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SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.ObjectRdcPanda.ModelRdc
public class ModelRdc
A program for computing all the backbond dihedral ($\phi$, $\psi$) angles of an $\alpha$-helix or a $\beta$-strand based on exact solution and a systematic search. The computed dihedral angles will (a) satisfy the experimental CH and NH RDCs as well as possible and (b) simultaneously have the ($\phi$, $\psi$) angles as close as possible to their average values in the PDB. However, the minimum is defined with respect to the all the backbone angles and all the RDCs for a secondary element, not just one residue. Please see the paper for the detail. In other words, the target function consists of terms representing, respectively, the deviation from the average helix and the deviation from the measured RDCs. Also included are programs for building models from a sequence of ($\phi, \psi$) angles and eight backbone angles with values beings set to be their averages extracted from 23 ultra-high resolution PDBS with protons built in. Written by Lincong Wang (2001-2005) and Jianyang (Michael) Zeng (2005-2009).
Nested Class Summary | |
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static class |
ModelRdc.mdComparator
The Class mdComparator. |
Constructor Summary | |
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ModelRdc()
Instantiates a new model rdc. |
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ModelRdc(int No)
Instantiates a new model rdc. |
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ModelRdc(int no,
java.lang.String re,
double x,
double y)
Instantiates a new model rdc. |
Method Summary | |
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double[] |
addCoords(double[] n1,
double[] n2)
adding two vectors. |
Pdb |
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. |
java.util.Vector |
coordByBackwardNew(double phi,
double psi,
double[] n1,
double[] nh1,
double[] ca1,
int residueNo)
By Michael Zeng. |
Pdb |
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 |
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. |
double[] |
dirCos(double[] vec)
cal the directioal cosines of the vector vec. |
double |
getPhi()
Gets the phi. |
double |
getPsi()
Gets the psi. |
java.lang.String |
getResidue()
Gets the residue. |
int |
getResidueNo()
Gets the residue no. |
double[][] |
haCoCoords(double phi,
double[] n1,
double[] nh1,
double[] ca1)
A method for computing coordinates of backbone atoms. |
double[][] |
haCoCoords(double phi,
double[] n1,
double[] nh1,
double[] ca1,
boolean first)
A method for computing coordinates of backbone atoms. |
double |
interAngle(double[] v1,
double[] v2)
calculate the angles between two vectors v1 and v2 The returned angle is in the [0,Pi] range. |
double[] |
internuclearVec(double[] n1,
double[] n2)
Compute the internuclear vector between two atoms. |
double |
length(double[] v1)
compute the length of a vector v1. |
java.util.Vector |
minBeta(java.util.Vector rdcVec1,
java.util.Vector rdcVec2,
double[] rdc1Cal,
double[] rdc2Cal,
java.util.Vector pdbVec2,
double Syy,
double Szz,
double rmsd1,
double rmsd2,
java.util.Vector pdbS1,
java.util.Vector hbVecOfE12,
int nCycle,
double weight4Angles,
double hbWeight,
boolean debugDFS,
boolean printResults)
A recusive function to compute all the backbone Phi/Psi for an n-residue fragment. |
java.util.Vector |
minBeta2(java.util.Vector rdcVec1,
java.util.Vector rdcVec2,
double[] rdc1Cal,
double[] rdc2Cal,
java.util.Vector pdbVec2,
double Syy,
double Szz,
double rmsd1,
double rmsd2,
java.util.Vector pdbS1,
java.util.Vector pdbS2,
java.util.Vector hbVecOfE12,
java.util.Vector hbVecOfE13,
int nCycle,
double weight4Angles,
double hbWeight,
boolean debugDFS,
boolean printResults)
A recusive function to compute all the backbone Phi/Psi for an n-residue fragment. |
java.util.Vector |
minHelix_old(java.util.Vector rdcVec1,
java.util.Vector rdcVec2,
double[] rdc1Cal,
double[] rdc2Cal,
java.util.Vector 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 fragment. |
