public static CTestgrad Testgrad(string testgradpath
, Tinker.Xyz xyz
, Tinker.Prm prm
, string tempbase //=null
, string[] keys
, Dictionary <string, string[]> optOutSource // = null
)
{
var tmpdir = HDirectory.CreateTempDirectory(tempbase);
string currpath = HEnvironment.CurrentDirectory;
CTestgrad testgrad;
{
HEnvironment.CurrentDirectory = tmpdir.FullName;
if (testgradpath == null)
{
string resbase = "HTLib2.Bioinfo.HTLib2.Bioinfo.External.Tinker.Resources.tinker_6_2_06.";
HResource.CopyResourceTo <Tinker>(resbase + "testgrad.exe", "testgrad.exe");
testgradpath = "testgrad.exe";
}
xyz.ToFile("test.xyz", false);
prm.ToFile("test.prm");
string keypath = null;
if (keys != null && keys.Length > 0)
{
keypath = "test.key";
HFile.WriteAllLines(keypath, keys);
}
testgrad = TestgradImpl(testgradpath, "test.xyz", "test.prm", keypath, optOutSource);
}
HEnvironment.CurrentDirectory = currpath;
try{ tmpdir.Delete(true); } catch {}
return(testgrad);
}
public static CTesthess Testhess
(string testhesspath
, Tinker.Xyz xyz
, Tinker.Prm prm
, string tempbase //=null
, string[] keys
, Dictionary <string, string[]> optOutSource // =null
, Func <int, int, HessMatrix> HessMatrixZeros // =null
)
{
var tmpdir = HDirectory.CreateTempDirectory(tempbase);
string currpath = HEnvironment.CurrentDirectory;
CTesthess testhess;
{
HEnvironment.CurrentDirectory = tmpdir.FullName;
if (testhesspath == null)
{
string resbase = "HTLib2.Bioinfo.HTLib2.Bioinfo.External.Tinker.Resources.tinker_6_2_01.";
HResource.CopyResourceTo <Tinker>(resbase + "testhess.exe", "testhess.exe");
testhesspath = "testhess.exe";
}
xyz.ToFile("test.xyz", false);
prm.ToFile("test.prm");
string keypath = null;
if ((keys != null) && (keys.Length > 0))
{
keypath = "test.key";
HFile.WriteAllLines(keypath, keys);
}
testhess = Testhess(testhesspath, "test.xyz", "test.prm", keypath, optOutSource, HessMatrixZeros);
testhess.xyz = xyz;
testhess.prm = prm;
}
HEnvironment.CurrentDirectory = currpath;
try{ tmpdir.Delete(true); } catch {}
string test_eig = "true";
if (test_eig == "false")
{
Vector D;
using (new Matlab.NamedLock(""))
{
Matlab.PutSparseMatrix("testeig.H", testhess.hess.GetMatrixSparse(), 3, 3);
Matlab.Execute("testeig.H = (testeig.H + testeig.H')/2;");
Matlab.Execute("[testeig.V, testeig.D] = eig(full(testeig.H));");
Matlab.Execute("testeig.D = diag(testeig.D);");
D = Matlab.GetVector("testeig.D");
Matlab.Execute("clear testeig;");
}
}
return(testhess);
}
public static ONewton Newton(string tinkerpath
, Tinker.Xyz xyz
, Tinker.Xyz.Atom.Format xyz_atoms_format
, Tinker.Prm prm
, string tempbase
, string copytemp // = null
, string param
//, string precondition // = "A" // Precondition via Auto/None/Diag/Block/SSOR/ICCG [A] : A
//, double gradCriterion // = 0.01 // Enter RMS Gradient per Atom Criterion [0.01] : 0.001
, IList <Tinker.Xyz.Atom> atomsToFix // = null
, bool pause // = false
, params string[] keys
)
{
if (HDebug.IsDebuggerAttached && atomsToFix != null)
{
Dictionary <int, Tinker.Xyz.Atom> xyzatoms = xyz.atoms.ToIdDictionary();
foreach (var atom in atomsToFix)
{
HDebug.Assert(object.ReferenceEquals(atom, xyzatoms[atom.Id]));
}
}
Tinker.Xyz minxyz;
string[] minlog;
using (var temp = new HTempDirectory(tempbase, copytemp))
{
temp.EnterTemp();
if (tinkerpath == null)
{
