public static Trans3 GetTrans(IList <Vector> C1, IList <Anisou> anisou1, IList <Vector> C2, HPack <double> optEnergy = null)
{
int size = C1.Count;
HDebug.Assert(size == C1.Count, size == C2.Count);
Vector[] C1s = C1.ToArray().Clone(3);
Vector[] C2s = C2.ToArray().Clone(3);
double[] W1s = new double[size * 3];
double[] enrgs = new double[size * 3];
for (int i = 0; i < size; i++)
{
HDebug.Assert(anisou1[i].eigvals[0] >= 0); W1s[i * 3 + 0] = (anisou1[i].eigvals[0] <= 0) ? 0 : 1 / anisou1[i].eigvals[0];
HDebug.Assert(anisou1[i].eigvals[1] >= 0); W1s[i * 3 + 1] = (anisou1[i].eigvals[1] <= 0) ? 0 : 1 / anisou1[i].eigvals[1];
HDebug.Assert(anisou1[i].eigvals[2] >= 0); W1s[i * 3 + 2] = (anisou1[i].eigvals[2] <= 0) ? 0 : 1 / anisou1[i].eigvals[2];
enrgs[i * 3 + 0] = enrgs[i * 3 + 1] = enrgs[i * 3 + 2] = double.NaN;
}
//Trans3 trans = ICP3.OptimalTransform(C2, C1);
Trans3 trans = new Trans3(new double[] { 0, 0, 0 }, 1, Quaternion.UnitRotation);// = transICP3.OptimalTransformWeighted(C2, C1, W1s);
int iter = 0;
int iter_max = 1000;
//double enrg = double.NaN;
while (iter < iter_max)
{
iter++;
Vector[] C2sUpdated = trans.GetTransformed(C2s);
//for(int i=0; i<size; i++)
System.Threading.Tasks.Parallel.For(0, size, delegate(int i)
{
for (int j = 0; j < 3; j++)
{
Vector planeNormal = anisou1[i].axes[j];
Vector planeBase = C1[i];
Vector query = C2sUpdated[i * 3 + j];
Vector closest = query - LinAlg.DotProd(planeNormal, query - planeBase) * planeNormal;
HDebug.AssertTolerance(0.00001, LinAlg.DotProd(closest - planeBase, planeNormal));
C1s[i * 3 + j] = closest;
enrgs[i * 3 + j] = W1s[i * 3 + j] * (query - closest).Dist2;
}
});
Trans3 dtrans = ICP3.OptimalTransformWeighted(C2sUpdated, C1s, W1s);
trans = Trans3.AppendTrans(trans, dtrans);
double max_dtrans_matrix = (dtrans.TransformMatrix - LinAlg.Eye(4)).ToArray().HAbs().HMax();
if (max_dtrans_matrix < 0.0000001)
{
break;
}
}
if (optEnergy != null)
{
optEnergy.value = enrgs.Sum() / size;
}
return(trans);
}
public static void WriteResult(string pdbid, List <Pdb.Atom>[] ensemble, List <Trans3[]> trajtrans, string pathroot)
{
List <Pdb.Atom> atoms = ensemble[0];
int size = ensemble[0].Count;
double bfactor0_min = double.PositiveInfinity;
double bfactor0_max = double.NegativeInfinity;
double anisou_eigvalthres = 0.00001 * 0.00001;
{
Trans3[] trans = trajtrans.First();
List <Vector>[] lensemble = new List <Vector> [ensemble.Length];
for (int i = 0; i < ensemble.Length; i++)
{
lensemble[i] = new List <Vector>(trans[i].GetTransformed(ensemble[i].ListCoord()));
}
Vector[] coords = new Vector[size];
Anisou[] anisous = new Anisou[size];
double[] bfactors = new double[size];
DetermineMeanConf(lensemble, coords);
DetermineThrmlFluc(lensemble, coords, anisous, bfactors, anisou_eigvalthres);
List <double>[] bfactorss = new List <double> [ensemble.Length];
for (int i = 0; i < bfactorss.Length; i++)
{
bfactorss[i] = new List <double>(bfactors);
}
List <int> idxCa = atoms.IndexOfAtoms(atoms.SelectByName("CA"));
bfactor0_min = bfactors.HSelectByIndex(idxCa).HMinNth(idxCa.Count / 10);
bfactor0_max = bfactors.HSelectByIndex(idxCa).HMaxNth(idxCa.Count / 10);
Pdb.ToFile(pathroot + "ensemble.000.pdb", atoms, lensemble, bfactorss);
Pdb.ToFile(pathroot + "ensemble.000.anisou.1.pdb", atoms, coords, anisous: anisous.GetUs(1), bfactors: bfactors, append: false);