java.util.Vector<Pdb> |
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> |
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> |
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> |
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> |
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 |
minTurns(java.util.Vector h1Vec,
java.util.Vector asgVec,
java.util.Vector pdbVec1,
java.util.Vector pdbVec2,
java.util.Vector rdcVec1,
java.util.Vector rdcVec2,
double Syy,
double Szz,
int no1,
int no2,
double a1,
double a2)
Compute the turns based on NOEs and RDCs. |
java.util.Vector |
modelBuild(double[] phiArr,
double[] psiArr,
double[] n1,
double[] nh1,
double[] ca1,
int no1,
boolean first)
Build model (compute the coordinates of backbone atoms (N, NH, CA, CO, O and HA) from the standard geometry and Phi/Psi angle. |
java.util.Vector |
modelBuild(java.util.Vector phiPsiVec,
double[] n1,
double[] nh1,
double[] ca1)
Build model (compute the coordinates of backbone atoms (N, NH, CA, CO, O and HA) from the standard geometry and Phi/Psi angle. |
java.util.Vector |
modelBuild(java.util.Vector phiPsiVec,
double[] n1,
double[] nh1,
double[] ca1,
boolean isLink)
Model build. |
java.util.Vector |
modelBuildLoopBackward(java.util.Vector phiPsiVec,
double[] nCoord,
double[] nhCoord,
double[] caCoord,
int startNo,
int endNo)
By Michael Zeng. |
double[][] |
nNhCaCal(double phi,
double psi,
double[] n,
double[] nh,
double[] ca)
A method for computing coordinates of backbone atoms. |
double[][] |
nNhCaCal(double phi,
double psi,
double[] n,
double[] nh,
double[] ca,
boolean first)
A method for computing coordinates of backbone atoms. |
double[][] |
nNhCaHaByBackward(double phi,
double psi,
double[] n1,
double[] nh1,
double[] ca1)
A method for computing coordinates of backbone atoms backward: with direasing residue no. |
void |
PrintAllByGridSearch(java.util.Vector vecHelixBB,
java.util.Vector<Dipolar> rdc1Vec,
java.util.Vector<Dipolar> rdc2Vec,
double Syy,
double Szz,
double resolution,
double rdcRmsdThreshold)
Prints the all by grid search. |
java.util.Vector |
refineHelix(java.util.Vector rdcVec1,
java.util.Vector rdcVec2,
double[] n2ca,
double Syy,
double Szz,
java.util.Map heliceMap)
For computing the Helix. |
java.util.Vector<Pdb> |
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> |
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> |
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> |
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> |
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 |
refineSaupe(java.util.Vector rdc1Vec,
java.util.Vector rdc2Vec,
double[] saupe,
double[] ramaFilter,
double phiAve,
double psiAve,
int refineCycle,
int nCycle,
boolean debugDFS,
boolean printResults,
java.util.Vector vecTalos)
Refine Saupe elements from an initial model. |
java.util.Vector |
refineSaupe2(java.util.Vector pdbVec,
java.util.Vector paraVec,
java.util.Vector eRdc1Vec,
java.util.Vector eRdc2Vec,
java.util.Vector helixRdc1,
java.util.Vector helixRdc2,
double[] saupeSave)
This is an old function. |
java.util.Vector<Pdb> |
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 |
refineSaupe4RDCsWOAT(java.util.Vector rdc1Vec,
java.util.Vector rdc2Vec,
java.util.Vector rdcCaCoVec,
java.util.Vector rdcCoNVec,
double[] saupe,
double[] ramaFilter,
double phiAve,
double psiAve,
int refineCycle,
int nCycle,
boolean debugDFS,
boolean printResults,
java.util.Vector vecTalos)
Refine Saupe elements from an initial model. |
java.util.Vector |
refineSaupe4RDCsWOAT(java.util.Vector vecPreBB,
java.util.Vector pdbVec,
java.util.Vector rdc1Vec,
java.util.Vector rdc2Vec,
java.util.Vector rdcCaCoVec,
java.util.Vector rdcCoNVec,
double[] saupe,
double[] ramaFilter,
double phiAve,
double psiAve,
int refineCycle,
int nCycle,
boolean debugDFS,
boolean printResults,
java.util.Vector vecTalos,
double wtCoCa,
double wtCoN,
int starNo,
int endNo,
java.util.Vector vecSeq)
Refine Saupe elements from an initial model. |
java.util.Vector |
refineStrand(java.util.Vector rdc1Vec,
java.util.Vector rdc2Vec,
