public static void GetEnergies(AlignData data1, IList <Vector> coords2
, out double pot_rmsd, out double pot_enrg, out double pot_enrg_full, out double pot_enrg_anisou
, Pdb pdb2 = null
, string pdb2outpath = null
)
{
Anisou[] anisous1;// = data1.GetAnisous();
double[] bfactor1;
{
List <Mode> modes = new List <Mode>(data1.GetModes());
for (int i = 0; i < 6; i++)
{
modes.RemoveAt(0);
}
bfactor1 = HBioinfo.GetBFactor(modes.ToArray(), data1.masses);
HDebug.Assert(data1.size == bfactor1.Length);
anisous1 = Anisou.FromBFactor(bfactor1, scale: 10000 * 1000);
}
//Trans3 trans = MinAnisou.GetTrans(data1.coords, anisous1, coords2);
Trans3 trans = GetTrans(data1.coords, bfactor1, coords2);
List <Vector> coords2trans = new List <Vector>(trans.GetTransformed(coords2));
if (pdb2 != null && pdb2outpath != null)
{
data1.pdb.ToFile(pdb2outpath, coords2trans, anisous: anisous1.GetUs());
}
pot_rmsd = data1.GetRmsdFrom(coords2trans);
pot_enrg = data1.GetEnergyFromDiag(coords2trans);
pot_enrg_full = data1.GetEnergyFromFull(coords2trans);
pot_enrg_anisou = data1.GetEnergyFromAnisou(coords2trans);
}
public static void Align(IList <Vector> C1
, IList <Anisou> anisou1
, ref List <Vector> C2
, HPack <List <Vector> > optMoveC2 = null
, HPack <Trans3> outTrans = null
, HPack <double> optEnergy = null
)
{
Trans3 trans = GetTrans(C1, anisou1, C2, optEnergy: optEnergy);
Vector[] nC2 = trans.GetTransformed(C2).ToArray();
if (optMoveC2 != null)
{
optMoveC2.value = new List <Vector>(nC2.Length);
for (int i = 0; i < nC2.Length; i++)
{
optMoveC2.value.Add(nC2[i] - C2[i]);
}
}
if (outTrans != null)
{
outTrans.value = trans;
}
C2 = new List <Vector>(nC2);
}
public static void Align(IList <Vector> C1
, IList <Anisou> anisou1
, ref IList <Vector> C2
, ref IList <Anisou> anisou2
, HPack <Trans3> outTrans = null
, HPack <double> optEnergy = null
)
{
Trans3 trans = GetTrans(C1, anisou1, C2, anisou2, optEnergy: optEnergy);
C2 = new List <Vector>(C2);
anisou2 = new List <Anisou>(anisou2);
Vector[] nC2 = trans.GetTransformed(C2).ToArray();
for (int i = 0; i < C2.Count; i++)
{
Vector p2i = C2[i];
Anisou a2i = anisou2[i];
Vector np2i = trans.DoTransform(p2i);
Anisou na2i = a2i.Clone();
na2i.eigvecs[0] = (trans.DoTransform(p2i + a2i.eigvecs[0]) - np2i).UnitVector();
na2i.eigvecs[1] = (trans.DoTransform(p2i + a2i.eigvecs[1]) - np2i).UnitVector();
na2i.eigvecs[2] = (trans.DoTransform(p2i + a2i.eigvecs[2]) - np2i).UnitVector();
C2[i] = np2i;
anisou2[i] = na2i;
}
if (outTrans != null)
{
outTrans.value = trans;
}
}
public static void Align(IList <Vector> C1
, ref List <Vector> C2
, HPack <List <Vector> > optMoveC2 = null
, HPack <Trans3> outTrans = null
, HPack <double> optRmsd = null
)
{
Trans3 trans = GetTrans(C1, C2);
Vector[] nC2 = trans.GetTransformed(C2).ToArray();
if (optMoveC2 != null)
{
optMoveC2.value = new List <Vector>(nC2.Length);
for (int i = 0; i < nC2.Length; i++)
{
optMoveC2.value[i] = nC2[i] - C2[i];
}
}
if (optRmsd != null)
{
optRmsd.value = 0;
for (int i = 0; i < nC2.Length; i++)
{
optRmsd.value += (nC2[i] - C1[i]).Dist2;
}
optRmsd.value /= nC2.Length;
}
C2 = new List <Vector>(nC2);
if (outTrans != null)
{
outTrans.value = trans.Clone();
}
}
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 Align(List <Vector> coords1
, ref List <Vector> coords2
, int maxiteration = int.MaxValue
, HPack <List <Trans3[]> > outTrajTrans = null
)
{
List <Vector>[] ensemble = new List <Vector>[]
{
coords1.HClone(),
coords2.HClone()
};
Align(ref ensemble, maxiteration: maxiteration, outTrajTrans: outTrajTrans);
Trans3 trans = MinRMSD.GetTrans(coords1, ensemble[0]);
Vector[] ensemble0 = trans.GetTransformed(ensemble[0]).ToArray();
Vector[] ensemble1 = trans.GetTransformed(ensemble[1]).ToArray();
