public static HessCoarseResiIter.HessInfoCoarseResiIter GetHessCoarseResiIter_SymrcmBlockWise
(Hess.HessInfo hessinfo
, Vector[] coords
, double?symrcm_filter_blckwise_interact // null (use 1 as default)
, ILinAlg ila
, int clus_width ///= 18 | (18,500) is good for large sparse proteins
, int num_atom_merge ///= 500 | (14,400) is good for small densely packed globular proteins
, double thres_zeroblk ///= 0.001 | 0.001 could be fairly good for ssNMA (possibly for sbNMA and NMA, too)
, string[] nameToKeep
)
{
if (clus_width <= 0)
{
throw new Exception("clus_width should be > 0");
}
HessCoarseResiIter.FuncGetIdxKeepListRemv GetIdxKeepListRemv = delegate(object[] latoms, Vector[] lcoords)
{
Universe.Atom[] lunivatoms = latoms.HToType(null as Universe.Atom[]);
return(HessCoarseResiIter.GetIdxKeepListRemv_ResiCluster_SymrcmBlockWise(lunivatoms, lcoords, hessinfo.hess, clus_width, num_atom_merge, symrcm_filter_blckwise_interact, nameToKeep));
};
return(HessCoarseResiIter.GetHessCoarseResiIter
(hessinfo, coords, GetIdxKeepListRemv, ila, thres_zeroblk
, HessCoarseResiIter.IterOption.Matlab_experimental
));
}
public static HessCoarseResiIter.HessInfoCoarseResiIter GetHessCoarseResiIter_BlockWise
(Hess.HessInfo hessinfo
, Vector[] coords
, ILinAlg ila
, int clus_width ///= 18 | (18,500) is good for large sparse proteins
, int num_atom_merge ///= 500 | (14,400) is good for small densely packed globular proteins
, double thres_zeroblk ///= 0.001 | 0.001 could be fairly good for ssNMA (possibly for sbNMA and NMA, too)
, IList <Universe.Atom> keeps
, HessCoarseResiIter.IterOption iteropt
, params string[] options
)
{
if (clus_width <= 0)
{
throw new Exception("clus_width should be > 0");
}
HessCoarseResiIter.FuncGetIdxKeepListRemv GetIdxKeepListRemv = delegate(object[] latoms, Vector[] lcoords)
{
Universe.Atom[] lunivatoms = latoms.HToType(null as Universe.Atom[]);
return(HessCoarseResiIter.GetIdxKeepListRemv_ResiCluster2(lunivatoms, lcoords, clus_width, num_atom_merge, keeps));
};
return(HessCoarseResiIter.GetHessCoarseResiIter
(hessinfo, coords, GetIdxKeepListRemv, ila, thres_zeroblk
, iteropt
, options: options
));
}
public static HessForcInfo From(Hess.HessInfo hessinfo)
{
return(new HessForcInfo {
atoms = hessinfo.atoms,
mass = hessinfo.mass,
coords = hessinfo.coords,
hess = hessinfo.hess,
});
}
public static HessForcInfo From(Hess.HessInfo hessinfo, Vector[] forc)
{
return(new HessForcInfo {
atoms = hessinfo.atoms,
mass = hessinfo.mass,
coords = hessinfo.coords,
hess = hessinfo.hess,
forc = forc,
});
}
public static HessCoarseResiIter.HessInfoCoarseResiIter GetHessCoarseResiIter_SymrcmAtomWise
(Hess.HessInfo hessinfo
, Vector[] coords
, ILinAlg ila
, int num_atom_merge ///= 500 | (14,400) is good for small densely packed globular proteins
, double thres_zeroblk ///= 0.001 | 0.001 could be fairly good for ssNMA (possibly for sbNMA and NMA, too)
, string[] nameToKeep
)
{
HessCoarseResiIter.FuncGetIdxKeepListRemv GetIdxKeepListRemv = delegate(object[] latoms, Vector[] lcoords)
{
Universe.Atom[] lunivatoms = latoms.HToType(null as Universe.Atom[]);
return(HessCoarseResiIter.GetIdxKeepListRemv_ResiCluster_SymrcmAtomWise(lunivatoms, lcoords, hessinfo.hess, num_atom_merge, thres_zeroblk, nameToKeep));
};
return(HessCoarseResiIter.GetHessCoarseResiIter
(hessinfo, coords, GetIdxKeepListRemv, ila, thres_zeroblk
, HessCoarseResiIter.IterOption.Matlab_experimental
));
}
public static HessCoarseResiIter.HessInfoCoarseResiIter GetHessCoarseResiIter_BlockWise
(Hess.HessInfo hessinfo
, Vector[] coords
, ILinAlg ila
, int clus_width ///= 18 | (18,500) is good for large sparse proteins