double Syy,
double Szz,
double[] ramaFilter,
double phiAve,
double psiAve,
int refineCycle,
int initialCycle,
double w4Angles,
double resolution,
boolean debugDFS,
boolean printResults)
For computing the first Strand which is NOT H-bonded to others. |
java.util.Vector |
refineStrand(java.util.Vector rdc1Vec,
java.util.Vector rdc2Vec,
double Syy,
double Szz,
double phiAve,
double psiAve,
int refineCycle,
int initialCycle,
double resolution,
double angleWeight,
double hbWeight,
java.util.Vector pdbS1,
java.util.Vector hBVecOfE21,
boolean printEulerSearch,
boolean debugDFS,
boolean printResults)
For computing the others Strands which IS H-bonded to others. |
java.util.Vector |
refineStrand2(java.util.Vector rdc1Vec,
java.util.Vector rdc2Vec,
double Syy,
double Szz,
double phiAve,
double psiAve,
int refineCycle,
int initialCycle,
double resolution,
double angleWeight,
double hbWeight,
java.util.Vector pdbE1,
java.util.Vector HbondVec,
boolean printEulerSearch,
boolean debugDFS,
boolean printResults)
For computing the others Strands which IS H-bonded to others. |
java.lang.String |
toString()
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Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public ModelRdc()
public ModelRdc(int No)
No
- the nopublic ModelRdc(int no, java.lang.String re, double x, double y)
no
- the nore
- the rex
- the xy
- the yMethod Detail |
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public int getResidueNo()
public java.lang.String getResidue()
public double getPhi()
public double getPsi()
public java.lang.String toString()
toString
in class java.lang.Object
public double length(double[] v1)
v1
- the v1
public double interAngle(double[] v1, double[] v2)
v1
- the v1v2
- the v2
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[] addCoords(double[] n1, double[] n2)
n1
- the coordinate (direction cosine) for vector n1n2
- the coordinate (direction cosine) for vector n2
public double[][] haCoCoords(double phi, double[] n1, double[] nh1, double[] ca1)
phi
- The backbone \phi anglen1
- the direction cosine for amide nitrogen of the original residuenh1
- the direction cosine for amide protonca1
- the direction cosine for Ca
public double[][] haCoCoords(double phi, double[] n1, double[] nh1, double[] ca1, boolean first)
phi
- The backbone \phi anglen1
- the direction cosine for amide nitrogen of the original residuenh1
- the direction cosine for amide protonca1
- the direction cosine for Cafirst
- whether the residue is the first residue of the fragment, if it is the first the
rotational matrix should be identity
public void PrintAllByGridSearch(java.util.Vector vecHelixBB, java.util.Vector<Dipolar> rdc1Vec, java.util.Vector<Dipolar> rdc2Vec, double Syy, double Szz, double resolution, double rdcRmsdThreshold)
vecHelixBB
- the vec helix bbrdc1Vec
- the rdc1 vecrdc2Vec
- the rdc2 vecSyy
- the syySzz
- the szzresolution
- the resolutionrdcRmsdThreshold
- the rdc rmsd thresholdpublic double[][] nNhCaCal(double phi, double psi, double[] n, double[] nh, double[] ca)
phi
- The backbone \phi anglepsi
- The backbone \psi anglen
- the nnh
- the nhca
- the ca
public double[][] nNhCaCal(double phi, double psi, double[] n, double[] nh, double[] ca, boolean first)
phi
- The backbone \phi anglepsi
- The backbone \psi anglefirst
- whether the residue is the first residue of the fragmentn
- the nnh
- the nhca
- the ca
public double[][] nNhCaHaByBackward(double phi, double psi, double[] n1, double[] nh1, double[] ca1)
phi
- The backbone \phi_i anglepsi
- The backbone \psi_i anglen1
- the coordinate of amide nitrogen of the residue (i+1)nh1
- the coordinate of amide proton atom of residue (i+1)ca1
- the coordinates of Ca atom of residue (i+1)
public Pdb coordByBackward(double phi, double psi, double[] n1, double[] nh1, double[] ca1, int residueNo, java.lang.String resid1)
phi
- The backbone \phi_i anglepsi
- The backbone \psi_i anglen1
- the coordinate of amide nitrogen of the residue (i+1)nh1
- the coordinate of amide proton atom of residue (i+1)ca1
