public HessInfo GetSubHessInfoByBlockHess(IList <int> idxs, ILinAlg ila)
{
// GetSubHessInfoByBlockHess(idxSele, ila, "pinv")
Vector idxmass = mass.ToArray().HSelectByIndex(idxs);
object[] idxatoms = atoms.HSelectByIndex(idxs);
Vector[] idxcoords = coords.HSelectByIndex(idxs);
HessMatrix idxhess = null;
if (ila != null)
{
idxhess = Hess.GetHessCoarseBlkmat(hess, idxs, ila);
}
else
{
idxhess = Hess.GetHessCoarseBlkmat(hess, idxs);
}
return(new HessInfo
{
mass = idxmass,
atoms = idxatoms,
coords = idxcoords,
hess = idxhess,
numZeroEigval = numZeroEigval,
});
}
public Mode[] GetModesMassWeighted(bool delhess, ILinAlg la)
{
Matrix mwhess = GetHessMassWeighted(delhess);
Mode[] mwmodes = Hess.GetModesFromHess(mwhess, la);
return(mwmodes);
}
private static void FourthTerm(IList <Vector> caArray, double Epsilon, HessMatrix hessian, int i, int j)
{
int[] idx = new int[] { i, j };
Vector[] lcaArray = new Vector[] { caArray[idx[0]], caArray[idx[1]] };
Matrix lhess = FourthTerm(lcaArray, Epsilon);
for (int c = 0; c < 2; c++)
{
for (int dc = 0; dc < 3; dc++)
{
for (int r = 0; r < 2; r++)
{
for (int dr = 0; dr < 3; dr++)
{
hessian[idx[c] * 3 + dc, idx[r] * 3 + dr] += lhess[c * 3 + dc, r *3 + dr];
}
}
}
}
if (HDebug.IsDebuggerAttachedWithProb(0.1))
{
if (caArray.Count == 2)
{
// avoid stack overflow
return;
}
HessMatrix lhess0 = new double[6, 6];
FourthTerm(lcaArray, Epsilon, lhess0, 0, 1);
FourthTerm(lcaArray, Epsilon, lhess0, 1, 0);
double r2 = (lcaArray[0] - lcaArray[1]).Dist2;
Matrix dhess0 = (120 * Epsilon / r2) * Hess.GetHessAnm(lcaArray, double.PositiveInfinity);
HDebug.AssertToleranceMatrix(0.00000001, lhess0 - dhess0);
}
}
public static void FirstTerm(IList <Vector> caArray, double K_r, HessMatrix hessian, int i, int j)
{
int[] idx = new int[] { i, j };
Vector[] lcaArray = new Vector[] { caArray[idx[0]], caArray[idx[1]] };
Matrix lhess = FirstTerm(lcaArray, K_r);
double maxabs_lhess = lhess.ToArray().HAbs().HMax();
HDebug.Assert(maxabs_lhess < 10000);
for (int c = 0; c < 2; c++)
{
for (int dc = 0; dc < 3; dc++)
{
for (int r = 0; r < 2; r++)
{
for (int dr = 0; dr < 3; dr++)
{
hessian[idx[c] * 3 + dc, idx[r] * 3 + dr] += lhess[c * 3 + dc, r *3 + dr];
}
}
}
}
if (HDebug.IsDebuggerAttached)
{
Matrix anm = (2 * K_r) * Hess.GetHessAnm(lcaArray, double.PositiveInfinity);
HDebug.AssertToleranceMatrix(0.00000001, lhess - anm);
}
}
public static bool GetModesSelftest()
{
if (GetModesSelftest_DoTest == false)
{
return(true);
}
GetModesSelftest_DoTest = false;
string pdbpath = @"C:\Users\htna\htnasvn_htna\VisualStudioSolutions\Library2\HTLib2.Bioinfo\Bioinfo.Data\pdb\1MJC.pdb";
if (HFile.Exists(pdbpath) == false)
{
return(false);
}
Pdb pdb = Pdb.FromFile(pdbpath);
for (int i = 0; i < pdb.atoms.Length; i++)
{
HDebug.Assert(pdb.atoms[0].altLoc == pdb.atoms[i].altLoc);
HDebug.Assert(pdb.atoms[0].chainID == pdb.atoms[i].chainID);
}
List <Vector> coords = pdb.atoms.ListCoord();
double cutoff = 13;
Matrix hess = Hess.GetHessAnm(coords.ToArray(), cutoff).ToArray();
Matrix modes;
Vector freqs;
GetModes(hess, out modes, out freqs);
return(true);
}
public static Mode[] PCA(IList <Vector[]> confs, Vector[] meanconf, Vector masses, Func <Matrix, Tuple <Matrix, Vector> > fnEig = null)
{
int size = meanconf.Length;
int size3 = size * 3;
Matrix cov = Matrix.Zeros(size3, size3);
Vector vmeanconf = Vector.FromBlockvector(meanconf);
foreach (Vector[] conf in confs)
{
Vector vconf = Vector.FromBlockvector(conf);
Vector dvconf = vconf - vmeanconf;
LinAlg.AddToM.VVt(cov, dvconf); // hess += dvconf * dvcond'
}
cov /= confs.Count;
Vector invmasses = new double[masses.Size]; // inverse mass
for (int i = 0; i < masses.Size; i++)
{
invmasses[i] = 1 / masses[i];
}
Matrix mwcov = Hess.GetMassWeightedHess(cov, invmasses); // just reuse Hess.GetMassWeightedHess(...)
Mode[] mwmodes = PCA(mwcov, confs.Count, fnEig);
Mode[] modes = mwmodes.GetMassReduced(masses.ToArray()).ToArray(); // just reuse ListMode.GetMassDeweighted(...)
return(modes);
}
public Mode[] GetModes(ILinAlg la)
{
if (_modes == null)
{
_modes = Hess.GetModesFromHess(hess, la);
}
return(_modes);
}
public static bool SelfTest()
{
HDebug.Verify(Hess.GetHessAnmSelfTest());
HDebug.Verify(Hess.GetHessGnmSelfTest());
HDebug.Verify(Hess.GetModesSelftest());
HDebug.Verify(Hess.GetBFactorSelfTest());
//HDebug.Verify(Hess.HessSbNMA.SelfTest());
return(true);
}
public static PFSM GetHessFSM(IList <Vector> coords, Matrix pwspring, Matrix pwforce, ILinAlg la)
{
HDebug.ToDo("check!!");
int size = coords.Count;
Matrix khess = Hess.GetHessAnm(coords, pwspring.ToArray());
Matrix invkhess;
{
var HH = la.ToILMat(khess);
HDebug.Assert(false); // try to use eig, instead of pinv
var invHH = la.PInv(HH);
HH.Dispose();
//var VVDD = la.EigSymm(HH);
invkhess = invHH.ToArray();
invHH.Dispose();
}
Matrix npwforce = Hess.GetHessFSM_GetEqlibForc(coords, khess, invkhess, pwforce);
Matrix pwdist = coords.Pwdist();
Matrix anm = Hess.GetHessAnm(coords, double.PositiveInfinity);
MatrixBySparseMatrix fhess = MatrixBySparseMatrix.Zeros(size * 3, size * 3, 3);
for (int i = 0; i < size; i++)
{
for (int j = 0; j < size; j++)
{
if (i == j)
{
continue;
}
int[] idxi = new int[] { i *3 + 0, i *3 + 1, i *3 + 2 };
int[] idxj = new int[] { j *3 + 0, j *3 + 1, j *3 + 2 };
// ANM_ij
MatrixByArr fhess_ij = anm.SubMatrix(idxi, idxj).ToArray();
// ANM_ij - GNM_ij = ANM_ij - I_33
fhess_ij[0, 0] += 1;
fhess_ij[1, 1] += 1;
fhess_ij[2, 2] += 1;
// fij/rij * (ANM_ij - GNM_ij)
fhess_ij *= (npwforce[i, j] / pwdist[i, j]);
fhess.SetBlock(i, j, fhess_ij);
fhess.SetBlock(i, i, fhess.GetBlock(i, i) - fhess_ij);
}
}
return(new PFSM
{
KHess = khess,
FHess = fhess,
});
}
public static MixHessInfo GetHessMixSbNMA(Universe univ, IList <Vector> coords, ILinAlg la
, IList <ResInfo> lstResAllAtom, double nbondMaxDist, out string errmsg
, bool bGetIntmInfo, string strBkbnReso
)
{
// nbondMaxDist = double.PositiveInfinity
MixModel.FnGetHess GetHess = delegate(Universe luniv, IList <Vector> lcoords, int[] idxAll, int[] idxBuffer, int[] idxCoarse, int[] idxBackbone)
{
var hessinfo = Hess.GetHessSbNMA(luniv, lcoords, nbondMaxDist);
return(hessinfo);
};
return(MixModel.GetHessMixModel(univ, coords, la, lstResAllAtom, GetHess, out errmsg, bGetIntmInfo, strBkbnReso));
}
public static HessMatrix GetHessApproxAnm(Vector[] coords, HessMatrix hess, string option, ILinAlg ila)
{
int nresi = coords.Length;
HDebug.Assert(nresi * 3 == hess.ColSize);
HDebug.Assert(nresi * 3 == hess.RowSize);
double[,] Kij = new double[nresi, nresi];
for (int c = 0; c < nresi; c++)
{
for (int r = c + 1; r < nresi; r++)
{
HessMatrix anmCR = Hess.GetHessAnm(coords.HSelectByIndex(new int[] { c, r }));
//Matrix anmCR = anm.SubMatrix(new int[] { 0, 1, 2 }, new int[] { 3, 4, 5 });
int[] idxs = new int[] { c *3 + 0, c *3 + 1, c *3 + 2, r *3 + 0, r *3 + 1, r *3 + 2 };
HessMatrix hessCR = new HessMatrixDense {
hess = hess.SubMatrix(idxs, idxs)
};
hessCR = Hess.CorrectHessDiag(hessCR);
Vector vecHessCR = hessCR.GetColVectorList().ToVector();
