public static bool GetModesSelftest()
{
if (GetModesSelftest_DoTest == false)
{
return(true);
}
GetModesSelftest_DoTest = false;
string pdbpath = @"C:\Users\htna\htnasvn_htna\VisualStudioSolutions\Library2\HTLib2.Bioinfo\Bioinfo.Data\pdb\1MJC.pdb";
if (HFile.Exists(pdbpath) == false)
{
return(false);
}
Pdb pdb = Pdb.FromFile(pdbpath);
for (int i = 0; i < pdb.atoms.Length; i++)
{
HDebug.Assert(pdb.atoms[0].altLoc == pdb.atoms[i].altLoc);
HDebug.Assert(pdb.atoms[0].chainID == pdb.atoms[i].chainID);
}
List <Vector> coords = pdb.atoms.ListCoord();
double cutoff = 13;
Matrix hess = Hess.GetHessAnm(coords.ToArray(), cutoff).ToArray();
Matrix modes;
Vector freqs;
GetModes(hess, out modes, out freqs);
return(true);
}
public static Pdb GetPdb(string pdbid, bool forceToRedownload = false)
{
List <string> pdblines = GetPdbLines(pdbid, forceToRedownload);
Pdb pdb = Pdb.FromLines(pdblines);
return(pdb);
}
public static Universe Build(string pdbpath, string toppath, ITextLogger logger)
{
Pdb pdb = Pdb.FromFile(pdbpath);
Top top = Top.FromFile(toppath);
return(Build(pdb, top, logger));
}
public Pdb GetPdb()
{
Pdb pdb = PdbDatabase.GetPdb(pdbid);
pdb = pdb.GetNoAltloc();
return(pdb);
}
public static CPsfgenExt PsfgenExt
(Pdb pdb
, string[] toplines
, string[] parlines
, Pdb alignto
, HOptions options
)
{
string[] psfgen_lines = null;
List <Tuple <string, string, Pdb.IAtom[]> > lstSegFileAtoms = new List <Tuple <string, string, Pdb.IAtom[]> >();
var pdb_iatoms = pdb.iatoms;
foreach (var ch_iatoms in pdb_iatoms.GroupChainID())
{
lstSegFileAtoms.Add(new Tuple <string, string, Pdb.IAtom[]>
(ch_iatoms.Key + ""
, null
, ch_iatoms.Value.ToArray()
));
}
return(PsfgenExt
(lstSegFileAtoms, toplines, parlines, alignto, psfgen_lines
, options: options
));
}
public Pdb GetNoAltloc()
{
Pdb pdb = this.Clone();
char[] toremove = pdb.atoms.ListAltLoc().HListCommonT().ToArray();
toremove = toremove.HRemoveAll(' ');
if (toremove.Length >= 1)
{
toremove = toremove.HRemoveAll(toremove[0]);
}
for (int i = 0; i < pdb.elements.Length; i++)
{
char?altLoc = null;
if (pdb.elements[i] is Pdb.Atom)
{
altLoc = (pdb.elements[i] as Pdb.Atom).altLoc;
}
if (pdb.elements[i] is Pdb.Hetatm)
{
altLoc = (pdb.elements[i] as Pdb.Hetatm).altLoc;
}
if ((altLoc != null) && toremove.Contains(altLoc.Value))
{
pdb.elements[i] = null;
}
}
pdb = new Pdb(pdb.elements);
return(pdb);
}
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 SelectCommonAtoms(Pdb pdb1, string ChainIDs1, out List <Atom> atoms1
, Pdb pdb2, string ChainIDs2, out List <Atom> atoms2
)
{
SelectCommonAtoms(pdb1.atoms, ChainIDs1, out atoms1
, pdb2.atoms, ChainIDs2, out atoms2
);
}
public static Universe Build(Tinker.Xyz xyz, Tinker.Prm prm, Pdb pdb0, Tinker.Xyz xyz0, double tolCoordPdbXyz /*=0.002*/)
{
Universe univ = Build(xyz0, prm, pdb0, tolCoordPdbXyz);
Vector[] coords = xyz.atoms.HListCoords();
univ.SetCoords(coords);
return(univ);
}
public static void Align(string pdbpath1, string pdbpath2, string alignedpath2)
{
Pdb pdb1 = Pdb.FromFile(pdbpath1); List <Pdb.Atom> atoms1 = pdb1.atoms.SelectByChainID().SelectByAltLoc();
