public static Universe Build(string pdbpath, string toppath, ITextLogger logger)
{
Pdb pdb = Pdb.FromFile(pdbpath);
Top top = Top.FromFile(toppath);
return(Build(pdb, top, logger));
}
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 void Align(string pdbpath1, string pdbpath2, string alignedpath2)
{
Pdb pdb1 = Pdb.FromFile(pdbpath1); List <Pdb.Atom> atoms1 = pdb1.atoms.SelectByChainID().SelectByAltLoc();
Pdb pdb2 = Pdb.FromFile(pdbpath2); List <Pdb.Atom> atoms2 = pdb2.atoms.SelectByChainID().SelectByAltLoc();
Align(atoms1, ref atoms2);
Pdb.ToFile(alignedpath2, atoms2);
}
public static AlignData FromFiles(string path_pdb, string path_hess, IList <double> masses, string cachebase = null)
{
AlignData data = new AlignData();
data.pdb = Pdb.FromFile(path_pdb);
data.coords = data.pdb.atoms.ListCoord();
data.cachebase = cachebase;
int n = data.coords.Count;
{ // data.hess
List <string> lines = HFile.ReadLines(path_hess).ToList();
int row, col;
{
string[] tokens = lines[1].Split(new char[] { ' ', ',', '\t' }, StringSplitOptions.RemoveEmptyEntries);
HDebug.Assert(tokens.Length == 2);
row = int.Parse(tokens[0]);
col = int.Parse(tokens[1]);
HDebug.Assert(row == col);
}
HDebug.Assert(row == n * 3, col == n * 3);
MatrixByArr[,] hess = new MatrixByArr[n, n];
for (int c = 0; c < n; c++)
{
for (int r = 0; r < n; r++)
{
hess[c, r] = new double[3, 3];
}
}
for (int c = 0; c < col; c++)
{
string line = lines[c + 2];
string[] tokens = line.Split(new char[] { ' ', ',', '\t' }, StringSplitOptions.RemoveEmptyEntries);
HDebug.Assert(tokens.Length == row);
for (int r = 0; r < row; r++)
{
double val = double.Parse(tokens[r]);
hess[c / 3, r / 3][c % 3, r % 3] += val;
hess[r / 3, c / 3][r % 3, c % 3] += val;
}
}
for (int c = 0; c < n; c++)
{
for (int r = 0; r < n; r++)
{
hess[c, r] /= 2;
}
}
data.hess = hess;
}
data.masses = masses.ToArray();
return(data);
}
public static void SelfTest(string rootpath, string[] args)
{
{
Pdb pdb = Pdb.FromFile(rootpath + @"\Sample\alanin.pdb");
List <Vector> coords = pdb.atoms.ListCoord();
coords[0] = new Vector(0, 1, 2);
pdb.ToFile(rootpath + @"\Sample\alanin.updated.pdb", coords);
}
{
Pdb pdb = Pdb.FromFile(rootpath + @"\Sample\1a6g.pdb");
//pdb.CollectResidues();
}
}
public static Pdb FromPdbid
(string pdbid
, string cachebase // null or @"K:\PdbUnzippeds\$PDBID$.pdb"
, bool?download // null or false
)
{
if (cachebase == null)
{
cachebase = @"K:\PdbUnzippeds\$PDBID$.pdb";
}
if (download == null)
{
download = false;
}
string pdbpath = cachebase.Replace("$PDBID$", pdbid);
if (HFile.Exists(pdbpath))
{
var pdb = Pdb.FromFile(pdbpath);
var last = pdb.elements.Last();
if (last is Pdb.End)
{
return(pdb);
}
if (last.line.Length == 80)
{
return(pdb);
}
if (download.Value)
{ // redownload
pdb = Pdb.FromPdbid(pdbid);
pdb.ToFile(pdbpath);
}
return(pdb);
}
else if (download.Value)
{
Pdb pdb = Pdb.FromPdbid(pdbid);
if (pdb != null)
{
pdb.ToFile(pdbpath);
return(pdb);
}
}
return(null);
}
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);
}
public static Top FromPdb(string pdbpath
, string ff = "charmm27"
, string water = "none"
, HPack <Pdb> optout_confout = null
)
{
Top top;
FileInfo pdbinfo = new FileInfo(pdbpath);
string currdir = HEnvironment.CurrentDirectory;
DirectoryInfo temproot = HDirectory.CreateTempDirectory();
HEnvironment.CurrentDirectory = temproot.FullName;
{
HFile.Copy(pdbinfo.FullName, "protein.pdb");
RunPdb2gmx(f: "protein.pdb"
, o: "confout.pdb"
, p: "topol.top"
, q: "clean.pdb"
, ff: ff
, water: water
, merge: "all"
, lineStderr: null
, lineStdout: null
);
top = Top.FromFile("topol.top");
if (optout_confout != null)
{
optout_confout.value = Pdb.FromFile("confout.pdb");
}
}
HEnvironment.CurrentDirectory = currdir;
