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 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 Anisou[] FromCoords(List <Vector[]> ensemble, Vector[] meanconf = null, double eigvalthres = double.NegativeInfinity)
{
int size = ensemble[0].Length;
Anisou[] anisous = new Anisou[size];
HDebug.AssertNotNull(ensemble);
System.Threading.Tasks.Parallel.For(0, size, delegate(int ai)
//for(int ai=0; ai<size; ai++)
{
Vector mean = meanconf[ai];
MatrixByArr cov = new double[3, 3];
{
for (int ei = 0; ei < ensemble.Count; ei++)
{
Vector vec = ensemble[ei][ai] - mean;
cov += LinAlg.VVt(vec, vec);
}
}
anisous[ai] = Anisou.FromMatrix(cov, eigvalthres: eigvalthres);
}
);
return(anisous);
}
public Anisou Clone()
{
Anisou anis = new Anisou();
anis.U = this.U;
anis.eigvecs = this.eigvecs;
anis.eigvals = this.eigvals;
return(anis);
}
public static Anisou[] FromMatrix(IList <MatrixByArr> Us)
{
Anisou[] anisous = new Anisou[Us.Count];
for (int i = 0; i < anisous.Length; i++)
{
anisous[i] = FromMatrix(Us[i]);
}
return(anisous);
}
public static Anisou FromValues(MatrixByArr U, Vector[] eigvecs, double[] eigvals)
{
Anisou anisou = new Anisou();
anisou.U = U.CloneT();
anisou.eigvecs = eigvecs.HClone <Vector>(); HDebug.Assert(eigvecs.Length == 3, eigvecs[0].Size == 3, eigvecs[1].Size == 3, eigvecs[2].Size == 3);
anisou.eigvals = eigvals.HClone <double>(); HDebug.Assert(eigvals.Length == 3);
return(anisou);
}
public static List <Anisou> ListBioAnisou(this IList <Pdb.Anisou> anisous)
{
int size = anisous.Count;
Anisou[] bioanisou = new Anisou[size];
for (int i = 0; i < size; i++)
{
bioanisou[i] = Anisou.FromMatrix(anisous[i].U);
}
return(new List <Anisou>(bioanisou));
}
public Anisou[] GetAnisous()
{
if (_anisous != null)
{
return(_anisous);
}
MatrixByArr hess = MatrixByArr.FromMatrixArray(this.hess);
_anisous = Anisou.FromHessian(hess, masses, scale: 10000000, cachepath: cachebase + "Anisous.data");
//_anisous = Bioinfo.GetAnisou(GetModes(), masses, scale: 10000000);
return(_anisous);
}
public static Anisou[] FromBFactor(double[] bfactor, double scale = 10000 *1000)
{
Anisou[] anisou = new Anisou[bfactor.Length];
for (int i = 0; i < anisou.Length; i++)
{
double rad2 = bfactor[i];
MatrixByArr U = new double[3, 3] {
{ rad2, 0, 0 }, { 0, rad2, 0 }, { 0, 0, rad2 }
};
anisou[i] = Anisou.FromMatrix(U * scale);
}
return(anisou);
}
public static List <Tuple <Anisou, int> > UpdateAnisous(Element[] elements)
{
int[] collection = Collect(elements, Anisou.RecordName);
List <Tuple <Anisou, int> > anisous = new List <Tuple <Anisou, int> >();
foreach (int idx in collection)
{
string line = elements[idx].line;
Anisou anisou = Anisou.FromString(line);
elements[idx] = anisou;
anisous.Add(new Tuple <Anisou, int>(anisou, idx));
}
return(anisous);
}
public static void DetermineThrmlFluc(List <Vector>[] ensemble, Vector[] meanconf, Anisou[] anisous, double[] bfactors, double eigvalthres)
{
#region old code
//int size = ensemble[0].Count;
//
//Debug.AssertNotNull(ensemble);
//Parallel.For(0, size, delegate(int ai)
////for(int i=0; i<size; i++)
//{
// Vector mean = meanconf[ai];
// Matrix cov = new double[3, 3];
// {
// for(int ei=0; ei<ensemble.Length; ei++)
// {
// Vector vec = ensemble[ei][ai] - mean;
// cov += Matrix.VVt(vec, vec);
// }
// }
// anisous[ai] = Anisou.FromMatrix(cov);
// if(anisous[ai].eigvals[0] < eigvalthres) anisous[ai].eigvals[0] = 0;
// if(anisous[ai].eigvals[1] < eigvalthres) anisous[ai].eigvals[1] = 0;
// if(anisous[ai].eigvals[2] < eigvalthres) anisous[ai].eigvals[2] = 0;
// Debug.Assert((anisous[ai].eigvals[0] == 0 && anisous[ai].eigvals[1] == 0 && anisous[ai].eigvals[2] == 0) == false);
// if(bfactors != null) bfactors[ai] = (cov[0, 0] + cov[1, 1] + cov[2, 2]);
//}
//);
#endregion
List <Vector[]> lensemble = new List <Vector[]>();
