public static Matrix3 RepairRotation(Matrix3 R)
{
Vector3 u;
Double theta = Matrix3.AngleAndAxis(R, out u);
Double absu = Vector3.Abs(u);
u = u * (1.0 / absu);
return(Matrix3.Rotation(u, theta));
}
private void SaveOverlayStates(String ofilename)
{
String fullfname = ofilename + ".pml";
Vector3 u; Double theta;
using (StreamWriter sw = new StreamWriter(fullfname, false))
{
sw.Write("# Overlay of structures ");
for (Int32 j = 0; j < _dataToSave.Length - 1; j++)
{
sw.Write(_dataToSave[j].InternalNumber.ToString() + ", ");
}
sw.WriteLine(_dataToSave[_dataToSave.Length - 1].InternalNumber.ToString());
for (Int32 i = 0; i < molecules.Count; i++)
{
sw.WriteLine("load " + molecules[i].FullFileName);
}
SimulationResult sr;
for (Int32 j = 0; j < _dataToSave.Length; j++)
{
sr = _dataToSave[j];
for (Int32 i = 0; i < molecules.Count; i++)
{
theta = Matrix3.AngleAndAxis(sr.Rotation[i], out u) * 180.0 / Math.PI;
sw.WriteLine("copy _tmp" + i.ToString() + ", " + molecules[i].Name);
sw.WriteLine("rotate [" + u.ToString() + "], " + theta.ToString("F3")
+ ", _tmp" + i.ToString() + ", origin=[" + molecules[i].CM.ToString() + "]");
sw.WriteLine("translate [" + sr.Translation[i].ToString() + "], _tmp" + i.ToString());
}
sw.WriteLine("select object _tmp*");
if (_bestfit)
{
sw.WriteLine("translate [" + sr.BestFitTranslation.ToString() + "], sele");
theta = Matrix3.AngleAndAxis(sr.BestFitRotation, out u) * 180.0 / Math.PI;
sw.WriteLine("rotate [" + u.ToString() + "], " + theta.ToString("F3")
+ ", sele, origin=[0, 0, 0]");
}
sw.WriteLine("save _tmp.pdb, sele");
sw.WriteLine("load _tmp.pdb, " + filenametextBox.Text);
sw.WriteLine("delete _tmp*");
}
for (Int32 i = 0; i < molecules.Count; i++)
{
sw.WriteLine("delete " + molecules[i].Name);
}
sw.Close();
}
}
/// <summary>
/// Do one iteration
/// </summary>
/// <param name="normF">Sum of F*F</param>
/// <param name="normT">Sum of T*T</param>
/// <param name="K">Kinetic energy</param>
/// <returns>Potential energy (before the iteration)</returns>
private double Iterate(out double normF, out double normT, out double K)
{
double E, theta, thetaw, abst, absw;
Molecule m;
Vector3 force_i, torque_i, tmpt, v, w;
Matrix3 tmpr;
E = ForceAndTorque();
CheckForClashes(true);
E += Eclash;
normF = 0; normT = 0.0; K = 0.0;
for (int i = 0; i < Nmolecules; i++)
{
m = _molecules[i];
tmpt = translationm1[i];
tmpr = rotation[i] * Matrix3.Transpose(rotationm1[i]);
translationm1[i] = translation[i];
rotationm1[i] = rotation[i];
force_i = force[i];
normF += force_i * force_i;
torque_i = torque[i];
normT += torque_i * torque_i;
translation[i] = translation[i] * (2.0 - viscosity) - tmpt * (1.0 - viscosity)
+ force_i * (dt * dt / m.Mass);
v = (translation[i] - tmpt) * 0.5 * rdt;
K += 0.5 * m.Mass * (v * v);
abst = torque_i.Normalize();
theta = dt * dt * abst / m.SimpleI;
thetaw = Matrix3.AngleAndAxis(tmpr, out w);
rotation[i] = Matrix3.Rotation(torque_i, theta) * Matrix3.Rotation(w, -thetaw * viscosity)
* tmpr * rotation[i];
absw = thetaw * rdt;
K += 0.5 * m.SimpleI * absw * absw;
}
return(E);
}
private void SaveSimulationResult(SimulationResult sr, String fname, Boolean addpdbsave)
{
String converged = sr.Converged ? " (converged)" : " (not converged)";
String fullfname = fname + ".pml";
Vector3 u; Double theta;
using (StreamWriter sw = new StreamWriter(fullfname, false))
{
sw.WriteLine("# Energy = " + sr.E.ToString("F8") + converged);
for (Int32 i = 0; i < molecules.Count; i++)
{
sw.WriteLine("load " + molecules[i].FullFileName);
}
for (Int32 i = 1; i < molecules.Count; i++)
{
theta = Matrix3.AngleAndAxis(sr.Rotation[i], out u) * 180.0 / Math.PI;
sw.WriteLine("rotate [" + u.ToString() + "], " + theta.ToString("F3")
+ ", " + molecules[i].Name + ", origin=[" + molecules[i].CM.ToString() + "]");
sw.WriteLine("translate [" + sr.Translation[i].ToString() + "], " + molecules[i].Name);
}
if (_bestfit)
{
sw.WriteLine("select all");
sw.WriteLine("translate [" + sr.BestFitTranslation.ToString() + "], sele");
theta = Matrix3.AngleAndAxis(sr.BestFitRotation, out u) * 180.0 / Math.PI;
sw.WriteLine("rotate [" + u.ToString() + "], " + theta.ToString("F3")
+ ", sele, origin=[0, 0, 0]");
}
if (addpdbsave)
{
sw.WriteLine("select all");
sw.WriteLine("save " + fname + ".pdb, sele");
}
String lpnames = "";
if (lpcheckBox.Checked)
{
Int32 im;
Vector3 r;
LabelingPosition lpref;
foreach (LabelingPosition l in labelingpos)
{
im = molecules.FindIndex(l.Molecule);
if ((sr.SimulationMethod & SimulationMethods.Refinement) != 0)
{
lpref = sr.RefinedLabelingPositions.Find(l.Name);
}
else
{
lpref = l;
}
r = sr.Rotation[im] * (lpref - molecules[im].CM) + molecules[im].CM + sr.Translation[im];
sw.WriteLine("pseudoatom " + l.Name + ", pos=[" + r.ToString() + "]");
sw.WriteLine("label " + l.Name + ", \"" + l.Name + "\"");
sw.WriteLine("show spheres, " + l.Name);
if (l.Dye == DyeType.Donor)
{
sw.WriteLine("color green, " + l.Name);
}
if (l.Dye == DyeType.Acceptor)
{
sw.WriteLine("color red, " + l.Name);
}
lpnames += " + " + l.Name;
}
}
if (_bestfit && lpnames != String.Empty)
{
sw.WriteLine("deselect");
sw.WriteLine("select " + lpnames.Substring(3));
sw.WriteLine("translate [" + sr.BestFitTranslation.ToString() + "], sele");
theta = Matrix3.AngleAndAxis(sr.BestFitRotation, out u) * 180.0 / Math.PI;
sw.WriteLine("rotate [" + u.ToString() + "], " + theta.ToString("F3")
+ ", sele, origin=[0, 0, 0]");
}
sw.WriteLine("deselect");
sw.Close();
}
}
