public SimulationBase(MoleculeList ms, LabelingPositionList lps, DistanceList ds)
{
this.Molecules = ms;
this.LabelingPositions = lps;
this.Distances = ds;
InitRnd();
}
private LabelingPositionList RedoAV()
{
LabelingPositionList lps_local = new LabelingPositionList(this.LabelingPositions.Count);
lps_local.AddRange(this.LabelingPositions);
AVEngine av = new AVEngine(mt, this.ProjectDataCopy.AVGlobalParameters);
LabelingPosition l;
Vector3 rmp;
int natom, nmol;
for (Int32 i = 0; i < lps_local.Count; i++)
{
l = lps_local[i];
if (l.AVData.AVType == AVSimlationType.None)
{
continue;
}
nmol = sr.Molecules.FindIndex(l.Molecule);
natom = Array.BinarySearch <Int32>(mt.OriginalAtomID, molstart[nmol], molnatoms[nmol], l.AVData.AtomID);
if (l.AVData.AVType == AVSimlationType.SingleDyeR)
{
av.Calculate1R(l.AVData.L, l.AVData.W, l.AVData.R, natom);
}
else if (l.AVData.AVType == AVSimlationType.ThreeDyeR)
{
av.Calculate3R(l.AVData.L, l.AVData.W, l.AVData.R1, l.AVData.R2, l.AVData.R3, natom);
}
rmp = Matrix3.Transpose(sr.Rotation[nmol]) * (av.Rmp - sr.Translation[nmol]
+ sr.Molecules[0].CM - sr.Molecules[nmol].CM) + sr.Molecules[nmol].CM;
l.X = rmp.X; l.Y = rmp.Y; l.Z = rmp.Z;
lps_local[i] = l;
}
return(lps_local);
}
private void AVinterface_Load(object sender, EventArgs e)
{
rmptextBox.Text = "Ready";
moleculescomboBox.Items.Clear();
if (_standalone)
{
_molecules = new MoleculeList(20);
}
for (Int32 i = 0; i < _molecules.Count; i++)
{
moleculescomboBox.Items.Add(_molecules[i].Name);
}
if (moleculescomboBox.Items.Count > 0)
{
moleculescomboBox.SelectedIndex = 0;
}
calculatebutton.Enabled = (_molecules.Count > 0);
// load default dye parameters
dyescomboBox.Items.AddRange(LinkerData.LinkerList);
dyescomboBox.SelectedIndex = 0;
simcombobox.SelectedIndex = 0;
_labelpos = new LabelingPositionList();
savebutton.Enabled = false;
addbutton.Enabled = false;
}
public FilterEngine(LabelingPositionList ls, DistanceList ds)
{
this.LabelingPositions = ls;
this.Distances = ds;
#if DEBUG
rnd = new Random(53672429);
#else
rnd = new Random();
#endif
// just in case default AV parameters
this.avparam.GridSize = 0.2;
this.avparam.MinGridSize = 0.4;
this.avparam.LinkerInitialSphere = 0.5;
this.avparam.LinkSearchNodes = 3;
this.avparam.ESamples = 200000;
}
public SpringEngine(MoleculeList ms, LabelingPositionList ls, DistanceList ds) : base(ms, ls, ds)
{
this.Nmolecules = ms.Count;
translation = new Vector3[Nmolecules];
rotation = new Matrix3[Nmolecules];
translationm1 = new Vector3[Nmolecules];
rotationm1 = new Matrix3[Nmolecules];
translationm2 = new Vector3[Nmolecules];
rotationm2 = new Matrix3[Nmolecules];
for (int i = 0; i < Nmolecules; i++)
{
rotation[i] = Matrix3.E;
rotationm1[i] = Matrix3.E;
}
force = new Vector3[Nmolecules];
torque = new Vector3[Nmolecules];
}
public ErrorEstimation(MoleculeList ms, LabelingPositionList ls, DistanceList ds) : base(ms, ls, ds)
{
}