for (int i = 0; i < ensemble.Length; i++)
{
lensemble.Add(ensemble[i].ToArray());
}
int size = ensemble[0].Count;
Anisou[] lanisous = Anisou.FromCoords(lensemble, meanconf: meanconf, eigvalthres: eigvalthres);
for (int i = 0; i < size; i++)
{
anisous[i] = lanisous[i];
if (bfactors != null)
{
bfactors[i] = anisous[i].bfactor;
}
}
}
public static Anisou FromCoords(IList <Vector> coords, Vector meancoord = null, double eigvalthres = double.NegativeInfinity)
{
if (meancoord == null)
{
meancoord = coords.Mean();
}
MatrixByArr cov = new double[3, 3];
{
for (int i = 0; i < coords.Count; i++)
{
Vector vec = coords[i] - meancoord;
cov += LinAlg.VVt(vec, vec);
}
}
Anisou anisou = Anisou.FromMatrix(cov, eigvalthres);
return(anisou);
}
public static Anisou[] FromHessian(Mode[] modesMassWeighted, double[] mass, double scale = 10000 *1000
, string cachepath = null
)
{
if (cachepath != null && HFile.Exists(cachepath))
{
List <Anisou> lstanisou;
HDebug.Verify(HSerialize.Deserialize(cachepath, null, out lstanisou));
return(lstanisou.ToArray());
}
int size = modesMassWeighted.Size();
HDebug.Assert(size == mass.Length);
Anisou[] anisous = new Anisou[size];
for (int i = 0; i < size; i++)
{
MatrixByArr invHii = new double[3, 3];
foreach (Mode mode in modesMassWeighted)
{
Vector modei = mode.GetEigvecOfAtom(i);
invHii = invHii + LinAlg.VVt(modei, modei) * mode.eigval;
}
MatrixByArr Ui = invHii * scale / mass[i];
anisous[i] = Anisou.FromMatrix(Ui);
}
if (cachepath != null)
{
HSerialize.Serialize(cachepath, null, new List <Anisou>(anisous));
}
return(anisous);
}
public static Anisou FromMatrix(MatrixByArr U, Func <MatrixByArr, Tuple <Vector[], double[]> > Eig, double eigvalthres = double.NegativeInfinity)
{
Anisou anisou = new Anisou();
anisou.U = U.CloneT();
anisou.eigvecs = new Vector[3];
anisou.eigvals = new double[3];
{
var eigvecval = Eig(anisou.U);
Vector[] eigvec = eigvecval.Item1;
double[] eigval = eigvecval.Item2;
if (eigval[0] < eigvalthres)
{
eigval[0] = 0;
}
if (eigval[1] < eigvalthres)
{
eigval[1] = 0;
}
if (eigval[2] < eigvalthres)
{
eigval[2] = 0;
}
HDebug.Assert((eigval[0] == 0 && eigval[1] == 0 && eigval[2] == 0) == false);
{ // normalize eigval and eigvec
double l;
l = eigvec[0].Dist; anisou.eigvecs[0] = eigvec[0] / l; anisou.eigvals[0] = eigval[0] * (l * l);
l = eigvec[1].Dist; anisou.eigvecs[1] = eigvec[1] / l; anisou.eigvals[1] = eigval[1] * (l * l);
l = eigvec[2].Dist; anisou.eigvecs[2] = eigvec[2] / l; anisou.eigvals[2] = eigval[2] * (l * l);
}
}
return(anisou);
}
public static Element UpdateElement(string line)
{
line = (line + " ").Substring(0, 80);
if (Header.IsHeader(line))
{
return(Header.FromString(line)); // Title Section
}
if (Title.IsTitle(line))
{
return(Title.FromString(line)); // Title Section
}
if (Compnd.IsCompnd(line))
{
return(Compnd.FromString(line)); // Title Section
}
if (Source.IsSource(line))
{
return(Source.FromString(line)); // Title Section
}
if (Keywds.IsKeywds(line))
{
return(Keywds.FromString(line)); // Title Section
}
if (Expdta.IsExpdta(line))
{
return(Expdta.FromString(line)); // Title Section
}
if (Nummdl.IsNummdl(line))
{
return(Nummdl.FromString(line)); // Title Section
}
if (Author.IsAuthor(line))
{
return(Author.FromString(line)); // Title Section
}
if (Revdat.IsRevdat(line))
{
return(Revdat.FromString(line)); // Title Section
}
if (Jrnl.IsJrnl(line))
{
return(Jrnl.FromString(line)); // Title Section
}
if (Remark.IsRemark(line))
{
return(Remark.FromString(line)); // Title Section
}
if (Seqres.IsSeqres(line))
{
return(Seqres.FromString(line)); // Primary Structure Section
}
if (Seqadv.IsSeqadv(line))
{
return(Seqadv.FromString(line)); // Primary Structure Section
}
if (Helix.IsHelix(line))
{
return(Helix.FromString(line)); // Secondary Structure Section
}
