public override SimulationResult Simulate()
{
PerturbDistances(1.0);
SimulationResult sr = base.Simulate();
sr.SimulationMethod |= SimulationMethods.ErrorEstimation;
return(sr);
}
public override SimulationResult Simulate()
{
SimulationResult srrefined = base.Simulate();
srrefined.SimulationMethod |= SimulationMethods.Refinement;
InitializeStructureForRefinement(srrefined);
srrefined.RefinedLabelingPositions = RedoAV();
srrefined.E = SetState(srrefined);
return(srrefined);
}
public override double SetState(SimulationResult sr0)
{
InitializeStructureForRefinement(sr0);
if ((sr0.SimulationMethod & SimulationMethods.Refinement) == 0 || sr0.RefinedLabelingPositions == null)
{
this.LabelingPositions = RedoAV();
}
else
{
this.LabelingPositions = sr0.RefinedLabelingPositions;
}
return(base.SetState(sr0));
}
/// <summary>
/// Combines units into one "molecule" (mainly to be able to redo AV). Only a few properties are copied
/// </summary>
/// <param name="sr">Structure</param>
public Molecule(SimulationResult sr)
{
MoleculeList units = sr.Molecules;
Prepared = false;
Name = "Structure " + sr.InternalNumber.ToString();
FullFileName = "";
Error = "";
NAtoms = 0;
for (int i = 0; i < units.Count; i++)
{
NAtoms += units[i].NAtoms;
}
AtomMass = new double[NAtoms];
vdWR = new double[NAtoms];
OriginalAtomID = new int[NAtoms];
Atoms = new string[NAtoms];
AtomsStandard = new string[NAtoms];
Mass = 0.0;
CM = new Vector3();
Molecule m, m0 = units[0];
int n = 0;
Vector3 r;
// local coordinates
XLocal = new double[NAtoms];
YLocal = new double[NAtoms];
ZLocal = new double[NAtoms];
for (int i = 0; i < units.Count; i++)
{
m = units[i];
for (int j = 0; j < m.NAtoms; j++)
{
r = sr.Rotation[i] * (new Vector3(m.XLocal[j], m.YLocal[j], m.ZLocal[j]))
- m0.CM + m.CM + sr.Translation[i];
XLocal[n] = r.X;
YLocal[n] = r.Y;
ZLocal[n] = r.Z;
AtomMass[n] = m.AtomMass[j];
vdWR[n] = m.vdWR[j];
OriginalAtomID[n] = m.OriginalAtomID[j];
Atoms[n] = m.Atoms[j];
AtomsStandard[n] = m.AtomsStandard[j];
n++;
}
}
}
public override double SetState(SimulationResult sr)
{
PrepareSimulation();
_originalstate = sr;
for (int i = 0; i < _molecules.Count; i++)
{
translation[i] = sr.Translation[i] - _molecules[0].CM + _molecules[i].CM;
rotation[i] = sr.Rotation[i];
}
double E = ForceAndTorque();
CheckForClashes(true);
return(E + Eclash);
}
/// <summary>
/// Best rotation to overlay with a reference structure
/// See Kabsch papers for details: Kabsch W. Acta Cryst. A32 (1976) 922, A34 (1978) 827
/// It is assumed that translations are already calculated in the same (weighted/unweighted) mode!!!