public Refinement(MoleculeList ms, LabelingPositionList ls, DistanceList ds) : base(ms, ls, ds)
{
}
private void PrepareSimulation()
{
// molecules
Nmolecules = _molecules.Count;
int maxatomsincluster = 0;
for (int i = 0; i < Nmolecules; i++)
{
minmass = Math.Min(minmass, _molecules[i].Mass);
maxatomsincluster = Math.Max(maxatomsincluster, _molecules[i].MaxAtomsInCluster);
}
// labeling positions
int im;
labelingpos_cm = new LabelingPositionList();
labelingpos_cm.AddRange(this._labelingpositions);
lpossim = new Vector3[labelingpos_cm.Count];
LtoM = new int[labelingpos_cm.Count];
// convert to local coordinates
for (int i = 0; i < labelingpos_cm.Count; i++)
{
im = _molecules.FindIndex(labelingpos_cm[i].Molecule);
LtoM[i] = im;
labelingpos_cm[i] -= _molecules[im].CM;
lpossim[i] = labelingpos_cm[i];
}
// distances
Distance dist_i;
DtoL1 = new int[_distances.Count];
DtoM1 = new int[_distances.Count];
DtoL2 = new int[_distances.Count];
DtoM2 = new int[_distances.Count];
kplus = new double[_distances.Count];
kminus = new double[_distances.Count];
drmaxplus = new double[_distances.Count];
drmaxminus = new double[_distances.Count];
double minerror = double.MaxValue;
for (int i = 0; i < _distances.Count; i++)
{
DtoL1[i] = labelingpos_cm.FindIndex(_distances[i].Position1);
DtoM1[i] = _molecules.FindIndex(labelingpos_cm.Find(_distances[i].Position1).Molecule);
DtoL2[i] = labelingpos_cm.FindIndex(_distances[i].Position2);
DtoM2[i] = _molecules.FindIndex(labelingpos_cm.Find(_distances[i].Position2).Molecule);
// check if bond
dist_i = _distances[i];
dist_i.IsBond = (labelingpos_cm[DtoL1[i]].Dye == DyeType.Unknown && labelingpos_cm[DtoL1[i]].AVData.AtomID > 0 &&
labelingpos_cm[DtoL1[i]].AVData.AVType == AVSimlationType.None && labelingpos_cm[DtoL2[i]].Dye == DyeType.Unknown &&
labelingpos_cm[DtoL2[i]].AVData.AtomID > 0 && labelingpos_cm[DtoL2[i]].AVData.AVType == AVSimlationType.None);
_distances[i] = dist_i;
// if bond, set small vdW radii to "exclude" from clashing
if (dist_i.IsBond)
{
foreach (var lp in new[] { labelingpos_cm[DtoL1[i]], labelingpos_cm[DtoL2[i]] })
{
int m = _molecules.FindIndex(lp.Molecule);
int natom = Array.BinarySearch <int>(_molecules[m].OriginalAtomID, lp.AVData.AtomID);
_molecules[m].vdWR[natom] = AtomData.vdWRNoClash;
int natom_cluster = Array.FindIndex <int>(_molecules[m].ClusteredAtomOriginalIndex, n => n == natom);
if (natom_cluster >= 0)
{
_molecules[m].ClusteredAtomvdwR[natom_cluster] = AtomData.vdWRNoClash;
System.Runtime.InteropServices.Marshal.Copy(new[] { (float)AtomData.vdWRNoClash }, 0,
FpsNativeWrapper.Aligned16(_molecules[m].XYZvdwRVectorArray) + (4 * natom_cluster + 3) * sizeof(float), 1);
}
}
}
// "spring constants"
kplus[i] = 2.0 / _distances[i].ErrPlus / _distances[i].ErrPlus;
kminus[i] = 2.0 / _distances[i].ErrMinus / _distances[i].ErrMinus;
//Console.Out.WriteLine("distance#" + i + " k+= " + kplus[i] + " k-= " + kminus[i] + " err+ " + _distances[i].ErrPlus + " err- " + _distances[i].ErrMinus);