- the coordinates of Ca atom of residue (i+1)residueNo
- the residue number of residue iresid1
- the name of the residue i
public java.util.Vector coordByBackwardNew(double phi, double psi, double[] n1, double[] nh1, double[] ca1, int residueNo)
phi
- The backbone \phi_i anglepsi
- The backbone \psi_i anglen1
- the coordinate of amide nitrogen of the residue (i+1)nh1
- the coordinate of amide proton atom of residue (i+1)ca1
- the coordinates of Ca atom of residue (i+1)residueNo
- the residue number of residue i
public Pdb coordByResidue(double phi, double psi, double[] n1, double[] nh1, double[] ca1, int residueNo, java.lang.String resid1, boolean first)
phi
- The backbone \phi anglepsi
- The backbone \psi anglen1
- the direction cosine for amide nitrogen of the original residuenh1
- the direction cosine for amide protonca1
- the direction cosine for CaresidueNo
- the residue numberresid1
- the name of the residuefirst
- whether the residue is the first residue of the fragment
public Pdb coordByResidueFull(double phi, double psi, double[] n1, double[] nh1, double[] ca1, int residueNo, java.lang.String resid1, boolean first)
phi
- The backbone \phi anglepsi
- The backbone \psi anglen1
- the direction cosine for amide nitrogen of the original residuenh1
- the direction cosine for amide protonca1
- the direction cosine for CaresidueNo
- the residue numberresid1
- the name of the residuefirst
- whether the residue is the first residue of the fragment
public java.util.Vector modelBuild(java.util.Vector phiPsiVec, double[] n1, double[] nh1, double[] ca1)
phiPsiVec
- an array of Phi/Psi angles for the fragment.n1
- the direction cosine for amide nitrogen of the first residuenh1
- the direction cosine for amide protonca1
- the direction cosine for Ca
public java.util.Vector modelBuild(java.util.Vector phiPsiVec, double[] n1, double[] nh1, double[] ca1, boolean isLink)
phiPsiVec
- the phi psi vecn1
- the n1nh1
- the nh1ca1
- the ca1isLink
- the is link
public java.util.Vector modelBuildLoopBackward(java.util.Vector phiPsiVec, double[] nCoord, double[] nhCoord, double[] caCoord, int startNo, int endNo)
phiPsiVec
- the vector for storing phi/psi anglesstartNo
- the first residue number, which is the end of backward computation.endNo
- the residue number of the last residue for starting the backward computation.nCoord
- the n coordnhCoord
- the nh coordcaCoord
- the ca coord
public java.util.Vector modelBuild(double[] phiArr, double[] psiArr, double[] n1, double[] nh1, double[] ca1, int no1, boolean first)
phiArr
- an array of Phi angles for the fragment.psiArr
- an array of Psi angles for the fragment.n1
- the direction cosine for amide nitrogen of the first residuenh1
- the direction cosine for amide protonca1
- the direction cosine for Cano1
- the residue number of the first residue of a fragmentfirst
- whether the residue is the first residue of the fragment
public java.util.Vector<Pdb> 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) throws JampackException
vecBB
- the vec bbrdc1Vec
- the rdc1 vecrdc2Vec
- the rdc2 vechelixRdcCaCoVec
- the helix rdc ca co vechelixRdcCoNVec
- the helix rdc co n vecSyy
- the syySzz
- the szzramaFilter
- the rama filterphiAve
- the phi avepsiAve
- the psi averefineCycle
- the refine cycleinitialCycle
- the initial cyclew4Angles
- the w4 anglesresolution
- the resolutiondebugDFS
- the debug dfsprintResults
- the print resultsvecTalos
- the vec talos
JampackException
- the jampack exceptionpublic java.util.Vector<Pdb> 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) throws JampackException
rdc1Vec
- NH RDCsrdc2Vec
- CH RDCsSyy
- the Saupe elementSzz
- the Saupe elementrefineCycle
- the number of cycles for iterating through the refinement
and computation of Saupe matrices.initialCycle
- the number of initial cycles for the DFS-based systematic search.w4Angles
- weight for the \phi and \psi angles in the score funtionresolution
- the resolution for the grid-search for the first peptide planedebugDFS
- for monitoring the progress in systematic search-based minimizationprintResults