coords2 = new List <Vector>(ensemble1);
}
public static void Align(List <Pdb.Atom> atoms1, ref List <Pdb.Atom> atoms2)
{
PdbStatic.SelectCommonAtoms(ref atoms1, ref atoms2);
List <Vector> coords1 = atoms1.ListCoord();
List <Vector> coords2 = atoms2.ListCoord();
Trans3 trans = GetTrans(coords1, coords2);
List <Vector> coords2a = new List <Vector>(trans.GetTransformed(coords2));
atoms2 = atoms2.CloneByUpdateCoord(coords2a);
}
public static void Align(IList <Vector> C1
, ref List <Vector> C2
, IList <double> weight
, HPack <Trans3> outTrans = null
)
{
Trans3 trans = GetTrans(C1, C2, weight);
Vector[] nC2 = trans.GetTransformed(C2).ToArray();
C2 = new List <Vector>(nC2);
if (outTrans != null)
{
outTrans.value = trans.Clone();
}
}
public static Trans3 GetTrans(IList <Vector> C1, IList <Vector> C2, HPack <int> optIter = null, HPack <List <double> > optListWeightSum = null)
{
HDebug.Assert(C1.Count == C2.Count);
int size = C1.Count;
if (optIter != null)
{
optIter.value = 0;
}
Trans3 trans0 = new Trans3(new double[3], 1, Quaternion.UnitRotation);
Trans3 trans1 = Geometry.AlignPointPoint.MinRMSD.GetTrans(C2, C1);
if (optListWeightSum != null)
{
optListWeightSum.value = new List <double>();
}
while ((trans0.TransformMatrix - trans1.TransformMatrix).ToArray().HAbs().HMax() > 0.00000001)
{
if (optIter != null)
{
optIter.value++;
}
Vector[] C2trans = trans1.GetTransformed(C2).ToArray();
double[] weight = new double[size];
double[] dist2s = new double[size];
for (int i = 0; i < size; i++)
{
double dist2 = (C1[i] - C2trans[i]).Dist2;
dist2 = HMath.Between(0.001, dist2, double.PositiveInfinity);
weight[i] = 1 / dist2;
dist2s[i] = dist2;
}
if (optListWeightSum != null)
{
optListWeightSum.value.Add(weight.Sum());
}
trans0 = trans1;
trans1 = Geometry.AlignPointPoint.MinRMSD.GetTrans(C2, C1, weight);
}
return(trans1);
}
public static void GetEnergies(AlignData data1, IList <Vector> coords2
, out double geo_rmsd, out double geo_enrg, out double geo_enrg_full, out double geo_enrg_anisou
, Pdb pdb2, string pdb2outpath
)
{
Trans3 trans = GetTrans(data1.coords, coords2);
List <Vector> coords2trans = new List <Vector>(trans.GetTransformed(coords2).ToArray());
if (pdb2 != null && pdb2outpath != null)
{
pdb2.ToFile(pdb2outpath, coords2);
}
geo_rmsd = data1.GetRmsdFrom(coords2trans);
geo_enrg = data1.GetEnergyFromDiag(coords2trans);
geo_enrg_full = data1.GetEnergyFromFull(coords2trans);
geo_enrg_anisou = data1.GetEnergyFromAnisou(coords2trans);
}
//public static Trans3 GetTrans(IList<Vector> C1, Matrix[] anisou1, IList<Vector> C2)
//{
// int size = C1.Count;
// Tuple<Vector[], double[]>[] eigs1 = new Tuple<Vector[], double[]>[size];
// {
// for(int i=0; i<size; i++)
// {
// Vector[] eigvec;
// double[] eigval;
// Debug.Verify(NumericSolver.Eig(anisou1[i], out eigvec, out eigval));
// { // normalize eigval and eigvec
// double l;
// l = eigvec[0].Dist; eigvec[0] /= l; eigval[0] *= (l*l); eigval[0] = Math.Pow(eigval[0], 2); Debug.Assert(eigval[0] >= 0);
// l = eigvec[1].Dist; eigvec[1] /= l; eigval[1] *= (l*l); eigval[1] = Math.Pow(eigval[1], 2); Debug.Assert(eigval[1] >= 0);
// l = eigvec[2].Dist; eigvec[2] /= l; eigval[2] *= (l*l); eigval[2] = Math.Pow(eigval[2], 2); Debug.Assert(eigval[2] >= 0);
// }
// {
// eigval[0] = 1 / eigval[0];
// eigval[1] = 1 / eigval[1];
// eigval[2] = 1 / eigval[2];
// }
// eigs1[i] = new Tuple<Vector[], double[]>(eigvec, eigval);
// }
// }
// return GetTrans(C1, eigs1, C2);
//}
public static void GetEnergies(AlignData data1, IList <Vector> coords2
, out double pot_rmsd, out double pot_enrg, out double pot_enrg_full, out double pot_enrg_anisou
, Pdb pdb2 = null
, string pdb2outpath = null
)
{
Anisou[] anisous1 = data1.GetAnisous();