Pdb.ToFile(pathroot + "ensemble.000.anisou.10.pdb", atoms, coords, anisous: anisous.GetUs(10), bfactors: bfactors, append: false);
Pdb.ToFile(pathroot + "ensemble.000.anisou.100.pdb", atoms, coords, anisous: anisous.GetUs(100), bfactors: bfactors, append: false);
Pdb.ToFile(pathroot + "ensemble.000.anisou.1000.pdb", atoms, coords, anisous: anisous.GetUs(1000), bfactors: bfactors, append: false);
Pdb.ToFile(pathroot + "ensemble.000.anisou.10000.pdb", atoms, coords, anisous: anisous.GetUs(10000), bfactors: bfactors, append: false);
}
int iter = trajtrans.Count - 1;
double bfactorn_min = double.PositiveInfinity;
double bfactorn_max = double.NegativeInfinity;
{
Trans3[] trans = new Trans3[ensemble.Length];
for (int j = 0; j < trans.Length; j++)
{
trans[j] = Trans3.UnitTrans;
}
for (int i = 0; i < trajtrans.Count; i++)
{
for (int j = 0; j < trans.Length; j++)
{
trans[j] = Trans3.AppendTrans(trans[j], trajtrans[i][j]);
}
}
List <Vector>[] lensemble = new List <Vector> [ensemble.Length];
for (int i = 0; i < ensemble.Length; i++)
{
lensemble[i] = new List <Vector>(trans[i].GetTransformed(ensemble[i].ListCoord()));
}
Vector[] coords = new Vector[size];
Anisou[] anisous = new Anisou[size];
double[] bfactors = new double[size];
DetermineMeanConf(lensemble, coords);
DetermineThrmlFluc(lensemble, coords, anisous, bfactors, anisou_eigvalthres);
List <double>[] bfactorss = new List <double> [ensemble.Length];
for (int i = 0; i < bfactorss.Length; i++)
{
bfactorss[i] = new List <double>(bfactors);
}
List <int> idxCa = atoms.IndexOfAtoms(atoms.SelectByName("CA"));
bfactorn_min = bfactors.HSelectByIndex(idxCa).HMinNth(idxCa.Count / 10);
bfactorn_max = bfactors.HSelectByIndex(idxCa).HMaxNth(idxCa.Count / 10);
Pdb.ToFile((pathroot + "ensemble.{finl}.pdb").Replace("{finl}", iter.ToString("000")), atoms, lensemble, bfactorss);
Pdb.ToFile((pathroot + "ensemble.{finl}.anisou.1.pdb").Replace("{finl}", iter.ToString("000")), atoms, coords, anisous: anisous.GetUs(1), bfactors: bfactors, append: false);
Pdb.ToFile((pathroot + "ensemble.{finl}.anisou.10.pdb").Replace("{finl}", iter.ToString("000")), atoms, coords, anisous: anisous.GetUs(10), bfactors: bfactors, append: false);
Pdb.ToFile((pathroot + "ensemble.{finl}.anisou.100.pdb").Replace("{finl}", iter.ToString("000")), atoms, coords, anisous: anisous.GetUs(100), bfactors: bfactors, append: false);
Pdb.ToFile((pathroot + "ensemble.{finl}.anisou.1000.pdb").Replace("{finl}", iter.ToString("000")), atoms, coords, anisous: anisous.GetUs(1000), bfactors: bfactors, append: false);
Pdb.ToFile((pathroot + "ensemble.{finl}.anisou.10000.pdb").Replace("{finl}", iter.ToString("000")), atoms, coords, anisous: anisous.GetUs(10000), bfactors: bfactors, append: false);
}
{
string[] lines = new string[] { @"load ensemble.{init}.pdb, {init}.align"
, @"load ensemble.{init}.anisou.10.pdb, {init}.anisou.10"
, @"load ensemble.{init}.anisou.100.pdb, {init}.anisou.100"
, @"load ensemble.{init}.anisou.1000.pdb, {init}.anisou.1000"
, @"load ensemble.{init}.anisou.10000.pdb, {init}.anisou.10000"
, @"load ensemble.{finl}.pdb, {finl}.align"
, @"load ensemble.{finl}.anisou.10.pdb, {finl}.anisou.10"
, @"load ensemble.{finl}.anisou.100.pdb, {finl}.anisou.100"
, @"load ensemble.{finl}.anisou.1000.pdb, {finl}.anisou.1000"