Thread.Sleep(100);
try{ temproot.Delete(true); } catch (Exception) {}
return(top);
}
public bool LoadCoordsFromPdb(string path)
{
Pdb pdb = Pdb.FromFile(path);
HDebug.Assert(this.pdb.atoms.Length == pdb.atoms.Length);
HDebug.Assert(this.size == pdb.atoms.Length);
Vector[] coords = new Vector[size];
for (int i = 0; i < size; i++)
{
if (this.pdb.atoms[i].name != pdb.atoms[i].name)
{
return(false);
}
if (this.pdb.atoms[i].resName != pdb.atoms[i].resName)
{
return(false);
}
coords[i] = pdb.atoms[i].coord;
}
SetCoords(coords);
return(true);
}
public static Universe Build(string xyzpath, bool loadxyzLatest, string prmpath, string pdbpath)
{
Tinker.Xyz xyz = Tinker.Xyz.FromFile(xyzpath, false);
Tinker.Xyz xyz1 = Tinker.Xyz.FromFile(xyzpath, loadxyzLatest);
Tinker.Prm prm = Tinker.Prm.FromFile(prmpath);
Pdb pdb = Pdb.FromFile(pdbpath);
Universe univ = Build(xyz, prm, pdb, 0.002);
if (HDebug.IsDebuggerAttached)
{
HDebug.Assert(xyz.atoms.Length == univ.size);
Vector[] xyzcoords = xyz.atoms.HListCoords();
Vector[] unvcoords = univ.GetCoords();
for (int i = 0; i < univ.size; i++)
{
Vector dcoord = xyzcoords[i] - unvcoords[i];
HDebug.AssertTolerance(0.00000001, dcoord);
}
}
univ.SetCoords(xyz1.atoms.HListCoords());
return(univ);
}
public static void GetPotential_SelfTest(string rootpath, string[] args)
{
if (GetPotential_SelfTest_do == false)
{
return;
}
GetPotential_SelfTest_do = false;
Namd.Psf psf = Namd.Psf.FromFile(rootpath + @"\Sample\alanin.psf");
Pdb pdb = Pdb.FromFile(rootpath + @"\Sample\alanin.pdb");
Namd.Prm prm = Namd.Prm.FromFileXPlor(rootpath + @"\Sample\alanin.params", new TextLogger());
Universe univ = Universe.Build(psf, prm, pdb, false);
List <ForceField.IForceField> frcflds = ForceField.GetMindyForceFields();
Vector[] forces = univ.GetVectorsZero();
MatrixByArr hessian = null;
Dictionary <string, object> cache = new Dictionary <string, object>();
double energy = univ.GetPotential(frcflds, ref forces, ref hessian, cache);
double toler = 0.000005;
HDebug.AssertTolerance(toler, SelfTest_alanin_energy - energy);
HDebug.AssertTolerance(toler, SelfTest_alanin_energy_bonds - (double)cache["energy_bonds "]);
HDebug.AssertTolerance(toler, SelfTest_alanin_energy_angles - (double)cache["energy_angles "]);
HDebug.AssertTolerance(toler, SelfTest_alanin_energy_dihedrals - (double)cache["energy_dihedrals "]);
HDebug.AssertTolerance(toler, SelfTest_alanin_energy_impropers - (double)cache["energy_impropers "]);
HDebug.AssertTolerance(toler, SelfTest_alanin_energy_nonbondeds - (double)cache["energy_nonbondeds"]);
HDebug.AssertTolerance(toler, SelfTest_alanin_energy_unknowns - (double)cache["energy_customs "]);
HDebug.AssertTolerance(toler, SelfTest_alanin_forces.GetLength(0) - forces.Length);
for (int i = 0; i < forces.Length; i++)
{
HDebug.Assert(forces[i].Size == 3);
HDebug.AssertTolerance(toler, SelfTest_alanin_forces[i, 0] - forces[i][0]);
HDebug.AssertTolerance(toler, SelfTest_alanin_forces[i, 1] - forces[i][1]);
HDebug.AssertTolerance(toler, SelfTest_alanin_forces[i, 2] - forces[i][2]);
}
}
public static List <string> Convert_PdbWaterBox_To_XyzWaterBox
(string path_solvbox_pdb //= @"K:\Temp\solvate\solvbox100.pdb";
)
{
Pdb pdb = Pdb.FromFile(path_solvbox_pdb);
var atoms = pdb.atoms;
HDebug.Assert(atoms.Length == 783_198);
string format_id = " {0,6}";
string format_coord = " {0,11:0.000000}";
List <string> lines = new List <string>();
lines.Add(string.Format(format_id, atoms.Length));
for (int i = 0; i < atoms.Length; i++)
{
var atom = atoms[i];
int id = i + 1;
//Tinker.Xyz.Atom
string sId = string.Format(format_id, id);
string sAtomType = null;
string sCoord = string.Format(format_coord, atom.x)
+ string.Format(format_coord, atom.y)