Pdb pdb2 = Pdb.FromFile(pdbpath2); List <Pdb.Atom> atoms2 = pdb2.atoms.SelectByChainID().SelectByAltLoc();
Align(atoms1, ref atoms2);
Pdb.ToFile(alignedpath2, atoms2);
}
public static AlignData FromFiles(string path_pdb, string path_hess, IList <double> masses, string cachebase = null)
{
AlignData data = new AlignData();
data.pdb = Pdb.FromFile(path_pdb);
data.coords = data.pdb.atoms.ListCoord();
data.cachebase = cachebase;
int n = data.coords.Count;
{ // data.hess
List <string> lines = HFile.ReadLines(path_hess).ToList();
int row, col;
{
string[] tokens = lines[1].Split(new char[] { ' ', ',', '\t' }, StringSplitOptions.RemoveEmptyEntries);
HDebug.Assert(tokens.Length == 2);
row = int.Parse(tokens[0]);
col = int.Parse(tokens[1]);
HDebug.Assert(row == col);
}
HDebug.Assert(row == n * 3, col == n * 3);
MatrixByArr[,] hess = new MatrixByArr[n, n];
for (int c = 0; c < n; c++)
{
for (int r = 0; r < n; r++)
{
hess[c, r] = new double[3, 3];
}
}
for (int c = 0; c < col; c++)
{
string line = lines[c + 2];
string[] tokens = line.Split(new char[] { ' ', ',', '\t' }, StringSplitOptions.RemoveEmptyEntries);
HDebug.Assert(tokens.Length == row);
for (int r = 0; r < row; r++)
{
double val = double.Parse(tokens[r]);
hess[c / 3, r / 3][c % 3, r % 3] += val;
hess[r / 3, c / 3][r % 3, c % 3] += val;
}
}
for (int c = 0; c < n; c++)
{
for (int r = 0; r < n; r++)
{
hess[c, r] /= 2;
}
}
data.hess = hess;
}
data.masses = masses.ToArray();
return(data);
}
static Pdb PsfgenExt_AlignTo(Pdb pdb, Pdb alignto)
{
var dictpdb = pdb.atoms.SelectByName("CA").GroupChainIDResSeq();
var dictaln = alignto.atoms.SelectByName("CA").GroupChainIDResSeq();
List <Vector> coordpdb = new List <Vector>();
List <Vector> coordaln = new List <Vector>();
foreach (char ch in dictpdb.Keys)
{
if (dictaln.ContainsKey(ch) == false)
{
continue;
}
foreach (var resi in dictpdb[ch].Keys)
{
var atompdb = dictpdb[ch][resi];
if (atompdb.Count != 1)
{
throw new HException(string.Format(">1 number of CA in chain {0} resi {1} in atompdb", ch, resi));
}
if (dictaln[ch].ContainsKey(resi) == false)
{
continue;
}
var atomaln = dictaln[ch][resi];
if (atomaln.Count != 1)
{
throw new HException(string.Format(">1 number of CA in chain {0} resi {1} in atomaln", ch, resi));
}
HDebug.Assert(coordpdb.Count == coordaln.Count);
coordpdb.Add(atompdb[0].coord);
coordaln.Add(atomaln[0].coord);
}
}
var trans = Align.MinRMSD.GetTrans(coordaln, coordpdb);
Dictionary <Pdb.IAtom, Vector> newcoords = new Dictionary <Pdb.IAtom, Vector>();
foreach (var atom in pdb.atoms)
{
newcoords.Add(atom, trans.DoTransform(atom.coord));
}
foreach (var atom in pdb.hetatms)
{
newcoords.Add(atom, trans.DoTransform(atom.coord));
}
var npdb = pdb.CloneUpdateCoord(newcoords);
return(npdb);
}
public static void SelfTest(string rootpath, string[] args)
{
{
Pdb pdb = Pdb.FromFile(rootpath + @"\Sample\alanin.pdb");
List <Vector> coords = pdb.atoms.ListCoord();
coords[0] = new Vector(0, 1, 2);
pdb.ToFile(rootpath + @"\Sample\alanin.updated.pdb", coords);
}
{
Pdb pdb = Pdb.FromFile(rootpath + @"\Sample\1a6g.pdb");
//pdb.CollectResidues();
}
}