Trans3 trans = GetTrans(data1.coords, anisous1, coords2);
List <Vector> coords2trans = new List <Vector>(trans.GetTransformed(coords2));
if (pdb2 != null && pdb2outpath != null)
{
pdb2.ToFile(pdb2outpath, coords2trans);
}
//data1.pdb.ToFile(pdb2outpath, coords2trans, anisous: anisous1.GetUs());
pot_rmsd = data1.GetRmsdFrom(coords2trans);
pot_enrg = data1.GetEnergyFromDiag(coords2trans);
pot_enrg_full = data1.GetEnergyFromFull(coords2trans);
pot_enrg_anisou = data1.GetEnergyFromAnisou(coords2trans);
}
public static Trans3 GetTrans(IList <Vector> C1
, IList <Vector> C2
, IList <double> weight
//, Pack<List<Vector>> C2new = null
)
{
if (HDebug.Selftest())
{
double[] tweight = new double[weight.Count];
for (int i = 0; i < tweight.Length; i++)
{
tweight[i] = 0.2;
}
Trans3 ttrans0 = GetTrans(C1, C2, tweight);
Trans3 ttrans1 = MinRMSD.GetTrans(C1, C2);
HDebug.AssertTolerance(0.0001, ttrans0.ds - ttrans1.ds);
HDebug.AssertTolerance(0.0001, ttrans0.dt - ttrans1.dt);
HDebug.AssertTolerance(0.0001, new Vector(ttrans0.dr.ToArray()) - ttrans1.dr.ToArray());
HDebug.AssertTolerance(0.0001, (ttrans0.TransformMatrix - ttrans1.TransformMatrix));
}
HDebug.Assert(C1.Count == C2.Count);
HDebug.Assert(C1.Count == weight.Count);
//Trans3 trans = ICP3.OptimalTransform(C2, C1);
Trans3 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;
}
//Debug.AssertTolerance(0.00000001, Math.Abs(RMSD1 - RMSD0));
}
return(trans);
}
public static Trans3 GetTrans(IList <Vector> C1
, IList <Vector> C2 // ref
//, Pack<List<Vector>> C2new = null
)
{
HDebug.Assert(C1.Count == C2.Count);
Trans3 trans = ICP3.OptimalTransform(C2, C1);
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;
}
RMSD0 /= C1.Count;
RMSD1 /= C1.Count;
//HDebug.AssertTolerance(0.00000001, Math.Abs(RMSD1 - RMSD0));
}
return(trans);
}
public static void Align(List <Vector> coords1, ref List <Vector> coords2)
{
Trans3 trans = GetTrans(coords1, coords2);
coords2 = new List <Vector>(trans.GetTransformed(coords2));
}
public static Trans3 GetTrans(IList <Vector> C1, IList <Vector> C2, HPack <int> optIter = null, HPack <List <double> > optListWeightSum = null)
{
HDebug.Assert(false);
HDebug.Assert(C1.Count == C2.Count);
int size = C1.Count;
if (optIter != null)
{
optIter.value = 0;
}
int iter = 0;
Trans3 trans0 = new Trans3(new double[3], 1, Quaternion.UnitRotation);
Trans3 trans1 = Geometry.AlignPointPoint.MinRMSD.GetTrans(C2, C1);
if (optListWeightSum != null)
{
optListWeightSum.value = new List <double>();
}
double maxdist = 0;
for (int i = 0; i < size; i++)
{
Vector diff = C1[i] - trans1.DoTransform(C2[i]); maxdist = Math.Max(maxdist, diff.Dist);
}
while ((trans0.TransformMatrix - trans1.TransformMatrix).ToArray().HAbs().HMax() > 0.00000001)
{
iter++;
if (optIter != null)
{
optIter.value++;
}
Vector[] C2trans = trans1.GetTransformed(C2).ToArray();
Vector dist2s = new double[size];
Vector dists = new double[size];
for (int i = 0; i < size; i++)
{
double dist2 = (C1[i] - C2trans[i]).Dist2;
dist2 = HMath.Between(0.00001, dist2, double.PositiveInfinity);
dist2s[i] = dist2;
dists[i] = Math.Sqrt(dist2);
}
//int[] idxsort = dist2s.ToArray().IdxSorted().Reverse();
Vector weight = dists.Clone() / dists.ToArray().Max();
for (int i = 0; i < size; i++)
{
double w = weight[i];
//w = (w*2-1)*4;
w = (w - 1) * 4;
w = 1 / (1 + Math.Exp(-1 * w));
weight[i] = w;
}
//weight[idxsort[i]] = (i <= 6) ? 1 : 0;
if (optListWeightSum != null)
{
optListWeightSum.value.Add(weight.Sum());
}
trans0 = trans1;
trans1 = Geometry.AlignPointPoint.MinRMSD.GetTrans(C2, C1, weight.ToArray());
maxdist = 0;
for (int i = 0; i < size; i++)
{
Vector diff = C1[i] - trans1.DoTransform(C2[i]); maxdist = Math.Max(maxdist, diff.Dist);
}
}
return(trans1);
}
