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 void Main
(string[] args
, string[] hesstypes
, double[] threszeroblks
)
{
string cachebase = @"K:\cache\CoarseGraining-20150111\proteins-177\";
string lockbase = cachebase + @"lock\"; if (HDirectory.Exists(lockbase) == false)
{
HDirectory.CreateDirectory(lockbase);
}
Dictionary <string, List <Tuple <double, double, double[]> > > data = new Dictionary <string, List <Tuple <double, double, double[]> > >();
foreach (string pdbid in pdbids)
{
if (locks.ContainsKey(pdbid) == false)
{
var filelock = HFile.LockFile(lockbase + pdbid);
if (filelock == null)
{
System.Console.WriteLine("{0} is locked", pdbid);
continue;
}
locks.Add(pdbid, filelock);
}
string pathbase = cachebase + pdbid + @"\";
// load univ
var pdb0 = Pdb.FromFile(pathbase + "xry-struc.pdb");
var xyz0 = Tinker.Xyz.FromFile(pathbase + "xry-struc.xyz", false);
var xyz1 = Tinker.Xyz.FromFile(pathbase + "min-struc-charmm22.xyz", false);
var prm = Tinker.Prm.FromFile(cachebase + "charmm22.prm");
if (HFile.Exists(pathbase + "min-struc-charmm22-screened.xyz") == false)
{
var newton = Tinker.Run.Newton
(xyz1, prm, tempbase
, null // copytemp
, "A 0.0001" // param
, null // atomsToFix
, false
, "CUTOFF 9", "TAPER"
);
newton.minxyz.ToFile(pathbase + "min-struc-charmm22-screened.xyz", false);
}
var xyz2 = Tinker.Xyz.FromFile(pathbase + "min-struc-charmm22-screened.xyz", false);
Universe univ = Universe.BuilderTinker.Build(xyz1, prm, pdb0, xyz0, 0.001);
Universe univ_scrn = Universe.BuilderTinker.Build(xyz2, prm, pdb0, xyz0, 0.001);
if (HDebug.IsDebuggerAttached)
{
var grad = Tinker.Run.Testgrad(xyz1, prm, tempbase);
var forc = grad.anlyts.GetForces(xyz1.atoms);
var mforc = forc.Dist().Max();
HDebug.Assert(mforc < 0.1);
grad = Tinker.Run.Testgrad(xyz2, prm, tempbase, new string[] { "CUTOFF 9", "TAPER" }
, optOutSource: null
);
forc = grad.anlyts.GetForces(xyz1.atoms);
mforc = forc.Dist().Max();
HDebug.Assert(mforc < 0.1);
}
System.Console.Write(pdbid + " : ");
foreach (string hesstype in hesstypes)
{
foreach (double threszeroblk in threszeroblks)
{
double GetHessCoarseResiIter_thres_zeroblk = threszeroblk;
Tuple <double, double, double[]> corr_wovlp_ovlps = GetQuality(pathbase, univ, univ_scrn, hesstype, GetHessCoarseResiIter_thres_zeroblk);
if (corr_wovlp_ovlps == null)
{
System.Console.Write(hesstype + "(Unknown exception ), ");
continue;
}
System.Console.Write(hesstype + "(");
System.Console.Write("thod " + threszeroblk + " : ");
System.Console.Write("corr {0,6:0.0000}, ", corr_wovlp_ovlps.Item1);
System.Console.Write("wovlp {0,6:0.0000} : ", corr_wovlp_ovlps.Item2);
System.Console.Write("{0}), ", corr_wovlp_ovlps.Item3.HToStringSeparated("{0,4:0.00}", ","));
string datakey = hesstype + "-" + threszeroblk;
if (data.ContainsKey(datakey) == false)
{
data.Add(datakey, new List <Tuple <double, double, double[]> >());
}
data[datakey].Add(corr_wovlp_ovlps);
}
}
System.Console.WriteLine();
}
System.Console.WriteLine("=================================================================================================");
System.Console.Write("avg : ");
foreach (string hesstype in hesstypes)
{