+ string.Format(format_coord, atom.z);
string sAtomId = null;
string sBondedId = null;
switch (i % 3)
{
case 0:
{
HDebug.Assert(atom.name == " OH2");
sAtomType = " OT ";
sAtomId = " 101";
sBondedId = string.Format(format_id, id + 1)
+ string.Format(format_id, id + 2);
//ATOM 1 OH2 TIP3W 1 -39.757 -43.987 -44.549 1.00 0.00 WT1 O
//ATOM 2 H1 TIP3W 1 -38.939 -43.594 -44.737 1.00 0.00 WT1 H
//ATOM 3 H2 TIP3W 1 -39.487 -44.929 -44.474 1.00 0.00 WT1 H
// 36944 OT 26.427752 -2.676966 -11.003556 101 36945 36946
// 36945 HT 25.722690 -1.988586 -10.960428 88 36944
// 36946 HT 25.928766 -3.441458 -11.365251 88 36944
}
break;
case 1:
{
HDebug.Assert(atom.name == " H1 ");
sAtomType = " HT ";
sAtomId = " 88";
sBondedId = string.Format(format_id, id - 1);
}
break;
case 2:
{
HDebug.Assert(atom.name == " H2 ");
sAtomType = " HT ";
sAtomId = " 88";
sBondedId = string.Format(format_id, id - 2);
}
break;
}
HDebug.Assert(sId != null);
HDebug.Assert(sAtomType != null);
HDebug.Assert(sCoord != null);
HDebug.Assert(sAtomId != null);
HDebug.Assert(sBondedId != null);
string line = sId + sAtomType + sCoord + sAtomId + sBondedId;
lines.Add(line);
}
//HFile.WriteAllLines(path_solvbox_pdb.Replace(".pdb",".xyz"), lines);
return(lines);
}
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();
}
public static void SelfTest(string pdbname, string psfname, string prmname, string xyzname)
{
using (var temp = new HTempDirectory(@"C:\temp\", null))
{
temp.EnterTemp();
{
string resbase = "HTLib2.Bioinfo.HTLib2.Bioinfo.External.Tinker.Resources.selftest.";
HResource.CopyResourceTo <Tinker>(resbase + pdbname, pdbname);
HResource.CopyResourceTo <Tinker>(resbase + psfname, psfname);
HResource.CopyResourceTo <Tinker>(resbase + "par_all27_prot_lipid.inp", prmname);
if (xyzname != null)
{
HResource.CopyResourceTo <Tinker>(resbase + xyzname, xyzname);
}
HResource.CopyResourceTo <Tinker>(resbase + "charmm22.prm", "charmm22.prm");
{
var pdb = Pdb.FromFile(pdbname);
var psf = Namd.Psf.FromFile(psfname);
var prm = Namd.Prm.FromFile(prmname);
var xyz_prm = BuildFromNamd(pdb, psf, prm);
xyz_prm.Item1.ToFile("TinkFromNamd.xyz", false);
xyz_prm.Item2.ToFile("TinkFromNamd.prm");
}
if (xyzname != null)
{
var xyz0 = Xyz.FromFile("TinkFromNamd.xyz", false);
var prm0 = Prm.FromFile("TinkFromNamd.prm");
var grad0 = Run.Testgrad(xyz0, prm0, @"C:\temp\"
//, "VDWTERM NONE"
//, "CHARGETERM NONE"
//, "BONDTERM NONE"
//, "ANGLETERM NONE"
//, "UREYTERM NONE"
//, "IMPROPTERM NONE"
//, "TORSIONTERM NONE"
);
var forc0 = grad0.anlyts.GetForces(xyz0.atoms);
var xyz1 = Xyz.FromFile(xyzname, false);
var prm1 = Prm.FromFile("charmm22.prm");
var grad1 = Run.Testgrad(xyz1, prm1, @"C:\temp\"
//, "VDWTERM NONE"
//, "CHARGETERM NONE"
//, "BONDTERM NONE"
//, "ANGLETERM NONE"
//, "UREYTERM NONE"
//, "IMPROPTERM NONE"
//, "TORSIONTERM NONE"
);
var forc1 = grad1.anlyts.GetForces(xyz1.atoms);
{
KDTree.KDTree <object> kdtree = new KDTree.KDTree <object>(3);
var atoms0 = xyz0.atoms;
for (int i = 0; i < atoms0.Length; i++)
{
kdtree.insert(atoms0[i].Coord, i);
}
var atoms1 = xyz1.atoms;
int[] idx1to0 = new int[atoms1.Length];
for (int i1 = 0; i1 < atoms1.Length; i1++)
{
Vector coord1 = atoms1[i1].Coord;
int i0 = (int)kdtree.nearest(coord1);
Vector coord0 = atoms0[i0].Coord;
kdtree.delete(coord0);
idx1to0[i0] = i1;
}
atoms1 = atoms1.HSelectByIndex(idx1to0);
forc1 = forc1.HSelectByIndex(idx1to0);
}
Vector[] dforc = VectorBlock.PwSub(forc0, forc1).ToArray();
double[] dforcl = dforc.Dist();
double max_dforc = dforc.Dist().Max();
HDebug.Exception(max_dforc < 1); // 0.72682794387667848
{
double EB = Math.Abs(grad0.enrgCmpnt.EB - grad1.enrgCmpnt.EB); HDebug.Exception(EB < 0.1);