/// </summary>
/// <param name="refsr">reference structure</param>
/// <param name="weighted">apply weights = mass</param>
public void CalculateBestFitRotation(SimulationResult refsr, Boolean weighted)
{
if (Double.IsNaN(this.E) || Double.IsNaN(refsr.E))
{
this.BestFitRotation = Matrix3.E;
return;
}
Vector3 r, r1, r2;
Int32 NAtomstotal = 0, n;
Molecule m;
Double w;
for (Int32 i = 0; i < this.Molecules.Count; i++)
{
NAtomstotal += this.Molecules[i].NAtoms;
}
// rotation
Mapack.Matrix Rxt = new Mapack.Matrix(NAtomstotal, 3);
Mapack.Matrix Ry = new Mapack.Matrix(3, NAtomstotal);
n = 0;
for (Int32 i = 0; i < this.Molecules.Count; i++)
{
m = this.Molecules[i];
for (Int32 j = 0; j < m.NAtoms; j++)
{
r = new Vector3(m.XLocal[j], m.YLocal[j], m.ZLocal[j]);
r1 = this.Rotation[i] * r + this.Translation[i] + m.CM + this.BestFitTranslation;
r2 = refsr.Rotation[i] * r + refsr.Translation[i] + m.CM + refsr.BestFitTranslation;
w = weighted ? m.AtomMass[j] : 1.0;
Rxt[n, 0] = r1.X; Rxt[n, 1] = r1.Y; Rxt[n, 2] = r1.Z;
Ry[0, n] = r2.X * w; Ry[1, n] = r2.Y * w; Ry[2, n] = r2.Z * w;
n++;
}
}
// Kabsch solution
Mapack.Matrix R = Ry * Rxt;
Mapack.SingularValueDecomposition svdR = new Mapack.SingularValueDecomposition(R);
Mapack.Matrix V = svdR.VMatrix;
Mapack.Matrix rS = new Mapack.Matrix(3, 3);
rS[0, 0] = 1.0 / svdR.Diagonal[0];
rS[1, 1] = 1.0 / svdR.Diagonal[1];
rS[2, 2] = (R.Determinant > 0.0) ? 1.0 / svdR.Diagonal[2] : -1.0 / svdR.Diagonal[2];
Mapack.Matrix Um = R * V * rS * V.Transpose();
Matrix3 U = new Matrix3(Um[0, 0], Um[0, 1], Um[0, 2],
Um[1, 0], Um[1, 1], Um[1, 2], Um[2, 0], Um[2, 1], Um[2, 2]);
this.BestFitRotation = Matrix3.RepairRotation(U);
}
private void InitializeStructureForRefinement(SimulationResult sr0)
{
sr = sr0;
mt = new Molecule(sr);
molstart = new int[sr.Molecules.Count];
molnatoms = new int[sr.Molecules.Count];
molstart[0] = 0;
for (int i = 1; i < sr.Molecules.Count; i++)
{
molstart[i] = molstart[i - 1] + sr.Molecules[i - 1].NAtoms;
}
for (int i = 0; i < sr.Molecules.Count; i++)
{
molnatoms[i] = sr.Molecules[i].NAtoms;
}
}
public override SimulationResult Simulate()
{
// initial energy
Elast = ForceAndTorque();
CheckForClashes(true);
Elast += Eclash;
int ntotal = 0; // current number of iterations
int nsuccessfull = 0; // number of successfull iterations
//const int nsuccessfull_max = 2000; // required number of successfull iterations between snapshots
// simulate: main loop
do
{
nsuccessfull += this.Iterate() ? 1 : 0;
ntotal++;
} while (nsuccessfull < this.SimulationParameters.MaxIterations);//while (ntotal < this.SimulationParameters.MaxIterations && nsuccessfull < nsuccessfull_max);
// save result
SimulationResult sr = new SimulationResult();
for (int i = 0; i < translation.Length; i++)
{
this.rotation[i] = Matrix3.RepairRotation(rotation[i]);
}
sr.E = ForceAndTorque();
CheckForClashes(true);
sr.E += Eclash;
sr.ParentStructure = _originalstate.InternalNumber;
sr.Eclash = Eclash;
sr.Ebond = Ebond;
sr.Converged = (ntotal < this.SimulationParameters.MaxIterations);
sr.SimulationMethod = _originalstate.SimulationMethod | SimulationMethods.MetropolisSampling;
sr.Translation = new Vector3[translation.Length];
sr.Rotation = new Matrix3[translation.Length];
for (int i = 0; i < translation.Length; i++)
{
sr.Translation[i] = Matrix3.Transpose(rotation[0]) * (translation[i] - translation[0])
- _molecules[i].CM + _molecules[0].CM;
this.rotation[i] = Matrix3.RepairRotation(rotation[i]);
sr.Rotation[i] = Matrix3.RepairRotation(Matrix3.Transpose(rotation[0]) * rotation[i]);
}
sr.Molecules = _molecules;
sr.CalculateBestFitTranslation(false);
return(sr);
}
/// <summary>
/// Randomly redistributes subunits until no clashes are detected
/// </summary>
public override double SetState()
{
Vector3 tshake;
Vector3 ushake;