Vector vecAnmCR = anmCR.GetColVectorList().ToVector();
double Kcr;
switch (option)
{
case "match magnitude": Kcr = vecHessCR.Dist / vecAnmCR.Dist; break;
case "least-mean square": Kcr = LinAlg.VtV(vecAnmCR, vecHessCR) / LinAlg.VtV(vecAnmCR, vecAnmCR); break;
default: throw new NotImplementedException();
}
if (Kcr < 0)
{
HDebug.Assert(false);
}
HDebug.Assert(Kcr >= 0);
double mag2cahessCR = vecAnmCR.Dist;
double mag2caAnmCR = vecHessCR.Dist;
double mag2caAnmCRx = (Kcr * anmCR).GetColVectorList().ToVector().Dist;
Kij[c, r] = Kij[r, c] = Kcr;
}
}
//return Kij;
return(Hess.GetHessAnm(coords, Kij));
throw new NotImplementedException();
}
public HessMatrix SubMatrixByAtomsImpl(bool ignNegIdx, IList <int> idxAtoms)
{
if (SubMatrixByAtomsImpl_selftest)
{
SubMatrixByAtomsImpl_selftest = false;
Vector[] tcoords = new Vector[] {
new Vector(1, 2, 3),
new Vector(1, 3, 2),
new Vector(1, 2, 9),
};
HessMatrix thess0 = Hess.GetHessAnm(tcoords);
int[] tidxs = new int[] { 0, 2 };
HessMatrix thess1a = thess0.SubMatrixByAtoms(false, tidxs);
HessMatrix thess1b = new double[, ]
{
{ thess0[0, 0], thess0[0, 1], thess0[0, 2], thess0[0, 6], thess0[0, 7], thess0[0, 8] },
{ thess0[1, 0], thess0[1, 1], thess0[1, 2], thess0[1, 6], thess0[1, 7], thess0[1, 8] },
{ thess0[2, 0], thess0[2, 1], thess0[2, 2], thess0[2, 6], thess0[2, 7], thess0[2, 8] },
{ thess0[6, 0], thess0[6, 1], thess0[6, 2], thess0[6, 6], thess0[6, 7], thess0[6, 8] },
{ thess0[7, 0], thess0[7, 1], thess0[7, 2], thess0[7, 6], thess0[7, 7], thess0[7, 8] },
{ thess0[8, 0], thess0[8, 1], thess0[8, 2], thess0[8, 6], thess0[8, 7], thess0[8, 8] },
};
// thess1a = Hess.CorrectHessDiag(thess1a); // diagonal of original matrix contains the interaction between 0-1 and 1-2 also,
// HessMatrix thess1b = Hess.GetHessAnm(tcoords.HSelectByIndex(tidxs)); // while new generated hessian matrix does not.
Matrix tdiffhess = thess1a - thess1b;
double max_tdiffhess = tdiffhess.ToArray().HAbs().HMax();
HDebug.Exception(0 == max_tdiffhess);
}
HessMatrix nhess = SubMatrixByAtomsImpl(ignNegIdx, idxAtoms, idxAtoms, true);
if (HDebug.IsDebuggerAttached && idxAtoms.Count < 1000)
{
List <int> idx3Atoms = new List <int>();
foreach (int idx in idxAtoms)
{
for (int i = 0; i < 3; i++)
{
idx3Atoms.Add(idx * 3 + i);
}
}
Matrix tnhess = this.SubMatrix(idx3Atoms, idx3Atoms);
double max2_tdiffhess = (nhess - tnhess).ToArray().HAbs().HMax();
HDebug.AssertTolerance(0.00000001, max2_tdiffhess);
}
return(nhess);
}
public static HessInfo GetHessSsNMA
(Universe univ
, IList <Vector> coords
, IEnumerable <Universe.Bond> bonds
, IEnumerable <Universe.Angle> angles
, IEnumerable <Universe.Improper> impropers
, IEnumerable <Universe.Dihedral> dihedrals
, IEnumerable <Universe.Nonbonded> nonbondeds
, IEnumerable <Universe.Nonbonded14> nonbonded14s
, double?maxAbsSpring = null
, double?K_r = 340.00
, double?K_theta = 45.00
, double?K_ub = 10.00
, double?K_psi = 70.00
, double?K_chi = 1.00
, double?n = 1
, string k_vdW = "Unif"
//, bool setNanForEmptyAtom // =true
)
{
bool vdW = true; // use vdW
bool elec = false; // ignore electrostatic
double D = double.PositiveInfinity; // dielectric constant for Tinker is "1"
bool ignNegSpr = true; // ignore negative spring (do not add the spring into hessian matrix)
//maxAbsSpring = Math.Pow(10, 9);
HessMatrix hess = null;
hess = STeM.GetHessBond(coords, bonds, K_r, hessian: hess);
hess = STeM.GetHessAngle(coords, angles, true, K_theta, K_ub, hessian: hess);
hess = STeM.GetHessImproper(coords, impropers, K_psi, hessian: hess, useArnaud96: true);
hess = STeM.GetHessDihedral(coords, dihedrals, K_chi, n, hessian: hess, useAbsSpr: true, useArnaud96: true);
hess = HessSpr.GetHessNonbond(coords, nonbondeds, D, k_vdW, hessian: hess, vdW: vdW, elec: elec, ignNegSpr: ignNegSpr, maxAbsSpring: maxAbsSpring);
hess = HessSpr.GetHessNonbond(coords, nonbonded14s, D, k_vdW, hessian: hess, vdW: vdW, elec: elec, ignNegSpr: ignNegSpr, maxAbsSpring: maxAbsSpring);
//if(setNanForEmptyAtom)
Hess.UpdateHessNaN(hess, coords);
return(new HessInfo
{
hess = hess,
mass = univ.GetMasses(),
atoms = univ.atoms.ToArray(),
coords = coords.HCloneVectors().ToArray(),
numZeroEigval = 6,
});
}
public static HessInfo GetHessEAnm
(Universe univ
, IList <Vector> coords
, IEnumerable <Tuple <int, int, double> > enumKij
, bool b_bonds
, bool b_angles
, bool b_impropers
, bool b_dihedrals
)
{
//bool vdW = true; // use vdW
//bool elec = false; // ignore electrostatic
//double D = double.PositiveInfinity; // dielectric constant for Tinker is "1"
//bool ignNegSpr = true; // ignore negative spring (do not add the spring into hessian matrix)
HessMatrix hess = null;
hess = Hess.GetHessAnm(coords, enumKij);
if (b_bonds)
{
hess = STeM.GetHessBond(coords, univ.bonds, 340.00, hessian: hess);
}
if (b_angles)
{
hess = STeM.GetHessAngle(coords, univ.angles, true, 45.00, 10.00, hessian: hess);
}
if (b_impropers)
{
hess = STeM.GetHessImproper(coords, univ.impropers, 70.00, hessian: hess, useArnaud96: true);
}
if (b_dihedrals)
{
hess = STeM.GetHessDihedral(coords, univ.dihedrals, 1.00, 1, hessian: hess, useAbsSpr: true, useArnaud96: true);
}
Hess.UpdateHessNaN(hess, coords);
return(new HessInfo
{
hess = hess,
mass = univ.GetMasses(),
atoms = univ.atoms.ToArray(),
coords = coords.HCloneVectors().ToArray(),
numZeroEigval = 6,
});
}
public static double[] GetBFactor(Mode[] modes, double[] mass = null)
{
if (HDebug.Selftest())
#region selftest
{
using (new Matlab.NamedLock("SELFTEST"))
{
Matlab.Clear("SELFTEST");
Matlab.Execute("SELFTEST.hess = rand(30);");
Matlab.Execute("SELFTEST.hess = SELFTEST.hess + SELFTEST.hess';");
Matlab.Execute("SELFTEST.invhess = inv(SELFTEST.hess);");
Matlab.Execute("SELFTEST.bfactor3 = diag(SELFTEST.invhess);");
Matlab.Execute("SELFTEST.bfactor = SELFTEST.bfactor3(1:3:end) + SELFTEST.bfactor3(2:3:end) + SELFTEST.bfactor3(3:3:end);");
MatrixByArr selftest_hess = Matlab.GetMatrix("SELFTEST.hess");
Mode[] selftest_mode = Hess.GetModesFromHess(selftest_hess);
Vector selftest_bfactor = BFactor.GetBFactor(selftest_mode);
Vector selftest_check = Matlab.GetVector("SELFTEST.bfactor");
Vector selftest_diff = selftest_bfactor - selftest_check;
HDebug.AssertTolerance(0.00000001, selftest_diff);
Matlab.Clear("SELFTEST");
}
}
#endregion
int size = modes[0].size;
if (mass != null)
{
HDebug.Assert(size == mass.Length);
}
double[] bfactor = new double[size];
for (int i = 0; i < size; i++)
{
foreach (Mode mode in modes)
{
bfactor[i] += mode.eigvec[i * 3 + 0] * mode.eigvec[i * 3 + 0] / mode.eigval;
bfactor[i] += mode.eigvec[i * 3 + 1] * mode.eigvec[i * 3 + 1] / mode.eigval;
bfactor[i] += mode.eigvec[i * 3 + 2] * mode.eigvec[i * 3 + 2] / mode.eigval;
}
if (mass != null)
{
bfactor[i] /= mass[i];
}
}
return(bfactor);
}
public static Tuple <double, double, double[]> GetQuality
(string pathbase
, Universe univ
, Universe univ_scrn
, string hesstype
, double GetHessCoarseResiIter_thres_zeroblk
)
{
Universe luniv;
Func <Hess.HessInfo> GetHessInfo;