- for printing the results for each iterationwtCoCa
- the weight for CoCa RDCwtCoN
- the weight for NCo RDCvecPreBB
- previous strcturevecBB
- the vec bbhelixRdcCaCoVec
- the helix rdc ca co vechelixRdcCoNVec
- the helix rdc co n vecramaFilter
- the rama filterphiAve
- the phi avepsiAve
- the psi avevecTalos
- the vec talosstarNo
- the star noendNo
- the end novecSeq
- the vec seq
JampackException
- the jampack exceptionpublic java.util.Vector<Pdb> 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) throws JampackException
vecBB
- the vec bbrdc1Vec
- the rdc1 vecrdc2Vec
- the rdc2 vecSyy
- the syySzz
- the szzramaFilter
- the rama filterphiAve
- the phi avepsiAve
- the psi averefineCycle
- the refine cycleinitialCycle
- the initial cyclew4Angles
- the w4 anglesresolution
- the resolutiondebugDFS
- the debug dfsprintResults
- the print resultsvecTalos
- the vec talos
JampackException
- the jampack exceptionpublic java.util.Vector<Pdb> 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)
rdcVec1
- an array of CH RDCs for the fragmentrdcVec2
- an array of NH RDCs for the fragmentrdc1Cal
- an array for storing the back-computed RDcsrdc2Cal
- an array for storing the back-computed RDcspdbVec
- the pdb vector previously computed or build from scratch.debugDFS
- if true, print out the information for debuggingprintResults
- if true, print out the information for debuggingisHelix
- if true, the last \psi angle is the average value for helix, otherwise, for betaSyy
- the syySzz
- the szzrmsd1
- the rmsd1rmsd2
- the rmsd2nCycle
- the n cycleweightAngles
- the weight angles
public java.util.Vector<Pdb> 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) throws JampackException
rdcVec1
- an array of CH RDCs for the fragmentrdcVec2
- an array of NH RDCs for the fragmentrdc1Cal
- an array for storing the back-computed RDcsrdc2Cal
- an array for storing the back-computed RDcspdbVec
- the pdb vector previously computed or build from scratch.debugDFS
- if true, print out the information for debuggingprintResults
- if true, print out the information for debuggingisHelix
- if true, the last \psi angle is the average value for helix, otherwise, for betaSyy
- the syySzz
- the szzrmsd1
- the rmsd1rmsd2
- the rmsd2nCycle
- the n cycleweightAngles
- the weight anglesvecTalos
- the vec talos
JampackException
- the jampack exceptionpublic java.util.Vector<Pdb> 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) throws JampackException
rdcVec1
- an array of CH RDCs for the fragmentrdcVec2
- an array of NH RDCs for the fragmentrdc1Cal
- an array for storing the back-computed RDcsrdc2Cal
- an array for storing the back-computed RDcspdbVec
- the pdb vector previously computed or build from scratch.debugDFS
- if true, print out the information for debuggingprintResults
- if true, print out the information for debuggingisHelix
- if true, the last \psi angle is the average value for helix, otherwise, for betavecTalos
- talos angle tablewtCoCa
- weight for CaCo rdcwtCoN
- weight for CoN RDChelixRdcCaCoVec
- the helix rdc ca co vechelixRdcCoNVec
- the helix rdc co n vecSyy
- the syySzz
- the szzrmsd1
- the rmsd1rmsd2
- the rmsd2nCycle
- the n cycleweightAngles
- the weight angles
JampackException
- the jampack exceptionpublic java.util.Vector<Pdb> 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) throws JampackException
vecPrePdb
- previous structurerdcVec1
- an array of CH RDCs for the fragmentrdcVec2
- an array of NH RDCs for the fragmentrdc1Cal
- an array for storing the back-computed RDcsrdc2Cal
- an array for storing the back-computed RDcspdbVec
- the pdb vector previously computed or build from scratch.debugDFS
- if true, print out the information for debuggingprintResults
- if true, print out the information for debuggingisHelix
- if true, the last \psi angle is the average value for helix, otherwise, for betavecTalos
- talos angle tablewtCoCa
- weight for CaCo rdcwtCoN
- weight for CoN RDChelixRdcCaCoVec
- the helix rdc ca co vechelixRdcCoNVec
- the helix rdc co n vecSyy
- the syySzz