string resbase = "HTLib2.Bioinfo.HTLib2.Bioinfo.External.Tinker.Resources.tinker_6_2_06.";
HResource.CopyResourceTo <Tinker>(resbase + "newton.exe", "newton.exe");
tinkerpath = "newton.exe";
}
xyz.ToFile("prot.xyz", false);
prm.ToFile("prot.prm");
List <string> keylines = new List <string>(keys);
if (atomsToFix != null)
{
foreach (var atom in atomsToFix)
{
Vector coord = atom.Coord;
double force_constant = 10000; // force constant in kcal/Å2 for the harmonic restraint potential
string keyline = string.Format("RESTRAIN-POSITION {0} {1} {2} {3} {4}", atom.Id, coord[0], coord[1], coord[2], force_constant);
keylines.Add(keyline);
}
}
HFile.WriteAllLines("prot.key", keylines);
// Precondition via Auto/None/Diag/Block/SSOR/ICCG [A] : A
// Enter RMS Gradient per Atom Criterion [0.01] : 0.001
//bool pause = false;
string command = tinkerpath;
command += string.Format(" prot.xyz prot.prm");
command += string.Format(" -k prot.key");
command += string.Format(" {0}", param);
HProcess.StartAsBatchInConsole("newton.bat", pause
, "time /t >> prot.log"
, command //+" >> prot.log"
, "time /t >> prot.log"
);
HDebug.Assert(HFile.Exists("prot.xyz_2"));
HDebug.Assert(HFile.Exists("prot.xyz_3") == false);
minxyz = Tinker.Xyz.FromFile("prot.xyz_2", false, xyz_atoms_format);
minlog = HFile.ReadAllLines("prot.log");
temp.QuitTemp();
}
return(new ONewton
{
minxyz = minxyz,
minlog = minlog
});
}
public static OMinimize Minimize(string minimizepath
, Tinker.Xyz xyz
, Tinker.Xyz.Atom.Format xyz_atoms_format
, Tinker.Prm prm
, string tempbase
, string copytemp // = null
, string param
, IList <Tinker.Xyz.Atom> atomsToFix // = null
, bool pause // = false
, params string[] keys
)
{
if (HDebug.IsDebuggerAttached && atomsToFix != null)
{
Dictionary <int, Tinker.Xyz.Atom> xyzatoms = xyz.atoms.ToIdDictionary();
foreach (var atom in atomsToFix)
{
HDebug.Assert(object.ReferenceEquals(atom, xyzatoms[atom.Id]));
}
}
Tinker.Xyz minxyz;
string[] minlog;
using (var temp = new HTempDirectory(tempbase, copytemp))
{
temp.EnterTemp();
xyz.ToFile("prot.xyz", false);
prm.ToFile("prot.prm");
List <string> keylines = new List <string>();
//if(grdmin != null)
//{
// string keyline = string.Format("GRDMIN {0}", grdmin.Value);
// keylines.Add(keyline);
//}
if (atomsToFix != null)
{
foreach (var atom in atomsToFix)
{
Vector coord = atom.Coord;
double force_constant = 10000; // force constant in kcal/Å2 for the harmonic restraint potential
string keyline = string.Format("RESTRAIN-POSITION {0} {1} {2} {3} {4}", atom.Id, coord[0], coord[1], coord[2], force_constant);
keylines.Add(keyline);
}
}
if (keys != null)
{
keylines.AddRange(keys);
}
HFile.WriteAllLines("prot.key", keylines);
// Enter RMS Gradient per Atom Criterion [0.01] :
string command = minimizepath;
command += " prot.xyz prot.prm";
command += " -k prot.key < param.txt";
HFile.WriteAllLines("param.txt", param.HSplit());
//command += string.Format(" >> prot.log");
HProcess.StartAsBatchInConsole("minimize.bat", pause
, "time /t >> prot.log"
, command
, "time /t >> prot.log"
);
HDebug.Assert(HFile.Exists("prot.xyz_2"));
HDebug.Assert(HFile.Exists("prot.xyz_3") == false);
minxyz = Tinker.Xyz.FromFile("prot.xyz_2", false, xyz.atoms_format);
minlog = HFile.ReadAllLines("prot.log");
temp.QuitTemp();
}
return(new OMinimize
{
minxyz = minxyz,
minlog = minlog
});
}