if (Sheet.IsSheet(line))
{
return(Sheet.FromString(line)); // Secondary Structure Section
}
if (Site.IsSite(line))
{
return(Site.FromString(line)); // Miscellaneous Features Section
}
if (Cryst1.IsCryst1(line))
{
return(Cryst1.FromString(line)); // Crystallographic and Coordinate Transformation Section
}
if (Anisou.IsAnisou(line))
{
return(Anisou.FromString(line)); // Coordinate Section
}
if (Atom.IsAtom(line))
{
return(Atom.FromString(line)); // Coordinate Section
}
if (Endmdl.IsEndmdl(line))
{
return(Endmdl.FromString(line)); // Coordinate Section
}
if (Hetatm.IsHetatm(line))
{
return(Hetatm.FromString(line)); // Coordinate Section
}
if (Model.IsModel(line))
{
return(Model.FromString(line)); // Coordinate Section
}
if (Siguij.IsSiguij(line))
{
return(Siguij.FromString(line)); // Coordinate Section
}
if (Ter.IsTer(line))
{
return(Ter.FromString(line)); // Coordinate Section
}
if (Conect.IsConect(line))
{
return(Conect.FromString(line)); // Connectivity Section
}
if (Master.IsMaster(line))
{
return(Master.FromString(line)); // Bookkeeping Section
}
if (End.IsEnd(line))
{
return(End.FromString(line)); // Bookkeeping Section
}
if (line.Substring(0, 6) == "DBREF ")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "SEQRES")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "MODRES")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "HET ")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "HETNAM")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "FORMUL")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "SSBOND")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "LINK ")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "ORIGX1")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "ORIGX2")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "ORIGX3")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "SCALE1")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "SCALE2")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "SCALE3")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "CISPEP")
{
return(new Element(line)); // Connectivity Annotation Section
}
if (line.Substring(0, 6) == "HETSYN")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "SEQADV")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "SPRSDE")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "MTRIX1")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "MTRIX2")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "MTRIX3")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "MDLTYP")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "SPLIT ")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "CAVEAT")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "OBSLTE")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "HYDBND")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "SLTBRG")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "TVECT ")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "DBREF1")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "DBREF2")
{
return(new Element(line));
}
if (line.Substring(0, 6) == "SIGATM")
{
return(new Element(line));
}
HDebug.Assert(false);
return(new Element(line));
}
public static Anisou[] FromHessian(MatrixByArr hessMassWeighted, double[] mass, double scale = 10000 *1000
, string cachepath = null
)
{
/// Estimation of "anisotropic temperature factors" (ANISOU)
///
/// delta = hess^-1 * force
/// = (0 + V7*V7'/L7 + V8*V8'/L8 + V9*V9'/L9 + ...) * force (* assume that 1-6 eigvecs/eigvals are ignored, because rot,trans *)
///
/// Assume that force[i] follows gaussian distributions N(0,1). Here, if there are 1000 samples, let denote i-th force as fi, and its j-th element as fi[j]
/// Then, $V7' * fi = si7, V8' * fi = si8, ...$ follows gaussian distribution N(0,1), too.
