// see SimulationResult.CalculateBestFitRotation
public void CalculateBestFitRotation(Molecule mref, Molecule m)
{
int NAtomstotal = Math.Min(mref.NAtoms, m.NAtoms);
// rotation
Mapack.Matrix Rxt = new Mapack.Matrix(NAtomstotal, 3);
Mapack.Matrix Ry = new Mapack.Matrix(3, NAtomstotal);
for (int j = 0; j < NAtomstotal; j++)
{
Rxt[j, 0] = m.XLocal[j]; Rxt[j, 1] = m.YLocal[j]; Rxt[j, 2] = m.ZLocal[j];
Ry[0, j] = mref.XLocal[j]; Ry[1, j] = mref.YLocal[j]; Ry[2, j] = mref.ZLocal[j];
}
// Kabsch solution
Mapack.Matrix R = Ry * Rxt;
Mapack.SingularValueDecomposition svdR = new Mapack.SingularValueDecomposition(R);
Mapack.Matrix V = svdR.VMatrix;
Mapack.Matrix rS = new Mapack.Matrix(3, 3);
rS[0, 0] = 1.0 / svdR.Diagonal[0];
rS[1, 1] = 1.0 / svdR.Diagonal[1];
rS[2, 2] = (R.Determinant > 0.0) ? 1.0 / svdR.Diagonal[2] : -1.0 / svdR.Diagonal[2];
Mapack.Matrix Um = R * V * rS * V.Transpose();
Matrix3 U = new Matrix3(Um[0, 0], Um[0, 1], Um[0, 2],
Um[1, 0], Um[1, 1], Um[1, 2], Um[2, 0], Um[2, 1], Um[2, 2]);
this.BestFitRotation = Matrix3.RepairRotation(U);
}
/// <summary>
/// Best rotation to overlay with a reference structure
/// See Kabsch papers for details: Kabsch W. Acta Cryst. A32 (1976) 922, A34 (1978) 827
/// It is assumed that translations are already calculated in the same (weighted/unweighted) mode!!!
/// </summary>
/// <param name="refsr">reference structure</param>
/// <param name="weighted">apply weights = mass</param>
public void CalculateBestFitRotation(SimulationResult refsr, Boolean weighted)
{
if (Double.IsNaN(this.E) || Double.IsNaN(refsr.E))
{
this.BestFitRotation = Matrix3.E;
return;
}
Vector3 r, r1, r2;
Int32 NAtomstotal = 0, n;
Molecule m;
Double w;
for (Int32 i = 0; i < this.Molecules.Count; i++)
{
NAtomstotal += this.Molecules[i].NAtoms;
}
// rotation
Mapack.Matrix Rxt = new Mapack.Matrix(NAtomstotal, 3);
Mapack.Matrix Ry = new Mapack.Matrix(3, NAtomstotal);
n = 0;
for (Int32 i = 0; i < this.Molecules.Count; i++)
{
m = this.Molecules[i];
for (Int32 j = 0; j < m.NAtoms; j++)
{
r = new Vector3(m.XLocal[j], m.YLocal[j], m.ZLocal[j]);
r1 = this.Rotation[i] * r + this.Translation[i] + m.CM + this.BestFitTranslation;
r2 = refsr.Rotation[i] * r + refsr.Translation[i] + m.CM + refsr.BestFitTranslation;
w = weighted ? m.AtomMass[j] : 1.0;
Rxt[n, 0] = r1.X; Rxt[n, 1] = r1.Y; Rxt[n, 2] = r1.Z;
Ry[0, n] = r2.X * w; Ry[1, n] = r2.Y * w; Ry[2, n] = r2.Z * w;
n++;
}
}
// Kabsch solution
Mapack.Matrix R = Ry * Rxt;
Mapack.SingularValueDecomposition svdR = new Mapack.SingularValueDecomposition(R);
Mapack.Matrix V = svdR.VMatrix;
Mapack.Matrix rS = new Mapack.Matrix(3, 3);
rS[0, 0] = 1.0 / svdR.Diagonal[0];
rS[1, 1] = 1.0 / svdR.Diagonal[1];
rS[2, 2] = (R.Determinant > 0.0) ? 1.0 / svdR.Diagonal[2] : -1.0 / svdR.Diagonal[2];
Mapack.Matrix Um = R * V * rS * V.Transpose();
Matrix3 U = new Matrix3(Um[0, 0], Um[0, 1], Um[0, 2],
Um[1, 0], Um[1, 1], Um[1, 2], Um[2, 0], Um[2, 1], Um[2, 2]);
this.BestFitRotation = Matrix3.RepairRotation(U);
}
/// <summary>
/// Obtain polynomial coefficients
/// </summary>
public void Convert()
{
if (_x == null || _x.Length < _order + 1 || _y == null || _y.Length < _order + 1)
{
_c = new Double[] { 0.0, 1.0 };
return;
}
Int32 n = orderbox.Value + 1;
Int32 m = _x.Length;
Mapack.Matrix A = new Mapack.Matrix(m, n);
