private void SaveDistances(String rfilename)
{
LabelingPosition l1, l2;
LabelingPosition[] l1index = new LabelingPosition[dist.Count];
LabelingPosition[] l2index = new LabelingPosition[dist.Count];
Double R;
using (StreamWriter sw = new StreamWriter(rfilename + "_Rmp.txt", false))
{
sw.Write("Structure\tNumber");
for (Int32 i = 0; i < dist.Count; i++)
{
l1 = labelingpos.Find(dist[i].Position1);
l2 = labelingpos.Find(dist[i].Position2);
l1index[i] = l1;
l2index[i] = l2;
sw.Write('\t' + l1.Name + '_' + l2.Name);
}
sw.WriteLine();
for (Int32 j = 0; j < _dataToSave.Length; j++)
{
sw.Write(filenametextBox.Text + _dataToSave[j].InternalNumber.ToString() + '\t' + _dataToSave[j].InternalNumber.ToString());
for (Int32 i = 0; i < dist.Count; i++)
{
sw.Write('\t' + _dataToSave[j].ModelDistance(l1index[i], l2index[i]).ToString("F3"));
}
sw.WriteLine();
}
sw.Close();
}
// saving converted distances if requested
if (dist.DataType != DistanceDataType.Rmp)
{
using (StreamWriter sw = new StreamWriter(rfilename + '_' + dist.DataType.ToString() + ".txt", false))
{
sw.Write("Structure\tNumber");
for (Int32 i = 0; i < dist.Count; i++)
{
l1 = labelingpos.Find(dist[i].Position1);
l2 = labelingpos.Find(dist[i].Position2);
sw.Write('\t' + l1.Name + '_' + l2.Name);
}
sw.WriteLine();
for (Int32 j = 0; j < _dataToSave.Length; j++)
{
sw.Write(filenametextBox.Text + _dataToSave[j].InternalNumber.ToString() + '\t' + _dataToSave[j].InternalNumber.ToString());
for (Int32 i = 0; i < dist.Count; i++)
{
R = (l1index[i].Dye != DyeType.Unknown && l2index[i].Dye != DyeType.Unknown) ?
Distance.Convert(_dataToSave[j].ModelDistance(l1index[i], l2index[i]), _globalcf) : _dataToSave[j].ModelDistance(l1index[i], l2index[i]);
sw.Write('\t' + R.ToString("F3"));
}
sw.WriteLine();
}
sw.Close();
}
}
}
public static LabelingPosition operator -(LabelingPosition l, Vector3 v)
{
LabelingPosition l1 = l;
l1.X = l.X - v.X;
l1.Y = l.Y - v.Y;
l1.Z = l.Z - v.Z;
return(l1);
}
/// <summary>
/// Calculates the accesible volume for a given labeling position.
/// </summary>
/// <param name="lp">Labeling position</param>
public void Calculate(LabelingPosition lp)
{
if (lp.AVData.AVType == AVSimlationType.SingleDyeR)
{
this.Calculate1R(lp.AVData.L, lp.AVData.W, lp.AVData.R,
Array.BinarySearch <Int32>(this.mol.OriginalAtomID, lp.AVData.AtomID));
}
else if (lp.AVData.AVType == AVSimlationType.ThreeDyeR)
{
this.Calculate3R(lp.AVData.L, lp.AVData.W, lp.AVData.R1, lp.AVData.R2, lp.AVData.R3,
Array.BinarySearch <Int32>(this.mol.OriginalAtomID, lp.AVData.AtomID));
}
else
{
throw new ArgumentException("Cannot calculate AV for a labeling position of type " + lp.AVData.AVType.ToString());
}
}
private void addbutton_Click(object sender, EventArgs e)
{
if (_lastcalculated == null)
{
return;
}
LabelingPosition l = new LabelingPosition();
l.Molecule = _lastcalculated.Name;
l.Name = lpnametextBox.Text;
l.X = ave.Rmp.X; l.Y = ave.Rmp.Y; l.Z = ave.Rmp.Z;
l.Dye = this.DradioButton.Checked ? DyeType.Donor : DyeType.Acceptor;
l.AVData.AVType = (AVSimlationType)(simcombobox.SelectedIndex + 1);
l.AVData.AVReady = true; l.AVData.AtomID = atomIDnumericBoxInt32.Value;
l.AVData.L = LnumericBoxDouble.Value; l.AVData.W = WnumericBoxDouble.Value;
l.AVData.R = R1numericBoxDouble.Value; l.AVData.R1 = R1numericBoxDouble.Value;
l.AVData.R2 = R2numericBoxDouble.Value; l.AVData.R3 = R3numericBoxDouble.Value;
_labelpos.Add(l);
}
/// <summary>
/// Model distance between labeling positions l1 and l2
/// </summary>
/// <param name="l1">position 1</param>
/// <param name="l2">position 2</param>
/// <returns>Model distance</returns>
public Double ModelDistance(LabelingPosition l1, LabelingPosition l2)
{
Int32 im1 = this.Molecules.FindIndex(l1.Molecule);
Int32 im2 = this.Molecules.FindIndex(l2.Molecule);
// take refined LPs if available
LabelingPosition lp1ref, lp2ref;
if ((this.SimulationMethod & SimulationMethods.Refinement) != 0 && this.RefinedLabelingPositions != null)
{
lp1ref = this.RefinedLabelingPositions.Find(l1.Name);
lp2ref = this.RefinedLabelingPositions.Find(l2.Name);
}
else
{
lp1ref = l1;
lp2ref = l2;
}
Vector3 d = this.Rotation[im1] * (lp1ref - this.Molecules[im1].CM) + this.Molecules[im1].CM + this.Translation[im1]
- this.Rotation[im2] * (lp2ref - this.Molecules[im2].CM) - this.Molecules[im2].CM - this.Translation[im2];
return(Vector3.Abs(d));
}