switch (hesstype)
{
case "NMA": luniv = univ; GetHessInfo = delegate() { return(Hess.GetHessNMA(luniv, luniv.GetCoords(), tempbase, 16)); }; break;
case "scrnNMA": luniv = univ_scrn; GetHessInfo = delegate() { return(Hess.GetHessNMA(luniv, luniv.GetCoords(), tempbase, 16, "CUTOFF 9", "TAPER")); }; break;
case "sbNMA": luniv = univ; GetHessInfo = delegate() { return(Hess.GetHessSbNMA(luniv, luniv.GetCoords(), double.PositiveInfinity)); }; break;
case "ssNMA": luniv = univ; GetHessInfo = delegate() { return(Hess.GetHessSsNMA(luniv, luniv.GetCoords(), double.PositiveInfinity)); }; break;
case "eANM": luniv = univ; GetHessInfo = delegate() { return(Hess.GetHessEAnm(luniv, luniv.GetCoords())); }; break;
case "AA-ANM": luniv = univ; GetHessInfo = delegate() { return(Hess.GetHessAnm(luniv, luniv.GetCoords(), 4.5)); }; break;
default:
throw new HException();
}
string pathcache = pathbase + string.Format("{0}.{1}.txt", hesstype, GetHessCoarseResiIter_thres_zeroblk);
Tuple <double, double, double[]> corr_wovlp_ovlps;
try
{
corr_wovlp_ovlps = GetQuality(pathcache, luniv, GetHessInfo, GetHessCoarseResiIter_thres_zeroblk);
return(corr_wovlp_ovlps);
}
catch
{
return(null);
}
}
//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));
}
public static bool GetBFactorSelfTest(string pdbpath, double cutoff, double corr, int round, InfoPack extra)
{
if (HFile.Exists(pdbpath) == false)
{
return(false);
}
Pdb pdb = Pdb.FromFile(pdbpath);
for (int i = 0; i < pdb.atoms.Length; i++)
{
HDebug.Assert(pdb.atoms[0].altLoc == pdb.atoms[i].altLoc);
HDebug.Assert(pdb.atoms[0].chainID == pdb.atoms[i].chainID);
}
List <Pdb.Atom> atoms = new List <Pdb.Atom>();
for (int i = 0; i < pdb.atoms.Length; i++)
{
Pdb.Atom atom = pdb.atoms[i];
if (atom.name.Trim().ToUpper() == "CA")
{
atoms.Add(atom);
}
}
List <Vector> coords = atoms.ListCoord();
Matrix hess = Hess.GetHessAnm(coords, cutoff);
InfoPack lextra = new InfoPack();
Vector bfactor = GetBFactor(hess, 0.00000001, null, lextra);
if (extra != null)
{
extra["num_zero_eigvals"] = lextra["num_zero_eigvals"];
extra["eigenvalues"] = lextra["eigenvalues"];
}
double corr_comp = pdb.CorrBFactor(atoms.ListName(), atoms.ListResSeq(), bfactor.ToArray());
corr_comp = Math.Round(corr_comp, round);
HDebug.Assert(corr == corr_comp);
return(corr == corr_comp);
}
/// Lei Zhou and Steven A. Siegelbaum,
/// Effects of Surface Water on Protein Dynamics Studied by a Novel Coarse-Grained Normal Mode Approach
/// Biophysical Journal, Volume 94, May 2008
/// http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2292380/pdf/3461.pdf
///
/// Divide Hessian matrix into heavy atoms and others:
/// Hess = [ HH HL ]
/// [ LH LL ],
/// where H and L imply heavy and light atoms, respectively.
///
/// Using block inverse matrix
/// [A B]-1 = [ (A-B D^-1 C)^-1 ... ]
/// [C D] [ ... ... ],
/// find the HH coarse-grain block of Hessian matrix:
/// Hess_HH = HH - HL * LL^-1 * LH
public static HessMatrix GetHessCoarseBlkmat(Matrix hess, IList <int> idx_heavy, ILinAlg ila, double?chkDiagToler, string invtype, params object[] invopt)
{
List <int> idxhess = new List <int>();
foreach (int idx in idx_heavy)
{
idxhess.Add(idx * 3 + 0);
idxhess.Add(idx * 3 + 1);
idxhess.Add(idx * 3 + 2);
}
HessMatrix hess_HH = new HessMatrixDense {
hess = hess.InvOfSubMatrixOfInv(idxhess, ila, invtype, invopt)
};
if (chkDiagToler == null)
{
chkDiagToler = 0.000001;
}
HDebug.Assert(Hess.CheckHessDiag(hess_HH, chkDiagToler.Value));
return(hess_HH);
}
public static HessMatrix GetHess(Universe univ)
{
Vector[] coords = univ.GetCoords();
HessMatrix hessian_spr = HessMatrixSparse.ZerosSparse(univ.size * 3, univ.size * 3);
Universe.Nonbondeds_v1 nonbondeds = new Universe.Nonbondeds_v1(univ.atoms, univ.size, 12);
nonbondeds.UpdateNonbondeds(coords, 0);
hessian_spr = STeM.GetHessBond(coords, univ.bonds, null, hessian: hessian_spr); HDebug.Verify(Hess.CheckHessDiag(hessian_spr, 0.000001, "non-computable exception while generating STeM hess_spr with bond"));
hessian_spr = STeM.GetHessAngle(coords, univ.angles, true, null, null, hessian: hessian_spr); HDebug.Verify(Hess.CheckHessDiag(hessian_spr, 0.000001, "non-computable exception while generating STeM hess_spr with angle"));
hessian_spr = STeM.GetHessImproper(coords, univ.impropers, null, hessian: hessian_spr); HDebug.Verify(Hess.CheckHessDiag(hessian_spr, 0.000001, "non-computable exception while generating STeM hess_spr with improper"));
hessian_spr = STeM.GetHessDihedral(coords, univ.dihedrals, null, null, hessian: hessian_spr); HDebug.Verify(Hess.CheckHessDiag(hessian_spr, 0.000001, "non-computable exception while generating STeM hess_spr with dihedral"));
hessian_spr = STeM.GetHessVdw(coords, univ.nonbonded14s.GetEnumerable(), null, null, hessian: hessian_spr); HDebug.Verify(Hess.CheckHessDiag(hessian_spr, 0.000001, "non-computable exception while generating STeM hess_spr with vdw14"));
hessian_spr = STeM.GetHessElec(coords, univ.nonbonded14s.GetEnumerable(), hessian: hessian_spr); HDebug.Verify(Hess.CheckHessDiag(hessian_spr, 0.000001, "non-computable exception while generating STeM hess_spr with elec14"));
hessian_spr = STeM.GetHessVdw(coords, nonbondeds.GetEnumerable(), null, null, hessian: hessian_spr); HDebug.Verify(Hess.CheckHessDiag(hessian_spr, 0.000001, "non-computable exception while generating STeM hess_spr with vdw"));
hessian_spr = STeM.GetHessElec(coords, nonbondeds.GetEnumerable(), hessian: hessian_spr); HDebug.Verify(Hess.CheckHessDiag(hessian_spr, 0.000001, "non-computable exception while generating STeM hess_spr with elec"));
//hessian_spr = GetHessSprElec(coords, nonbondeds , hessian: hessian_spr); Debug.Verify(Hess.CheckHessDiag(hessian_spr));
//hessian_spr = GetHessSprVdw(coords, nonbondeds , hessian: hessian_spr); Debug.Verify(Hess.CheckHessDiag(hessian_spr));
hessian_spr = Hess.CorrectHessDiag(hessian_spr); HDebug.Verify(Hess.CheckHessDiag(hessian_spr, 0.000001, "non-computable exception while generating STeM hess_spr"));
return(hessian_spr);
}
public HessMatrix GetHessMassWeighted(bool delhess)
{
HessMatrix mwhess;
if (delhess)
{
mwhess = hess;
hess = null;
}
else
{
mwhess = hess.CloneHess();
}
double[] mass3 = new double[mass.Size * 3];
for (int i = 0; i < mass3.Length; i++)
{
mass3[i] = mass[i / 3];
}
Hess.UpdateMassWeightedHess(mwhess, mass3);
return(mwhess);
}
public static double GetSprTensor(Vector[] coords, HessMatrix hess, int atm1, int atm2, IList <int> atms, ILinAlg ila)
{
HDebug.Assert(atms.Count == atms.HUnion().Length);
int[] idxs = atms.HUnion();
idxs = idxs.HRemoveAll(atm1);
idxs = idxs.HRemoveAll(atm2);
idxs = idxs.HInsert(0, atm2);
idxs = idxs.HInsert(0, atm1);
HDebug.Assert(idxs.HExcept(atms).HExcept(atm1, atm2).Length == 0);
HDebug.Assert(idxs[0] == atm1);
HDebug.Assert(idxs[1] == atm2);
HessMatrix H = hess.ReshapeByAtom(idxs);
H = Hess.GetHessFixDiag(H);
HDebug.Assert(H.ColSize == H.RowSize, H.RowSize == idxs.Length * 3);
// H should have 6 zero eigenvalues !!