Mapack.Matrix B = new Mapack.Matrix(m, 1);
if (_inverse)
{
for (Int32 i = 0; i < m; i++)
{
A[i, 0] = 1.0;
for (Int32 j = 1; j < n; j++)
{
A[i, j] = A[i, j - 1] * _y[i];
}
B[i, 0] = _x[i];
}
}
else
{
for (Int32 i = 0; i < m; i++)
{
A[i, 0] = 1.0;
for (Int32 j = 1; j < n; j++)
{
A[i, j] = A[i, j - 1] * _x[i];
}
B[i, 0] = _y[i];
}
}
Mapack.Matrix Csolve = A.Solve(B);
_c = new Double[n];
for (Int32 j = 0; j < n; j++)
{
_c[j] = Csolve[j, 0];
}
coeftsarray.Value = _c;
// error
Mapack.Matrix E = A * Csolve - B;
errorBoxDouble.Value = E.FrobeniusNorm / Math.Sqrt((Double)m);
}
// process a structure
public double CalculateChi2(ref FilteringResult fr)
{
Molecule m;
if (fr.MoleculeWeakReference == null || !fr.MoleculeWeakReference.TryGetTarget(out m))
{
m = new Molecule(fr.FullFileName);
}
fr.MoleculeWeakReference = new WeakReference <Molecule>(m);
if (m.Error.Length > 0)
{
System.Windows.Forms.MessageBox.Show("Error reading file " + fr.FullFileName + ": " + m.Error, "Error",
System.Windows.Forms.MessageBoxButtons.OK, System.Windows.Forms.MessageBoxIcon.Error);
return(MiscData.ENotCalculated);
}
AVEngine av = new AVEngine(m, avparam);
Int32 natom, ilp = 0, ilp1, ilp2, iref, nref_total = 0;
List <Vector3[]> avcache = new List <Vector3[]>(labelingpos.Count);
Vector3[] t;
Vector3[] rmp = new Vector3[labelingpos.Count];
Vector3 cr, cm; Matrix3 U;
ReferenceAtom rr;
Double R06 = _filterParameters.R0 * _filterParameters.R0 * _filterParameters.R0 *
_filterParameters.R0 * _filterParameters.R0 * _filterParameters.R0,
dr, refrmsd_t = 0.0;
fr.E = 0.0;
fr.InvalidR = 0;
fr.RefRMSD = 0.0;
fr.Sigma1 = 0;
fr.Sigma2 = 0;
fr.Sigma3 = 0;
foreach (LabelingPosition l in this.labelingpos)
{
// calculate AVs and mean positions
if (l.AVData.AVType == AVSimlationType.SingleDyeR)
{
natom = Array.BinarySearch <Int32>(m.OriginalAtomID, l.AVData.AtomID);
av.Calculate1R(l.AVData.L, l.AVData.W, l.AVData.R, natom);
t = new Vector3[av.R.Length];
Array.Copy(av.R, t, av.R.Length);
avcache.Add(t);
rmp[ilp++] = av.Rmp;
}
else if (l.AVData.AVType == AVSimlationType.ThreeDyeR)
{
natom = Array.BinarySearch <Int32>(m.OriginalAtomID, l.AVData.AtomID);
av.Calculate3R(l.AVData.L, l.AVData.W, l.AVData.R1, l.AVData.R2, l.AVData.R3, natom);
t = new Vector3[av.R.Length];
Array.Copy(av.R, t, av.R.Length);
avcache.Add(t);
rmp[ilp++] = av.Rmp;
}
else if (l.AVData.AVType == AVSimlationType.None && referenceAtoms[ilp].Length > 0)
{
// align reference atoms with the structure
// translation
cr = new Vector3();
cm = new Vector3();
for (iref = 0; iref < referenceAtoms[ilp].Length; iref++)
{
rr = referenceAtoms[ilp][iref];
natom = rr.ConvertedN;
cr += rr;
cm += new Vector3(m.XLocal[natom] + m.CM.X, m.YLocal[natom] + m.CM.Y, m.ZLocal[natom] + m.CM.Z);
}
cr *= -1.0 / ((Double)referenceAtoms[ilp].Length);
cm *= -1.0 / ((Double)referenceAtoms[ilp].Length);
// rotation: see also SimulationResult.CalculateBestFitRotation
Mapack.Matrix Rxt = new Mapack.Matrix(referenceAtoms[ilp].Length, 3);
Mapack.Matrix Ry = new Mapack.Matrix(3, referenceAtoms[ilp].Length);
for (iref = 0; iref < referenceAtoms[ilp].Length; iref++)
{
rr = referenceAtoms[ilp][iref];
natom = rr.ConvertedN;
Rxt[iref, 0] = rr.X + cr.X; Rxt[iref, 1] = rr.Y + cr.Y; Rxt[iref, 2] = rr.Z + cr.Z;
Ry[0, iref] = m.XLocal[natom] + m.CM.X + cm.X;