double EA = Math.Abs(grad0.enrgCmpnt.EA - grad1.enrgCmpnt.EA); HDebug.Exception(EA < 0.1);
double EBA = Math.Abs(grad0.enrgCmpnt.EBA - grad1.enrgCmpnt.EBA); HDebug.Exception(EBA < 0.1);
double EUB = Math.Abs(grad0.enrgCmpnt.EUB - grad1.enrgCmpnt.EUB); HDebug.Exception(EUB < 0.1);
double EAA = Math.Abs(grad0.enrgCmpnt.EAA - grad1.enrgCmpnt.EAA); HDebug.Exception(EAA < 0.1);
double EOPB = Math.Abs(grad0.enrgCmpnt.EOPB - grad1.enrgCmpnt.EOPB); HDebug.Exception(EOPB < 0.1);
double EOPD = Math.Abs(grad0.enrgCmpnt.EOPD - grad1.enrgCmpnt.EOPD); HDebug.Exception(EOPD < 0.1);
double EID = Math.Abs(grad0.enrgCmpnt.EID - grad1.enrgCmpnt.EID); HDebug.Exception(EID < 0.1); // 0.0019000000000000128 : N-terminus (and C-terminus) information is/are inconsistent betweeen namd-charmm and tink-charmm22
double EIT = Math.Abs(grad0.enrgCmpnt.EIT - grad1.enrgCmpnt.EIT); HDebug.Exception(EIT < 0.1);
double ET = Math.Abs(grad0.enrgCmpnt.ET - grad1.enrgCmpnt.ET); HDebug.Exception(ET < 0.5); // 0.33029999999999404 : N-terminus (and C-terminus) information is/are inconsistent betweeen namd-charmm and tink-charmm22
double EPT = Math.Abs(grad0.enrgCmpnt.EPT - grad1.enrgCmpnt.EPT); HDebug.Exception(EPT < 0.1);
double EBT = Math.Abs(grad0.enrgCmpnt.EBT - grad1.enrgCmpnt.EBT); HDebug.Exception(EBT < 0.1);
double ETT = Math.Abs(grad0.enrgCmpnt.ETT - grad1.enrgCmpnt.ETT); HDebug.Exception(ETT < 0.1);
double EV = Math.Abs(grad0.enrgCmpnt.EV - grad1.enrgCmpnt.EV); HDebug.Exception(EV < 0.1);
double EC = Math.Abs(grad0.enrgCmpnt.EC - grad1.enrgCmpnt.EC); HDebug.Exception(EC < 0.5); // 0.37830000000002428
double ECD = Math.Abs(grad0.enrgCmpnt.ECD - grad1.enrgCmpnt.ECD); HDebug.Exception(ECD < 0.1);
double ED = Math.Abs(grad0.enrgCmpnt.ED - grad1.enrgCmpnt.ED); HDebug.Exception(ED < 0.1);
double EM = Math.Abs(grad0.enrgCmpnt.EM - grad1.enrgCmpnt.EM); HDebug.Exception(EM < 0.1);
double EP = Math.Abs(grad0.enrgCmpnt.EP - grad1.enrgCmpnt.EP); HDebug.Exception(EP < 0.1);
double ER = Math.Abs(grad0.enrgCmpnt.ER - grad1.enrgCmpnt.ER); HDebug.Exception(ER < 0.1);
double ES = Math.Abs(grad0.enrgCmpnt.ES - grad1.enrgCmpnt.ES); HDebug.Exception(ES < 0.1);
double ELF = Math.Abs(grad0.enrgCmpnt.ELF - grad1.enrgCmpnt.ELF); HDebug.Exception(ELF < 0.1);
double EG = Math.Abs(grad0.enrgCmpnt.EG - grad1.enrgCmpnt.EG); HDebug.Exception(EG < 0.1);
double EX = Math.Abs(grad0.enrgCmpnt.EX - grad1.enrgCmpnt.EX); HDebug.Exception(EX < 0.1);
}
}
}
temp.QuitTemp();
}
//{
// //string pathbase = @"C:\Users\htna.IASTATE\svn\htnasvn_htna\Research.bioinfo.prog.NAMD\1A6G\New folder\";
// string pathbase = @"C:\Users\htna.IASTATE\svn\htnasvn_htna\Research.bioinfo.prog.NAMD\1A6G\";
// string toplbase = @"C:\Users\htna.IASTATE\svn\htnasvn_htna\Research.bioinfo.prog.NAMD\top_all27_prot_lipid\";
// var pdb = Pdb .FromFile(pathbase+"1A6G.psfgen.pdb");
// var psf = Namd.Psf.FromFile(pathbase+"1A6G.psfgen.psf");
// var prm = Namd.Prm.FromFile(toplbase+"par_all27_prot_na.prm");
//
// pdb = Pdb .FromFile(@"K:\Tim-8TIM,1TPH,1M6J\Tim-1M6J\1M6J.psfgen.pdb");
// psf = Namd.Psf.FromFile(@"K:\Tim-8TIM,1TPH,1M6J\Tim-1M6J\1M6J.psfgen.psf");
// prm = Namd.Prm.FromFile(@"K:\Tim-8TIM,1TPH,1M6J\Tim-1M6J\par_all27_prot_lipid.inp");
// var xyz_prm = BuildFromNamd(pdb, psf, prm);
// xyz_prm.Item1.ToFile(@"C:\temp\TinkFromNamd.xyz", false);
// xyz_prm.Item2.ToFile(@"C:\temp\TinkFromNamd.prm");
//}
}
public static void SelfTest(string rootpath, string[] args)
{
//{
// Pdb pdb = Pdb.FromFile(rootpath + @"\Sample\1a6g.pdb");
// HTLib2.Bioinfo.Universe.Build(pdb);
//}
GetPotential_SelfTest(rootpath, args);
Universe univ = null;
string sample = null;
//sample = "1a6g_autopsf.unfolded";
//sample = "1a6g_autopsf";
switch (sample)
{
case "alanin":