- the szzrmsd1
- the rmsd1rmsd2
- the rmsd2nCycle
- the n cycleweightAngles
- the weight anglesstartNo
- the start noendNo
- the end novecSeq
- the vec seq
JampackException
- the jampack exceptionpublic java.util.Vector<Pdb> 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)
rdcVec1
- an array of CH RDCs for the fragmentrdcVec2
- an array of NH RDCs for the fragmentrdc1Cal
- an array for storing the back-computed RDcsrdc2Cal
- an array for storing the back-computed RDcspdbVec
- the pdb vector previously computed or build from scratch.debugDFS
- if true, print out the information for debuggingprintResults
- if true, print out the information for debuggingisHelix
- if true, the last \psi angle is the average value for helix, otherwise, for betaSyy
- the syySzz
- the szzrmsd1
- the rmsd1rmsd2
- the rmsd2nCycle
- the n cycleweightAngles
- the weight anglesNhRdcRmsd
- the nh rdc rmsdChRdcRmsd
- the ch rdc rmsd
public java.util.Vector minHelix_old(java.util.Vector rdcVec1, java.util.Vector rdcVec2, double[] rdc1Cal, double[] rdc2Cal, java.util.Vector pdbVec, double Syy, double Szz, double rmsd1, double rmsd2, int nCycle, double weightAngles, boolean debugDFS, boolean printResults, boolean isHelix)
rdcVec1
- an array of CH RDCs for the fragmentrdcVec2
- an array of NH RDCs for the fragmentrdc1Cal
- the rdc1 calrdc2Cal
- the rdc2 calpdbVec
- the pdb vecSyy
- the syySzz
- the szzrmsd1
- the rmsd1rmsd2
- the rmsd2nCycle
- the n cycleweightAngles
- the weight anglesdebugDFS
- the debug dfsprintResults
- the print resultsisHelix
- the is helix
public java.util.Vector<Pdb> refineSaupe3(java.util.Vector<Pdb> pdbVec, java.util.Vector<Dipolar> nhRdc, java.util.Vector<Dipolar> cahaRdc, double[] saupeSave)
pdbVec
- the Pdb vector before the updatesaupeSave
- for saving the computed Saupe elements {Syy, Szz, rmsd4NHRDC, rmsd4CHRDC}nhRdc
- the nh rdccahaRdc
- the caha rdc
public java.util.Vector minBeta(java.util.Vector rdcVec1, java.util.Vector rdcVec2, double[] rdc1Cal, double[] rdc2Cal, java.util.Vector pdbVec2, double Syy, double Szz, double rmsd1, double rmsd2, java.util.Vector pdbS1, java.util.Vector hbVecOfE12, int nCycle, double weight4Angles, double hbWeight, boolean debugDFS, boolean printResults)
rdcVec1
- an array of CH RDCs for the fragmentrdcVec2
- an array of NH RDCs for the fragmentrdc1Cal
- has the back-computed CH RDCs for handling missing datardc2Cal
- has the back-computed NH RDCs for handling missing dataSyy
- Saupe elementsSzz
- Saupe elementsrmsd1
- the CH RDC rmsd before the refinementrmsd2
- the NH RDC rmsd before the refinementpdbS1
- the computed Strands H-bonded to the to be refined StrandhbVecOfE12
- the vector with H-bond information between the two strandspdbVec2
- the pdb vec2nCycle
- the n cycleweight4Angles
- the weight4 angleshbWeight
- the hb weightdebugDFS
- the debug dfsprintResults
- the print results
public java.util.Vector minBeta2(java.util.Vector rdcVec1, java.util.Vector rdcVec2, double[] rdc1Cal, double[] rdc2Cal, java.util.Vector pdbVec2, double Syy, double Szz, double rmsd1, double rmsd2, java.util.Vector pdbS1, java.util.Vector pdbS2, java.util.Vector hbVecOfE12, java.util.Vector hbVecOfE13, int nCycle, double weight4Angles, double hbWeight, boolean debugDFS, boolean printResults)
rdcVec1
- an array of CH RDCs for the fragmentrdcVec2
- an array of NH RDCs for the fragmentrdc1Cal
- has the back-computed CH RDCs for handling missing datardc2Cal
- has the back-computed NH RDCs for handling missing dataSyy
- Saupe elementsSzz
- Saupe elementsrmsd1
- the CH RDC rmsd before the refinementrmsd2
- the NH RDC rmsd before the refinementpdbS1
- the computed Strands H-bonded to the to be refined StrandhbVecOfE12
- the vector with H-bond information between the two strandspdbVec2
- the pdb vec2pdbS2
- the pdb s2hbVecOfE13
- the hb vec of e13nCycle
- the n cycleweight4Angles
- the weight4 angleshbWeight
- the hb weightdebugDFS
- the debug dfsprintResults
- the print results
