCseigenValues
- for saving the computed {Syy, Szz, rmsd4NHRDC, rmsd4CHRDC
public Matrix bestFit4RDCs(java.util.Vector pdbVec, java.util.Vector nhRdc, java.util.Vector cahaRdc, java.util.Vector cacoRdc, java.util.Vector conRdc, double[] rdc1Cal, double[] rdc2Cal, double[] eigenValues)
pdbVec
- CoordinatesnhRdc
- the measured NH rdcscahaRdc
- the measured CH rdcsrdc1Cal
- for saving back-computed NH Rdcs including those of missing experimental RDCsrdc2Cal
- for saving back-computed CH Rdcs including those of missing experimental RDCseigenValues
- for saving the computed {Syy, Szz, rmsd4NHRDC, rmsd4CHRDCcacoRdc
- the caco rdcconRdc
- the con rdc
public double 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)
pdbVec
- the pdb coordinatesrdcVec
- the meausred RDC valuesatom1
- the atoms of which the internuclear vector has RDC valuesatom2
- the atoms of which the internuclear vector has RDC valuesSxx
- the three diagonalized Saupe elementsSyy
- the three diagonalized Saupe elementsSzz
- the three diagonalized Saupe elementsrdcRatio
- the relative strength of RDCsrdcBc
- an array for returning the back-computed RDCsmm
- the matrix used to rotate the original PDB frame to one of POFsquareRmsd
- the variable for computing overall Rmsd, added by zengsize
- the size of experimental RDCs, added by zeng
public double 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)
pdbVec
- the pdb coordinatesrdcVec
- the meausred RDC valuesatom1
- the atoms of which the internuclear vector has RDC valuesatom2
- the atoms of which the internuclear vector has RDC valuesSxx
- the three diagonalized Saupe elementsSyy
- the three diagonalized Saupe elementsSzz
- the three diagonalized Saupe elementsrdcRatio
- the relative strength of RDCsrdcBc
- an array for returning the back-computed RDCsmm
- the matrix used to rotate the original PDB frame to one of POFsquareRmsd
- the variable for computing overall Rmsd, added by zengsize
- the size of experimental RDCs, added by zeng
public double 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)
pdbVec
- the pdb coordinatesrdcVec
- the meausred RDC valuesatom1
- the atoms of which the internuclear vector has RDC valuesatom2
- the atoms of which the internuclear vector has RDC valuesmm
- the matrix used to rotate the original PDB frame to one of POFSxx
- the three diagonalized Saupe elementsSyy
- the three diagonalized Saupe elementsSzz
- the three diagonalized Saupe elementsrdcRatio
- the relative strength of RDCsrdcBc
- an array for returning the back-computed RDCssquareRmsd
- the variable for computing overall Rmsd, added by zengsize
- the size of experimental RDCs, added by zeng
public double 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)
pdbVec
- the pdb coordinatesrdcVec
- the meausred RDC valuesatom1
- the atoms of which the internuclear vector has RDC valuesatom2
- the atoms of which the internuclear vector has RDC valuesmm
- the matrix used to rotate the original PDB frame to one of POFSxx
- the three diagonalized Saupe elementsSyy
- the three diagonalized Saupe elementsSzz
- the three diagonalized Saupe elementsrdcRatio
- the relative strength of RDCsrdcBc
- an array for returning the back-computed RDCssquareRmsd
- the variable for computing overall Rmsd, added by zengsize
- the size of experimental RDCs, added by zeng
public double 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)
pdbVec
- the pdb coordinatesrdcVec
- the meausred RDC valuesatom1
- the atoms of which the internuclear vector has RDC valuesatom2
- the atoms of which the internuclear vector has RDC valuesmm
- the matrix used to rotate the original PDB frame to one of POFSxx
- the three diagonalized Saupe elementsSyy
- the three diagonalized Saupe elementsSzz
- the three diagonalized Saupe elementsrdcRatio
- the relative strength of RDCs
public double 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)
pdbVec
- the pdb coordinatesrdcVec
- the meausred RDC valuesatom1
- the atoms of which the internuclear vector has RDC valuesatom2
- the atoms of which the internuclear vector has RDC valuesmm
- the matrix used to rotate the original PDB frame to one of POFSxx
- the three diagonalized Saupe elementsSyy
- the three diagonalized Saupe elementsSzz
- the three diagonalized Saupe elementsrdcRatio
- the relative strength of RDCsrdcBc