// since it is the original hessian matrix.
Vector u12 = (coords[atm2] - coords[atm1]).UnitVector();
Matrix S12 = Matrix.Zeros(idxs.Length * 3, 6);
for (int i = 0; i < 6; i++)
{
S12[i, i] = 1;
}
Matrix invkij = GetInvSprTensorSymm(H, S12, ila);
HDebug.Assert(invkij.ColSize == 1, invkij.RowSize == 1);
HDebug.Assert(invkij[0, 0] > 0);
double kij = 1 / invkij[0, 0];
return(kij);
}
public static Vector[] GetRotTran(Vector[] coords, double[] masses)
{
#region source rtbProjection.m
/// rtbProjection.m
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
/// function [P, xyz] = rtbProjection(xyz, mass)
/// % the approach is to find the inertia. compute the principal axes. and then use them to determine directly translation or rotation.
///
/// n = size(xyz, 1); % n: the number of atoms
/// if nargin == 1
/// mass = ones(n,1);
/// end
///
/// M = sum(mass);
/// % find the mass center.
/// m3 = repmat(mass, 1, 3);
/// center = sum (xyz.*m3)/M;
/// xyz = xyz - center(ones(n, 1), :);
///
/// mwX = sqrt (m3).*xyz;
/// inertia = sum(sum(mwX.^2))*eye(3) - mwX'*mwX;
/// [V,D] = eig(inertia);
/// tV = V'; % tV: transpose of V. Columns of V are principal axes.
/// for i=1:3
/// trans{i} = tV(ones(n,1)*i, :); % the 3 translations are along principal axes
/// end
/// P = zeros(n*3, 6);
/// for i=1:3
/// rotate{i} = cross(trans{i}, xyz);
/// temp = mat2vec(trans{i});
/// P(:,i) = temp/norm(temp);
/// temp = mat2vec(rotate{i});
/// P(:,i+3) = temp/norm(temp);
/// end
/// m3 = mat2vec(sqrt(m3));
/// P = repmat (m3(:),1,size(P,2)).*P;
/// % now normalize columns of P
/// P = P*diag(1./normMat(P,1));
///
/// function vec = mat2vec(mat)
/// % convert a matrix to a vector, extracting data *row-wise*.
/// vec = reshape(mat',1,prod(size(mat)));
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
#endregion
if (HDebug.Selftest())
#region selftest
{
// get test coords and masses
Vector[] tcoords = Pdb.FromLines(SelftestData.lines_1EVC_pdb).atoms.ListCoord().ToArray();
double[] tmasses = new double[tcoords.Length];
for (int i = 0; i < tmasses.Length; i++)
{
tmasses[i] = 1;
}
// get test rot/trans RTB vectors
Vector[] trottra = GetRotTran(tcoords, tmasses);
HDebug.Assert(trottra.Length == 6);
// get test ANM
var tanm = Hess.GetHessAnm(tcoords);
// size of vec_i == 1
for (int i = 0; i < trottra.Length; i++)
{
double dist = trottra[i].Dist;
HDebug.Assert(Math.Abs(dist - 1) < 0.00000001);
}
// vec_i and vec_j must be orthogonal
for (int i = 0; i < trottra.Length; i++)
{
for (int j = i + 1; j < trottra.Length; j++)
{
double dot = LinAlg.VtV(trottra[i], trottra[j]);
HDebug.Assert(Math.Abs(dot) < 0.00000001);
}
}
// vec_i' * ANM * vec_i == 0
for (int i = 0; i < trottra.Length; i++)
{
double eigi = LinAlg.VtMV(trottra[i], tanm, trottra[i]);
HDebug.Assert(Math.Abs(eigi) < 0.00000001);
Vector tvecx = trottra[i].Clone();
tvecx[1] += (1.0 / tvecx.Size) * Math.Sign(tvecx[1]);
tvecx = tvecx.UnitVector();
double eigix = LinAlg.VtMV(tvecx, tanm, tvecx);
HDebug.Assert(Math.Abs(eigix) > 0.00000001);
}
}
#endregion
Vector[] rottran;
using (new Matlab.NamedLock(""))
{
Matlab.PutMatrix("xyz", coords.ToMatrix(), true);
Matlab.Execute("xyz = xyz';");
Matlab.PutVector("mass", masses);
//Matlab.Execute("function [P, xyz] = rtbProjection(xyz, mass) ");
//Matlab.Execute("% the approach is to find the inertia. compute the principal axes. and then use them to determine directly translation or rotation. ");
Matlab.Execute(" ");
Matlab.Execute("n = size(xyz, 1); % n: the number of atoms ");
//Matlab.Execute("if nargin == 1; ");
//Matlab.Execute(" mass = ones(n,1); ");
//Matlab.Execute("end ");
Matlab.Execute(" ");
Matlab.Execute("M = sum(mass); ");
Matlab.Execute("% find the mass center. ");
Matlab.Execute("m3 = repmat(mass, 1, 3); ");
Matlab.Execute("center = sum (xyz.*m3)/M; ");
Matlab.Execute("xyz = xyz - center(ones(n, 1), :); ");
Matlab.Execute(" ");
Matlab.Execute("mwX = sqrt (m3).*xyz; ");
Matlab.Execute("inertia = sum(sum(mwX.^2))*eye(3) - mwX'*mwX; ");
Matlab.Execute("[V,D] = eig(inertia); ");
Matlab.Execute("tV = V'; % tV: transpose of V. Columns of V are principal axes. ");
Matlab.Execute("for i=1:3 \n"
+ " trans{i} = tV(ones(n,1)*i, :); % the 3 translations are along principal axes \n"
+ "end \n");
Matlab.Execute("P = zeros(n*3, 6); ");
Matlab.Execute("mat2vec = @(mat) reshape(mat',1,prod(size(mat))); ");
Matlab.Execute("for i=1:3 \n"
+ " rotate{i} = cross(trans{i}, xyz); \n"
+ " temp = mat2vec(trans{i}); \n"
+ " P(:,i) = temp/norm(temp); \n"
+ " temp = mat2vec(rotate{i}); \n"
+ " P(:,i+3) = temp/norm(temp); \n"
+ "end ");
Matlab.Execute("m3 = mat2vec(sqrt(m3)); ");
Matlab.Execute("P = repmat (m3(:),1,size(P,2)).*P; ");
//Matlab.Execute("% now normalize columns of P "); // already normalized
//Matlab.Execute("normMat = @(x) sqrt(sum(x.^2,2)); "); // already normalized
//Matlab.Execute("P = P*diag(1./normMat(P,1)); "); // already normalized
//Matlab.Execute(" "); // already normalized
//////////////////////////////////////////////////////////////////////////////////////////////////////
//Matlab.Execute("function vec = mat2vec(mat) ");
//Matlab.Execute("% convert a matrix to a vector, extracting data *row-wise*. ");
//Matlab.Execute("vec = reshape(mat',1,prod(size(mat))); ");
//////////////////////////////////////////////////////////////////////////////////////////////////////
//Matlab.Execute("function amp = normMat(x) ");
//Matlab.Execute("amp = sqrt(sum(x.^2,2)); ");
Matrix xyz = Matlab.GetMatrix("xyz", true);
Matrix P = Matlab.GetMatrix("P", true);
rottran = P.GetColVectorList();
}
return(rottran);
}
public static CTesthess ReadHess
(Xyz xyz
, string outputpath
, Dictionary <string, string[]> optOutSource // =null
, Func <int, int, HessMatrix> HessMatrixZeros // =null
)
{
int size = xyz.atoms.Length;
#region format: output.txt
/// ######################################################################
/// ##########################################################################
/// ### ###
/// ### TINKER --- Software Tools for Molecular Design ###
/// ## ##
/// ## Version 6.2 February 2013 ##
/// ## ##
/// ## Copyright (c) Jay William Ponder 1990-2013 ##
/// ### All Rights Reserved ###
/// ### ###
/// ##########################################################################
/// ######################################################################
///
///
/// Atoms with an Unusual Number of Attached Atoms :
///
/// Type Atom Name Atom Type Expected Found
///
/// Valence 1496-NR2 69 2 3
/// Valence 2438-FE 107 6 5
///
/// Diagonal Hessian Elements for Each Atom :
///
/// Atom X Y Z
///
/// 1 1445.9830 1358.3447 1484.8642
/// 2 212.9895 294.4584 604.5062
/// 3 187.1986 751.6727 125.0336
/// 4 813.4799 132.1743 151.5707
/// ...
