public SimulationBase(MoleculeList ms, LabelingPositionList lps, DistanceList ds)
{
this.Molecules = ms;
this.LabelingPositions = lps;
this.Distances = ds;
InitRnd();
}
private void AVinterface_Load(object sender, EventArgs e)
{
rmptextBox.Text = "Ready";
moleculescomboBox.Items.Clear();
if (_standalone)
{
_molecules = new MoleculeList(20);
}
for (Int32 i = 0; i < _molecules.Count; i++)
{
moleculescomboBox.Items.Add(_molecules[i].Name);
}
if (moleculescomboBox.Items.Count > 0)
{
moleculescomboBox.SelectedIndex = 0;
}
calculatebutton.Enabled = (_molecules.Count > 0);
// load default dye parameters
dyescomboBox.Items.AddRange(LinkerData.LinkerList);
dyescomboBox.SelectedIndex = 0;
simcombobox.SelectedIndex = 0;
_labelpos = new LabelingPositionList();
savebutton.Enabled = false;
addbutton.Enabled = false;
}
/// <summary>
/// Combines units into one "molecule" (mainly to be able to redo AV). Only a few properties are copied
/// </summary>
/// <param name="sr">Structure</param>
public Molecule(SimulationResult sr)
{
MoleculeList units = sr.Molecules;
Prepared = false;
Name = "Structure " + sr.InternalNumber.ToString();
FullFileName = "";
Error = "";
NAtoms = 0;
for (int i = 0; i < units.Count; i++)
{
NAtoms += units[i].NAtoms;
}
AtomMass = new double[NAtoms];
vdWR = new double[NAtoms];
OriginalAtomID = new int[NAtoms];
Atoms = new string[NAtoms];
AtomsStandard = new string[NAtoms];
Mass = 0.0;
CM = new Vector3();
Molecule m, m0 = units[0];
int n = 0;
Vector3 r;
// local coordinates
XLocal = new double[NAtoms];
YLocal = new double[NAtoms];
ZLocal = new double[NAtoms];
for (int i = 0; i < units.Count; i++)
{
m = units[i];
for (int j = 0; j < m.NAtoms; j++)
{
r = sr.Rotation[i] * (new Vector3(m.XLocal[j], m.YLocal[j], m.ZLocal[j]))
- m0.CM + m.CM + sr.Translation[i];
XLocal[n] = r.X;
YLocal[n] = r.Y;
ZLocal[n] = r.Z;
AtomMass[n] = m.AtomMass[j];
vdWR[n] = m.vdWR[j];
OriginalAtomID[n] = m.OriginalAtomID[j];
Atoms[n] = m.Atoms[j];
AtomsStandard[n] = m.AtomsStandard[j];
n++;
}
}
}
public SpringEngine(MoleculeList ms, LabelingPositionList ls, DistanceList ds) : base(ms, ls, ds)
{
this.Nmolecules = ms.Count;
translation = new Vector3[Nmolecules];
rotation = new Matrix3[Nmolecules];
translationm1 = new Vector3[Nmolecules];
rotationm1 = new Matrix3[Nmolecules];
translationm2 = new Vector3[Nmolecules];
rotationm2 = new Matrix3[Nmolecules];
for (int i = 0; i < Nmolecules; i++)
{
rotation[i] = Matrix3.E;
rotationm1[i] = Matrix3.E;
}
force = new Vector3[Nmolecules];
torque = new Vector3[Nmolecules];
}
public ErrorEstimation(MoleculeList ms, LabelingPositionList ls, DistanceList ds) : base(ms, ls, ds)
{
}
public Refinement(MoleculeList ms, LabelingPositionList ls, DistanceList ds) : base(ms, ls, ds)
{
}
private double Elast; // energy after last iteration
public MetropolisSampler(MoleculeList ms, LabelingPositionList ls, DistanceList ds) : base(ms, ls, ds)
{
this.IsContinuous = true;
}
public AVinterface(MoleculeList ms)
{
_molecules = ms;
_standalone = false;
InitializeComponent();
}