{
List <ForceField.IForceField> frcflds = ForceField.GetMindyForceFields();
double k = 0.0001;
double threshold = 0.001;
//int iter = univ.Minimize_ConjugateGradient_v0(frcflds, k, threshold);
int randomPurturb = 0; // no random purturbation
bool[] atomsMovable = null; // update all atoms
int iter_conjgrad;
{
Namd.Psf psf = Namd.Psf.FromFile(rootpath + @"\Sample\alanin.psf");
Pdb pdb = Pdb.FromFile(rootpath + @"\Sample\alanin.pdb");
Namd.Prm prm = Namd.Prm.FromFileXPlor(rootpath + @"\Sample\alanin.params", new TextLogger());
univ = Universe.Build(psf, prm, pdb, false);
//frcflds = new List<ForceField.IForceField>();
//frcflds.Add(new ForceField.MindyBond());
//frcflds.Add(new ForceField.MindyAngle());
//frcflds.Add(new ForceField.MindyDihedral());
//frcflds.Add(new ForceField.MindyImproper());
//frcflds.Add(new ForceField.MindyNonbondedLennardJones());
//frcflds.Add(new ForceField.MindyNonbondedElectrostatic());
//iter_conjgrad = univ.Minimize_ConjugateGradient_v1(0, frcflds, k, 0.1, null, threshold, randomPurturb, atomsMovable, new MinimizeLogger_PrintEnergyForceMag(), null, null);
//frcflds = new List<ForceField.IForceField>();
//frcflds.Add(new ForceField.MindyBond());
//frcflds.Add(new ForceField.MindyAngle());
//frcflds.Add(new ForceField.MindyImproper());
//frcflds.Add(new ForceField.MindyNonbondedLennardJones());
//frcflds.Add(new ForceField.MindyNonbondedElectrostatic());
//iter_conjgrad = univ.Minimize_ConjugateGradient_v1(0, frcflds, k*0.1, 0.1, null, threshold, randomPurturb, atomsMovable, new MinimizeLogger_PrintEnergyForceMag(), null, null);
frcflds = new List <ForceField.IForceField>();
if (HDebug.False)
{
frcflds.Add(new ForceField.MindyBond());
}
else
{
frcflds.Add(new ForceField.PwBond());
}
if (HDebug.False)
{
frcflds.Add(new ForceField.MindyAngle());
}
else
{
frcflds.Add(new ForceField.PwAngle());
}
frcflds.Add(new ForceField.MindyDihedral());
if (HDebug.False)
{
frcflds.Add(new ForceField.MindyImproper());
}
else
{
frcflds.Add(new ForceField.PwImproper());
}
if (HDebug.False)
{
frcflds.Add(new ForceField.MindyNonbondedElectrostatic());
}
else
{
frcflds.Add(new ForceField.PwElec());
}
if (HDebug.False)
{
frcflds.Add(new ForceField.MindyNonbondedLennardJones());
}
else
{
frcflds.Add(new ForceField.PwVdw());
}
univ.LoadCoords(@"D:\xxxx.coords");
iter_conjgrad = univ.Minimize_ConjugateGradient_v1(0, frcflds, k, 0.01, null, threshold, randomPurturb, atomsMovable, new MinimizeLogger_PrintEnergyForceMag(), null, null);
univ.SaveCoords(@"D:\xxxx.coords");
System.Console.WriteLine("=======================================================================");
System.Console.WriteLine("=======================================================================");
System.Console.WriteLine("=======================================================================");
}
{
//Psf psf = Psf.FromFile(rootpath + @"\Sample\alanin.psf");
//Pdb pdb = Pdb.FromFile(rootpath + @"\Sample\alanin.pdb");
//Prm prm = Prm.FromFileXPlor(rootpath + @"\Sample\alanin.params", new TextLogger());
//univ = Universe.Build(psf, prm, pdb);
//frcflds = new List<ForceField.IForceField>();
//if(true) frcflds.Add(new ForceField.MindyBond()); else frcflds.Add(new ForceField.PwBond());
//if(true) frcflds.Add(new ForceField.MindyAngle()); else frcflds.Add(new ForceField.PwAngle());
//frcflds.Add(new ForceField.MindyDihedral());
//if(true) frcflds.Add(new ForceField.MindyImproper()); else frcflds.Add(new ForceField.PwImproper());
//if(true) frcflds.Add(new ForceField.MindyNonbondedElectrostatic()); else frcflds.Add(new ForceField.PwElec());
//if(true) frcflds.Add(new ForceField.MindyNonbondedLennardJones()); else frcflds.Add(new ForceField.PwVdw());