/// Its moved position by k-th eigen component is determined then, as
/// dik = (Vk * Vk' / Lk) * Fi
/// = Vk / Lk * (Vk' * Fi)
/// = Vk / Lk * Sik.
/// Additionally, the moved position j-th atom is:
/// dik[j] = Vk[j] / Lk[j] * Sik.
/// and its correlation matrix is written as (because its mean position is 0 !!!):
/// Cik[j] = dik[j] * dik[j]'
/// = [dik[j]_x * dik[j]_x dik[j]_x * dik[j]_y dik[j]_x * dik[j]_z]
/// [dik[j]_y * dik[j]_x dik[j]_y * dik[j]_y dik[j]_y * dik[j]_z]
/// [dik[j]_z * dik[j]_x dik[j]_z * dik[j]_y dik[j]_z * dik[j]_z]
/// = (Vk[j] * Vk[j]') / (Lk[j]*Lk[j]) * (Sik*Sik).
///
/// Note that Sik*Sik follows the chi-square distribution, because Sik follows the gaussian distribution N(0,1).
/// Additionally, note that the thermal fluctuation is (not one projection toward k-th eigen component with only i-th force, but) the results of 1..i.. forced movements and 1..k.. eigen components.
/// Therefore, for j-th atom, the accumulation of the correlation over all forces (1..i..) with all eigen components (1..k..) is:
/// C[j] = sum_{i,k} {(Vk[j] * Vk[j]') / (Lk[j]*Lk[j]) * (Sik*Sik)}.
///
/// Here, Sik is normal distribution independent to i and k. Therefore, the mean of C[j] is
/// E(C[j]) = E( sum_{i,k} {(Vk[j] * Vk[j]') / (Lk[j]*Lk[j]) * (Sik*Sik)} )
/// = sum_{i,k} E( (Vk[j] * Vk[j]') / (Lk[j]*Lk[j]) * (Sik*Sik) )
/// = sum_{i,k} { (Vk[j] * Vk[j]') / (Lk[j]*Lk[j]) * E(Sik*Sik) }
/// = sum_{i,k} { (Vk[j] * Vk[j]') / (Lk[j]*Lk[j]) * 1 } (* because mean of E(x*x)=1 where x~N(0,1) *)
/// = sum_{k} { (Vk[j] * Vk[j]') / (Lk[j]*Lk[j]) }
///
/// Note that E(C[j]) is same to the j-th diagonal component of inverse hessian matrix (except, the eigenvalues are squared).
///
/// Fixation: Gromacx generate the ensemble X by
/// X[j] = sum_{k} {Vk / sqrt(Lk[j]) / sqrt(mass[j]) * x_k},
/// where x~N(0,1). However, the above is assumed as
/// X[j] = sum_{k} {Vk / Lk[j] * x_k}.