, @"load ensemble.{finl}.anisou.10000.pdb, {finl}.anisou.10000"
, @"load ..\theseus\{pdbid}_theseus_sup.pdb, theseus"
, @"align theseus, {finl}.align"
, @"orient {finl}.align"
, @"zoom {finl}.align"
, @""
, @"select sele, name ca and ({init}.anisou.* or {finl}.anisou.*)"
, @"hide everything"
, @"show ellipsoids, sele"
, @"delete sele"
, @""
, @"cartoon loop"
, @"set cartoon_loop_radius, 0.1"
, @"set all_states"
, @"show cartoon, {init}.align or {finl}.align"
, @"show cartoon, theseus"
, @"disable all"
, @""
, @"spectrum b, rainbow, minimum={bfactor-min}, maximum={bfactor-max}"
, @"spectrum b, rainbow, minimum=0, maximum=50"
, @"show line"
, @"enable {init}.align; png ..\{pdbid}-{init}-line.png; disable {init}.align;"
, @"enable {finl}.align; png ..\{pdbid}-{finl}-line.png; disable {finl}.align;"
, @"hide line"
, @"enable {init}.align; png ..\{pdbid}-{init}.png; disable {init}.align;"
, @"enable {finl}.align; png ..\{pdbid}-{finl}.png; disable {finl}.align;"
, @"enable theseus; png ..\{pdbid}-theseus.png; disable theseus;"
, @"enable {init}.align"
, @"enable {finl}.align"
, @"enable theseus" };
lines = lines.HReplace("{init}", "000");
lines = lines.HReplace("{finl}", iter.ToString("000"));
lines = lines.HReplace("{pdbid}", pdbid);
lines = lines.HReplace("{bfactor-min}", bfactorn_min.ToString());
lines = lines.HReplace("{bfactor-max}", bfactorn_max.ToString());
string pmlpath = pathroot + "align.pml";
HFile.WriteAllLines(pmlpath, lines);
{
HFile.AppendAllLines(pmlpath, "quit");
string curdirectory = System.Environment.CurrentDirectory;
string pmldirectory = pmlpath.Substring(0, pmlpath.LastIndexOf('\\') + 1);
System.Environment.CurrentDirectory = pmldirectory;
System.Diagnostics.ProcessStartInfo pymolStartInfo = new System.Diagnostics.ProcessStartInfo(@"C:\Program Files (x86)\PyMOL\PyMOL\PymolWin.exe ", "\"" + pmlpath + "\"");
pymolStartInfo.WindowStyle = System.Diagnostics.ProcessWindowStyle.Minimized;
System.Diagnostics.Process pymol = System.Diagnostics.Process.Start(pymolStartInfo);
//pymol.win
pymol.WaitForExit();
System.Environment.CurrentDirectory = curdirectory;
HFile.WriteAllLines(pmlpath, lines);
}
{
List <string> lines_notheseus = new List <string>();
for (int i = 0; i < lines.Length; i++)
{
if (lines[i].Contains("theseus") == false)
{
lines_notheseus.Add(lines[i]);
}
}
HFile.WriteAllLines(pathroot + "align.notheseus.pml", lines);
}
}
}
public static Trans3 GetTrans(IList <Vector> C1, IList <Anisou> anisou1, IList <Vector> C2, IList <Anisou> anisou2, HPack <double> optEnergy = null)
{
int size = C1.Count;
HDebug.Assert(size == C1.Count, size == C2.Count);
Vector[] srcs = new Vector[size * 3 * 2]; // sources
Vector[] tars = new Vector[size * 3 * 2]; // targets
double[] weis = new double[size * 3 * 2]; // weights
double[] engs = new double[size * 3 * 2]; // energies
//for(int i=0; i<size; i++)
//{
// Debug.Assert(anisou1[i].eigvals[0] >= 0); W1s[i*3+0] = (anisou1[i].eigvals[0] <= 0) ? 0 : 1 / anisou1[i].eigvals[0];
// Debug.Assert(anisou1[i].eigvals[1] >= 0); W1s[i*3+1] = (anisou1[i].eigvals[1] <= 0) ? 0 : 1 / anisou1[i].eigvals[1];
// Debug.Assert(anisou1[i].eigvals[2] >= 0); W1s[i*3+2] = (anisou1[i].eigvals[2] <= 0) ? 0 : 1 / anisou1[i].eigvals[2];
// enrgs[i*3+0] = enrgs[i*3+1] = enrgs[i*3+2] = double.NaN;
//}
//Trans3 trans = ICP3.OptimalTransform(C2, C1);