public static HMutation[] FromPdb(string wtpdbid, IList <string> pdbids, Func <string, Pdb> FnLoadPdb)
{
HMutation[] mutations = new HMutation[pdbids.Count];
for (int i = 0; i < pdbids.Count; i++)
{
Pdb wtpdb = FnLoadPdb(wtpdbid);
Pdb mutpdb = FnLoadPdb(pdbids[i]);
mutations[i] = FromPdb
(wtpdb, mutpdb
, wt_pdbid: wtpdbid
, mut_pdbid: pdbids[i]
);
}
return(mutations);
}
public static Pdb FromPdbid
(string pdbid
, string cachebase // null or @"K:\PdbUnzippeds\$PDBID$.pdb"
, bool?download // null or false
)
{
if (cachebase == null)
{
cachebase = @"K:\PdbUnzippeds\$PDBID$.pdb";
}
if (download == null)
{
download = false;
}
string pdbpath = cachebase.Replace("$PDBID$", pdbid);
if (HFile.Exists(pdbpath))
{
var pdb = Pdb.FromFile(pdbpath);
var last = pdb.elements.Last();
if (last is Pdb.End)
{
return(pdb);
}
if (last.line.Length == 80)
{
return(pdb);
}
if (download.Value)
{ // redownload
pdb = Pdb.FromPdbid(pdbid);
pdb.ToFile(pdbpath);
}
return(pdb);
}
else if (download.Value)
{
Pdb pdb = Pdb.FromPdbid(pdbid);
if (pdb != null)
{
pdb.ToFile(pdbpath);
return(pdb);
}
}
return(null);
}
//public static PdbInfo GetPdbInfo(string pdbid, string pdbpath)
//{
// if(HFile.Exists(pdbpath) == false)
// Pdb.FromPdbid(pdbid, cachepath: pdbpath);
// Pdb pdb = Pdb.FromFile(pdbpath);
// return GetPdbInfo(pdbid, pdb);
//}
//static PdbInfo GetPdbInfo(Pdb pdb)
//{
// return GetPdbInfo("", pdb);
//}
static PdbInfo GetPdbInfo(string pdbid, Pdb pdb)
{
PdbInfo pdbinfo = new PdbInfo
{
pdbid = pdbid,
keywords = pdb.elements.ListType <Pdb.Keywds>().ListKeyword().ToArray(),
numAtom = pdb.atoms.Length,
numAnisou = pdb.anisous.Length,
numModel = pdb.elements.ListType <Pdb.Model>().Count,
numChain = pdb.atoms.ListChainID().HListCommonT().Count,
numAltloc = pdb.atoms.ListAltLoc().HListCommonT().Count,
numResidue = pdb.atoms.ListResSeq().HListCommonT().Count,
};
return(pdbinfo);
}
public static void PCA(string pdbpath, string outpathroot, double scaleAnimation)
{
HDebug.ToDo();
Pdb.Atom[] meanconf;
Matrix modes;
Vector freq;
PCA(pdbpath, out meanconf, out modes, out freq);
for (int i = 0; i < freq.Size; i++)
{
string outpath = outpathroot + i.ToString("00") + ".pdb";
Vector[] mode = (modes.GetColVector(i) * scaleAnimation / freq[i]).ToVectors(3);
Pdb.ToFileAnimated(outpath, meanconf, mode);
}
}
public static Pdb CopyPdbOccupancyForMergedPsf(Pdb copyto, Pdb copyfrom1, Pdb copyfrom2)
{
KDTreeDLL.KDTree <Pdb.Atom> kdtree = new KDTreeDLL.KDTree <Pdb.Atom>(3);
foreach (var atom in copyfrom1.atoms)
{
kdtree.insert(atom.coord, atom);
}
foreach (var atom in copyfrom2.atoms)
{
kdtree.insert(atom.coord, atom);
}
Pdb pdb = copyto.Clone();
List <string> nlines = new List <string>();
for (int i = 0; i < pdb.elements.Length; i++)
{
var elemi = pdb.elements[i];
if ((elemi is Pdb.Atom) == false)
{
nlines.Add(elemi.line);
}
else
{
var atomi = elemi as Pdb.Atom;
var atomx = kdtree.nearest(atomi.coord);
HDebug.Assert(atomi.coord[0] == atomx.coord[0]);
HDebug.Assert(atomi.coord[1] == atomx.coord[1]);
HDebug.Assert(atomi.coord[2] == atomx.coord[2]);
/// 55 - 60 Real(6.2) occupancy Occupancy.
