Example #1
0
 public SimulationBase(MoleculeList ms, LabelingPositionList lps, DistanceList ds)
 {
     this.Molecules         = ms;
     this.LabelingPositions = lps;
     this.Distances         = ds;
     InitRnd();
 }
Example #2
0
        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;
        }
Example #3
0
 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];
 }
Example #4
0
        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));
        }
Example #5
0
 public ErrorEstimation(MoleculeList ms, LabelingPositionList ls, DistanceList ds) : base(ms, ls, ds)
 {
 }
Example #6
0
 public Refinement(MoleculeList ms, LabelingPositionList ls, DistanceList ds) : base(ms, ls, ds)
 {
 }
Example #7
0
        private double Elast; // energy after last iteration

        public MetropolisSampler(MoleculeList ms, LabelingPositionList ls, DistanceList ds) : base(ms, ls, ds)
        {
            this.IsContinuous = true;
        }