univ.atoms[0].Coord += new Vector(0.1, 0.1, 0.1);
//iter_conjgrad = univ.Minimize_ConjugateGradient_v1(0, frcflds, k, 0.001, null, threshold, randomPurturb, atomsMovable, new MinimizeLogger_PrintEnergyForceMag(), null, null);
iter_conjgrad = univ.Minimize_ConjugateGradient_AtomwiseUpdate(frcflds,
threshold: threshold,
k: k,
max_atom_movement: 0.001,
max_iteration: null,
atomsMovable: atomsMovable,
logger: new MinimizeLogger_PrintEnergyForceMag()
);
}
k = 0.0005;
HDebug.Assert(false);
//int iter_stepdsnt = univ.Minimize_SteepestDescent(frcflds, k, threshold, System.Console.Error);
}
break;
case "1a6g_autopsf":
{
Namd.Psf psf = Namd.Psf.FromFile(rootpath + @"\Sample\1a6g_autopsf.psf");
Pdb pdb = Pdb.FromFile(rootpath + @"\Sample\1a6g_autopsf.pdb");
Namd.Prm prm = Namd.Prm.FromFile(rootpath + @"\Sample\1a6g_autopsf.prm", new TextLogger());
univ = Universe.Build(psf, prm, pdb, false);
List <ForceField.IForceField> frcflds = ForceField.GetMindyForceFields();
double threshold = 0.001;
string minimize_ver = "v1";
switch (minimize_ver)
{
//case "v2":
// {
// double atom_max_move = 0.03;
// int iter_conjgrad = univ.Minimize_ConjugateGradient_v2(frcflds, atom_max_move, threshold, System.Console.Error);
// break;
// }
case "v1":
{
double k = 0.0001;
int randomPurturb = 0; // no random purturbation
bool[] atomsMovable = null; // update all atoms
int iter_conjgrad = univ.Minimize_ConjugateGradient_v1(0, frcflds, k, 0.1, null, threshold, randomPurturb, atomsMovable, new MinimizeLogger_PrintEnergyForceMag(), null, null);
break;
}
default:
goto case "v1";
}
//atom_max_move = 0.03;
//int iter_stepdsnt = univ.Minimize_SteepestDescent(frcflds, atom_max_move, threshold, System.Console.Error);
}
break;
case "1a6g_autopsf.unfolded":
{
Namd.Psf psf = Namd.Psf.FromFile(rootpath + @"\Sample\1a6g_autopsf.psf");
Pdb pdb = Pdb.FromFile(rootpath + @"\Sample\1a6g_autopsf.pdb");
{
Random rand = new Random(1);
List <Vector> coords = pdb.atoms.ListCoord();
for (int i = 0; i < coords.Count; i++)
{
double x = i * 0.1 + rand.NextDouble() * 0.01;
double y = i * 0.1 + rand.NextDouble() * 0.01;
double z = i * 0.1 + rand.NextDouble() * 0.01;
coords[i] = new Vector(x, y, z);
}
pdb.ToFile(rootpath + @"\Sample\1a6g_autopsf.unfolded.pdb", coords);
pdb = Pdb.FromFile(rootpath + @"\Sample\1a6g_autopsf.unfolded.pdb");
}
Namd.Prm prm = Namd.Prm.FromFile(rootpath + @"\Sample\1a6g_autopsf.prm", new TextLogger());
univ = Universe.Build(psf, prm, pdb, false);
List <ForceField.IForceField> frcflds = ForceField.GetMindyForceFields();
double threshold = 0.01;
string minimize_ver = "v1";
switch (minimize_ver)
{
//case "v2":
// {
// double atom_max_move = 0.1;
// int iter_conjgrad = univ.Minimize_ConjugateGradient_v2(frcflds, atom_max_move, threshold, System.Console.Error);
// break;
// }
case "v1":
{
double k = 0.0001;
int randomPurturb = 100;
bool[] atomsMovable = null; // updates all atoms
int iter_conjgrad = univ.Minimize_ConjugateGradient_v1(0, frcflds, k, 0.1, null, threshold, randomPurturb, atomsMovable, new MinimizeLogger_PrintEnergyForceMag(), null, null);
break;
}
default:
goto case "v1";
}
//atom_max_move = 0.03;
//int iter_stepdsnt = univ.Minimize_SteepestDescent(frcflds, atom_max_move, threshold, System.Console.Error);
}
break;
default:
goto case "alanin";
}
}
public static bool Main(string[] args, ILinAlg la)
{
string cachebase = @"K:\cache\CoarseGraining-20150111\proteins-177\";
foreach (var pdbid_corr_ovlps in lst_pdbid_corr_ovlps)
{
string pdbid = pdbid_corr_ovlps.Item1;
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");
var xyz2 = Tinker.Xyz.FromFile(pathbase + "min-struc-charmm22-screened.xyz", false);
#region generating "min-struc-charmm22-screened.xyz"