char[] line = atomi.line.ToCharArray();
line[55 - 1] = atomx.line[55 - 1];
line[56 - 1] = atomx.line[56 - 1];
line[57 - 1] = atomx.line[57 - 1];
line[58 - 1] = atomx.line[58 - 1];
line[59 - 1] = atomx.line[59 - 1];
line[60 - 1] = atomx.line[60 - 1];
string nline = line.HToString();
nlines.Add(nline);
Pdb.Atom natomi = Pdb.Atom.FromString(nline);
pdb.elements[i] = natomi;
}
}
return(pdb);
}
public double GetRMSD(Pdb pdb, char selAltLoc = 'A', bool includeHydrogen = false)
{
List <Tuple <int, int> > idxs_univ2pdb = GetIndex(pdb, selAltLoc, includeHydrogen);
List <int> atomidxs = new List <int>();
List <Vector> atomcoords = new List <Vector>();
foreach (Tuple <int, int> idx_univ2pdb in idxs_univ2pdb)
{
int atomidx = idx_univ2pdb.Item1;
Vector atomcoord = pdb.atoms[idx_univ2pdb.Item2].coord;
atomidxs.Add(atomidx);
atomcoords.Add(atomcoord);
}
return(GetRMSD(atomidxs, atomcoords));
}
public Pdb CloneByRemoveHeader()
{
Pdb pdb = CloneSelectType
//( "TITLE "
//, "REMARK"
//, "CRYST1"
("MODEL "
, "ATOM "
, "TER "
, "ENDMDL"
, "ANISOU"
, "HETATM"
, "SIGUIJ"
, "CONECT"
);
return(pdb);
}
public Pdb CloneRemoveHetatm()
{
Pdb pdb = CloneSelectType
(null
, "HEADER", "TITLE", "COMPND", "SOURCE", "KEYWDS", "EXPDTA", "AUTHOR", "REVDAT", "JRNL", "REMARK" //
, "DBREF", "SEQRES", "SEQADV" //
, "HET", "HETNAM", "FORMUL" //
, "HELIX", "SHEET" //
, "LINK" //
, "SITE" //
, "CRYST1", "ORIGX1", "ORIGX2", "ORIGX3", "SCALE1", "SCALE2", "SCALE3", "MTRIX1", "MTRIX2", "MTRIX3" //
, "MODEL", "ATOM", "ANISOU", "SIGUIJ", "TER", "ENDMDL" // , "HETATM"
, "CONECT" //
, "MASTER", "END" //
);
return(pdb);
}
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 HMutation FromPdb
(Pdb wtpdb, Pdb mutpdb
, string wt_pdbid = null, string mut_pdbid = null
, int?wt_pdb_model = null, char?wt_pdb_altLoc = null, char?wt_pdb_chainID = null, char?wt_pdb_iCode = null
, int?mut_pdb_model = null, char?mut_pdb_altLoc = null, char?mut_pdb_chainID = null, char?mut_pdb_iCode = null
)
{
if ((wtpdb.models.Length >= 2) && wt_pdb_model == null)
{
wt_pdb_model = 0;
} // HDebug.Assert(false);
if ((mutpdb.models.Length >= 2) && mut_pdb_model == null)
{
mut_pdb_model = 0;
} // HDebug.Assert(false);
Pdb.Atom[] wt_atoms = wtpdb.SelectAtoms(imodel: wt_pdb_model, altLoc: wt_pdb_altLoc, chainID: wt_pdb_chainID, iCode: wt_pdb_iCode);
Pdb.Atom[] mut_atoms = mutpdb.SelectAtoms(imodel: mut_pdb_model, altLoc: mut_pdb_altLoc, chainID: mut_pdb_chainID, iCode: mut_pdb_iCode);
Pdb.Residue[] wt_resis = wt_atoms.ListResidue();
Pdb.Residue[] mut_resis = mut_atoms.ListResidue();
Tuple <string, int>[] wt_resn_resi = wt_resis.HListResNameSeq();