double angleshake, uz, uxy, uphi;
Matrix3 rotshake;
int lastshaked;
PrepareSimulation();
_originalstate = new SimulationResult()
{
InternalNumber = -1
};
for (int i = 0; i < _molecules.Count; i++)
{
translation[i] = new Vector3(0.0, 0.0, 0.0);
rotation[i] = Matrix3.E;
}
do
{
for (int i = 1; i < _molecules.Count; i++)
{
lastshaked = 0;
if (!_molecules[i].Selected)
{
tshake = (new Vector3(_rnd.NextDouble(), _rnd.NextDouble(), _rnd.NextDouble()) + (-0.5)) * 10.0;
translation[i] += tshake;
lastshaked = i;
uz = -1.0 + _rnd.NextDouble() * 2.0;
uxy = Math.Sqrt(1.0 - uz * uz);
uphi = _rnd.NextDouble() * 2.0 * Math.PI;
ushake = new Vector3(uxy * Math.Cos(uphi), uxy * Math.Sin(uphi), uz);
angleshake = 2.0 * Math.PI * _rnd.NextDouble();
rotshake = Matrix3.Rotation(ushake, angleshake);
rotation[i] = rotshake * rotation[i];
}
else
{
translation[i] = translation[lastshaked] + _molecules[i].CM - _molecules[lastshaked].CM;
rotation[i] = rotation[lastshaked];
}
}
}while (CheckForClashes(false));
return(ForceAndTorque());
}
public override double SetState(SimulationResult sr)
{
// set model distances as "true"
Distance rmodeltmp;
DistanceList rlisttmp = new DistanceList(this.Distances.Count);
rlisttmp.AddRange(this.Distances);
for (Int32 i = 0; i < rlisttmp.Count; i++)
{
rmodeltmp = rlisttmp[i];
rmodeltmp.R = sr.ModelDistance(this.LabelingPositions.Find(rmodeltmp.Position1),
this.LabelingPositions.Find(rmodeltmp.Position2));
rlisttmp[i] = rmodeltmp;
}
this.Distances = rlisttmp;
return(base.SetState(sr));
}
/// <summary>
/// RMSD compared to another structure
/// </summary>
/// <param name="sr_other">another structure</param>
/// <returns>rmsd value</returns>
public Double RMSD(SimulationResult sr_other, Boolean bestfit, Boolean selected_only)
{
Double sd = 0.0;
Matrix3 U;
Vector3 r, t;
Int32 NAtomstotal = 0;
Molecule m;
if (bestfit)
{
this.CalculateBestFitRotation(sr_other, false);
}
for (Int32 i = 0; i < this.Molecules.Count; i++)
{
m = this.Molecules[i];
if (selected_only && !m.Selected)
{
continue;
}
if (bestfit)
{
U = this.BestFitRotation * this.Rotation[i] - sr_other.Rotation[i];
t = this.BestFitRotation * (this.Translation[i] + m.CM + this.BestFitTranslation)
- sr_other.Translation[i] - m.CM - sr_other.BestFitTranslation;
}
else
{
U = this.Rotation[i] - sr_other.Rotation[i];
t = this.Translation[i] - sr_other.Translation[i];
}
for (Int32 j = 0; j < m.NAtoms; j++)
{
r = new Vector3(m.XLocal[j], m.YLocal[j], m.ZLocal[j]);
sd += Vector3.SquareNormDiff(U * r, t);
}
NAtomstotal += m.NAtoms;
}
return(Math.Sqrt(sd / (Double)NAtomstotal));
}
private void SaveEnergyTable(String efilename)
{
String fname = this.filenametextBox.Text;
SimulationResult tmp;
using (StreamWriter sw = new StreamWriter(efilename, false))
{
_rmsdref = _vsref ? _rmsdref : _dataToSave[0];
String rmsrefdtext = "RMSD vs " + _rmsdref.InternalNumber;
sw.WriteLine("File\tchi2\tchi2_bond\tchi2_clash\tConvergence\tMethod\t" + "RMSD vs previous" +
'\t' + rmsrefdtext + '\t' + rmsrefdtext + " (selected)");
tmp = _dataToSave[0];
sw.WriteLine(String.Format("{0}{1}\t{2:F8}\t{3:F4}\t{4:F4}\t{5}\t{6}\t---\t{7:F6}\t{8:F6}", fname, tmp.InternalNumber,
tmp.E, tmp.Ebond, tmp.Eclash, tmp.Converged, tmp.SimulationMethod, tmp.RMSD(_rmsdref, _bestfit), tmp.RMSD(_rmsdref, _bestfit, true)));
for (Int32 i = 1; i < _dataToSave.Length; i++)
{
tmp = _dataToSave[i];
sw.WriteLine(String.Format("{0}{1}\t{2:F8}\t{3:F4}\t{4:F4}\t{5}\t{6}\t{7:F6}\t{8:F6}\t{9:F6}", fname, tmp.InternalNumber,
tmp.E, tmp.Ebond, tmp.Eclash, tmp.Converged, tmp.SimulationMethod,
tmp.RMSD(_dataToSave[i - 1], _bestfit), tmp.RMSD(_rmsdref, _bestfit), tmp.RMSD(_rmsdref, _bestfit, true)));
}
sw.Close();
}
}
/// <summary>
/// Sets an initial state of the simulation from an intermediate result. Must be overriden in the derived class.