//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);
//}
#endregion
Universe univ = Universe.BuilderTinker.Build(xyz1, prm, pdb0, xyz0, 0.001);
System.Console.Write("{0}: ", pdbid);
HessInfo NMA_hessinfo = GetHessNMA(xyz1, prm, tempbase);
Mode[] NMA_modes = NMA_hessinfo.GetModesMassReduced();
Mode[] NMA_nzmodes = NMA_modes.HSelectFrom(6);
Vector NMA_bfactor = NMA_nzmodes.GetBFactor().ToArray();
HessInfo sbNMA_hessinfo = GetHessSbNMA(univ, xyz1.atoms.HListCoords(), 12, null, true, true, true, true, true, true, null, null, null, null, null, null, null, null, null, null, null, null);
Mode[] sbNMA_modes = sbNMA_hessinfo.GetModesMassReduced();
Mode[] sbNMA_nzmodes = sbNMA_modes.HSelectFrom(6);
Vector sbNMA_bfactor = sbNMA_nzmodes.GetBFactor().ToArray();
double corr = HBioinfo.BFactor.Corr(NMA_bfactor, sbNMA_bfactor);
double ovlp0 = Math.Abs(LinAlg.VtV(NMA_nzmodes[0].eigvec.UnitVector(), sbNMA_nzmodes[0].eigvec.UnitVector()));
double ovlp1 = Math.Abs(LinAlg.VtV(NMA_nzmodes[1].eigvec.UnitVector(), sbNMA_nzmodes[1].eigvec.UnitVector()));
double ovlp2 = Math.Abs(LinAlg.VtV(NMA_nzmodes[2].eigvec.UnitVector(), sbNMA_nzmodes[2].eigvec.UnitVector()));
double ovlp3 = Math.Abs(LinAlg.VtV(NMA_nzmodes[3].eigvec.UnitVector(), sbNMA_nzmodes[3].eigvec.UnitVector()));
double ovlp4 = Math.Abs(LinAlg.VtV(NMA_nzmodes[4].eigvec.UnitVector(), sbNMA_nzmodes[4].eigvec.UnitVector()));
double ovlp5 = Math.Abs(LinAlg.VtV(NMA_nzmodes[5].eigvec.UnitVector(), sbNMA_nzmodes[5].eigvec.UnitVector()));
double ovlp6 = Math.Abs(LinAlg.VtV(NMA_nzmodes[6].eigvec.UnitVector(), sbNMA_nzmodes[6].eigvec.UnitVector()));
double ovlp7 = Math.Abs(LinAlg.VtV(NMA_nzmodes[7].eigvec.UnitVector(), sbNMA_nzmodes[7].eigvec.UnitVector()));
double ovlp8 = Math.Abs(LinAlg.VtV(NMA_nzmodes[8].eigvec.UnitVector(), sbNMA_nzmodes[8].eigvec.UnitVector()));
double ovlp9 = Math.Abs(LinAlg.VtV(NMA_nzmodes[9].eigvec.UnitVector(), sbNMA_nzmodes[9].eigvec.UnitVector()));
System.Console.Write("corr {0:0.0000}, ", corr);
System.Console.Write("ovlp0 {0:0.0000}, ", ovlp0);
System.Console.Write("ovlp1 {0:0.0000}, ", ovlp1);
System.Console.Write("ovlp2 {0:0.0000}, ", ovlp2);
System.Console.Write("ovlp3 {0:0.0000}, ", ovlp3);
System.Console.Write("ovlp4 {0:0.0000}, ", ovlp4);
System.Console.Write("ovlp5 {0:0.0000}, ", ovlp5);
System.Console.Write("ovlp6 {0:0.0000}, ", ovlp6);
System.Console.Write("ovlp7 {0:0.0000}, ", ovlp7);
System.Console.Write("ovlp8 {0:0.0000}, ", ovlp8);
System.Console.Write("ovlp9 {0:0.0000}, ", ovlp9);
System.Console.WriteLine();
}
return(true);
}
public static bool GetHessAnmSelfTest()
{
if (HDebug.Selftest() == false)
{
return(true);
}
string pdbpath = @"C:\Users\htna\svn\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;
Matlab.Execute("clear");
Matlab.PutMatrix("x", Matrix.FromRowVectorList(coords).ToArray());
Matlab.PutValue("cutoffR", cutoff);
Matlab.Execute(@"% function cx = contactsNew(x, cutoffR)
% Contact matrix within cutoff distance.
% Author: Guang Song
% New: 10/25/2006
%
%n = size(x,1);
% Method 1: slow
%for i=1:n
% center = x(i,:);
% distSqr(:,i) = sum((x-center(ones(n,1),:)).^2,2);
%end
%cx = sparse(distSqr<=cutoffR^2);
% Method 2: fast! about 28 times faster when array size is 659x3
%tot = zeros(n,n);
%for i=1:3
% xi = x(:,ones(n,1)*i);
% %tmp = (xi - xi.').^2;
% %tot = tot + tmp;
% tot = tot + (xi - xi.').^2;
%end
%cx = sparse(tot<=cutoffR^2);
% Method 3: this implementation is the shortest! but sligtly slower than
% method 2
%xn = x(:,:,ones(n,1)); % create n copy x
%xnp = permute(xn,[3,2,1]);
%tot = sum((xn-xnp).^2,2); % sum along x, y, z
%cx = sparse(permute(tot,[1,3,2])<=cutoffR^2);
% put it into one line like below actually slows it down. Don't do that.