/// 2507 178.7277 479.7434 243.4103
/// 2508 969.8813 977.2507 1845.6726
/// 2509 390.1648 232.0577 1029.6844
/// 2510 322.3674 337.8749 996.8230
///
/// Sum of Diagonal Hessian Elements : 5209042.9060
///
/// Hessian Matrix written to File : test.hes
#endregion
Tuple <int, double, double, double>[] outDiagHessElems = new Tuple <int, double, double, double> [size];
double?outSumDiagHessElem = null;
string outHessMatFile = null;
string outHessFormat = null;
{
string step = "";
foreach (string _line in HFile.ReadLines(outputpath))
{
string line = _line.Trim();
if (line.Length == 0)
{
continue;
}
if (line.Trim().StartsWith("#"))
{
continue;
}
if (line.Contains(" :"))
{
if (line.Contains("Atoms with an Unusual Number of Attached Atoms"))
{
step = ""; continue;
}
else if (line.Contains("Diagonal Hessian Elements for Each Atom"))
{
step = "hess diagonal"; continue;
}
else if (line.Contains("Sum of Diagonal Hessian Elements"))
{
step = "sum hess diagonal";
}
else if (line.Contains("Hessian Matrix written to File"))
{
step = "full hess file";
}
else if (line.Contains("Hessian Sparse Matrix written to File"))
{
step = "sparse hess file";
}
else if (line.Contains("Select Smaller Size for Sparse Hessian Matrix"))
{
continue;
}
else
{
HDebug.Assert(false);
continue;
}
}
switch (step)
{
case "":
continue;
case "hess diagonal":
{
string[] tokens = line.Split().HRemoveAll("");
if (tokens[0] == "Atom")
{
continue;
}
int Atom = int.Parse(tokens[0]); // ; if( int.TryParse(tokens[0], out Atom) == false) continue;
double X = double.Parse(tokens[1]); // ; if(double.TryParse(tokens[1], out X) == false) continue;
double Y = double.Parse(tokens[2]); // ; if(double.TryParse(tokens[2], out Y) == false) continue;
double Z = double.Parse(tokens[3]); // ; if(double.TryParse(tokens[3], out Z) == false) continue;
HDebug.Assert(outDiagHessElems[Atom - 1] == null);
outDiagHessElems[Atom - 1] = new Tuple <int, double, double, double>(Atom, X, Y, Z);
}
continue;
case "sum hess diagonal":
{
string[] tokens = line.Split().HRemoveAll("");
double sum = double.Parse(tokens.Last()); // if(double.TryParse(tokens.Last(), out sum) == false) continue;
outSumDiagHessElem = sum;
}
step = "";
continue;
case "full hess file": outHessFormat = "full matrix"; goto case "hess file";
case "sparse hess file": outHessFormat = "sparse matrix"; goto case "hess file";
case "hess file":
{
string[] tokens = line.Split().HRemoveAll("");
string outputpath_dir = HFile.GetFileInfo(outputpath).Directory.FullName;
outHessMatFile = outputpath_dir + "\\" + tokens.Last();
}
step = "";
continue;
default:
HDebug.Assert(false);
step = "";
continue;
}
}
}
#region Format: test.hes
/// Diagonal Hessian Elements (3 per Atom)
///
/// 1445.9830 1358.3447 1484.8642 212.9895 294.4584 604.5062
/// 187.1986 751.6727 125.0336 813.4799 132.1743 151.5707
/// 1167.7472 1188.3459 1162.5475 268.8291 498.0188 143.2438
/// ...
/// Off-diagonal Hessian Elements for Atom 1 X
/// 23.0878 14.6380 -214.0545 96.9308 -186.7740 -205.1460
/// -208.7035 -28.9630 -788.9124 39.6748 126.4491 -190.5074
/// ...
/// Off-diagonal Hessian Elements for Atom 1 Y
/// -64.1616 97.2697 -292.3813 264.1922 -184.4701 -728.8687
/// -109.9103 15.4168 -152.5717 -11.7733 18.8369 -188.4875
/// ...
/// Off-diagonal Hessian Elements for Atom 1 Z
/// -155.9409 219.8782 -610.0622 -10.0041 -62.8209 -156.1112
/// 77.0829 -14.2127 -166.0525 53.1834 -97.4207 -347.9315
/// ...
/// Off-diagonal Hessian Elements for Atom 2 X
/// -106.5166 185.8395 19.7546 -10.0094 25.8072 -8.1335
/// 35.8501 -64.8320 3.8761 -13.8893 9.4266 0.1312
/// ...
///
/// ...
///
/// Off-diagonal Hessian Elements for Atom 2508 X
/// 488.4590 -69.2721 -338.4824 -155.1656 253.3732 -297.4214
/// -164.8301 -191.3769
/// Off-diagonal Hessian Elements for Atom 2508 Y
/// 74.0161 -149.1060 -273.4863 176.4975 -170.6527 -341.1639
/// -263.6141
/// Off-diagonal Hessian Elements for Atom 2508 Z
/// 304.9942 223.7496 -851.3028 -242.9481 -310.7953 -821.2532
/// Off-diagonal Hessian Elements for Atom 2509 X
/// 198.4498 -331.6530 78.8172 17.3909 -30.0512
/// Off-diagonal Hessian Elements for Atom 2509 Y
/// -227.5916 25.7235 74.5131 -53.2690
/// Off-diagonal Hessian Elements for Atom 2509 Z
/// 46.7873 20.7615 -168.0704
/// Off-diagonal Hessian Elements for Atom 2510 X
/// 252.6853 247.2963
/// Off-diagonal Hessian Elements for Atom 2510 Y
/// 343.6797
#endregion
HessMatrix hess;
{
if (HessMatrixZeros != null)
{
hess = HessMatrixZeros(size * 3, size * 3);
}
else
{
switch (outHessFormat)
{
case "full matrix": hess = HessMatrixDense.ZerosDense(size * 3, size * 3); break;
case "sparse matrix": hess = HessMatrixSparse.ZerosSparse(size * 3, size * 3); break;
default: hess = null; break;
}
}
//HDebug.SetEpsilon(hess);
string step = "";
int diagidx = -1;
int offidx1 = -1;
int offidx2 = -1;
/// string[] lines = HFile.ReadAllLines(outHessMatFile);
/// GC.WaitForFullGCComplete();
/// object[] tokenss = new object[lines.Length];
///
/// Parallel.For(0, lines.Length, delegate(int i)
/// //for(int i=0; i<lines.Length; i++)
/// {
/// string line = lines[i];
/// string[] stokens = line.Trim().Split().RemoveAll("");
/// if(stokens.Length != 0)
/// {
/// double[] dtokens = new double[stokens.Length];
/// for(int j=0; j<stokens.Length; j++)
/// if(double.TryParse(stokens[j], out dtokens[j]) == false)
/// {
/// tokenss[i] = stokens;
/// goto endfor;
/// }
/// tokenss[i] = dtokens;
/// }
/// endfor: ;
/// });
/// System.IO.StreamReader matreader = HFile.OpenText(outHessMatFile);
/// while(matreader.EndOfStream == false)
/// for(int i=0; i<lines.Length; i++)
/// foreach(string line in lines)
foreach (string line in HFile.HEnumAllLines(outHessMatFile))
{
/// string line = lines[i];
/// string line = matreader.ReadLine();
string[] tokens = line.Trim().Split().HRemoveAll("");
if (tokens.Length == 0)
{
continue;
}
/// if(tokenss[i] == null)
/// continue;
/// string[] stokens = (tokenss[i] as string[]);
if (tokens[0] == "Diagonal" && tokens[1] == "Hessian" && tokens[2] == "Elements")
{
step = "Diagonal"; diagidx = 0; continue;
}
if (tokens[0] == "Off-diagonal" && tokens[1] == "Hessian" && tokens[2] == "Elements")
{
step = "Off-diagonal"; offidx1++; offidx2 = offidx1 + 1; continue;