/// </summary>
/// <param name="sr">Starting structure.</param>
/// <returns>"Energy".</returns>
public virtual double SetState(SimulationResult sr)
{
throw new NotImplementedException();
}
private void SaveSimulationResult(SimulationResult sr, String fname, Boolean addpdbsave)
{
String converged = sr.Converged ? " (converged)" : " (not converged)";
String fullfname = fname + ".pml";
Vector3 u; Double theta;
using (StreamWriter sw = new StreamWriter(fullfname, false))
{
sw.WriteLine("# Energy = " + sr.E.ToString("F8") + converged);
for (Int32 i = 0; i < molecules.Count; i++)
{
sw.WriteLine("load " + molecules[i].FullFileName);
}
for (Int32 i = 1; i < molecules.Count; i++)
{
theta = Matrix3.AngleAndAxis(sr.Rotation[i], out u) * 180.0 / Math.PI;
sw.WriteLine("rotate [" + u.ToString() + "], " + theta.ToString("F3")
+ ", " + molecules[i].Name + ", origin=[" + molecules[i].CM.ToString() + "]");
sw.WriteLine("translate [" + sr.Translation[i].ToString() + "], " + molecules[i].Name);
}
if (_bestfit)
{
sw.WriteLine("select all");
sw.WriteLine("translate [" + sr.BestFitTranslation.ToString() + "], sele");
theta = Matrix3.AngleAndAxis(sr.BestFitRotation, out u) * 180.0 / Math.PI;
sw.WriteLine("rotate [" + u.ToString() + "], " + theta.ToString("F3")
+ ", sele, origin=[0, 0, 0]");
}
if (addpdbsave)
{
sw.WriteLine("select all");
sw.WriteLine("save " + fname + ".pdb, sele");
}
String lpnames = "";
if (lpcheckBox.Checked)
{
Int32 im;
Vector3 r;
LabelingPosition lpref;
foreach (LabelingPosition l in labelingpos)
{
im = molecules.FindIndex(l.Molecule);
if ((sr.SimulationMethod & SimulationMethods.Refinement) != 0)
{
lpref = sr.RefinedLabelingPositions.Find(l.Name);
}
else
{
lpref = l;
}
r = sr.Rotation[im] * (lpref - molecules[im].CM) + molecules[im].CM + sr.Translation[im];
sw.WriteLine("pseudoatom " + l.Name + ", pos=[" + r.ToString() + "]");
sw.WriteLine("label " + l.Name + ", \"" + l.Name + "\"");
sw.WriteLine("show spheres, " + l.Name);
if (l.Dye == DyeType.Donor)
{
sw.WriteLine("color green, " + l.Name);
}
if (l.Dye == DyeType.Acceptor)
{
sw.WriteLine("color red, " + l.Name);
}
lpnames += " + " + l.Name;
}
}
if (_bestfit && lpnames != String.Empty)
{
sw.WriteLine("deselect");
sw.WriteLine("select " + lpnames.Substring(3));
sw.WriteLine("translate [" + sr.BestFitTranslation.ToString() + "], sele");
theta = Matrix3.AngleAndAxis(sr.BestFitRotation, out u) * 180.0 / Math.PI;
sw.WriteLine("rotate [" + u.ToString() + "], " + theta.ToString("F3")
+ ", sele, origin=[0, 0, 0]");
}
sw.WriteLine("deselect");
sw.Close();
}
}
public override SimulationResult Simulate()
{
double E, K, Etot, theta, abst, normF, normT;
Molecule m;
Vector3 tnorm;
// select dt and do the first time step
E = ForceAndTorque();
CheckForClashes(true);
E = E + Eclash;
dt = dr4dt / Math.Sqrt(2.0 * Math.Max(E, Nmolecules) / minmass) * SimulationParameters.TimeStepFactor;
rdt = 1.0 / dt;
Etot_last = E;
double Mtot = 0.0, ktot = 0.0;
for (int i = 0; i < Nmolecules; i++)
{
Mtot += _molecules[i].Mass;
}
