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; }