Ry[1, iref] = m.YLocal[natom] + m.CM.Y + cm.Y;
Ry[2, iref] = m.ZLocal[natom] + m.CM.Z + cm.Z;
}
// Kabsch solution
Mapack.Matrix R = Ry * Rxt;
Mapack.SingularValueDecomposition svdR = new Mapack.SingularValueDecomposition(R);
Mapack.Matrix V = svdR.VMatrix;
Mapack.Matrix rS = new Mapack.Matrix(3, 3);
rS[0, 0] = 1.0 / svdR.Diagonal[0];
rS[1, 1] = 1.0 / svdR.Diagonal[1];
rS[2, 2] = (R.Determinant > 0.0) ? 1.0 / svdR.Diagonal[2] : -1.0 / svdR.Diagonal[2];
Mapack.Matrix Um = R * V * rS * V.Transpose();
U = new Matrix3(Um[0, 0], Um[0, 1], Um[0, 2],
Um[1, 0], Um[1, 1], Um[1, 2], Um[2, 0], Um[2, 1], Um[2, 2]);
U = Matrix3.RepairRotation(U);
// reference rmsd
for (iref = 0; iref < referenceAtoms[ilp].Length; iref++)
{
rr = referenceAtoms[ilp][iref];
natom = rr.ConvertedN;
refrmsd_t += Vector3.SquareNormDiff(U * (rr + cr),
new Vector3(m.XLocal[natom], m.YLocal[natom], m.ZLocal[natom]) + m.CM + cm);
nref_total++;
}
rmp[ilp++] = U * (l + cr) - cm;
avcache.Add(new Vector3[0]);
}
else
{
rmp[ilp++] = l;
avcache.Add(new Vector3[0]);
}
}
// calculate mp and FRET distances
Distance d, dmp;
Int32 activeR = 0;
fr.RModel = new DistanceList(dist.Count);
fr.RmpModel = new DistanceList(dist.Count);
fr.RmpModel.DataType = dist.DataType;
for (Int32 i = 0; i < dist.Count; i++)
{
dmp = new Distance();
d = new Distance();
dmp.Position1 = dist[i].Position1;
dmp.Position2 = dist[i].Position2;
d.Position1 = dist[i].Position1;
d.Position2 = dist[i].Position2;
ilp1 = labelingpos.FindIndex(d.Position1);
ilp2 = labelingpos.FindIndex(d.Position2);
dmp.R = Vector3.Abs(rmp[ilp1] - rmp[ilp2]);
if (dist.DataType == DistanceDataType.Rmp ||
labelingpos[ilp1].AVData.AVType == AVSimlationType.None || labelingpos[ilp2].AVData.AVType == AVSimlationType.None)
{
d.R = dmp.R; // i.e. no clouds -> Rmp
}
else if (dist.DataType == DistanceDataType.RDAMeanE)
{
if (avcache[ilp1].Length == 0 || avcache[ilp2].Length == 0)
{
d.R = Double.NaN;
}
else
{
d.R = FpsNativeWrapper.RdaMeanEFromAv(avcache[ilp1], avcache[ilp1].Length, avcache[ilp2], avcache[ilp2].Length,
avparam.ESamples, rnd.Next(), this._filterParameters.R0);
}
}
else if (dist.DataType == DistanceDataType.RDAMean)
{
if (avcache[ilp1].Length == 0 || avcache[ilp2].Length == 0)
{
d.R = Double.NaN;
}
else
{
d.R = FpsNativeWrapper.RdaMeanFromAv(avcache[ilp1], avcache[ilp1].Length, avcache[ilp2], avcache[ilp2].Length,
avparam.ESamples, rnd.Next());
}
}
fr.RModel.Add(d);
fr.RmpModel.Add(dmp);
dr = d.R - dist[i].R;
if (Double.IsNaN(d.R))
{
fr.InvalidR++;
}
else if (!this._filterParameters.OptimizeSelected || dist[i].IsSelected)
{
fr.E += dr > 0.0 ? dr * dr / dist[i].ErrPlus / dist[i].ErrPlus :
dr * dr / dist[i].ErrMinus / dist[i].ErrMinus;
activeR++;
if (dr > dist[i].ErrPlus)
{
fr.Sigma1++;
}
if (dr > 2.0 * dist[i].ErrPlus)
{
fr.Sigma2++;
}
if (dr > 3.0 * dist[i].ErrPlus)
{
fr.Sigma3++;
}
if (dr < -dist[i].ErrMinus)
{
fr.Sigma1++;
}
if (dr < -2.0 * dist[i].ErrMinus)
{
fr.Sigma2++;
}
if (dr < -3.0 * dist[i].ErrMinus)
{
fr.Sigma3++;
}
}
}
fr.E = fr.E / (Double)activeR;
fr.RefRMSD = nref_total == 0 ? 0.0 : Math.Sqrt(refrmsd_t / (Double)nref_total);
return(fr.E);
}
public void SetDMatrix(Mapack.Matrix Mat)
{
ParamicsPuppetMaster.EditDemands EDM = new ParamicsPuppetMaster.EditDemands(TestC.ParamicsPath, Mat);
}