/// In order to apply the assumption by the Gromacs ensemble, The equation should be fixed as
/// E(C[j]) = sum_{k} { (Vk[j] * Vk[j]') / (sqrt(Lk[j])*sqrt(Lk[j])) }
/// = sum_{k} { (Vk[j] * Vk[j]') / Lk[j] / mass[j] }
///
int size = mass.Length;
HDebug.Assert(hessMassWeighted.RowSize == size * 3, hessMassWeighted.ColSize == size * 3);
Anisou[] anisous = new Anisou[size];
if (cachepath != null && HFile.Exists(cachepath))
{
List <Anisou> lstanisou;
HDebug.Verify(HSerialize.Deserialize <List <Anisou> >(cachepath, null, out lstanisou));
anisous = lstanisou.ToArray();
return(anisous);
}
// anisotropic temperature factors
using (new Matlab.NamedLock("ANISOU"))
{
Matlab.Clear("ANISOU");
Matlab.PutMatrix("ANISOU.H", hessMassWeighted);
Matlab.Execute("[ANISOU.V,ANISOU.D] = eig(ANISOU.H);");
Matlab.Execute("ANISOU.D = diag(ANISOU.D);"); // get diagonal
{
Matlab.Execute("[ANISOU.sortD, ANISOU.sortIdxD] = sort(abs(ANISOU.D));"); // sorted index of abs(D)
Matlab.Execute("ANISOU.D(ANISOU.sortIdxD(1:6)) = 0;"); // set the 6 smallest eigenvalues as zero
//Matlab.Execute("ANISOU.D(ANISOU.D < 0) = 0;"); // set negative eigenvalues as zero
}
//{
// Matlab.Execute("ANISOU.D(1:6) = 0;");
//}
Matlab.Execute("ANISOU.invD = 1 ./ ANISOU.D;"); // set invD
Matlab.Execute("ANISOU.invD(ANISOU.D == 0) = 0;"); // set Inf (by divided by zero) as zero
//Matlab.Execute("ANISOU.D = ANISOU.D .^ 2;"); // assume the gromacs ensemble condition
Matlab.Execute("ANISOU.invH = ANISOU.V * diag(ANISOU.invD) * ANISOU.V';");
for (int i = 0; i < size; i++)
{
string idx = string.Format("{0}:{1}", i * 3 + 1, i * 3 + 3);
MatrixByArr U = Matlab.GetMatrix("ANISOU.invH(" + idx + "," + idx + ")");
U *= (scale / mass[i]);
anisous[i] = Anisou.FromMatrix(U);
}
Matlab.Clear("ANISOU");
}
if (cachepath != null)
{
HSerialize.Serialize(cachepath, null, new List <Anisou>(anisous));
}
return(anisous);
}
public static void ToFile(string filepath
, IList <Atom> atoms
, IList <Vector> coords = null
, IList <MatrixByArr> anisous = null
, double?anisouScale = null
, IList <double> bfactors = null
, bool append = false
, IList <string> headers = null
, int?modelidx = null
)
{
List <string> lines = new List <string>();
int size = atoms.Count;
if (coords != null)
{
HDebug.Assert(size == coords.Count);
}
if (anisous != null)
{
HDebug.Assert(size == anisous.Count);
}
//if(anisouScale != null) Debug.Assert(size == anisouScale.Count);
if (headers != null)
{
lines.AddRange(headers);
}
{
// 1 2 3 4 5 6 7 8
// 12345678901234567890123456789012345678901234567890123456789012345678901234567890
// "MODEL 1 "
string line = "MODEL 1 ";
if (modelidx != null)
{
line.Replace("1", modelidx.Value.ToString());
}
line = line.Substring(0, 80);
lines.Add(line);
}
for (int i = 0; i < size; i++)
{
Atom atom = atoms[i];
if (atom == null)
{
continue;
}
{
if (coords != null)
{
double x = coords[i][0];
double y = coords[i][1];
double z = coords[i][2];
atom = Atom.FromString(atom.GetUpdatedLine(x, y, z));
}
if (bfactors != null)
{
atom = Atom.FromString(atom.GetUpdatedLineTempFactor(bfactors[i]));
}
lines.Add(atom.line);
}
{
if (anisous != null)
{
MatrixByArr U = anisous[i];
if (anisouScale != null)
{
U = U * anisouScale.Value;
}
Anisou anisou = Anisou.FromAtom(atom, U.ToArray().HToInt());
