public static bool SelfTest_1AAC()
{
Pdb.Atom[] atoms_ca = new Pdb.Atom[]
{
#region 1AAC text of CA atoms
Pdb.Atom.FromString("ATOM 2 CA ASP A 1 25.378 -18.141 21.012 1.00 23.28 C "),
Pdb.Atom.FromString("ATOM 10 CA LYS A 2 24.390 -18.799 17.407 1.00 12.32 C "),
Pdb.Atom.FromString("ATOM 19 CA ALA A 3 25.772 -15.617 15.840 1.00 10.31 C "),
Pdb.Atom.FromString("ATOM 24 CA THR A 4 28.837 -13.442 16.439 1.00 9.47 C "),
Pdb.Atom.FromString("ATOM 31 CA ILE A 5 28.913 -9.665 15.865 1.00 7.94 C "),
Pdb.Atom.FromString("ATOM 39 CA PRO A 6 31.906 -8.243 13.886 1.00 8.02 C "),
Pdb.Atom.FromString("ATOM 46 CA SER A 7 31.049 -4.632 14.810 1.00 7.70 C "),
Pdb.Atom.FromString("ATOM 52 CA GLU A 8 28.768 -3.589 17.658 1.00 10.01 C "),
Pdb.Atom.FromString("ATOM 73 CA PRO A 10 26.932 0.412 12.498 1.00 7.09 C "),
Pdb.Atom.FromString("ATOM 80 CA PHE A 11 29.488 1.217 9.844 1.00 6.81 C "),
Pdb.Atom.FromString("ATOM 91 CA ALA A 12 29.431 2.815 6.390 1.00 6.76 C "),
Pdb.Atom.FromString("ATOM 96 CA ALA A 13 28.012 1.036 3.320 1.00 8.60 C "),
Pdb.Atom.FromString("ATOM 101 CA ALA A 14 31.392 1.654 1.659 1.00 11.18 C "),
Pdb.Atom.FromString("ATOM 106 CA GLU A 15 33.092 -0.407 4.404 1.00 9.76 C "),
Pdb.Atom.FromString("ATOM 115 CA VAL A 16 31.115 -3.590 3.763 1.00 12.85 C "),
Pdb.Atom.FromString("ATOM 122 CA ALA A 17 33.429 -6.584 3.205 1.00 20.32 C "),
Pdb.Atom.FromString("ATOM 127 CA ASP A 18 34.080 -7.894 -0.306 1.00 27.64 C "),
Pdb.Atom.FromString("ATOM 135 CA GLY A 19 31.708 -10.634 -1.313 1.00 26.92 C "),
Pdb.Atom.FromString("ATOM 139 CA ALA A 20 29.393 -9.683 1.528 1.00 19.57 C "),
Pdb.Atom.FromString("ATOM 144 CA ILE A 21 25.881 -11.238 1.583 1.00 11.70 C "),
Pdb.Atom.FromString("ATOM 152 CA VAL A 22 23.847 -8.061 1.553 1.00 7.77 C "),
Pdb.Atom.FromString("ATOM 159 CA VAL A 23 20.196 -7.501 2.410 1.00 6.37 C "),
Pdb.Atom.FromString("ATOM 166 CA ASP A 24 19.093 -3.982 1.466 1.00 6.66 C "),
Pdb.Atom.FromString("ATOM 174 CA ILE A 25 16.500 -2.121 3.513 1.00 7.21 C "),
Pdb.Atom.FromString("ATOM 182 CA ALA A 26 14.398 0.375 1.556 1.00 8.41 C "),
Pdb.Atom.FromString("ATOM 187 CA LYS A 27 10.724 1.489 1.214 1.00 9.80 C "),
Pdb.Atom.FromString("ATOM 201 CA MET A 28 10.147 0.295 4.838 1.00 8.69 C "),
Pdb.Atom.FromString("ATOM 209 CA LYS A 29 10.882 -3.362 4.004 1.00 9.09 C "),
Pdb.Atom.FromString("ATOM 223 CA TYR A 30 13.753 -5.845 4.132 1.00 6.32 C "),
Pdb.Atom.FromString("ATOM 235 CA GLU A 31 14.275 -6.364 0.381 1.00 9.00 C "),