}
if (tokens[0] == "Off-diagonal" && tokens[1] == "sparse" && tokens[2] == "Hessian" &&
tokens[3] == "Indexes/Elements" && tokens[4] == "for" && tokens[5] == "Atom")
{
step = "Off-diagonal sparse";
offidx1 = (int.Parse(tokens[6]) - 1) * 3;
switch (tokens[7])
{
case "X": break;
case "Y": offidx1 += 1; break;
case "Z": offidx1 += 2; break;
default: throw new HException();
}
continue;
}
/// double[] dtokens = (tokenss[i] as double[]);
/// tokens = new string[20];
/// for(int i=0; i*12<line.Length; i++)
/// tokens[i] = line.Substring(i*12, 12).Trim();
/// tokens = tokens.HRemoveAll("").ToArray();
/// tokens = tokens.HRemoveAll(null).ToArray();
switch (step)
{
case "Diagonal":
{
/// foreach(double val in dtokens)
foreach (string token in tokens)
{
HDebug.Assert(token.Last() != ' ');
double val = double.Parse(token);
HDebug.Assert(hess[diagidx, diagidx] == 0);
hess[diagidx, diagidx] = val;
diagidx++;
}
}
continue;
case "Off-diagonal":
{
/// foreach(double val in dtokens)
foreach (string token in tokens)
{
HDebug.Assert(token.Last() != ' ');
//double val = double.Parse(token);
double val;
bool succ = double.TryParse(token, out val);
if (succ == false)
{
HDebug.Assert(false);
goto case "exception 0";
}
if (size < 3000)
{
HDebug.Assert(hess[offidx1, offidx2] == 0);
HDebug.Assert(hess[offidx2, offidx1] == 0);
}
if (val != 0)
{
hess[offidx1, offidx2] = val;
hess[offidx2, offidx1] = val;
}
offidx2++;
}
}
continue;
case "Off-diagonal sparse":
{
HDebug.Assert(tokens.Length % 2 == 0);
for (int i = 0; i < tokens.Length; i += 2)
{
HDebug.Assert(tokens[i].Last() != ' ');
HDebug.Assert(tokens[i + 1].Last() != ' ');
//double val = double.Parse(token);
double val;
bool succ = true;
succ &= int.TryParse(tokens[i], out offidx2); offidx2--;
succ &= double.TryParse(tokens[i + 1], out val);
if (succ == false)
{
HDebug.Assert(false);
goto case "exception 0";
}
if (size < 3000)
{
HDebug.Assert(hess[offidx1, offidx2] == 0);
HDebug.Assert(hess[offidx2, offidx1] == 0);
}
if (val != 0)
{
hess[offidx1, offidx2] = val;
hess[offidx2, offidx1] = val;
}
}
}
continue;
default:
HDebug.Assert(false);
goto case "exception 1";
case "exception 0":
throw new HException("incomplete hessian file (0)");
case "exception 1":
throw new HException("incomplete hessian file (1)");
}
throw new HException("incomplete hessian file (2)");
}
/// matreader.Close();
if (HDebug.IsDebuggerAttached && size < 3000)
{
//for(int c=0; c<size*3; c++)
// for(int r=0; r<size*3; r++)
// if(hess[c, r] == double.Epsilon)
// throw new Exception("incomplete hessian file (3)");
//
//for(int c=0; c<size*3; c++)
//{
// double sum = 0;
// double max = double.NegativeInfinity;
// for(int r=0; r<size*3; r++)
// {
// max = Math.Max(max, hess[c, r]);
// sum += hess[c, r];
// HDebug.Assert(hess[c, r] != double.Epsilon);
// }
// HDebug.Assert(Math.Abs(sum) < max/1000);
// HDebug.AssertTolerance(0.1, sum);
//}
Hess.CheckHessDiag(hess, 0.1, null);
for (int i = 0; i < size; i++)
{
HDebug.Assert(outDiagHessElems[i].Item1 == i + 1);
HDebug.AssertTolerance(0.000001, outDiagHessElems[i].Item2 - hess[i * 3 + 0, i * 3 + 0]);
HDebug.AssertTolerance(0.000001, outDiagHessElems[i].Item3 - hess[i * 3 + 1, i * 3 + 1]);
HDebug.AssertTolerance(0.000001, outDiagHessElems[i].Item4 - hess[i * 3 + 2, i * 3 + 2]);
}
}
}
if (optOutSource != null)
{
optOutSource.Add("test.hes", HFile.HEnumAllLines(outHessMatFile).ToArray());
}
return(new CTesthess
{
hess = hess,
xyz = xyz,
});
}
public HessMatrix CorrectHessDiag()
{
return(Hess.CorrectHessDiag(this));
}
public static double GetSprScalar(Vector[] coords, HessMatrix hess, int atm1, int atm2, IList <int> atms, ILinAlg ila)
{
HDebug.Assert(atms.Count == atms.HUnion().Length);
int[] idxs = atms.HUnion();
idxs = idxs.HRemoveAll(atm1);
idxs = idxs.HRemoveAll(atm2);
idxs = idxs.HInsert(0, atm2);
idxs = idxs.HInsert(0, atm1);
HDebug.Assert(idxs.HExcept(atms).HExcept(atm1, atm2).Length == 0);
HDebug.Assert(idxs[0] == atm1);
HDebug.Assert(idxs[1] == atm2);
HessMatrix H = hess.ReshapeByAtom(idxs);
H = Hess.GetHessFixDiag(H);
HDebug.Assert(H.ColSize == H.RowSize, H.RowSize == idxs.Length * 3);
// H should have 6 zero eigenvalues !!
// since it is the original hessian matrix.
// return "0" spring if there is no connect between atm1 and atm2
{
Graph <int, object> g = new Graph <int, object>();
for (int i = 0; i < H.ColBlockSize; i++)
{
g.AddNode(i);
}
foreach (var bc_br_bval in H.EnumBlocks())
{
int bc = bc_br_bval.Item1;
int br = bc_br_bval.Item2;
if (bc > br)
{
continue;
}
g.AddEdge(bc, br, new object());
//g.AddEdge(br, bc, new object()); // g is bi-directional graph
}
var paths = g.FindPathShortest(g.GetNode(0), new Graph <int, object> .Node[] { g.GetNode(1) });
if (paths == null)
{
// if there is no path between 0 <-> 1, then there is no spring
return(0);
}
}
Vector u12 = (coords[atm2] - coords[atm1]).UnitVector();
Matrix S12 = new double[idxs.Length * 3, 1];
S12[0, 0] = u12[0]; S12[1, 0] = u12[1]; S12[2, 0] = u12[2];
S12[3, 0] = -u12[0]; S12[4, 0] = -u12[1]; S12[5, 0] = -u12[2];
Matrix invkij = GetInvSprTensorSymm(H, S12, ila);
HDebug.Assert(invkij.ColSize == 1, invkij.RowSize == 1);
HDebug.Assert(invkij[0, 0] > 0);
double kij = 1 / invkij[0, 0];
return(kij);
}
public static Quality GetQuality
(string pathcache
, Universe univ
, Func <Hess.HessInfo> GetHessInfo
, double GetHessCoarseResiIter_thres_zeroblk
)
{
double corr = double.NaN;
double wovlp = double.NaN;
double sparsityall = double.NaN;
double sparsityca = double.NaN;
double[] ovlps = new double[]
{
double.NaN, double.NaN, double.NaN, double.NaN, double.NaN,
double.NaN, double.NaN, double.NaN, double.NaN, double.NaN,
};
double[] eigvals = new double[]
{
double.NaN, double.NaN, double.NaN, double.NaN, double.NaN,
double.NaN, double.NaN, double.NaN, double.NaN, double.NaN,
};
try
{
Hess.HessInfo hessinfo = GetHessInfo();
double lsparsityall = 1 - hessinfo.hess.RatioUsedBlocks;
Mode[] camodes_orig;
{
int[] idxca = (hessinfo.atoms as Universe.Atom[]).ListPdbAtomName(true).HIdxEqual("CA");
HessMatrix cahess = Hess.GetHessCoarseBlkmat(hessinfo.hess, idxca, "inv");
Mode[] lcamodes = Hess.GetModesFromHess(cahess, la);
var camodes_nzero_zero = lcamodes.SeparateTolerants();
