private LabelingPositionList RedoAV()
{
LabelingPositionList lps_local = new LabelingPositionList(this.LabelingPositions.Count);
lps_local.AddRange(this.LabelingPositions);
AVEngine av = new AVEngine(mt, this.ProjectDataCopy.AVGlobalParameters);
LabelingPosition l;
Vector3 rmp;
int natom, nmol;
for (Int32 i = 0; i < lps_local.Count; i++)
{
l = lps_local[i];
if (l.AVData.AVType == AVSimlationType.None)
{
continue;
}
nmol = sr.Molecules.FindIndex(l.Molecule);
natom = Array.BinarySearch <Int32>(mt.OriginalAtomID, molstart[nmol], molnatoms[nmol], l.AVData.AtomID);
if (l.AVData.AVType == AVSimlationType.SingleDyeR)
{
av.Calculate1R(l.AVData.L, l.AVData.W, l.AVData.R, natom);
}
else if (l.AVData.AVType == AVSimlationType.ThreeDyeR)
{
av.Calculate3R(l.AVData.L, l.AVData.W, l.AVData.R1, l.AVData.R2, l.AVData.R3, natom);
}
rmp = Matrix3.Transpose(sr.Rotation[nmol]) * (av.Rmp - sr.Translation[nmol]
+ sr.Molecules[0].CM - sr.Molecules[nmol].CM) + sr.Molecules[nmol].CM;
l.X = rmp.X; l.Y = rmp.Y; l.Z = rmp.Z;
lps_local[i] = l;
}
return(lps_local);
}
private void calculatebutton_Click(object sender, EventArgs e)
{
savebutton.Enabled = false;
addbutton.Enabled = false;
ave = _standalone ? new AVEngine(_molecules[moleculescomboBox.SelectedIndex]) :
new AVEngine(_molecules[moleculescomboBox.SelectedIndex], _avpar);
_lastcalculated = _molecules[moleculescomboBox.SelectedIndex];
if (simcombobox.SelectedIndex == 0) // simple AV
{
_lastparams = "molecule " + _lastcalculated.Name + " (" + _lastcalculated.FullFileName + "); atom "
+ atomIDnumericBoxInt32.Value.ToString() + " (" + atomnametextBox.Text + "); linker length = "
+ LnumericBoxDouble.Value.ToString() + " width = " + WnumericBoxDouble.Value.ToString()
+ " dye radius = " + R1numericBoxDouble.Value.ToString();
ave.Calculate1R(LnumericBoxDouble.Value, WnumericBoxDouble.Value, R1numericBoxDouble.Value, _natom);
}
else if (simcombobox.SelectedIndex == 1) // 3 radii
{
_lastparams = "molecule " + _lastcalculated.Name + " (" + _lastcalculated.FullFileName + "); atom "
+ atomIDnumericBoxInt32.Value.ToString() + " (" + atomnametextBox.Text + "); linker length = "
+ LnumericBoxDouble.Value.ToString() + " width = " + WnumericBoxDouble.Value.ToString()
+ " dye radii = " + R1numericBoxDouble.Value.ToString() + " / " + R2numericBoxDouble.Value.ToString()
+ " / " + R3numericBoxDouble.Value.ToString();
ave.Calculate3R(LnumericBoxDouble.Value, WnumericBoxDouble.Value,
R1numericBoxDouble.Value, R2numericBoxDouble.Value, R3numericBoxDouble.Value, _natom);
}
rmptextBox.Text = "Rmp = (" + ave.Rmp.ToString() + ")";
addbutton.Enabled = !_standalone;
savebutton.Enabled = true;
}
// 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);
}