public void logTrajectory(Universe univ, long iter, Vectors coords)
{
if (logpath == null)
{
return;
}
if (iter % logTrajectoryFrequency != 0)
{
return;
}
string pdbid = "";
if (univ.refs.ContainsKey("pdbid"))
{
pdbid = univ.refs["pdbid"].String;
}
string dir = logpath;
if (dir == "")
{
dir = "output-" + pdbid;
}
System.IO.Directory.CreateDirectory(dir);
string pdbname = string.Format("mini.conju.{0:D5}.pdb", iter);
univ.pdb.ToFile(dir + "\\" + pdbname, coords.ToArray());
if (iter % 100 == 0)
{
univ.SaveCoords(dir + "\\conformation.coords", coords);
}
string pmlloadname = (pdbid != "") ? pdbid : "eqlib";
try
{
System.IO.File.AppendAllLines(dir + "\\mini.conju.[animation].pml", new string[] { "load " + pdbname + ", " + pmlloadname });
}
catch (Exception)
{
}
}
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";
}
}