, int num_atom_merge ///= 500 | (14,400) is good for small densely packed globular proteins
, double thres_zeroblk ///= 0.001 | 0.001 could be fairly good for ssNMA (possibly for sbNMA and NMA, too)
)
{
string[] nameToKeep = new string[] { "CA" };
return(GetHessCoarseResiIter_BlockWise
(hessinfo
, coords
, ila
, clus_width
, num_atom_merge
, thres_zeroblk
, nameToKeep
));
}
public static HessCoarseResiIter.HessInfoCoarseResiIter GetHessCoarseResiIter
(Hess.HessInfo hessinfo
, Vector[] coords
, HessCoarseResiIter.FuncGetIdxKeepListRemv GetIdxKeepListRemv
, ILinAlg ila
, double thres_zeroblk = 0.001
, HessCoarseResiIter.IterOption iteropt = HessCoarseResiIter.IterOption.Matlab_experimental
, string[] options = null
)
{
return(HessCoarseResiIter.GetHessCoarseResiIter
(hessinfo: hessinfo
, coords: coords
, GetIdxKeepListRemv: GetIdxKeepListRemv
, ila: ila
, thres_zeroblk: thres_zeroblk
, iteropt: iteropt
, options: options
));
}
public static HessInfoCoarseResiIter GetHessCoarseResiIter
(Hess.HessInfo hessinfo
, Vector[] coords
, FuncGetIdxKeepListRemv GetIdxKeepListRemv
, ILinAlg ila
, double thres_zeroblk = 0.001
, IterOption iteropt = IterOption.Matlab_experimental
, string[] options = null
)
{
bool rediag = true;
HessMatrix H = null;
List <int>[] lstNewIdxRemv = null;
int numca = 0;
double[] reMass = null;
object[] reAtoms = null;
Vector[] reCoords = null;
Tuple <int[], int[][]> idxKeepRemv = null;
//System.Console.WriteLine("begin re-indexing hess");
{
object[] atoms = hessinfo.atoms;
idxKeepRemv = GetIdxKeepListRemv(atoms, coords);
int[] idxKeep = idxKeepRemv.Item1;
int[][] idxsRemv = idxKeepRemv.Item2;
{
List <int> check = new List <int>();
check.AddRange(idxKeep);
foreach (int[] idxRemv in idxsRemv)
{
check.AddRange(idxRemv);
}
check = check.HToHashSet().ToList();
if (check.Count != coords.Length)
{
throw new Exception("the re-index contains the duplicated atoms or the missing atoms");
}
}
List <int> idxs = new List <int>();
idxs.AddRange(idxKeep);
foreach (int[] idxRemv in idxsRemv)
{
idxs.AddRange(idxRemv);
}
HDebug.Assert(idxs.Count == idxs.HToHashSet().Count);
H = hessinfo.hess.ReshapeByAtom(idxs);
numca = idxKeep.Length;
reMass = hessinfo.mass.ToArray().HSelectByIndex(idxs);
reAtoms = hessinfo.atoms.ToArray().HSelectByIndex(idxs);
reCoords = coords.HSelectByIndex(idxs);
int nidx = idxKeep.Length;
lstNewIdxRemv = new List <int> [idxsRemv.Length];
for (int i = 0; i < idxsRemv.Length; i++)
{
lstNewIdxRemv[i] = new List <int>();
foreach (var idx in idxsRemv[i])
{
lstNewIdxRemv[i].Add(nidx);
nidx++;
}
}
HDebug.Assert(nidx == lstNewIdxRemv.Last().Last() + 1);
HDebug.Assert(nidx == idxs.Count);
}
GC.Collect(0);
HDebug.Assert(numca == H.ColBlockSize - lstNewIdxRemv.HListCount().Sum());
//if(bool.Parse("false"))
{
if (bool.Parse("false"))
#region
{
int[] idxKeep = idxKeepRemv.Item1;
int[][] idxsRemv = idxKeepRemv.Item2;
Pdb.Atom[] pdbatoms = hessinfo.atomsAsUniverseAtom.ListPdbAtoms();
Pdb.ToFile(@"C:\temp\coarse-keeps.pdb", pdbatoms.HSelectByIndex(idxKeep), false);
if (HFile.Exists(@"C:\temp\coarse-graining.pdb"))
{
HFile.Delete(@"C:\temp\coarse-graining.pdb");
}
foreach (int[] idxremv in idxsRemv.Reverse())
{
List <Pdb.Element> delatoms = new List <Pdb.Element>();
foreach (int idx in idxremv)
{
if (pdbatoms[idx] == null)
{
continue;
}
string line = pdbatoms[idx].GetUpdatedLine(coords[idx]);
Pdb.Atom delatom = Pdb.Atom.FromString(line);
delatoms.Add(delatom);
}
Pdb.ToFile(@"C:\temp\coarse-graining.pdb", delatoms.ToArray(), true);
}
}
#endregion
if (bool.Parse("false"))
#region
{
// export matrix to matlab, so the matrix can be checked in there.