if (bool.Parse("false"))
{
camodes_nzero_zero = lcamodes.SeparateTolerantsByCountSigned(6);
} /// manually fix 3LKY, 4EDL
if (camodes_nzero_zero.Item2.Length != 6)
{
throw new HException("# zero-eigval != 6");
}
camodes_orig = camodes_nzero_zero.Item1;
}
GC.Collect();
Vector cabfactor_orig = camodes_orig.GetBFactor().ToArray();
double lsparsityca;
Mode[] camodes_iter;
Mode[] camodes;
{
var coords = univ.GetCoords();
var cahess = Hess.GetHessCoarseResiIter_BlockWise(hessinfo, coords, la, 18, 500, GetHessCoarseResiIter_thres_zeroblk);
lsparsityca = 1 - cahess.hess.RatioUsedBlocks;
camodes = Hess.GetModesFromHess(cahess.hess, la);
var camodes_nzero_zero = camodes.SeparateTolerantsByCountSigned(6);
if (camodes_nzero_zero.Item2.Length != 6)
{
throw new HException("# zero-eigval != 6");
}
camodes_iter = camodes_nzero_zero.Item1;
}
GC.Collect();
Vector cabfactor_iter = camodes_iter.GetBFactor().ToArray();
corr = HBioinfo.BFactor.Corr(cabfactor_orig, cabfactor_iter);
var lwovlp = HBioinfo.OverlapWeightedByEigval(camodes_orig, camodes_iter, la, false, "corresponding index");
wovlp = lwovlp.woverlap;
sparsityall = lsparsityall;
sparsityca = lsparsityca;
ovlps = new double[]
{
lwovlp.overlaps[0], lwovlp.overlaps[1], lwovlp.overlaps[2], lwovlp.overlaps[3], lwovlp.overlaps[4],
lwovlp.overlaps[5], lwovlp.overlaps[6], lwovlp.overlaps[7], lwovlp.overlaps[8], lwovlp.overlaps[9],
};
eigvals = new double[]
{
camodes[0].eigval, camodes[1].eigval, camodes[2].eigval, camodes[3].eigval, camodes[4].eigval,
camodes[5].eigval, camodes[6].eigval, camodes[7].eigval, camodes[8].eigval, camodes[9].eigval,
};
}
catch (Exception e)
{
if (e.Message != "# zero-eigval != 6")
{
throw;
}
}
return(new Quality
{
corr = corr,
wovlp = wovlp,
sparsity_all = sparsityall,
sparsity_ca = sparsityca,
ovlps = ovlps,
eigvals = eigvals,
});
}
public static void TestTuLiangDataSet()
{
System.Console.WriteLine("pdbid : ANM(TuLiang -> mine), STeM(TuLiang -> mine)");
foreach (STeM.DataSet data in STeM.TuLiangDataSet)
{
Pdb pdb = PdbDatabase.GetPdb(data.pdbid);
int numChain = pdb.atoms.ListChainID().HListCommonT().Count;
HDebug.Assert(numChain == 1);
//List<Pdb.Atom> atoms = pdb.atoms.SelectByName("CA");
List <Pdb.Atom> atoms = pdb.atoms.SelectByAltLoc().SelectByName("CA");
//List<Pdb.Atom> atoms = pdb.atoms.SelectByDefault().SelectByName("CA");
List <Vector> coords = atoms.ListCoord();
Vector bfactors = atoms.ListTempFactor().ToArray();
Matrix hessANM = Hess.GetHessAnm(coords, 12);
Mode[] modeANM = Hess.GetModesFromHess(hessANM);
modeANM = modeANM.SelectExceptSmallSix();
Vector bfactorANM = modeANM.GetBFactor().ToArray();
double corrANM = HBioinfo.BFactor.Corr(bfactors, bfactorANM);
//Matrix hessGNM = ENM.GnmHessian(coords, 12);
//Mode[] modeGNM = Hess.GetModes(hessGNM);
//Vector bfactorGNM = modeGNM.GetBFactor().ToArray();
//double corrGNM = BFactor.Corr(bfactors, bfactorGNM);
HessMatrix hessSTeM = STeM.GetHessCa_matlab(coords);
//Matrix hessSTeM = STeM.GetHessCa(coords);
Mode[] modeSTeM = Hess.GetModesFromHess(hessSTeM);
modeSTeM = modeSTeM.SelectExceptSmallSix();
Vector bfactorSTeM = modeSTeM.GetBFactor().ToArray();
double corrSTeM = HBioinfo.BFactor.Corr(bfactors, bfactorSTeM);
System.Console.Write(data.pdbid);
System.Console.Write(" : ANM({0:0.00}) -> {1:0.0000})", data.ANM, corrANM);
System.Console.Write(" : STeM({0:0.00}) -> {1:0.0000})", data.STeM, corrSTeM);
System.Console.WriteLine();
}
/// Capture of result...
///
/// pdbid : ANM(TuLiang -> mine), STeM(TuLiang -> mine)
/// 1AAC : ANM(0.70) -> 0.6918) : STeM(0.76) -> 0.7538)
/// 1ADS : ANM(0.77) -> 0.7807) : STeM(0.71) -> 0.7142)
/// 1AHC : ANM(0.79) -> 0.7953) : STeM(0.61) -> 0.6117)
/// 1AKY : ANM(0.56) -> 0.5675) : STeM(0.60) -> 0.6023)
/// 1AMM : ANM(0.56) -> 0.5951) : STeM(0.55) -> 0.5304)
#region ...
/// 1AMP : ANM(0.62) -> 0.5643) : STeM(0.68) -> 0.6739)
/// 1ARB : ANM(0.78) -> 0.7526) : STeM(0.83) -> 0.8253)
/// 1ARS : ANM(0.14) -> 0.1343) : STeM(0.41) -> 0.3646)
/// 1ARU : ANM(0.70) -> 0.7358) : STeM(0.79) -> 0.7921)
/// 1BKF : ANM(0.52) -> 0.4695) : STeM(0.50) -> 0.4940)
/// 1BPI : ANM(0.43) -> 0.4225) : STeM(0.57) -> 0.5588)
/// 1CDG : ANM(0.65) -> 0.6586) : STeM(0.71) -> 0.7068)
/// 1CEM : ANM(0.51) -> 0.5232) : STeM(0.76) -> 0.6735)
/// 1CNR : ANM(0.34) -> 0.3445) : STeM(0.42) -> 0.4190)
/// 1CNV : ANM(0.69) -> 0.6748) : STeM(0.68) -> 0.6775)
/// 1CPN : ANM(0.51) -> 0.5607) : STeM(0.56) -> 0.5535)
/// 1CSH : ANM(0.44) -> 0.4257) : STeM(0.57) -> 0.5755)
/// 1CTJ : ANM(0.47) -> 0.4889) : STeM(0.62) -> 0.6256)
/// 1CUS : ANM(0.74) -> 0.7416) : STeM(0.76) -> 0.7992)
/// 1DAD : ANM(0.28) -> 0.3461) : STeM(0.42) -> 0.4155)
/// 1DDT : ANM(0.21) -> 0.1899) : STeM(0.49) -> 0.4869)
/// 1EDE : ANM(0.67) -> 0.7044) : STeM(0.75) -> 0.7439)
/// 1EZM : ANM(0.56) -> 0.5609) : STeM(0.58) -> 0.5842)
/// 1FNC : ANM(0.29) -> 0.2663) : STeM(0.61) -> 0.6109)
/// 1FRD : ANM(0.54) -> 0.5933) : STeM(0.77) -> 0.7579)
/// 1FUS : ANM(0.40) -> 0.3935) : STeM(0.61) -> 0.6084)
/// 1FXD : ANM(0.58) -> 0.6291) : STeM(0.70) -> 0.6793)
/// 1GIA : ANM(0.68) -> 0.6655) : STeM(0.69) -> 0.6856)
/// 1GKY : ANM(0.36) -> 0.3833) : STeM(0.44) -> 0.4257)
/// 1GOF : ANM(0.75) -> 0.7614) : STeM(0.78) -> 0.7736)
/// 1GPR : ANM(0.65) -> 0.5689) : STeM(0.66) -> 0.6534)
/// 1HFC : ANM(0.63) -> 0.6313) : STeM(0.35) -> 0.7303)
/// 1IAB : ANM(0.36) -> 0.3262) : STeM(0.53) -> 0.5232)
/// 1IAG : ANM(0.34) -> 0.3464) : STeM(0.44) -> 0.4344)
/// 1IFC : ANM(0.61) -> 0.5054) : STeM(0.53) -> 0.5395)
/// 1IGD : ANM(0.18) -> 0.1874) : STeM(0.27) -> 0.2660)
/// 1IRO : ANM(0.82) -> 0.7949) : STeM(0.85) -> 0.8461)
/// 1JBC : ANM(0.72) -> 0.7380) : STeM(0.73) -> 0.7326)
/// 1KNB : ANM(0.63) -> 0.6615) : STeM(0.54) -> 0.5389)
/// 1LAM : ANM(0.53) -> 0.5324) : STeM(0.71) -> 0.7102)
/// 1LCT : ANM(0.52) -> 0.5488) : STeM(0.61) -> 0.6115)
/// 1LIS : ANM(0.16) -> 0.1674) : STeM(0.30) -> 0.2959)
/// 1LIT : ANM(0.65) -> 0.5715) : STeM(0.76) -> 0.7575)
/// 1LST : ANM(0.39) -> 0.3860) : STeM(0.73) -> 0.7283)
/// 1MJC : ANM(0.67) -> 0.6470) : STeM(0.61) -> 0.6164)
/// 1MLA : ANM(0.59) -> 0.5686) : STeM(0.54) -> 0.5404)
/// 1MRJ : ANM(0.66) -> 0.6708) : STeM(0.50) -> 0.4923)
/// 1NAR : ANM(0.62) -> 0.6257) : STeM(0.74) -> 0.7332)