Pdb.Atom.FromString("ATOM 244 CA THR A 32 15.144 -10.026 0.769 1.00 7.30 C "),
Pdb.Atom.FromString("ATOM 251 CA PRO A 33 12.722 -11.107 3.546 1.00 8.68 C "),
Pdb.Atom.FromString("ATOM 258 CA GLU A 34 13.757 -14.780 3.406 1.00 9.28 C "),
Pdb.Atom.FromString("ATOM 267 CA LEU A 35 17.468 -15.255 2.972 1.00 7.34 C "),
Pdb.Atom.FromString("ATOM 275 CA HIS A 36 19.181 -18.672 2.822 1.00 6.97 C "),
Pdb.Atom.FromString("ATOM 285 CA VAL A 37 22.841 -18.828 3.840 1.00 7.29 C "),
Pdb.Atom.FromString("ATOM 292 CA LYS A 38 25.361 -21.456 5.044 1.00 9.55 C "),
Pdb.Atom.FromString("ATOM 306 CA VAL A 39 26.828 -21.965 8.529 1.00 9.09 C "),
Pdb.Atom.FromString("ATOM 313 CA GLY A 40 29.717 -19.533 8.887 1.00 8.81 C "),
Pdb.Atom.FromString("ATOM 317 CA ASP A 41 28.343 -16.891 6.520 1.00 8.19 C "),
Pdb.Atom.FromString("ATOM 325 CA THR A 42 28.196 -13.227 7.468 1.00 7.95 C "),
Pdb.Atom.FromString("ATOM 332 CA VAL A 43 24.989 -11.395 6.512 1.00 6.02 C "),
Pdb.Atom.FromString("ATOM 339 CA THR A 44 25.158 -7.607 6.224 1.00 5.34 C "),
Pdb.Atom.FromString("ATOM 346 CA TRP A 45 22.054 -5.421 6.244 1.00 4.51 C "),
Pdb.Atom.FromString("ATOM 360 CA ILE A 46 22.453 -1.974 4.623 1.00 5.55 C "),
Pdb.Atom.FromString("ATOM 368 CA ASN A 47 19.890 0.774 5.248 1.00 6.52 C "),
Pdb.Atom.FromString("ATOM 376 CA ARG A 48 19.350 2.559 1.939 1.00 10.21 C "),
Pdb.Atom.FromString("ATOM 387 CA GLU A 49 16.823 5.111 3.196 1.00 12.44 C "),
Pdb.Atom.FromString("ATOM 396 CA ALA A 50 16.764 8.058 5.564 1.00 13.39 C "),
Pdb.Atom.FromString("ATOM 401 CA MET A 51 14.386 6.508 8.133 1.00 12.52 C "),
Pdb.Atom.FromString("ATOM 409 CA PRO A 52 16.509 4.566 10.725 1.00 9.20 C "),
Pdb.Atom.FromString("ATOM 416 CA HIS A 53 16.032 0.778 10.889 1.00 6.43 C "),
Pdb.Atom.FromString("ATOM 426 CA ASN A 54 17.658 -2.107 12.766 1.00 5.06 C "),
Pdb.Atom.FromString("ATOM 434 CA VAL A 55 17.296 -5.891 13.052 1.00 5.44 C "),
Pdb.Atom.FromString("ATOM 441 CA HIS A 56 15.979 -7.379 16.316 1.00 4.53 C "),
Pdb.Atom.FromString("ATOM 451 CA PHE A 57 15.920 -11.061 17.243 1.00 5.94 C "),
Pdb.Atom.FromString("ATOM 462 CA VAL A 58 13.932 -11.794 20.435 1.00 7.60 C "),
Pdb.Atom.FromString("ATOM 469 CA ALA A 59 15.316 -13.765 23.405 1.00 7.37 C "),
Pdb.Atom.FromString("ATOM 474 CA GLY A 60 16.074 -17.393 22.787 1.00 9.00 C "),
Pdb.Atom.FromString("ATOM 478 CA VAL A 61 16.521 -17.029 18.997 1.00 8.51 C "),
Pdb.Atom.FromString("ATOM 485 CA LEU A 62 20.244 -16.290 18.543 1.00 9.65 C "),
Pdb.Atom.FromString("ATOM 493 CA GLY A 63 21.156 -16.644 22.197 1.00 10.26 C "),
