public SimulationBase(MoleculeList ms, LabelingPositionList lps, DistanceList ds)
{
this.Molecules = ms;
this.LabelingPositions = lps;
this.Distances = ds;
InitRnd();
}
public FilterEngine(LabelingPositionList ls, DistanceList ds)
{
this.LabelingPositions = ls;
this.Distances = ds;
#if DEBUG
rnd = new Random(53672429);
#else
rnd = new Random();
#endif
// just in case default AV parameters
this.avparam.GridSize = 0.2;
this.avparam.MinGridSize = 0.4;
this.avparam.LinkerInitialSphere = 0.5;
this.avparam.LinkSearchNodes = 3;
this.avparam.ESamples = 200000;
}
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 override double SetState(SimulationResult sr)
{
// set model distances as "true"
Distance rmodeltmp;
DistanceList rlisttmp = new DistanceList(this.Distances.Count);
rlisttmp.AddRange(this.Distances);
for (Int32 i = 0; i < rlisttmp.Count; i++)
{
rmodeltmp = rlisttmp[i];
rmodeltmp.R = sr.ModelDistance(this.LabelingPositions.Find(rmodeltmp.Position1),
this.LabelingPositions.Find(rmodeltmp.Position2));
rlisttmp[i] = rmodeltmp;
}
this.Distances = rlisttmp;
return(base.SetState(sr));
}
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;
}