int[] idxca = HEnum.HEnumCount(numca).ToArray();
int[] idxoth = HEnum.HEnumFromTo(numca, coords.Length - 1).ToArray();
Matlab.Register(@"C:\temp\");
Matlab.PutSparseMatrix("H", H.GetMatrixSparse(), 3, 3);
Matlab.Execute("figure; spy(H)");
Matlab.Clear();
}
#endregion
if (bool.Parse("false"))
#region
{
HDirectory.CreateDirectory(@"K:\temp\$coarse-graining\");
{ // export original hessian matrix
List <int> cs = new List <int>();
List <int> rs = new List <int>();
foreach (ValueTuple <int, int, MatrixByArr> bc_br_bval in hessinfo.hess.EnumBlocks())
{
cs.Add(bc_br_bval.Item1);
rs.Add(bc_br_bval.Item2);
}
Matlab.Clear();
Matlab.PutVector("cs", cs.ToArray());
Matlab.PutVector("rs", rs.ToArray());
Matlab.Execute("hess = sparse(cs+1, rs+1, ones(size(cs)));");
Matlab.Execute("hess = float(hess);");
Matlab.Execute("figure; spy(hess)");
Matlab.Execute("cs = int32(cs+1);");
Matlab.Execute("rs = int32(rs+1);");
Matlab.Execute(@"save('K:\temp\$coarse-graining\hess-original.mat', 'cs', 'rs', '-v6');");
Matlab.Clear();
}
{ // export reshuffled hessian matrix
List <int> cs = new List <int>();
List <int> rs = new List <int>();
foreach (ValueTuple <int, int, MatrixByArr> bc_br_bval in H.EnumBlocks())
{
cs.Add(bc_br_bval.Item1);
rs.Add(bc_br_bval.Item2);
}
Matlab.Clear();
Matlab.PutVector("cs", cs.ToArray());
Matlab.PutVector("rs", rs.ToArray());
Matlab.Execute("H = sparse(cs+1, rs+1, ones(size(cs)));");
Matlab.Execute("H = float(H);");
Matlab.Execute("figure; spy(H)");
Matlab.Execute("cs = int32(cs+1);");
Matlab.Execute("rs = int32(rs+1);");
Matlab.Execute(@"save('K:\temp\$coarse-graining\hess-reshuffled.mat', 'cs', 'rs', '-v6');");
Matlab.Clear();
}
}
#endregion
if (bool.Parse("false"))
#region
{
int[] idxca = HEnum.HEnumCount(numca).ToArray();
int[] idxoth = HEnum.HEnumFromTo(numca, coords.Length - 1).ToArray();
HessMatrix A = H.SubMatrixByAtoms(false, idxca, idxca);
HessMatrix B = H.SubMatrixByAtoms(false, idxca, idxoth);
HessMatrix C = H.SubMatrixByAtoms(false, idxoth, idxca);
HessMatrix D = H.SubMatrixByAtoms(false, idxoth, idxoth);
Matlab.Clear();
Matlab.PutSparseMatrix("A", A.GetMatrixSparse(), 3, 3);
Matlab.PutSparseMatrix("B", B.GetMatrixSparse(), 3, 3);
Matlab.PutSparseMatrix("C", C.GetMatrixSparse(), 3, 3);
Matlab.PutSparseMatrix("D", D.GetMatrixSparse(), 3, 3);
Matlab.Clear();
}
#endregion
}
List <HessCoarseResiIterInfo> iterinfos = null;
{
object[] atoms = reAtoms; // reAtoms.HToType(null as Universe.Atom[]);
CGetHessCoarseResiIterImpl info = null;
switch (iteropt)
{
case IterOption.ILinAlg_20150329: info = GetHessCoarseResiIterImpl_ILinAlg_20150329(H, lstNewIdxRemv, thres_zeroblk, ila, false); break;
case IterOption.ILinAlg: info = GetHessCoarseResiIterImpl_ILinAlg(H, lstNewIdxRemv, thres_zeroblk, ila, false); break;
case IterOption.Matlab: info = GetHessCoarseResiIterImpl_Matlab(atoms, H, lstNewIdxRemv, thres_zeroblk, ila, false, options); break;