Pdb.Atom.FromString("ATOM 497 CA GLU A 64 19.729 -16.413 25.651 1.00 9.18 C "),
Pdb.Atom.FromString("ATOM 506 CA ALA A 65 19.129 -12.671 25.468 1.00 8.86 C "),
Pdb.Atom.FromString("ATOM 511 CA ALA A 66 17.408 -10.687 22.723 1.00 7.22 C "),
Pdb.Atom.FromString("ATOM 516 CA LEU A 67 19.808 -9.283 20.128 1.00 9.01 C "),
Pdb.Atom.FromString("ATOM 524 CA LYS A 68 18.504 -5.777 19.473 1.00 10.06 C "),
Pdb.Atom.FromString("ATOM 533 CA GLY A 69 20.805 -4.416 16.788 1.00 8.06 C "),
Pdb.Atom.FromString("ATOM 537 CA PRO A 70 21.868 -0.715 16.656 1.00 8.23 C "),
Pdb.Atom.FromString("ATOM 544 CA MET A 71 19.807 1.769 14.640 1.00 8.56 C "),
Pdb.Atom.FromString("ATOM 552 CA MET A 72 21.337 2.189 11.156 1.00 8.26 C "),
Pdb.Atom.FromString("ATOM 560 CA LYS A 73 21.086 5.638 9.601 1.00 9.59 C "),
Pdb.Atom.FromString("ATOM 574 CA LYS A 74 21.097 6.084 5.777 1.00 9.46 C "),
Pdb.Atom.FromString("ATOM 588 CA GLU A 75 23.892 4.149 4.097 1.00 9.45 C "),
Pdb.Atom.FromString("ATOM 602 CA GLN A 76 24.997 2.451 7.267 1.00 6.02 C "),
Pdb.Atom.FromString("ATOM 611 CA ALA A 77 25.416 -1.310 7.631 1.00 5.75 C "),
Pdb.Atom.FromString("ATOM 616 CA TYR A 78 25.448 -3.978 10.318 1.00 4.90 C "),
Pdb.Atom.FromString("ATOM 628 CA SER A 79 26.700 -7.612 10.117 1.00 5.13 C "),
Pdb.Atom.FromString("ATOM 634 CA LEU A 80 26.024 -10.884 11.899 1.00 5.65 C "),
Pdb.Atom.FromString("ATOM 642 CA THR A 81 27.969 -14.123 11.320 1.00 6.53 C "),
Pdb.Atom.FromString("ATOM 649 CA PHE A 82 25.693 -17.171 11.780 1.00 5.24 C "),
Pdb.Atom.FromString("ATOM 660 CA THR A 83 27.363 -20.163 13.449 1.00 6.79 C "),
Pdb.Atom.FromString("ATOM 667 CA GLU A 84 24.599 -22.785 13.726 1.00 6.27 C "),
Pdb.Atom.FromString("ATOM 676 CA ALA A 85 21.975 -24.045 11.260 1.00 7.61 C "),
Pdb.Atom.FromString("ATOM 681 CA GLY A 86 18.324 -23.142 11.886 1.00 7.35 C "),
Pdb.Atom.FromString("ATOM 685 CA THR A 87 15.680 -20.519 11.055 1.00 8.50 C "),
Pdb.Atom.FromString("ATOM 692 CA TYR A 88 16.009 -17.145 12.731 1.00 7.35 C "),
Pdb.Atom.FromString("ATOM 704 CA ASP A 89 13.191 -14.620 12.557 1.00 7.28 C "),
Pdb.Atom.FromString("ATOM 712 CA TYR A 90 13.740 -10.922 13.122 1.00 5.26 C "),
Pdb.Atom.FromString("ATOM 724 CA HIS A 91 11.902 -7.619 12.935 1.00 4.80 C "),
Pdb.Atom.FromString("ATOM 734 CA CYS A 92 12.663 -3.894 13.049 1.00 5.44 C "),
Pdb.Atom.FromString("ATOM 740 CA THR A 93 12.228 -2.579 16.647 1.00 6.60 C "),
Pdb.Atom.FromString("ATOM 747 CA PRO A 94 10.460 0.815 15.821 1.00 7.51 C "),
