public Mode[] GetModesMassWeighted(bool delhess, ILinAlg la)
{
Matrix mwhess = GetHessMassWeighted(delhess);
Mode[] mwmodes = Hess.GetModesFromHess(mwhess, la);
return(mwmodes);
}
public Mode[] GetModes(ILinAlg la)
{
if (_modes == null)
{
_modes = Hess.GetModesFromHess(hess, la);
}
return(_modes);
}
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 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,
});
}
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
}