%cx = sparse(permute(sum((xn-permute(xn,[3,2,1])).^2,2),[1,3,2])<=cutoffR^2);
%Method 4: using function pdist, which I just know
% this one line implementation is even faster. 2 times than method 2.
cx = sparse(squareform(pdist(x)<=cutoffR));
");
Matlab.Execute(@"% function [anm,xij,normxij] = baseHess(x,cx)
% Basic Hessian Matrix
% Author: Guang Song
% Created: Feb 23, 2005
% Rev: 11/09/06
%
% cx is the contact map. Also with gama info (new! 02/23/05)
dim = size(x,1);
nx = x(:,:,ones(1,dim));
xij = permute(nx,[3,1,2]) - permute(nx,[1,3,2]); % xj - xi for any i j
normxij = squareform(pdist(x)) + diag(ones(1,dim)); % + diag part added to avoid divided by zero.
anm = zeros(3*dim,3*dim);
for i=1:3
for j=1:3
tmp = xij(:,:,i).*xij(:,:,j).*cx./normxij.^2;
tmp = diag(sum(tmp)) - tmp;
anm(i:3:3*dim,j:3:3*dim) = tmp;
end
end
% if dR is scalar, then dR = 1, back to GNM.
%if abs(i-j) == 1 % virtual bonds. should stay around 3.81 A
% K33 = K33*100;
%end
anm = (anm+anm')/2; % make sure return matrix is symmetric (fix numeric error)
");
Matrix anm_gsong = Matlab.GetMatrix("anm");
Matlab.Execute("clear;");
Matrix anm = GetHessAnm(coords.ToArray(), cutoff);
if (anm_gsong.RowSize != anm.RowSize)
{
HDebug.Assert(false); return(false);
}
if (anm_gsong.ColSize != anm.ColSize)
{
HDebug.Assert(false); return(false);
}
for (int c = 0; c < anm.ColSize; c++)
{
for (int r = 0; r < anm.RowSize; r++)
{
if (Math.Abs(anm_gsong[c, r] - anm[c, r]) >= 0.00000001)
{
HDebug.Assert(false); return(false);
}
}
}
return(true);
}
public static Vector[] MinimizeLBfgs(IList <Pdb.Atom> atoms
, IList <Vector> coords = null
, string ff = null // -ff string select Force field, interactive by default. Use -h for information.
// "charmm27", ...
, string water = null // -water enum select Water model to use: select, none, spc, spce, tip3p, tip4p or tip5p
, double mdp_emtol = 0.001 // the minimization is converged when the maximum force is smaller than this value
, double mdp_emstep = 0.001 // initial step-size
)
{
Vector[] confout;
{
string currdir = HEnvironment.CurrentDirectory;
System.IO.DirectoryInfo temproot = HDirectory.CreateTempDirectory();
HEnvironment.CurrentDirectory = temproot.FullName;
{
if (coords != null)
{
HDebug.Assert(atoms.Count == coords.Count);
}
Pdb.ToFile("conf.pdb", atoms, coords: coords
, headers: new string[] { "CRYST1 " }
);
HFile.WriteAllLines("grompp-nm.mdp"
, new string[] { "; Parameters describing what to do, when to stop and what to save "
, "integrator = l-bfgs "
, "emtol = 0.001 "
, "emstep = 0.001 ; Energy step size "
, "nsteps = 5000000000 ; Maximum number of (minimization) steps to perform "
, " ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions "
, "nstlist = 1 ; Frequency to update the neighbor list and long range forces "
, "ns_type = grid ; Method to determine neighbor list (simple, grid) "
, "rlist = 1.0 ; Cut-off for making neighbor list (short range forces) ; htna 1.0-1.2 "
, "coulombtype = Shift "
, "rcoulomb = 1.0 "
, "rcoulomb_switch = 0.7 "
, "vdwtype = Shift "
, "rvdw = 1.0 "
, "rvdw_switch = 0.7 "
//," "
//," "
//,"nstxout = 1; (100) [steps] frequency to write coordinates to output trajectory file, the last coordinates are always written"
//,"nstvout = 1; (100) [steps] frequency to write velocities to output trajectory, the last velocities are always written "
//,"nstfout = 1; ( 0) [steps] frequency to write forces to output trajectory. "
});
RunPdb2gmx(f: "conf.pdb"
, o: "confout.pdb"
, p: "topol.top"
, i: "posre.itp"
, n: "clean.ndx"
, q: "clean.pdb"
, ff: "charmm27"
, water: "none"
, merge: "all"
, lineStderr: null
, lineStdout: null
);
RunGrompp(f: "grompp-nm.mdp"
, p: "topol.top"
, o: "topol-nm.tpr"
, c: "confout.pdb"
, lineStderr: null
, lineStdout: null
);
RunMdrun(s: "topol-nm.tpr"
, c: "confout.pdb"
, o: "traj.trr"
, g: "md.log"
//, mtx:"hessian.mtx"
//, pf:"pullf.xvg"
//, px:"pullx.xvg"
//, nt:"3"
, lineStderr: null
, lineStdout: null
);
Pdb pdbout = Pdb.FromFile("confout.pdb");
confout = pdbout.atoms.ListCoord().ToArray();
}
HEnvironment.CurrentDirectory = currdir;
Thread.Sleep(100);
try{ temproot.Delete(true); } catch (Exception) {}
}
HDebug.Assert(confout.Length == atoms.Count);
return(confout);
}