- an array for returning the back-computed RDCssquareRmsd
- the variable for computing overall Rmsd, added by zengsize
- the size of experimental RDCs, added by zengisPrint
- whether the RDC deviation at each residue is printed
public double 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)
pdbVec
- the pdb coordinatesrdcVec
- the meausred RDC valuesatom1
- the atoms of which the internuclear vector has RDC valuesatom2
- the atoms of which the internuclear vector has RDC valuesmm
- the matrix used to rotate the original PDB frame to one of POFSxx
- the three diagonalized Saupe elementsSyy
- the three diagonalized Saupe elementsSzz
- the three diagonalized Saupe elementsrdcRatio
- the relative strength of RDCs
public double 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)
pdbVec
- the pdb coordinatesrdcVec
- the meausred RDC valuesatom1
- the atoms of which the internuclear vector has RDC valuesatom2
- the atoms of which the internuclear vector has RDC valuesmm
- the matrix used to rotate the original PDB frame to one of POFSxx
- the three diagonalized Saupe elementsSyy
- the three diagonalized Saupe elementsSzz
- the three diagonalized Saupe elementsrdcRatio
- the relative strength of RDCsrdcBc
- an array for returning the back-computed RDCssquareRmsd
- the variable for computing overall Rmsd, added by zengsize
- the size of experimental RDCs, added by zengisPrint
- whether the RDC deviation is printed
public double 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)
pdbVec
- the pdb coordinatesrdcVec
- the meausred RDC valuesatom1
- the atoms of which the internuclear vector has RDC valuesatom2
- the atoms of which the internuclear vector has RDC valuesmm
- the matrix used to rotate the original PDB frame to one of POFSxx
- the three diagonalized Saupe elementsSyy
- the three diagonalized Saupe elementsSzz
- the three diagonalized Saupe elementsrdcRatio
- the relative strength of RDCs
public double 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)
pdbVec
- the pdb coordinatesrdcVec
- the meausred RDC valuesatom1
- the atoms of which the internuclear vector has RDC valuesatom2
- the atoms of which the internuclear vector has RDC valuesmm
- the matrix used to rotate the original PDB frame to one of POFSxx
- the three diagonalized Saupe elementsSyy
- the three diagonalized Saupe elementsSzz
- the three diagonalized Saupe elementsrdcRatio
- the relative strength of RDCsrdcBc
- an array for returning the back-computed RDCs
public double 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)
pdbVec
- the pdb coordinatesrdcVec
- the meausred RDC valuesatom1
- the atoms of which the internuclear vector has RDC valuesatom2
- the atoms of which the internuclear vector has RDC valuesSxx
- the three diagonalized Saupe elementsSyy
- the three diagonalized Saupe elementsSzz
- the three diagonalized Saupe elementsrdcRatio
- the relative strength of RDCsrdcBc
- an array for returning the back-computed RDCsmm
- the matrix used to rotate the original PDB frame to one of POF
public double[] BackCalRdcs(java.util.Vector pdbVec, java.util.Vector rdcVec, java.lang.String atom1, java.lang.String atom2, Matrix mm, double Sxx, double Syy, double Szz)
pdbVec
- the pdb coordinatesrdcVec
- the meausred RDC valuesatom1
- the atoms of which the internuclear vector has RDC valuesatom2
- the atom2mm
- the matrix used to rotate the original PDB frame to one of POFSxx
- the three diagonalized Saupe elementsSyy
- the syySzz
- the szz
public Matrix 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)
pdbVec
- coordinate vectorrdcVec1
- nh rdc vectorrdcVec2
- ch rdc vectorresolution
- resolution in the grid searchRdcRmsdThreshold
- rdc rmsd thresholdrmsds
- return rdc rmsd
return the best rotation matrix in terms of rdc rmsdSyy
- the syySzz
- the szzdebug
- the debug
public Matrix 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)
pdbVec
- a vector of Pdb object corresponding to the structural fragment.rdcVec1
- a vector of NH RDC valuesrdcVec2
- a vector of CH RDC valuesSzz
- the three diagonalized Saupe elementsSyy
- the three diagonalized Saupe elementsrmsds
- for returning the RDC RMSDs in the order of RDC for medium 1 and medium 2resolution
- the resolution in the grid-searchdebug
- if true, it will print the progress of the fittingrdcVecCaCo
