public static MatrixSparse <double> GetCorrMatrix(this IList <Mode> modes, IEnumerable <Tuple <int, int> > enumCorrCR)
{
Vector[][] eigvecs = new Vector[modes.Count][];
double[] eigvals = new double[modes.Count];
for (int i = 0; i < modes.Count; i++)
{
eigvals[i] = modes[i].eigval;
eigvecs[i] = modes[i].GetEigvecsOfAtoms();
}
int size = modes[0].size;
MatrixSparse <double> Dij = new MatrixSparse <double>(size, size);
Vector Dii = new double[size];
for (int i = 0; i < eigvals.Length; i++)
{
Vector[] eigvec = eigvecs[i];
double eigval = eigvals[i];
for (int c = 0; c < size; c++)
{
Dii[c] += (LinAlg.VtV(eigvec[c], eigvec[c]) / eigval);
}
foreach (var cr in enumCorrCR)
{
int c = cr.Item1;
int r = cr.Item2;
Dij[c, r] += (LinAlg.VtV(eigvec[c], eigvec[r]) / eigval);
}
}
foreach (var cr in enumCorrCR)
{
Dij[cr] = Dij[cr] / modes.Count;
}
Dii = Dii / modes.Count;
// Cij
foreach (var cr in enumCorrCR)
{
int c = cr.Item1;
int r = cr.Item2;
Dij[c, r] /= Math.Sqrt(Dii[c] * Dii[r]);
}
if (HDebug.IsDebuggerAttached)
{
Matrix tDij = GetCorrMatrix(modes);
foreach (var cr in enumCorrCR)
{
int c = cr.Item1;
int r = cr.Item2;
double err = Dij[c, r] - tDij[c, r];
HDebug.Exception(Math.Abs(err) < 0.00000001);
}
}
return(Dij);
}
public static T reshapeOrDeclare <T>(T target, MatrixSparse reference)
where T : MatrixSparse
{
if (target == null)
{
return(reference.createLike <T>());
}
else
{
target.reshape(reference.NumRows, reference.NumCols, reference.NonZeroLength);
}
return(target);
}
//public static IEnumerable<Tuple<int, int, double>> EnumHessAnmSpr_obsolete(IList<Vector> coords, double cutoff, double sprcst)
//{
// int size = coords.Count;
// double cutoff2 = cutoff*cutoff;
// //Matrix Kij = Matrix.Zeros(size, size);
// int num_springs = 0;
// for(int c=0; c<size; c++)
// {
// if(coords[c] == null) continue;
// for(int r=c+1; r<size; r++)
// {
// if(coords[r] == null) continue;
// double dist2 = (coords[c] - coords[r]).Dist2;
// if(dist2 <= cutoff2)
// {
// yield return new Tuple<int, int, double>(c, r, sprcst); //Kij[c, r] = sprcst;
// yield return new Tuple<int, int, double>(r, c, sprcst); //Kij[r, c] = sprcst;
// num_springs += 2;
// }
// }
// }
// double ratio_springs = ((double)num_springs) / (size*size);
// //return Kij;
//}
public static MatrixSparse <double> GetHessAnmBmat(IList <Vector> coords, double cutoff)
{
if (HDebug.Selftest())
{
var _coords = Pdb._smallest_protein_cacoords;
Matrix _Bmat = Hess.GetHessAnmBmat(_coords, 13).ToArray();
Matrix _BB = _Bmat * _Bmat.Tr();
Matrix _ANM = Hess.GetHessAnm(_coords, 13);
double _err = (_BB - _ANM).HAbsMax();
HDebug.Assert(_err < 0.00000001);
}
List <Tuple <int, int, double> > sprs = EnumHessAnmSpr(coords, cutoff, 1).ToList();
MatrixSparse <double> Bmat = new MatrixSparse <double>(3 * coords.Count, sprs.Count);
int spr_count = 0;
for (int ij = 0; ij < sprs.Count; ij++)
{
var spr = sprs[ij];
int ai = spr.Item1;
int aj = spr.Item2;
if (ai >= aj)
{
continue;
}
double kij = spr.Item3;
Vector coordi = coords[ai];
Vector coordj = coords[aj];
double sij = (coordi - coordj).Dist;
double xij = (coordj[0] - coordi[0]) / sij;
double yij = (coordj[1] - coordi[1]) / sij;
double zij = (coordj[2] - coordi[2]) / sij;
Bmat[(ai * 3 + 0), spr_count] = xij;
Bmat[(ai * 3 + 1), spr_count] = yij;
Bmat[(ai * 3 + 2), spr_count] = zij;
Bmat[(aj * 3 + 0), spr_count] = -xij;
Bmat[(aj * 3 + 1), spr_count] = -yij;
Bmat[(aj * 3 + 2), spr_count] = -zij;
spr_count++;
}
return(Bmat.GetSubMatrix(3 * coords.Count, spr_count));
}