/// 1NFP : ANM(0.23) -> 0.2561) : STeM(0.41) -> 0.4053)
/// 1NIF : ANM(0.42) -> 0.4139) : STeM(0.61) -> 0.6112)
/// 1NPK : ANM(0.53) -> 0.5654) : STeM(0.64) -> 0.5983)
/// 1OMP : ANM(0.61) -> 0.5857) : STeM(0.65) -> 0.6499)
/// 1ONC : ANM(0.55) -> 0.5789) : STeM(0.58) -> 0.5736)
/// 1OSA : ANM(0.36) -> 0.3596) : STeM(0.55) -> 0.5465)
/// 1OYC : ANM(0.78) -> 0.7708) : STeM(0.77) -> 0.7757)
/// 1PBE : ANM(0.53) -> 0.5341) : STeM(0.63) -> 0.6290)
/// 1PDA : ANM(0.60) -> 0.6240) : STeM(0.58) -> 0.5697)
/// 1PHB : ANM(0.56) -> 0.5919) : STeM(0.59) -> 0.5866)
/// 1PHP : ANM(0.59) -> 0.5852) : STeM(0.65) -> 0.6470)
/// 1PII : ANM(0.19) -> 0.2429) : STeM(0.28) -> 0.2871)
/// 1PLC : ANM(0.41) -> 0.3411) : STeM(0.42) -> 0.4239)
/// 1POA : ANM(0.54) -> 0.5944) : STeM(0.42) -> 0.4290)
/// 1POC : ANM(0.46) -> 0.4341) : STeM(0.39) -> 0.3878)
/// 1PPN : ANM(0.61) -> 0.5655) : STeM(0.67) -> 0.6757)
/// 1PTF : ANM(0.47) -> 0.4669) : STeM(0.54) -> 0.5349)
/// 1PTX : ANM(0.65) -> 0.5949) : STeM(0.62) -> 0.6167)
/// 1RA9 : ANM(0.48) -> 0.5029) : STeM(0.53) -> 0.5267)
/// 1RCF : ANM(0.59) -> 0.5629) : STeM(0.58) -> 0.5937)
/// 1REC : ANM(0.34) -> 0.3352) : STeM(0.49) -> 0.4884)
/// 1RIE : ANM(0.71) -> 0.7440) : STeM(0.52) -> 0.6806)
/// 1RIS : ANM(0.25) -> 0.2199) : STeM(0.47) -> 0.4779)
/// 1RRO : ANM(0.08) -> 0.1192) : STeM(0.36) -> 0.3266)
/// 1SBP : ANM(0.69) -> 0.6955) : STeM(0.67) -> 0.6668)
/// 1SMD : ANM(0.50) -> 0.5193) : STeM(0.67) -> 0.6713)
/// 1SNC : ANM(0.68) -> 0.6860) : STeM(0.72) -> 0.7275)
/// 1THG : ANM(0.50) -> 0.4982) : STeM(0.50) -> 0.4934)
/// 1TML : ANM(0.64) -> 0.6266) : STeM(0.58) -> 0.5728)
/// 1UBI : ANM(0.56) -> 0.5610) : STeM(0.61) -> 0.6235)
/// 1WHI : ANM(0.12) -> 0.1223) : STeM(0.38) -> 0.3713)
/// 1XIC : ANM(0.29) -> 0.2942) : STeM(0.47) -> 0.4624)
/// 2AYH : ANM(0.63) -> 0.6453) : STeM(0.82) -> 0.8157)
/// 2CBA : ANM(0.67) -> 0.6562) : STeM(0.80) -> 0.8054)
/// 2CMD : ANM(0.68) -> 0.6630) : STeM(0.62) -> 0.6106)
/// 2CPL : ANM(0.61) -> 0.6379) : STeM(0.72) -> 0.7131)
/// 2CTC : ANM(0.63) -> 0.6220) : STeM(0.75) -> 0.7495)
/// 2CY3 : ANM(0.51) -> 0.5150) : STeM(0.67) -> 0.6614)
/// 2END : ANM(0.63) -> 0.6307) : STeM(0.68) -> 0.6841)
/// 2ERL : ANM(0.74) -> 0.7400) : STeM(0.85) -> 0.8445)
/// 2HFT : ANM(0.63) -> 0.5503) : STeM(0.72) -> 0.7228)
/// 2IHL : ANM(0.62) -> 0.6632) : STeM(0.72) -> 0.7083)
/// 2MCM : ANM(0.78) -> 0.7774) : STeM(0.79) -> 0.7886)
/// 2MHR : ANM(0.65) -> 0.6117) : STeM(0.64) -> 0.6341)
/// 2MNR : ANM(0.46) -> 0.4762) : STeM(0.47) -> 0.4688)
/// 2PHY : ANM(0.54) -> 0.5160) : STeM(0.68) -> 0.6831)
/// 2RAN : ANM(0.43) -> 0.4072) : STeM(0.31) -> 0.3138)
/// 2RHE : ANM(0.28) -> 0.2074) : STeM(0.33) -> 0.3317)
/// 2RN2 : ANM(0.68) -> 0.6555) : STeM(0.75) -> 0.7478)
/// 2SIL : ANM(0.43) -> 0.4203) : STeM(0.51) -> 0.5127)
/// 2TGI : ANM(0.69) -> 0.6787) : STeM(0.73) -> 0.7391)
/// 3CHY : ANM(0.61) -> 0.5572) : STeM(0.68) -> 0.6885)
/// 3COX : ANM(0.71) -> 0.6925) : STeM(0.72) -> 0.7179)
/// 3EBX : ANM(0.22) -> 0.1913) : STeM(0.40) -> 0.3871)
/// 3GRS : ANM(0.44) -> 0.4431) : STeM(0.59) -> 0.5910)
/// 3LZM : ANM(0.60) -> 0.5867) : STeM(0.66) -> 0.6567)
/// 3PTE : ANM(0.68) -> 0.6788) : STeM(0.77) -> 0.7688)
/// 4FGF : ANM(0.41) -> 0.3695) : STeM(0.43) -> 0.4166)
/// 4GCR : ANM(0.73) -> 0.7077) : STeM(0.75) -> 0.7258)
/// 4MT2 : ANM(0.42) -> 0.3117) : STeM(0.46) -> 0.4547)
/// 5P21 : ANM(0.40) -> 0.3540) : STeM(0.45) -> 0.4521)
/// 7RSA : ANM(0.42) -> 0.4663) : STeM(0.59) -> 0.5938)
/// 8ABP : ANM(0.61) -> 0.6265) : STeM(0.62) -> 0.6182)
#endregion
}
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);
}
public static Tuple <double, double, double[]> GetQuality
(string pathcache
, Universe univ
, Func <Hess.HessInfo> GetHessInfo
, double GetHessCoarseResiIter_thres_zeroblk
)
{
if (HFile.Exists(pathcache) == false)
{
double corr = double.NaN;
double wovlp = double.NaN;
double[] ovlps = new double[]
{
double.NaN, double.NaN, double.NaN, double.NaN, double.NaN,
double.NaN, double.NaN, double.NaN, double.NaN, double.NaN,
};
try
{
Hess.HessInfo hessinfo = GetHessInfo();
Mode[] camodes_orig;
{
int[] idxca = (hessinfo.atoms as Universe.Atom[]).ListPdbAtomName(true).HIdxEqual("CA");
Matrix cahess = Hess.GetHessCoarseBlkmat(hessinfo.hess, idxca, "inv");
Mode[] lcamodes = Hess.GetModesFromHess(cahess, la);
var camodes_nzero_zero = lcamodes.SeparateTolerants();
if (bool.Parse("false"))
{
camodes_nzero_zero = lcamodes.SeparateTolerantsByCountSigned(6);
} /// manually fix 3LKY, 4EDL
if (camodes_nzero_zero.Item2.Length != 6)
{
throw new HException("# zero-eigval != 6");
}
camodes_orig = camodes_nzero_zero.Item1;
}
GC.Collect();
Vector cabfactor_orig = camodes_orig.GetBFactor().ToArray();
Mode[] camodes_iter;
{
var cahess = Hess.GetHessCoarseResiIter_BlockWise(hessinfo, univ.GetCoords(), la, 18, 500, GetHessCoarseResiIter_thres_zeroblk);
Mode[] lcamodes = Hess.GetModesFromHess(cahess.hess, la);
var camodes_nzero_zero = lcamodes.SeparateTolerantsByCountSigned(6);
if (camodes_nzero_zero.Item2.Length != 6)
{
throw new HException("# zero-eigval != 6");
}
camodes_iter = camodes_nzero_zero.Item1;
}
GC.Collect();
Vector cabfactor_iter = camodes_iter.GetBFactor().ToArray();
corr = HBioinfo.BFactor.Corr(cabfactor_orig, cabfactor_iter);
var lwovlp = HBioinfo.OverlapWeightedByEigval(camodes_orig, camodes_iter, la, false, "corresponding index");
wovlp = lwovlp.woverlap;
ovlps = new double[]
{
lwovlp.overlaps[0], lwovlp.overlaps[1], lwovlp.overlaps[2], lwovlp.overlaps[3], lwovlp.overlaps[4],
lwovlp.overlaps[5], lwovlp.overlaps[6], lwovlp.overlaps[7], lwovlp.overlaps[8], lwovlp.overlaps[9],
};
}
catch (Exception e)
{
if (e.Message != "# zero-eigval != 6")
{
throw;
}
}
HSerialize.SerializeText(pathcache, new double[]
{ corr, wovlp,
ovlps[0], ovlps[1], ovlps[2], ovlps[3], ovlps[4],
ovlps[5], ovlps[6], ovlps[7], ovlps[8], ovlps[9], });
}
{
double[] buff;
HSerialize.DeserializeText(pathcache, out buff);
double corr = buff[0];
double wovlp = buff[1];
double[] ovlps = new double[] { buff[2], buff[3], buff[4], buff[5], buff[6]
, buff[7], buff[8], buff[9], buff[10], buff[11] };
if (double.IsNaN(corr))
{
HDebug.Assert(false);
}
return(new Tuple <double, double, double[]>(corr, wovlp, ovlps));
}
}