public java.util.Vector minTurns(java.util.Vector h1Vec, java.util.Vector asgVec, java.util.Vector pdbVec1, java.util.Vector pdbVec2, java.util.Vector rdcVec1, java.util.Vector rdcVec2, double Syy, double Szz, int no1, int no2, double a1, double a2)
no1
- the first residue of the fragment (turn and loop)no2
- the last residue of the fragment (turn and loop)h1Vec
- resonance assignment sorted by H1 CS shift.asgVec
- the merged resonacs assigement and HN and HA NOEsrdcVec1
- the CH RDCrdcVec2
- the NH RDCa1
- the constant used to convert the intensity to distancea2
- the constant used to convert the intensity to distancepdbVec1
- the structure for the beginning side of turn or looppdbVec2
- the structure for the end side of turn or loopSyy
- the diagnolized Saupe elementsSzz
- the diagnolized Saupe elements
public java.util.Vector refineSaupe4RDCsWOAT(java.util.Vector rdc1Vec, java.util.Vector rdc2Vec, java.util.Vector rdcCaCoVec, java.util.Vector rdcCoNVec, double[] saupe, double[] ramaFilter, double phiAve, double psiAve, int refineCycle, int nCycle, boolean debugDFS, boolean printResults, java.util.Vector vecTalos) throws JampackException
rdc1Vec
- NH RDCsrdc2Vec
- CH RDCsrefineCycle
- the number of cycles for iterating through the refinement
and computation of Saupe matrices.nCycle
- the number of cycles for the refinement by DFS itself.ramaFilter
- the Ramachandran filter for the favorable phi and psi regionphiAve
- the average phi anglepsiAve
- the average psi angledebugDFS
- for monitoring the progress in systematic search-based minimizationprintResults
- for printing the results for each iterationrdcCaCoVec
- the rdc ca co vecrdcCoNVec
- the rdc co n vecsaupe
- the saupevecTalos
- the vec talos
JampackException
- the jampack exceptionpublic java.util.Vector refineSaupe4RDCsWOAT(java.util.Vector vecPreBB, java.util.Vector pdbVec, java.util.Vector rdc1Vec, java.util.Vector rdc2Vec, java.util.Vector rdcCaCoVec, java.util.Vector rdcCoNVec, double[] saupe, double[] ramaFilter, double phiAve, double psiAve, int refineCycle, int nCycle, boolean debugDFS, boolean printResults, java.util.Vector vecTalos, double wtCoCa, double wtCoN, int starNo, int endNo, java.util.Vector vecSeq) throws JampackException
rdc1Vec
- NH RDCsrdc2Vec
- CH RDCsrefineCycle
- the number of cycles for iterating through the refinement
and computation of Saupe matrices.nCycle
- the number of cycles for the refinement by DFS itself.ramaFilter
- the Ramachandran filter for the favorable phi and psi regionphiAve
- the average phi anglepsiAve
- the average psi angledebugDFS
- for monitoring the progress in systematic search-based minimizationprintResults
- for printing the results for each iterationvecPreBB
- the vec pre bbpdbVec
- the pdb vecrdcCaCoVec
- the rdc ca co vecrdcCoNVec
- the rdc co n vecsaupe
- the saupevecTalos
- the vec taloswtCoCa
- the wt co cawtCoN
- the wt co nstarNo
- the star noendNo
- the end novecSeq
- the vec seq
JampackException
- the jampack exceptionpublic java.util.Vector refineSaupe(java.util.Vector rdc1Vec, java.util.Vector rdc2Vec, double[] saupe, double[] ramaFilter, double phiAve, double psiAve, int refineCycle, int nCycle, boolean debugDFS, boolean printResults, java.util.Vector vecTalos) throws JampackException
rdc1Vec
- NH RDCsrdc2Vec
- CH RDCsrefineCycle
- the number of cycles for iterating through the refinement
and computation of Saupe matrices.nCycle
- the number of cycles for the refinement by DFS itself.ramaFilter
- the Ramachandran filter for the favorable phi and psi regionphiAve
- the average phi anglepsiAve
- the average psi angledebugDFS
- for monitoring the progress in systematic search-based minimizationprintResults
- for printing the results for each iterationsaupe
- the saupevecTalos
- the vec talos
JampackException
- the jampack exceptionpublic java.util.Vector refineSaupe2(java.util.Vector pdbVec, java.util.Vector paraVec, java.util.Vector eRdc1Vec, java.util.Vector eRdc2Vec, java.util.Vector helixRdc1, java.util.Vector helixRdc2, double[] saupeSave)
pdbVec
- the Pdb vector before the updateparaVec
- the set of parameters for computing fragment etc.eRdc1Vec
