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();
}
}
