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 Mode[] GetModes()
{ // determine eigvals and eigvecs
if (_modes != null)
{
return(_modes.HClone <Mode>());
}
MatrixByArr hess = MatrixByArr.FromMatrixArray(this.hess);
_modes = HBioinfo.GetModes(hess, cachebase + "Modes.data");
return(_modes.HClone <Mode>());
}
public static (List <(double freq, double dovlp)> freq1_dovlp, List <(double freq, double dovlp)> freq2_dovlp) DegeneratcyOverlap
(IList <Mode> modes1, double[] mass1, double[] mass2, IList <Mode> modes2
, ILinAlg ila, bool bResetUnitVector
, double degeneracy_tolerance // 3.0
, Matrix overlapsigned = null
)
{
if (overlapsigned == null)
{
overlapsigned = HBioinfo.OverlapSigned(modes1, mass1, mass2, modes2, ila, bResetUnitVector);
}
double[] freqs1 = modes1.ListFreq();
double[] freqs2 = modes2.ListFreq();
bool isfreqssorted = true;
{
for (int i = 1; i < freqs1.Length; i++)
{
isfreqssorted = isfreqssorted && (freqs1[i - 1] <= freqs1[i]); // ( sorted ) or ( freqs1[i-1] is close to zero )
}
for (int i = 1; i < freqs2.Length; i++)
{
isfreqssorted = isfreqssorted && (freqs2[i - 1] <= freqs2[i]); // ( sorted ) or ( freqs2[i-1] is close to zero )
}
}
int[] idx1sorted = null;
int[] idx2sorted = null;
if (isfreqssorted == false)
{
idx1sorted = freqs1.HIdxSorted();
idx2sorted = freqs2.HIdxSorted();
modes1 = modes1.HSelectByIndex(idx1sorted);
modes2 = modes2.HSelectByIndex(idx2sorted);
if (mass1 != null)
{
HDebug.Assert(mass1.Length == idx1sorted.Length); mass1 = mass1.HSelectByIndex(idx1sorted);
}
if (mass2 != null)
{
HDebug.Assert(mass2.Length == idx2sorted.Length); mass2 = mass2.HSelectByIndex(idx2sorted);
}
freqs1 = modes1.ListFreq();
freqs2 = modes2.ListFreq();
overlapsigned = HBioinfo.OverlapSigned(modes1, mass1, mass2, modes2, ila, bResetUnitVector);
}
if (HDebug.IsDebuggerAttached)
{
for (int i = 1; i < freqs1.Length; i++)
{
HDebug.Assert(freqs1[i - 1] <= freqs1[i]);
}
for (int i = 1; i < freqs2.Length; i++)
{
HDebug.Assert(freqs2[i - 1] <= freqs2[i]);
}
}
List <(double freq, double dovlp)> freq1_dovlp = new List <(double, double)>();
for (int i1 = 0; i1 < freqs1.Length; i1++)
{
double freq = freqs1[i1];
int i2a = Array.BinarySearch(freqs2, freq - degeneracy_tolerance);
int i2b = Array.BinarySearch(freqs2, freq + degeneracy_tolerance);
if (i2a == i2b)
{
freq1_dovlp.Add((freqs1[i1], 0));
continue;
}
if (i2a < 0)
{
i2a = ~i2a;
}
if (i2b < 0)
{
i2b = ~i2b;
}
HDebug.Assert(i2a < i2b);
double dovlp = 0;
for (int i2 = i2a; i2 < i2b; i2++)
{
dovlp += overlapsigned[i1, i2] * overlapsigned[i1, i2];
}
freq1_dovlp.Add((freqs1[i1], dovlp));
}
List <(double freq, double dovlp)> freq2_dovlp = new List <(double, double)>();
for (int i2 = 0; i2 < freqs2.Length; i2++)
{
double freq = freqs2[i2];
int i1a = Array.BinarySearch(freqs1, freq - degeneracy_tolerance);
int i1b = Array.BinarySearch(freqs1, freq + degeneracy_tolerance);
if (i1a == i1b)
{
freq2_dovlp.Add((freqs2[i2], 0));
continue;
}
if (i1a < 0)
{
i1a = ~i1a;
}
if (i1b < 0)
{
i1b = ~i1b;
}
HDebug.Assert(i1a < i1b);
double dovlp = 0;
for (int i1 = i1a; i1 < i1b; i1++)
{
dovlp += overlapsigned[i1, i2] * overlapsigned[i1, i2];
}
freq2_dovlp.Add((freqs2[i2], dovlp));
}
if (HDebug.IsDebuggerAttached)
{
HDebug.Assert(freqs1.Length == freq1_dovlp.Count);
HDebug.Assert(freqs2.Length == freq2_dovlp.Count);
for (int i = 0; i < freqs1.Length; i++)
{
HDebug.Assert(freqs1[i] == freq1_dovlp[i].freq);
}
for (int i = 0; i < freqs2.Length; i++)
{
HDebug.Assert(freqs2[i] == freq2_dovlp[i].freq);
}
}
return(freq1_dovlp, freq2_dovlp);
}
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));
}
}
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,
});
}