- RDC data for beta-strands //the following fours are just for convenienceeRdc2Vec
- RDC data for beta-strandshelixRdc1
- the helix rdc1helixRdc2
- the helix rdc2saupeSave
- the saupe save
public java.util.Vector<Pdb> 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)
vecBB
- the vec bbrdc1Vec
- the rdc1 vecrdc2Vec
- the rdc2 vecSyy
- the syySzz
- the szzramaFilter
- the rama filterphiAve
- the phi avepsiAve
- the psi averefineCycle
- the refine cycleinitialCycle
- the initial cyclew4Angles
- the w4 anglesresolution
- the resolutiondebugDFS
- the debug dfsprintResults
- the print resultsnhRdcRmsd
- the nh rdc rmsdchRdcRmsd
- the ch rdc rmsd
public java.util.Vector<Pdb> 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)
vecBB
- the vec bbrdc1Vec
- the rdc1 vecrdc2Vec
- the rdc2 vecSyy
- the syySzz
- the szzramaFilter
- the rama filterphiAve
- the phi avepsiAve
- the psi averefineCycle
- the refine cycleinitialCycle
- the initial cyclew4Angles
- the w4 anglesresolution
- the resolutiondebugDFS
- the debug dfsprintResults
- the print resultsnhRdcRmsd
- the nh rdc rmsdchRdcRmsd
- the ch rdc rmsd
public java.util.Vector refineHelix(java.util.Vector rdcVec1, java.util.Vector rdcVec2, double[] n2ca, double Syy, double Szz, java.util.Map heliceMap)
Syy
- the Saupe elementSzz
- the Saupe elementrdcVec1
- the rdc vec1rdcVec2
- the rdc vec2n2ca
- the n2caheliceMap
- the helice map
public java.util.Vector refineStrand(java.util.Vector rdc1Vec, java.util.Vector rdc2Vec, double Syy, double Szz, double[] ramaFilter, double phiAve, double psiAve, int refineCycle, int initialCycle, double w4Angles, double resolution, boolean debugDFS, boolean printResults)
rdc1Vec
- RDCs in medium 1rdc2Vec
- RDCs in medium 2refineCycle
- the number of cycles for iterating through the refinement
and computation of Saupe matrices.initialCycle
- the number of initial cycles for the DFS-based systematic search.ramaFilter
- the Ramachandran filter for the favorable phi and psi regionphiAve
- the average phi anglepsiAve
- the average psi anglew4Angles
- weight for the \phi and \psi angles in the score funtionresolution
- the resolution for the grid-search for the first peptide planedebugDFS
- for monitoring the progress in systematic search-based minimizationprintResults
- for printing the results for each iterationSyy
- the syySzz
- the szz
public java.util.Vector refineStrand(java.util.Vector rdc1Vec, java.util.Vector rdc2Vec, double Syy, double Szz, double phiAve, double psiAve, int refineCycle, int initialCycle, double resolution, double angleWeight, double hbWeight, java.util.Vector pdbS1, java.util.Vector hBVecOfE21, boolean printEulerSearch, boolean debugDFS, boolean printResults)
rdc1Vec
- RDCs in medium 1rdc2Vec
- RDCs in medium 2refineCycle
- the number of cycles for iterating through the refinement
and computation of Saupe matrices.Syy
- the syySzz
- the szzphiAve
- the phi avepsiAve
- the psi aveinitialCycle
- the initial cycleresolution
- the resolutionangleWeight
- the angle weighthbWeight
- the hb weightpdbS1
- the pdb s1hBVecOfE21
- the h b vec of e21printEulerSearch
- the print euler searchdebugDFS
- the debug dfsprintResults
- the print results
public java.util.Vector refineStrand2(java.util.Vector rdc1Vec, java.util.Vector rdc2Vec, double Syy, double Szz, double phiAve, double psiAve, int refineCycle, int initialCycle, double resolution, double angleWeight, double hbWeight, java.util.Vector pdbE1, java.util.Vector HbondVec, boolean printEulerSearch, boolean debugDFS, boolean printResults)
rdc1Vec
- RDCs in medium 1rdc2Vec
- RDCs in medium 2refineCycle
- the number of cycles for iterating through the refinement
and computation of Saupe matrices.Syy
- the syySzz
- the szzphiAve
- the phi avepsiAve
- the psi aveinitialCycle
- the initial cycleresolution
- the resolutionangleWeight
- the angle weighthbWeight
- the hb weightpdbE1
- the pdb e1HbondVec
- the hbond vecprintEulerSearch
- the print euler searchdebugDFS
- the debug dfsprintResults
- the print results
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