string line = anisou.line; //anisou.GetUpdatedU(anisous[i])
lines.Add(line);
}
}
}
lines.Add("ENDMDL ");
//int idx = 0;
//foreach(Element element in elements)
//{
// string line = element.line;
// if(typeof(Atom).IsInstanceOfType(element))
// {
// double x = coords[idx][0];
// double y = coords[idx][1];
// double z = coords[idx][2];
// Atom atom = (Atom)element;
// line = atom.GetUpdatedLine(x, y, z);
// idx++;
// }
// lines.Add(line);
//}
if (append == false)
{
HFile.WriteAllLines(filepath, lines);
}
else
{
StringBuilder text = new StringBuilder();
foreach (string line in lines)
{
text.AppendLine(line);
}
HFile.AppendAllText(filepath, text.ToString());
}
}
public Pdb CloneReplaceChainID(string IDfrom, string IDto)
{
if (IDfrom == null)
{
throw new ArgumentException("IDfrom is null");
}
if (IDto == null)
{
throw new ArgumentException("IDto is null");
}
if (IDfrom.Length != IDto.Length)
{
throw new ArgumentException("IDFrom.leng != IDto.leng");
}
Dictionary <char, char> from2to = GetPairChainID(IDfrom, IDto);
if (from2to.ContainsKey('_'))
{
throw new ArgumentException("wildkey('_') is not allowed in IDfrom");
}
Element[] newelements = new Element[elements.Length];
for (int i = 0; i < elements.Length; i++)
{
Element elem = elements[i];
char? ch = null;
if (elem is Atom)
{
HDebug.Assert(ch == null); ch = (elem as Atom).chainID;
}
if (elem is Hetatm)
{
HDebug.Assert(ch == null); ch = (elem as Hetatm).chainID;
}
if (elem is Anisou)
{
HDebug.Assert(ch == null); ch = (elem as Anisou).chainID;
}
if (ch != null)
{
if (from2to.ContainsKey(ch.Value))
{
if (from2to[ch.Value] == '_')
{
// if wildcard ('_') is in IDto, delete that atom
continue;
}
Element nelem = null;
if (elem is Atom)
{
if (nelem != null)
{
throw new HException("(nelem != null)");
}
Atom atom = elem as Atom;
nelem = Atom.FromData(
serial: atom.serial,
name: atom.name,
resName: atom.resName,
chainID: from2to[atom.chainID],
resSeq: atom.resSeq,
x: atom.x,
y: atom.y,
z: atom.z,
altLoc: atom.altLoc,
iCode: atom.iCode,
occupancy: atom.occupancy,
tempFactor: atom.tempFactor,
element: atom.element,
charge: atom.charge
);
}
if (elem is Hetatm)
{
if (nelem != null)
{
throw new HException("(nelem != null)");
}
Hetatm hetatm = elem as Hetatm;
nelem = Hetatm.FromData(
serial: hetatm.serial,
name: hetatm.name,
resName: hetatm.resName,
chainID: from2to[hetatm.chainID],
resSeq: hetatm.resSeq,
x: hetatm.x,
y: hetatm.y,
z: hetatm.z,
altLoc: hetatm.altLoc,
iCode: hetatm.iCode,
occupancy: hetatm.occupancy,
tempFactor: hetatm.tempFactor,
element: hetatm.element,
charge: hetatm.charge
);
}
if (elem is Anisou)
{
if (nelem != null)
{
throw new HException("(nelem != null)");
}
Anisou anisou = elem as Anisou;
nelem = Anisou.FromData(anisou.line
, chainID: from2to[anisou.chainID]
);
}
if (nelem == null)
{
throw new NotImplementedException();
}
elem = nelem;
}
}
newelements[i] = elem.UpdateElement();
}
newelements = newelements.HRemoveAll(null);
return(new Pdb(newelements));
}
public static Anisou[] BFactor2Anisou(IList <double> bfactor, double scale = 10000 *1000)
{
return(Anisou.FromBFactor(bfactor.ToArray(), scale: scale));
}
public static void Align(ref List <Vector>[] ensemble
, int maxiteration = int.MaxValue
, HPack <List <Trans3[]> > outTrajTrans = null
)
{
List <Vector>[] lensemble = ensemble.HClone <List <Vector> >();