Tuple <string, int>[] mut_resn_resi = mut_resis.HListResNameSeq();
Tuple <string, string, int, string>[] mutationinfos =
FromResnResi
(wt_resn_resi
, mut_resn_resi
, rngLcsLen: new Tuple <int, int>((int)(wt_resis.Length * 0.8), (int)(wt_resis.Length * 1.2))
);
return(new HMutation
{
wt_pdb = wtpdb, mut_pdb = mutpdb,
wt_pdbid = wt_pdbid, mut_pdbid = mut_pdbid,
wt_ResSeq = wt_resis.HListResSeq(), mut_ResSeq = mut_resis.HListResSeq(),
wt_ResName = wt_resis.HListResName(), mut_ResName = mut_resis.HListResName(),
wt_pdb_model = wt_pdb_model, mut_pdb_model = mut_pdb_model,
wt_pdb_altLoc = wt_pdb_altLoc, mut_pdb_altLoc = mut_pdb_altLoc,
wt_pdb_chainID = wt_pdb_chainID, mut_pdb_chainID = mut_pdb_chainID,
wt_pdb_iCode = wt_pdb_iCode, mut_pdb_iCode = mut_pdb_iCode,
mutationinfos = mutationinfos
});
}
public Pdb CloneRemoveResName(bool inAtom, bool inHetatm, params string[] resName)
{
HashSet <IAtom> iatomsInConect = ListIAtomInConect().HToHashSet();
HashSet <string> setResName = resName.HTrim().HToHashSet();
List <Element> nelements = new List <Element>();
int numRemove = 0;
int numRemoveInConect = 0;
foreach (Element element in elements)
{
string record = element.record.Trim();
bool remove = false;
if (inAtom && record == "ATOM")
{
if (resName.Contains((element as Atom).resName.Trim()))
{
remove = true;
}
}
if (inHetatm && record == "HETATM")
{
if (resName.Contains((element as Hetatm).resName.Trim()))
{
remove = true;
}
}
if (remove)
{
if (iatomsInConect.Contains(element as IAtom))
{
numRemoveInConect++;
}
numRemove++;
continue;
}
nelements.Add(element);
}
HDebug.Assert(numRemoveInConect == 0);
Pdb npdb = new Pdb(nelements);
return(npdb);
}
public static void ToPdbFileAnimated
(this Mode mode
, string filepath
, Pdb pdb
, IList <double> stepTimes = null
, double scale = 1
, int?modelidx = null
)
{
Pdb.ToFileAnimated
(filepath
, pdb.atoms
, mode.GetEigvecsOfAtoms(scale)
, stepTimes
, null
, null
, null
, modelidx
);
}
public static bool GetBFactorSelfTest(string pdbpath, double cutoff, double corr, int round, InfoPack extra)
{
if (HFile.Exists(pdbpath) == false)
{
return(false);
}
Pdb pdb = Pdb.FromFile(pdbpath);
for (int i = 0; i < pdb.atoms.Length; i++)
{
HDebug.Assert(pdb.atoms[0].altLoc == pdb.atoms[i].altLoc);
HDebug.Assert(pdb.atoms[0].chainID == pdb.atoms[i].chainID);
}
List <Pdb.Atom> atoms = new List <Pdb.Atom>();
for (int i = 0; i < pdb.atoms.Length; i++)
{
Pdb.Atom atom = pdb.atoms[i];
if (atom.name.Trim().ToUpper() == "CA")
{
atoms.Add(atom);
}
}
List <Vector> coords = atoms.ListCoord();
Matrix hess = Hess.GetHessAnm(coords, cutoff);
InfoPack lextra = new InfoPack();