Pdb.Atom.FromString("ATOM 754 CA HIS A 95 8.594 -0.728 12.857 1.00 7.46 C "),
Pdb.Atom.FromString("ATOM 764 CA PRO A 96 7.518 -4.286 13.932 1.00 7.59 C "),
Pdb.Atom.FromString("ATOM 771 CA PHE A 97 5.480 -4.778 10.739 1.00 7.30 C "),
Pdb.Atom.FromString("ATOM 782 CA MET A 98 8.923 -5.104 8.994 1.00 6.57 C "),
Pdb.Atom.FromString("ATOM 790 CA ARG A 99 9.707 -8.821 9.391 1.00 7.91 C "),
Pdb.Atom.FromString("ATOM 808 CA GLY A 100 12.343 -11.105 7.827 1.00 6.39 C "),
Pdb.Atom.FromString("ATOM 812 CA LYS A 101 14.085 -14.438 8.459 1.00 7.31 C "),
Pdb.Atom.FromString("ATOM 826 CA VAL A 102 17.523 -15.900 7.870 1.00 6.58 C "),
Pdb.Atom.FromString("ATOM 833 CA VAL A 103 17.552 -19.658 7.157 1.00 7.20 C "),
Pdb.Atom.FromString("ATOM 840 CA VAL A 104 21.061 -21.012 7.897 1.00 7.28 C "),
Pdb.Atom.FromString("ATOM 847 CA GLU A 105 21.699 -24.347 6.221 1.00 13.74 C "),
#endregion
};
Pdb.Atom[] atoms_r6 = new Pdb.Atom[]
{
Pdb.Atom.FromString("ATOM 42 CB PRO A 6 31.929 -8.271 12.386 1.00 7.98 C "),
Pdb.Atom.FromString("ATOM 43 CG PRO A 6 30.972 -9.378 12.022 1.00 9.48 C "),
Pdb.Atom.FromString("ATOM 44 CD PRO A 6 29.880 -9.313 13.099 1.00 8.27 C "),
};
{
HessMatrix hess = GetHessCa(atoms_ca.ListCoord());
InfoPack extra = new InfoPack();
//Vector bfactors = ENM.BFactorFromHessian(hess, null, 6, extra);
Vector bfactors = Hess.GetBFactor(hess, null, 6, extra);
Vector eigvals = (double[])extra["eigenvalues"];
int[] idxsorted_eigvals = eigvals.ToArray().HAbs().HIdxSorted();
for (int i = 0; i < 6; i++)
{
eigvals[idxsorted_eigvals[i]] = 0;
}
for (int i = 0; i < eigvals.Size; i++)
{
if (eigvals[i] < 0)
{
// return false, if there exists negative eigenvalue
HDebug.Assert(false);
return(false);
}
}
}
{
List <Pdb.Atom> atoms = new List <Pdb.Atom>();
atoms.AddRange(atoms_ca);
atoms.AddRange(atoms_r6);
HDebug.Assert(atoms[5].resSeq == 6);
List <int> idxs_ca = new List <int>(); for (int i = 0; i < atoms_ca.Length; i++)
{
idxs_ca.Add(i);
}
List <int> idxs_r6 = new List <int>(); for (int i = atoms_ca.Length; i < atoms.Count; i++)
{
idxs_r6.Add(i);
}
idxs_r6.InsertRange(0, new int[] { 3, 4, 5 });
List <Tuple <int, int> > list12 = new List <Tuple <int, int> >();
for (int i = 1; i < idxs_ca.Count; i++)
{
list12.Add(new Tuple <int, int>(idxs_ca[i - 1], idxs_ca[i]));
}
for (int i = 3; i < idxs_r6.Count; i++)
{
list12.Add(new Tuple <int, int>(idxs_r6[i - 1], idxs_r6[i]));
}
List <Tuple <int, int, int> > list123 = new List <Tuple <int, int, int> >();
for (int i = 2; i < idxs_ca.Count; i++)