drmaxplus[i] = SimulationParameters.MaxForce / kplus[i];
drmaxminus[i] = -SimulationParameters.MaxForce / kminus[i];
minerror = Math.Min(minerror, Math.Min(_distances[i].ErrPlus, _distances[i].ErrMinus));
}
// simulation parameters
kclash = 2.0 / SimulationParameters.ClashTolerance / SimulationParameters.ClashTolerance;
drmaxclash = -SimulationParameters.MaxForce / kclash;
dr4dt = Math.Min(SimulationParameters.ClashTolerance * 0.5, minerror);
}
/// <summary>
/// Read reference atoms from an LP file
/// </summary>
/// <param name="m">Example molecule</param>
/// <param name="classicpdb">True for pdb line format, false if tab-delimited</param>
public void ReadRefAtoms(Molecule m, Boolean classicpdb)
{
// re-read the lp file to get reference frames
referenceAtoms = new List <ReferenceAtom[]>(labelingpos.Count);
Int32 j;
String[] strdata;
strdata = System.IO.File.ReadAllLines(labelingpos.FullPath);
String[] tmpstr;
Double x, y, z;
Char[] separator = new Char[] { ' ', '\t' };
ReferenceAtom[] reftmp;
for (Int32 i = 0; i < strdata.Length; i++)
{
// find LP line
if (!LabelingPositionList.ValidLPLine(strdata[i]))
{
continue;
}
// now LP is found, count following pdb lines if any
j = 0;
if (classicpdb)
{
while (i + j + 1 < strdata.Length && strdata[i + j + 1].Length > 54 && strdata[i + j + 1].Substring(0, 4) == "ATOM")
{
j++;
}
}
else
{
while (i + j + 1 < strdata.Length && strdata[i + j + 1].Length > 10 && strdata[i + j + 1].Substring(0, 4) == "ATOM")
{
j++;
}
}
reftmp = new ReferenceAtom[j];
// read reference atoms
j = 0;
if (classicpdb)
{
while (i + j + 1 < strdata.Length && strdata[i + j + 1].Length > 54 && strdata[i + j + 1].Substring(0, 4) == "ATOM")
{
tmpstr = strdata[i + j + 1].Split(separator, StringSplitOptions.RemoveEmptyEntries);
reftmp[j].OriginalN = Int32.Parse(tmpstr[1]);
reftmp[j].ConvertedN = Array.BinarySearch <Int32>(m.OriginalAtomID, reftmp[j].OriginalN);
if (Double.TryParse(strdata[i + j + 1].Substring(30, 8), out x) &&
Double.TryParse(strdata[i + j + 1].Substring(38, 8), out y) &&
Double.TryParse(strdata[i + j + 1].Substring(46, 8), out z))
{
reftmp[j].X = x;
reftmp[j].Y = y;
reftmp[j].Z = z;
}
j++;
}
}
else
{
while (i + j + 1 < strdata.Length && strdata[i + j + 1].Length > 10 && strdata[i + j + 1].Substring(0, 4) == "ATOM")
{
tmpstr = strdata[i + j + 1].Split(separator, StringSplitOptions.RemoveEmptyEntries);
reftmp[j].OriginalN = Int32.Parse(tmpstr[1]);
reftmp[j].ConvertedN = Array.BinarySearch <Int32>(m.OriginalAtomID, reftmp[j].OriginalN);
if (Double.TryParse(tmpstr[6], out x) &&
Double.TryParse(tmpstr[7], out y) &&
Double.TryParse(tmpstr[8], out z))
{
reftmp[j].X = x;
reftmp[j].Y = y;
reftmp[j].Z = z;
}
j++;
}
}
referenceAtoms.Add(reftmp);
i += j;
}
}
private double Elast; // energy after last iteration
public MetropolisSampler(MoleculeList ms, LabelingPositionList ls, DistanceList ds) : base(ms, ls, ds)
{
this.IsContinuous = true;
}