private void PrepareSimulation()
{
// molecules
Nmolecules = _molecules.Count;
int maxatomsincluster = 0;
for (int i = 0; i < Nmolecules; i++)
{
minmass = Math.Min(minmass, _molecules[i].Mass);
maxatomsincluster = Math.Max(maxatomsincluster, _molecules[i].MaxAtomsInCluster);
}
// labeling positions
int im;
labelingpos_cm = new LabelingPositionList();
labelingpos_cm.AddRange(this._labelingpositions);
lpossim = new Vector3[labelingpos_cm.Count];
LtoM = new int[labelingpos_cm.Count];
// convert to local coordinates
for (int i = 0; i < labelingpos_cm.Count; i++)
{
im = _molecules.FindIndex(labelingpos_cm[i].Molecule);
LtoM[i] = im;
labelingpos_cm[i] -= _molecules[im].CM;
lpossim[i] = labelingpos_cm[i];
}
// distances
Distance dist_i;
DtoL1 = new int[_distances.Count];
DtoM1 = new int[_distances.Count];
DtoL2 = new int[_distances.Count];
DtoM2 = new int[_distances.Count];
kplus = new double[_distances.Count];
kminus = new double[_distances.Count];
drmaxplus = new double[_distances.Count];
drmaxminus = new double[_distances.Count];
double minerror = double.MaxValue;
for (int i = 0; i < _distances.Count; i++)
{
DtoL1[i] = labelingpos_cm.FindIndex(_distances[i].Position1);
DtoM1[i] = _molecules.FindIndex(labelingpos_cm.Find(_distances[i].Position1).Molecule);
DtoL2[i] = labelingpos_cm.FindIndex(_distances[i].Position2);
DtoM2[i] = _molecules.FindIndex(labelingpos_cm.Find(_distances[i].Position2).Molecule);
// check if bond
dist_i = _distances[i];
dist_i.IsBond = (labelingpos_cm[DtoL1[i]].Dye == DyeType.Unknown && labelingpos_cm[DtoL1[i]].AVData.AtomID > 0 &&
labelingpos_cm[DtoL1[i]].AVData.AVType == AVSimlationType.None && labelingpos_cm[DtoL2[i]].Dye == DyeType.Unknown &&
labelingpos_cm[DtoL2[i]].AVData.AtomID > 0 && labelingpos_cm[DtoL2[i]].AVData.AVType == AVSimlationType.None);
_distances[i] = dist_i;
// if bond, set small vdW radii to "exclude" from clashing
if (dist_i.IsBond)
{
foreach (var lp in new[] { labelingpos_cm[DtoL1[i]], labelingpos_cm[DtoL2[i]] })
{
int m = _molecules.FindIndex(lp.Molecule);
int natom = Array.BinarySearch <int>(_molecules[m].OriginalAtomID, lp.AVData.AtomID);
_molecules[m].vdWR[natom] = AtomData.vdWRNoClash;
int natom_cluster = Array.FindIndex <int>(_molecules[m].ClusteredAtomOriginalIndex, n => n == natom);
if (natom_cluster >= 0)
{
_molecules[m].ClusteredAtomvdwR[natom_cluster] = AtomData.vdWRNoClash;
System.Runtime.InteropServices.Marshal.Copy(new[] { (float)AtomData.vdWRNoClash }, 0,
FpsNativeWrapper.Aligned16(_molecules[m].XYZvdwRVectorArray) + (4 * natom_cluster + 3) * sizeof(float), 1);
}
}
}
// "spring constants"
kplus[i] = 2.0 / _distances[i].ErrPlus / _distances[i].ErrPlus;
kminus[i] = 2.0 / _distances[i].ErrMinus / _distances[i].ErrMinus;
//Console.Out.WriteLine("distance#" + i + " k+= " + kplus[i] + " k-= " + kminus[i] + " err+ " + _distances[i].ErrPlus + " err- " + _distances[i].ErrMinus);
drmaxplus[i] = SimulationParameters.MaxForce / kplus[i];
drmaxminus[i] = -SimulationParameters.MaxForce / kminus[i];
minerror = Math.Min(minerror, Math.Min(_distances[i].ErrPlus, _distances[i].ErrMinus));
}
// simulation parameters
kclash = 2.0 / SimulationParameters.ClashTolerance / SimulationParameters.ClashTolerance;
drmaxclash = -SimulationParameters.MaxForce / kclash;
dr4dt = Math.Min(SimulationParameters.ClashTolerance * 0.5, minerror);
}
// 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);
}