public static void GetEnergies(AlignData data1, IList <Vector> coords2
, out double pot_rmsd, out double pot_enrg, out double pot_enrg_full, out double pot_enrg_anisou
, Pdb pdb2 = null
, string pdb2outpath = null
)
{
Anisou[] anisous1;// = data1.GetAnisous();
double[] bfactor1;
{
List <Mode> modes = new List <Mode>(data1.GetModes());
for (int i = 0; i < 6; i++)
{
modes.RemoveAt(0);
}
bfactor1 = HBioinfo.GetBFactor(modes.ToArray(), data1.masses);
HDebug.Assert(data1.size == bfactor1.Length);
anisous1 = Anisou.FromBFactor(bfactor1, scale: 10000 * 1000);
}
//Trans3 trans = MinAnisou.GetTrans(data1.coords, anisous1, coords2);
Trans3 trans = GetTrans(data1.coords, bfactor1, coords2);
List <Vector> coords2trans = new List <Vector>(trans.GetTransformed(coords2));
if (pdb2 != null && pdb2outpath != null)
{
data1.pdb.ToFile(pdb2outpath, coords2trans, anisous: anisous1.GetUs());
}
pot_rmsd = data1.GetRmsdFrom(coords2trans);
pot_enrg = data1.GetEnergyFromDiag(coords2trans);
pot_enrg_full = data1.GetEnergyFromFull(coords2trans);
pot_enrg_anisou = data1.GetEnergyFromAnisou(coords2trans);
}
public static void GetEnergies(AlignData data1, IList <Vector> coords2
, out double geo_rmsd, out double geo_enrg, out double geo_enrg_full, out double geo_enrg_anisou
, Pdb pdb2, string pdb2outpath
)
{
Trans3 trans = GetTrans(data1.coords, coords2);
List <Vector> coords2trans = new List <Vector>(trans.GetTransformed(coords2).ToArray());
if (pdb2 != null && pdb2outpath != null)
{
pdb2.ToFile(pdb2outpath, coords2);
}
geo_rmsd = data1.GetRmsdFrom(coords2trans);
geo_enrg = data1.GetEnergyFromDiag(coords2trans);
geo_enrg_full = data1.GetEnergyFromFull(coords2trans);
geo_enrg_anisou = data1.GetEnergyFromAnisou(coords2trans);
}
//public static Trans3 GetTrans(IList<Vector> C1, Matrix[] anisou1, IList<Vector> C2)
//{
// int size = C1.Count;
// Tuple<Vector[], double[]>[] eigs1 = new Tuple<Vector[], double[]>[size];
// {
// for(int i=0; i<size; i++)
// {
// Vector[] eigvec;
// double[] eigval;
// Debug.Verify(NumericSolver.Eig(anisou1[i], out eigvec, out eigval));
// { // normalize eigval and eigvec
// double l;
// l = eigvec[0].Dist; eigvec[0] /= l; eigval[0] *= (l*l); eigval[0] = Math.Pow(eigval[0], 2); Debug.Assert(eigval[0] >= 0);
// l = eigvec[1].Dist; eigvec[1] /= l; eigval[1] *= (l*l); eigval[1] = Math.Pow(eigval[1], 2); Debug.Assert(eigval[1] >= 0);
// l = eigvec[2].Dist; eigvec[2] /= l; eigval[2] *= (l*l); eigval[2] = Math.Pow(eigval[2], 2); Debug.Assert(eigval[2] >= 0);
// }
// {
// eigval[0] = 1 / eigval[0];
// eigval[1] = 1 / eigval[1];
// eigval[2] = 1 / eigval[2];
// }
// eigs1[i] = new Tuple<Vector[], double[]>(eigvec, eigval);
// }
// }
// return GetTrans(C1, eigs1, C2);
//}
public static void GetEnergies(AlignData data1, IList <Vector> coords2
, out double pot_rmsd, out double pot_enrg, out double pot_enrg_full, out double pot_enrg_anisou
, Pdb pdb2 = null
, string pdb2outpath = null
)
{
Anisou[] anisous1 = data1.GetAnisous();
Trans3 trans = GetTrans(data1.coords, anisous1, coords2);
List <Vector> coords2trans = new List <Vector>(trans.GetTransformed(coords2));
if (pdb2 != null && pdb2outpath != null)
{
pdb2.ToFile(pdb2outpath, coords2trans);
}
//data1.pdb.ToFile(pdb2outpath, coords2trans, anisous: anisous1.GetUs());
pot_rmsd = data1.GetRmsdFrom(coords2trans);
pot_enrg = data1.GetEnergyFromDiag(coords2trans);
pot_enrg_full = data1.GetEnergyFromFull(coords2trans);
pot_enrg_anisou = data1.GetEnergyFromAnisou(coords2trans);
}