case IterOption.Matlab_experimental: info = GetHessCoarseResiIterImpl_Matlab_experimental(atoms, H, lstNewIdxRemv, thres_zeroblk, ila, false, options); break;
case IterOption.Matlab_IterLowerTri: info = GetHessCoarseResiIterImpl_Matlab_IterLowerTri(atoms, H, lstNewIdxRemv, thres_zeroblk, ila, false, options); break;
case IterOption.LinAlg_IterLowerTri: info = GetHessCoarseResiIterImpl_LinAlg_IterLowerTri.Do(atoms, H, lstNewIdxRemv, thres_zeroblk, ila, false, options); break;
}
;
H = info.H;
iterinfos = info.iterinfos;
}
//{
// var info = GetHessCoarseResiIterImpl_Matlab(H, lstNewIdxRemv, thres_zeroblk);
// H = info.H;
//}
GC.Collect(0);
if (HDebug.IsDebuggerAttached)
{
int nidx = 0;
int[] ikeep = idxKeepRemv.Item1;
foreach (int idx in ikeep)
{
bool equal = object.ReferenceEquals(hessinfo.atoms[idx], reAtoms[nidx]);
if (equal == false)
{
HDebug.Assert(false);
}
HDebug.Assert(equal);
nidx++;
}
}
if (rediag)
{
H = H.CorrectHessDiag();
}
//System.Console.WriteLine("finish fixing diag");
return(new HessInfoCoarseResiIter
{
hess = H,
mass = reMass.HSelectCount(numca),
atoms = reAtoms.HSelectCount(numca),
coords = reCoords.HSelectCount(numca),
numZeroEigval = 6,
iterinfos = iterinfos,
});
}
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 HessInfo GetHessMixAnm(IList <Vector> coords
, IList <int> lstIdxCa
, IList <int> lstIdxAll
, double CaCutoff, double CaSprcst
, double AaCutoff, double AaSprcst
)
{
int size = coords.Count;
Vector[] mixCoords = new Vector[size];
double[] cutoffs = new double[size]; cutoffs = cutoffs.HUpdateValueAll(double.NaN);
double[] sprcsts = new double[size]; sprcsts = sprcsts.HUpdateValueAll(double.NaN);
foreach (int idx in lstIdxCa)
{
mixCoords[idx] = coords[idx].Clone(); cutoffs[idx] = CaCutoff; sprcsts[idx] = CaSprcst;
}
foreach (int idx in lstIdxAll)
{
mixCoords[idx] = coords[idx].Clone(); cutoffs[idx] = AaCutoff; sprcsts[idx] = AaSprcst;
}
double[,] hesskij = new double[size, size]; hesskij = hesskij.HUpdateValueAll(double.NaN);
for (int i = 0; i < size; i++)
{
Vector coordi = mixCoords[i];
if (coordi == null)
{
continue;
}
double cutoffi = cutoffs[i];
double sprcsti = sprcsts[i];
double cutoffi3 = cutoffi * cutoffi * cutoffi;
for (int j = i; j < size; j++)
{
if (i == j)
{
hesskij[i, j] = 0;
continue;
}
Vector coordj = mixCoords[j];
if (coordj == null)
{
continue;
}
double cutoffj = cutoffs[j];
double sprcstj = sprcsts[j];
double cutoffj3 = cutoffj * cutoffj * cutoffj;
double distij = (coordi - coordj).Dist;
double cutoffij;
if (cutoffi == cutoffj)
{
cutoffij = cutoffi;
}
else
{
cutoffij = Math.Pow((cutoffi3 + cutoffj3) / 2, 1 / 3.0);
}
double sprcstij = 0;
if (distij < cutoffij)
{
sprcstij = (sprcsti + sprcstj) / 2;
}
hesskij[i, j] = sprcstij;
hesskij[j, i] = sprcstij;
}
}
HessMatrix hess = GetHessAnm(mixCoords, hesskij);
Vector mass = new double[size]; mass.SetValue(1);
var hessinfo = new Hess.HessInfo
{
hess = hess,
mass = mass,
coords = mixCoords,
atoms = null,
numZeroEigval = 6,
};
return(hessinfo);
}