for (int i = 0; i < kplus.Length; i++)
{
ktot += Math.Max(kplus[i], kminus[i]);
}
viscosity_per_dt = SimulationParameters.ViscosityFactor * 2.0 * dt * Math.Sqrt(ktot / Mtot);
viscosity = viscosity_per_dt * dt;
viscosity = Math.Max(minviscosity, viscosity);
viscosity = Math.Min(maxviscosity, viscosity);
for (int i = 0; i < Nmolecules; i++)
{
m = _molecules[i];
translationm1[i] = translation[i];
rotationm1[i] = rotation[i];
translation[i] += force[i] * (0.5 / m.Mass) * dt * dt;
abst = Vector3.Abs(torque[i]);
tnorm = torque[i] * (1.0 / abst);
theta = 0.5 * dt * dt * abst / m.SimpleI;
rotation[i] *= Matrix3.Rotation(tnorm, theta);
}
// main loop
int niter = 0, maxniter;
optimize_selected_now = (SimulationParameters.OptimizeSelected == OptimizeSelected.Selected ||
SimulationParameters.OptimizeSelected == OptimizeSelected.SelectedThenAll);
if (SimulationParameters.OptimizeSelected == OptimizeSelected.SelectedThenAll)
{
maxniter = SimulationParameters.MaxIterations / 2;
}
else
{
maxniter = SimulationParameters.MaxIterations;
}
do
{
E = Iterate(out normF, out normT, out K);
Etot = E + K;
niter++;
if ((niter << 28) == 0 || Eclash > 10.0 || Etot > Etot_last + maxdE)
{
Cleanup(ref Etot);
}
Etot_last = Etot;
}while (((normF > SimulationParameters.FTolerance) || (normT > SimulationParameters.TTolerance) ||
(K > SimulationParameters.KTolerance * Nmolecules)) && (niter < maxniter));
// repeat if selected then all
if (SimulationParameters.OptimizeSelected == OptimizeSelected.SelectedThenAll)
{
dt = dr4dt / Math.Sqrt(2.0 * Math.Max(E, Nmolecules) / minmass) * SimulationParameters.TimeStepFactor;
rdt = 1.0 / dt;
viscosity = SimulationParameters.ViscosityFactor * 2.0 * dt * Math.Sqrt(ktot / Mtot);
viscosity = Math.Max(minviscosity, viscosity);
viscosity = Math.Min(maxviscosity, viscosity);
niter = 0;
optimize_selected_now = false;
do
{
E = Iterate(out normF, out normT, out K);
Etot = E + K;
niter++;
if ((niter << 28) == 0 || Eclash > 10.0 || Etot > Etot_last + maxdE)
{
Cleanup(ref Etot);
}
Etot_last = Etot;
}while (((normF > SimulationParameters.FTolerance) || (normT > SimulationParameters.TTolerance) ||
(K > SimulationParameters.KTolerance * Nmolecules)) && (niter < maxniter));
}
SimulationResult sr = new SimulationResult();
sr.E = E;
sr.Eclash = Eclash;
sr.Ebond = Ebond;
sr.Converged = (niter < SimulationParameters.MaxIterations);
sr.Translation = new Vector3[Nmolecules];
sr.Rotation = new Matrix3[Nmolecules];
sr.ParentStructure = _originalstate.InternalNumber;
sr.SimulationMethod = _originalstate.SimulationMethod | SimulationMethods.Docking;
for (int i = 0; i < Nmolecules; i++)
{
sr.Translation[i] = Matrix3.Transpose(rotation[0]) * (translation[i] - translation[0])
- _molecules[i].CM + _molecules[0].CM;
sr.Rotation[i] = Matrix3.RepairRotation(Matrix3.Transpose(rotation[0]) * rotation[i]);
}
sr.Molecules = _molecules;
sr.CalculateBestFitTranslation(false);
return(sr);
}
public Double RMSD(SimulationResult sr2, Boolean bestfit)
{
return(this.RMSD(sr2, bestfit, false));
}