int size = lensemble[0].Count;
for (int i = 1; i < lensemble.Length; i++)
{
HDebug.Assert(size == lensemble[i].Count);
}
// initial alignment using RMSD
Trans3[] transs = new Trans3[lensemble.Length];
transs[0] = Trans3.UnitTrans;
Vector[] coords = new Vector[size];
Anisou[] anisous = new Anisou[size];
double anisou_eigvalthres = 0.00001 * 0.00001;
double[] bfactors = new double[size];
{
// set ensemble[0] as the initial mean structure
for (int i = 0; i < size; i++)
{
coords[i] = lensemble[0][0].Clone();
}
// set anisou as sphere (with radii as one)
Anisou U0 = Anisou.FromMatrix(new double[3, 3] {
{ 1, 0, 0 }, { 0, 1, 0 }, { 0, 0, 1 }
});
for (int i = 0; i < anisous.Length; i++)
{
anisous[i] = U0;
}
// set bfactor as one
for (int i = 0; i < bfactors.Length; i++)
{
bfactors[i] = 1;
}
}
//List<double>[] bfactorss = new List<double>[ensemble.Length];
//for(int i=0; i<bfactorss.Length; i++)
// bfactorss[i] = new List<double>(bfactors);
//Pdb.ToFile("ensemble.000.pdb", null, lensemble, bfactorss);
System.Console.WriteLine("begin iterative alignment");
double move2 = double.PositiveInfinity;
//double thres = 0.00001;// *size * lensemble.Length;
double thres = 0.00001;// *size * lensemble.Length;
//List<Pdb.Atom> atoms = null;
//while(thres < move2)
for (int iter = 0; iter < maxiteration; iter++)
{
transs = new Trans3[ensemble.Length];
move2 = Align(lensemble, coords, anisous, transs);
if (outTrajTrans != null)
{
outTrajTrans.value.Add(transs);
}
System.Console.WriteLine(iter + "th alignment done: (move " + move2 + " Å)");
if (move2 < thres)
{
break;
}
DetermineMeanConf(lensemble, coords);
DetermineThrmlFluc(lensemble, coords, anisous, null, anisou_eigvalthres);
}
ensemble = lensemble;
}
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 void ToFile(string filepath, IList <Vector> coords = null, IList <double> bfactors = null, IList <MatrixByArr> anisous = null, double anisous_scale = 1, bool append = false)
{
List <string> lines = new List <string>();
if (coords == null)
{
coords = this.atoms.ListCoord();
}
//Debug.Assert(atoms.Length == coords.Count);
int idx = 0;
foreach (Element element in elements)
{
//string line = element.line;
if (typeof(Atom).IsInstanceOfType(element))
{
double x = coords[idx][0];
double y = coords[idx][1];
double z = coords[idx][2];
Atom atom = (Atom)element;
atom = Atom.FromString(atom.GetUpdatedLine(x, y, z));
if (bfactors != null)
{
atom = Atom.FromString(atom.GetUpdatedLineTempFactor(bfactors[idx]));
}
lines.Add(atom.line);
if (anisous != null)
{
MatrixByArr anisoui = anisous[idx] * anisous_scale;
int[,] U = new int[3, 3] {
{ (int)anisoui[0, 0], (int)anisoui[0, 1], (int)anisoui[0, 2], },
{ (int)anisoui[1, 0], (int)anisoui[1, 1], (int)anisoui[1, 2], },
{ (int)anisoui[2, 0], (int)anisoui[2, 1], (int)anisoui[2, 2], },
};
Anisou anisou = Anisou.FromAtom(atom, U);
lines.Add(anisou.line);
}
idx++;
}
else if (typeof(Anisou).IsInstanceOfType(element) && anisous != null)
{
// skip because it is handled in the "Atom" part
}
else
{
lines.Add(element.line);
}
}
if (append == false)
{
HFile.WriteAllLines(filepath, lines);
}
else
{
StringBuilder text = new StringBuilder();
foreach (string line in lines)
{
text.AppendLine(line);
}
HFile.AppendAllText(filepath, text.ToString());
}
}
