// 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);
}
// two molecules
private Boolean CheckForClashes(int im1, int im2)
{
Molecule m1 = _molecules[im1];
Molecule m2 = _molecules[im2];
Vector3 dcm = translation[im1] - translation[im2], rc1, rc2;
// check clusters
Vector3[] rc2cache = new Vector3[m2.AtomClusters.Length];
double sumr, dsq, dx2, dy2, dz2;
Vector3 sumrv;
AtomCluster c1, c2;
Matrix3 rot1to2 = Matrix3.Transpose(rotation[im2]) * rotation[im1];
Matrix3 rot2to1 = Matrix3.Transpose(rot1to2);
Vector3 dcm1t = Matrix3.Transpose(rotation[im1]) * dcm;
Vector3 dcm2t = Matrix3.Transpose(rotation[im2]) * dcm;
int[] c2tocheck = new int[m2.AtomClusters.Length];
int j2, n2tocheck;
int[] mustbechecked1 = new int[m1.AtomClusters.Length];
int[] mustbechecked2 = new int[m2.AtomClusters.Length];
// check if we can skip some of m2
n2tocheck = 0;
for (int j = 0; j < m2.AtomClusters.Length; j++)
{
c2 = m2.AtomClusters[j];
rc2 = rot2to1 * c2 - dcm1t;
dx2 = rc2.X * rc2.X;
dy2 = rc2.Y * rc2.Y;
dz2 = rc2.Z * rc2.Z;
sumrv = m1.MaxRadius + c2.ClusterRadius;
if ((dy2 + dz2 <= sumrv.X * sumrv.X) && (dx2 + dz2 <= sumrv.Y * sumrv.Y) && (dx2 + dy2 <= sumrv.Z * sumrv.Z))
{
rc2cache[n2tocheck] = c2;
c2tocheck[n2tocheck++] = j;
}
}
for (int i = 0; i < m1.AtomClusters.Length; i++)
{
c1 = m1.AtomClusters[i];
rc1 = rot1to2 * c1 + dcm2t;
// if completely out of reach, skip the check
dx2 = rc1.X * rc1.X;
dy2 = rc1.Y * rc1.Y;
dz2 = rc1.Z * rc1.Z;
sumrv = m2.MaxRadius + c1.ClusterRadius;
if ((dy2 + dz2 > sumrv.X * sumrv.X) || (dx2 + dz2 > sumrv.Y * sumrv.Y) || (dx2 + dy2 > sumrv.Z * sumrv.Z))
{
continue;
}
// otherwise check selected clusters from m2
for (int j = 0; j < n2tocheck; j++)
{
j2 = c2tocheck[j];
rc2 = rc2cache[j];
c2 = m2.AtomClusters[j2];
dsq = Vector3.SquareNormDiff(rc1, rc2);
sumr = c1.ClusterRadius + c2.ClusterRadius;
if (dsq < sumr * sumr) // clusters overlap, check all atoms
{
mustbechecked1[i] = 1;
mustbechecked2[j2] = 1;
// clash |= CheckForClashes(c1, c2, im1, im2, dcm); // => replaced with unmanaged
}
}
}
// this runs in m1's coordinate system!
Vector3 fclash = new Vector3(), tclash1 = new Vector3(), tclash2 = new Vector3();
double dEClash = FpsNativeWrapper.CheckForClashes(FpsNativeWrapper.Aligned16(m1.XYZvdwRVectorArray),
FpsNativeWrapper.Aligned16(m2.XYZvdwRVectorArray), m1.AtomClusters, m2.AtomClusters,
m1.AtomClusters.Length, m2.AtomClusters.Length, mustbechecked1, mustbechecked2,
rot2to1, -dcm1t, kclash, ref fclash, ref tclash1, ref tclash2);
force[im1] += rotation[im1] * fclash;
force[im2] -= rotation[im1] * fclash;
torque[im1] += rotation[im1] * tclash1;
torque[im2] += rotation[im1] * tclash2;
Eclash += dEClash;
return(dEClash > 1.0e-8);
}
/// <summary>
/// Read reference atoms from an LP file
/// </summary>
/// <param name="m">Example molecule</param>
/// <param name="classicpdb">True for pdb line format, false if tab-delimited</param>
public void ReadRefAtoms(Molecule m, Boolean classicpdb)
{
// re-read the lp file to get reference frames
referenceAtoms = new List <ReferenceAtom[]>(labelingpos.Count);
Int32 j;
String[] strdata;
strdata = System.IO.File.ReadAllLines(labelingpos.FullPath);
String[] tmpstr;
Double x, y, z;
Char[] separator = new Char[] { ' ', '\t' };
ReferenceAtom[] reftmp;
for (Int32 i = 0; i < strdata.Length; i++)
{
// find LP line
if (!LabelingPositionList.ValidLPLine(strdata[i]))
{
continue;
}
// now LP is found, count following pdb lines if any
j = 0;
if (classicpdb)
{
while (i + j + 1 < strdata.Length && strdata[i + j + 1].Length > 54 && strdata[i + j + 1].Substring(0, 4) == "ATOM")
{
j++;
}
}
else
{
while (i + j + 1 < strdata.Length && strdata[i + j + 1].Length > 10 && strdata[i + j + 1].Substring(0, 4) == "ATOM")
{
j++;
}
}
reftmp = new ReferenceAtom[j];
// read reference atoms
j = 0;
if (classicpdb)
{
while (i + j + 1 < strdata.Length && strdata[i + j + 1].Length > 54 && strdata[i + j + 1].Substring(0, 4) == "ATOM")
{
tmpstr = strdata[i + j + 1].Split(separator, StringSplitOptions.RemoveEmptyEntries);
reftmp[j].OriginalN = Int32.Parse(tmpstr[1]);
reftmp[j].ConvertedN = Array.BinarySearch <Int32>(m.OriginalAtomID, reftmp[j].OriginalN);
if (Double.TryParse(strdata[i + j + 1].Substring(30, 8), out x) &&
Double.TryParse(strdata[i + j + 1].Substring(38, 8), out y) &&
Double.TryParse(strdata[i + j + 1].Substring(46, 8), out z))
{
reftmp[j].X = x;
reftmp[j].Y = y;
reftmp[j].Z = z;
}
j++;
}
}
else
{
while (i + j + 1 < strdata.Length && strdata[i + j + 1].Length > 10 && strdata[i + j + 1].Substring(0, 4) == "ATOM")
{
tmpstr = strdata[i + j + 1].Split(separator, StringSplitOptions.RemoveEmptyEntries);
reftmp[j].OriginalN = Int32.Parse(tmpstr[1]);
reftmp[j].ConvertedN = Array.BinarySearch <Int32>(m.OriginalAtomID, reftmp[j].OriginalN);
if (Double.TryParse(tmpstr[6], out x) &&
Double.TryParse(tmpstr[7], out y) &&
Double.TryParse(tmpstr[8], out z))
{
reftmp[j].X = x;
reftmp[j].Y = y;
reftmp[j].Z = z;
}
j++;
}
}
referenceAtoms.Add(reftmp);
i += j;
}
}