- the rdc vec ca cordcVecCoN
- the rdc vec co n
public Matrix 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)
pdbVec
- a vector of Pdb object corresponding to the structural fragment.rdcVec1
- a vector of NH RDC valuesrdcVec2
- a vector of CH RDC valuesSzz
- the three diagonalized Saupe elementsSyy
- the three diagonalized Saupe elementsrmsds
- for returning the RDC RMSDs in the order of RDC for medium 1 and medium 2resolution
- the resolution in the grid-searchdebug
- if true, it will print the progress of the fitting
public Matrix eulerFit_old(java.util.Vector pdbVec, java.util.Vector rdcVec1, java.util.Vector rdcVec2, double Syy, double Szz, double[] rmsds, double resolution, boolean debug)
pdbVec
- a vector of Pdb object corresponding to the structural fragment.rdcVec1
- a vector of NH RDC valuesrdcVec2
- a vector of CH RDC valuesrmsds
- for returning the RDC RMSDs in the order of RDC for medium 1 and medium 2resolution
- the resolution in the grid-searchdebug
- if true, it will print the progress of the fittingSyy
- the syySzz
- the szz
public Matrix fit4MissingRdc(java.util.Vector pdbVec, java.util.Vector rdcVec1, java.util.Vector rdcVec2, double Syy, double Szz, double[] rmsds, double resolution, boolean debug)
pdbVec
- a vector of Pdb object corresponding to the structural fragment.rdcVec1
- a vector of NH RDCrdcVec2
- a vector of CH RDCrmsds
- saving the RDC RMSDs and hbScore in the order: rmsdRDC1, rmsdRDC2, hbScore.resolution
- the resolution in grid search on angle spacedebug
- if true will print the progress of the searchSyy
- the syySzz
- the szz
public Matrix fit4MissingRdcHB(java.util.Vector pdbVec, java.util.Vector rdcVec1, java.util.Vector rdcVec2, double Syy, double Szz, java.util.Vector pdbVecA, double[] rmsds, double resolution, double weight4HB, java.util.Vector hbVec, boolean debug)
pdbVec
- a vector of Pdb object corresponding to the structural fragment.rdcVec1
- a vector of NH RDCrdcVec2
- a vector of CH RDCrmsds
- saving the RDC RMSDs and hbScore in the order: rmsdRDC1, rmsdRDC2, hbScore.resolution
- the resolution in grid search on angle spaceweight4HB
- relative weight for the H-bond in the score functionpdbVecA
- the H-bond parter of current fragment being searchedhbVec
- the identity of H-bondsdebug
- if true will print the progress of the searchSyy
- the syySzz
- the szz
public Matrix fit4MissingRdcHB2(java.util.Vector pdbVec, java.util.Vector rdcVec1, java.util.Vector rdcVec2, double Syy, double Szz, java.util.Vector pdbVecA1, java.util.Vector pdbVecA2, double[] rmsds, double resolution, double weight4HB, java.util.Vector hbVec1, java.util.Vector hbVec2, boolean debug)
pdbVec
- a vector of Pdb object corresponding to the structural fragment.rdcVec1
- a vector of NH RDCrdcVec2
- a vector of CH RDCrmsds
- saving the RDC RMSDs and hbScore in the order: rmsdRDC1, rmsdRDC2, hbScore.resolution
- the resolution in grid search on angle spaceweight4HB
- relative weight for the H-bond in the score functionpdbVecA1
- the H-bond parter of current fragment being searchedpdbVecA2
- another H-bond parter of current fragment being searcheddebug
- if true will print the progress of the searchSyy
- the syySzz
- the szzhbVec1
- the hb vec1hbVec2
- the hb vec2
public Matrix eulerFitHB(java.util.Vector pdbVec, java.util.Vector rdcVec1, java.util.Vector rdcVec2, double[] saupe, Matrix rot, double[] rmsds, double resolution, double weight4HB, java.util.Vector pdbVecS1, java.util.Vector hbVec, Matrix mat4Dirs, boolean debug)
pdbVec
- a vector of Pdb object corresponding to the structural fragment.rdcVec1
- a vector of RDC values from medium 1rdcVec2
- a vector of RDC values from medium 2saupe
- four diagnolized Saupe elements in the order of {Syy1, Szz1, Syy2, Szz2}rot
- The relative rotation matrix between the 2 POFs.rmsds
- saving the RDC RMSDs and hbScore in the order: rmsdRDC1, rmsdRDC2, hbScore.resolution
- the resolution in grid search on angle spaceweight4HB
- relative weight for the H-bond in the score functionpdbVecS1
- the H-bond parter of current fragment being searchedhbVec
- the identity of H-bondsmat4Dirs
- the matrix specifying one of the possible orientations.debug
- if true will print the progress of the search
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