foreach (double threszeroblk in threszeroblks)
{
string datakey = hesstype + "-" + threszeroblk;
List <Tuple <double, double, double[]> > datai = data[datakey];
double[] lst_corr = datai.HListItem1().ToArray();
double[] lst_wovlp = datai.HListItem2().ToArray();
double[][] lst_ovlps = datai.HListItem3().ToArray();
double corr = lst_corr.HRemoveAll(double.NaN).Average();
double wovlp = lst_wovlp.HRemoveAll(double.NaN).Average();
double[] ovlps = new double[10];
for (int i = 0; i < 10; i++)
{
double[] lst_ovlpsi = new double[lst_ovlps.Length];
for (int j = 0; j < lst_ovlps.Length; j++)
{
lst_ovlpsi[j] = lst_ovlps[j][i];
}
ovlps[i] = lst_ovlpsi.HRemoveAll(double.NaN).Average();
}
System.Console.Write(hesstype + "(");
System.Console.Write("thod " + threszeroblk + " : ");
System.Console.Write("corr {0,6:0.0000}, ", corr);
System.Console.Write("wovlp {0,6:0.0000} : ", wovlp);
System.Console.Write("{0}), ", ovlps.HToStringSeparated("{0,4:0.00}", ","));
}
}
System.Console.WriteLine();
System.Console.Write("min : ");
foreach (string hesstype in hesstypes)
{
foreach (double threszeroblk in threszeroblks)
{
string datakey = hesstype + "-" + threszeroblk;
List <Tuple <double, double, double[]> > datai = data[datakey];
double[] lst_corr = datai.HListItem1().ToArray();
double[] lst_wovlp = datai.HListItem2().ToArray();
double[][] lst_ovlps = datai.HListItem3().ToArray();
double corr = lst_corr.HRemoveAll(double.NaN).Min();
double wovlp = lst_wovlp.HRemoveAll(double.NaN).Min();
double[] ovlps = new double[10];
for (int i = 0; i < 10; i++)
{
double[] lst_ovlpsi = new double[lst_ovlps.Length];
for (int j = 0; j < lst_ovlps.Length; j++)
{
lst_ovlpsi[j] = lst_ovlps[j][i];
}
ovlps[i] = lst_ovlpsi.HRemoveAll(double.NaN).Min();
}
System.Console.Write(hesstype + "(");
System.Console.Write("thod " + threszeroblk + " : ");
System.Console.Write("corr {0,6:0.0000}, ", corr);
System.Console.Write("wovlp {0,6:0.0000} : ", wovlp);
System.Console.Write("{0}), ", ovlps.HToStringSeparated("{0,4:0.00}", ","));
}
}
System.Console.WriteLine();
System.Console.Write("#miss: ");
foreach (string hesstype in hesstypes)
{
foreach (double threszeroblk in threszeroblks)
{
string datakey = hesstype + "-" + threszeroblk;
List <Tuple <double, double, double[]> > datai = data[datakey];
double[] lst_corr = datai.HListItem1().ToArray();
double[] lst_wovlp = datai.HListItem2().ToArray();
double[][] lst_ovlps = datai.HListItem3().ToArray();
int cnt_corr = lst_corr.Length - lst_corr.HRemoveAll(double.NaN).Length;
int cnt_wovlp = lst_wovlp.Length - lst_wovlp.HRemoveAll(double.NaN).Length;
int[] cnt_ovlps = new int[10];
for (int i = 0; i < 10; i++)
{
double[] lst_ovlpsi = new double[lst_ovlps.Length];
for (int j = 0; j < lst_ovlps.Length; j++)
{
lst_ovlpsi[j] = lst_ovlps[j][i];
}
cnt_ovlps[i] = lst_ovlpsi.Length - lst_ovlpsi.HRemoveAll(double.NaN).Length;
}
System.Console.Write(hesstype + "(");
System.Console.Write("thod " + threszeroblk + " : ");
System.Console.Write("corr {0,6}, ", cnt_corr);
System.Console.Write("wovlp {0,6} : ", cnt_wovlp);
System.Console.Write("{0}), ", cnt_ovlps.HToStringSeparated("{0,4}", ","));
}
}
System.Console.WriteLine();
}