{
list123.Add(new Tuple <int, int, int>(idxs_ca[i - 2], idxs_ca[i - 1], idxs_ca[i]));
}
for (int i = 3; i < idxs_r6.Count; i++)
{
list123.Add(new Tuple <int, int, int>(idxs_r6[i - 2], idxs_r6[i - 1], idxs_r6[i]));
}
List <Tuple <int, int, int, int> > list1234 = new List <Tuple <int, int, int, int> >();
for (int i = 3; i < idxs_ca.Count; i++)
{
list1234.Add(new Tuple <int, int, int, int>(idxs_ca[i - 3], idxs_ca[i - 2], idxs_ca[i - 1], idxs_ca[i]));
}
for (int i = 3; i < idxs_r6.Count; i++)
{
list1234.Add(new Tuple <int, int, int, int>(idxs_r6[i - 3], idxs_r6[i - 2], idxs_r6[i - 1], idxs_r6[i]));
}
List <Tuple <int, int> > listNonbond = new List <Tuple <int, int> >();
for (int i = 0; i < idxs_ca.Count; i++)
{
for (int j = i + 4; j < idxs_ca.Count; j++)
{
listNonbond.Add(new Tuple <int, int>(idxs_ca[i], idxs_ca[j]));
}
}
for (int i = 0; i < idxs_r6.Count; i++)
{
for (int j = i + 4; j < idxs_r6.Count; j++)
{
listNonbond.Add(new Tuple <int, int>(idxs_r6[i], idxs_r6[j]));
}
}
List <Vector> coords = atoms.ListCoord();
HessMatrix hessian = HessMatrixSparse.ZerosSparse(atoms.Count * 3, atoms.Count * 3);
double Epsilon = 0.36;
double K_r = 100 * Epsilon;
double K_theta = 20 * Epsilon;
double K_phi1 = 1 * Epsilon;
double K_phi3 = 0.5 * Epsilon;
for (int i = 0; i < list12.Count; i++)
{
FirstTerm(coords, K_r, hessian, list12[i].Item1, list12[i].Item2);
}
for (int i = 0; i < list123.Count; i++)
{
SecondTerm(coords, K_theta, hessian, list123[i].Item1, list123[i].Item2, list123[i].Item3);
}
for (int i = 0; i < list1234.Count; i++)
{
ThirdTerm(coords, K_phi1, K_phi3, hessian, list1234[i].Item1, list1234[i].Item2, list1234[i].Item3, list1234[i].Item4);
}
for (int i = 0; i < listNonbond.Count; i++)
{
FourthTerm(coords, Epsilon, hessian, listNonbond[i].Item1, listNonbond[i].Item2);
}
InfoPack extra = new InfoPack();
//Vector bfactors = ENM.BFactorFromHessian(hessian, null, 6, extra);
Vector bfactors = Hess.GetBFactor(hessian, null, 6, extra);
Vector eigvals = (double[])extra["eigenvalues"];
int[] idxsorted_eigvals = eigvals.ToArray().HAbs().HIdxSorted();
for (int i = 0; i < 6; i++)
{
eigvals[idxsorted_eigvals[i]] = 0;
}
for (int i = 0; i < eigvals.Size; i++)
{
if (eigvals[i] < 0)
{
// return false, if there exists negative eigenvalue
HDebug.Assert(false);
return(false);
}
}
}
//{
// Debug.Assert(atoms_ca[5].resSeq == 6);
// Pdb.Atom[] atoms_resi6 = new Pdb.Atom[]
// {
// atoms_ca[5],
// Pdb.Atom.FromString("ATOM 42 CB PRO A 6 31.929 -8.271 12.386 1.00 7.98 C "),