Trans3 trans = new Trans3(new double[] { 0, 0, 0 }, 1, Quaternion.UnitRotation);// = transICP3.OptimalTransformWeighted(C2, C1, W1s);
int iter = 0;
int iter_max = 1000;
//double enrg = double.NaN;
while (iter < iter_max)
{
iter++;
//for(int i=0; i<size; i++)
System.Threading.Tasks.Parallel.For(0, size, delegate(int i)
{
for (int j = 0; j < 3; j++)
{
Vector p1 = C1[i];
Vector n1 = anisou1[i].axes[j];
double w1 = anisou1[i].eigvals[j]; w1 = (w1 <= 0) ? 0 : 1 / w1;
Vector p2 = trans.DoTransform(C2[i]);
Vector n2 = (trans.DoTransform(C2[i] + anisou2[i].axes[j]) - p2).UnitVector();
double w2 = anisou2[i].eigvals[j]; w2 = (w2 <= 0) ? 0 : 1 / w2;
Vector clo12 = p2 - LinAlg.DotProd(n1, p2 - p1) * n1; // closest point from p1 to plane2
Vector clo21 = p1 - LinAlg.DotProd(n2, p1 - p2) * n2; // closest point from p1 to plane2
HDebug.AssertTolerance(0.00001, LinAlg.DotProd(clo12 - p1, n1));
HDebug.AssertTolerance(0.00001, LinAlg.DotProd(clo21 - p2, n2));
// p2 -> (pt closest to p2 on plane1 with w1)
srcs[(i * 3 + j) * 2 + 0] = p2;
tars[(i * 3 + j) * 2 + 0] = clo12;
weis[(i * 3 + j) * 2 + 0] = w1;
engs[(i * 3 + j) * 2 + 0] = w1 * (p2 - clo12).Dist2;
// inverse of {p1 -> (pt closest to p1 on plane2 with w2)}
// = (pt closest to p1 on plane2 with w2) -> p1
srcs[(i * 3 + j) * 2 + 1] = clo21;
tars[(i * 3 + j) * 2 + 1] = p1;
weis[(i * 3 + j) * 2 + 1] = w2;
engs[(i * 3 + j) * 2 + 1] = w2 * (clo21 - p1).Dist2;
}
});
Trans3 dtrans = ICP3.OptimalTransformWeighted(srcs, tars, weis);
trans = Trans3.AppendTrans(trans, dtrans);
double max_dtrans_matrix = (dtrans.TransformMatrix - LinAlg.Eye(4)).ToArray().HAbs().HMax();
if (max_dtrans_matrix < 0.0000001)
{
break;
}
}
if (optEnergy != null)
{
optEnergy.value = engs.Sum() / size;
}
return(trans);
}
public static Trans3 GetTrans(IList <Vector> C1, IList <double> bfactor, IList <Vector> C2)
{
Trans3 trans;
double[] weight = new double[bfactor.Count];
{
for (int i = 0; i < weight.Length; i++)
{
weight[i] = 1.0 / bfactor[i];
}
}
{
int size = C1.Count;
Vector MassCenter1 = new double[3];
Vector MassCenter2 = new double[3];
{
double weight_sum = 0;
for (int i = 0; i < size; i++)
{
weight_sum += weight[i];
MassCenter1 += weight[i] * C1[i];
MassCenter2 += weight[i] * C2[i];
}
MassCenter1 = MassCenter1 / weight_sum;
MassCenter2 = MassCenter2 / weight_sum;
}
Vector[] nc1 = new Vector[size];
Vector[] nc2 = new Vector[size];
{
for (int i = 0; i < size; i++)
{
nc1[i] = C1[i] - MassCenter1;
nc2[i] = C2[i] - MassCenter2;
}
}
Quaternion rot = ICP3.OptimalRotationWeighted(nc2, nc1, weight);
Quaternion urot = Quaternion.UnitRotation;
Trans3 trans1 = new Trans3(-MassCenter2, 1, urot);
Trans3 trans2 = new Trans3(new double[3], 1, rot);
Trans3 trans3 = new Trans3(MassCenter1, 1, urot);
trans = trans1;
trans = Trans3.AppendTrans(Trans3.AppendTrans(trans1, trans2), trans3);
HDebug.AssertTolerance(0.00000001, trans.DoTransform(MassCenter2) - MassCenter1);
return(trans);
}
// /// original source
// {
// trans = ICP3.OptimalTransformWeighted(C2, C1, weight);
// if(HDebug.IsDebuggerAttached)
// {
// Vector[] C2updated = trans.GetTransformed(C2).ToArray();
// double RMSD0 = 0;
// double RMSD1 = 0;
// for(int i=0; i<C1.Count; i++)
// {
// RMSD0 += (C1[i]-C2[i]).Dist2;
// RMSD1 += (C1[i]-C2updated[i]).Dist2;
// }
// HDebug.Assert(RMSD1 <= RMSD0);
// }
// return trans;
// }
}