// Pdb.Atom.FromString("ATOM 43 CG PRO A 6 30.972 -9.378 12.022 1.00 9.48 C "),
// Pdb.Atom.FromString("ATOM 44 CD PRO A 6 29.880 -9.313 13.099 1.00 8.27 C "),
// };
// Matrix hess_ca = GetHessCa(atoms_ca.ListCoord());
// Matrix hess_resi6 = GetHessCa(atoms_resi6.ListCoord());
//
// int size_ca = atoms_ca.Length;
// int size_r6 = atoms_resi6.Length - 1;
// Matrix hess = new double[(size_ca+size_r6)*3,(size_ca+size_r6)*3];
// for(int c = 0; c < hess.ColSize; c++)
// for(int r = 0; r < hess.RowSize; r++)
// hess[c, r] = double.NaN;
// for(int c = 0; c < hess_ca.ColSize; c++)
// for(int r = 0; r < hess_ca.RowSize; r++)
// hess[c, r] = hess_ca[c, r];
// for(int c = 0; c < hess_resi6.ColSize; c++)
// for(int r = 0; r < hess_resi6.RowSize; r++)
// {
// if(c < 3 && r < 3) { int c0=5 *3+ c ; int r0=5 *3+ r ; Debug.Assert(double.IsNaN(hess[c0, r0]) ==false); hess[c0, r0] = hess_resi6[c, r]; }
// else if(c < 3 && r >= 3) { int c0=5 *3+ c ; int r0=size_ca*3+(r-3); Debug.Assert(double.IsNaN(hess[c0, r0]) == true); hess[c0, r0] = hess_resi6[c, r]; }
// else if(c >= 3 && r < 3) { int c0=size_ca*3+(c-3); int r0=5 *3+ r ; Debug.Assert(double.IsNaN(hess[c0, r0]) == true); hess[c0, r0] = hess_resi6[c, r]; }
// else if(c >= 3 && r >= 3) { int c0=size_ca*3+(c-3); int r0=size_ca*3+(r-3); Debug.Assert(double.IsNaN(hess[c0, r0]) == true); hess[c0, r0] = hess_resi6[c, r]; }
// else Debug.Assert(false);
// }
// for(int j = size_ca * 3; j < (size_ca + size_r6) * 3; j++)
// {
// for(int i = 0; i < 5*3; i++)
// {
// Debug.Assert(double.IsNaN(hess[i, j]) == true); hess[i, j] = 0;
// Debug.Assert(double.IsNaN(hess[j, i]) == true); hess[j, i] = 0;
// }
// for(int i = 6*3; i < size_ca * 3; i++)
// {
// Debug.Assert(double.IsNaN(hess[i, j]) == true); hess[i, j] = 0;
// Debug.Assert(double.IsNaN(hess[j, i]) == true); hess[j, i] = 0;
// }
// }
// for(int c = 0; c < hess.ColSize; c++)
// for(int r = 0; r < hess.RowSize; r++)
// Debug.Assert(double.IsNaN(hess[c, r]) == false);
//
// InfoPack extra = new InfoPack();
// Vector bfactors = ENM.BFactorFromHessian(hess, null, 6, extra);
// Vector eigvals = (double[])extra["eigenvalues"];
// int[] idxsorted_eigvals = eigvals.ToArray().Abs().IdxSorted();
// for(int i = 0; i < 6; i++) eigvals[idxsorted_eigvals[i]] = 0;
// for(int i = 0; i < eigvals.Size; i++)
// if(eigvals[i] < 0)
// {
// // return false, if there exists negative eigenvalue
// Debug.Assert(false);
// return false;
// }
//}
return(true);
}