Vector bfactor = GetBFactor(hess, 0.00000001, null, lextra);
if (extra != null)
{
extra["num_zero_eigvals"] = lextra["num_zero_eigvals"];
extra["eigenvalues"] = lextra["eigenvalues"];
}
double corr_comp = pdb.CorrBFactor(atoms.ListName(), atoms.ListResSeq(), bfactor.ToArray());
corr_comp = Math.Round(corr_comp, round);
HDebug.Assert(corr == corr_comp);
return(corr == corr_comp);
}
//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 void ToFileAnimated(string filepath
, IList <Atom> atoms
, IList <Vector> velocities
, IList <double> stepTimes = null
, IList <Vector> coords = null
, IList <double> bfactors = null
, IList <Element> headers = null
, int?modelidx = null
)
{
if (coords == null)
{
coords = atoms.ListCoord();
}
if (stepTimes == null)
{
stepTimes = new double[] { 0.0, -0.1, -0.2, -0.3, -0.4, -0.5, -0.6, -0.7, -0.8, -0.9, -1.0,
-1.0, -0.9, -0.8, -0.7, -0.6, -0.5, -0.4, -0.3, -0.2, -0.1, 0.0,
0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0,
1.0, 0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3, 0.2, 0.1, 0.0, }
}
;
bool append = false;
for (int i = 0; i < stepTimes.Count; i++)
{
List <Vector> lcoords = coords.PwAdd(velocities, stepTimes[i]);
List <string> lheaders = null;
if ((append == false) && (headers != null))
{
lheaders = headers.ToLines();
}
Pdb.ToFile(filepath, atoms, coords: lcoords, append: append, headers: lheaders, bfactors: bfactors
, modelidx: modelidx
);
append = true;
}
}
}
public static void FromFile(string filepath, out Pdb[] pdbs)
{
string[] lines = System.IO.File.ReadAllLines(filepath);
Element[] elements = new Element[lines.Length];
for (int i = 0; i < lines.Length; i++)
{
elements[i] = new Element(lines[i]);
}
elements = elements.UpdateElement();
List <List <Element> > ensembles;
{
ensembles = new List <List <Element> >();
ensembles.Add(new List <Element>());
for (int i = 0; i < elements.Length; i++)
{
//ensembles.Last().Add(elements[i]);
if (Atom.IsAtom(elements[i].line))
{
ensembles.Last().Add(elements[i]);
}
if (Endmdl.IsEndmdl(elements[i].line))
{
ensembles.Add(new List <Element>());
}
}
if (ensembles.Last().Count == 0)
{
ensembles.Remove(ensembles.Last());
}
}
pdbs = new Pdb[ensembles.Count];
for (int i = 0; i < ensembles.Count; i++)
{
pdbs[i] = new Pdb(ensembles[i].ToArray());
}
}
public static Top FromPdb(string pdbpath
, string ff = "charmm27"
, string water = "none"
, HPack <Pdb> optout_confout = null
)
{
Top top;
FileInfo pdbinfo = new FileInfo(pdbpath);
string currdir = HEnvironment.CurrentDirectory;
DirectoryInfo temproot = HDirectory.CreateTempDirectory();
HEnvironment.CurrentDirectory = temproot.FullName;
{
HFile.Copy(pdbinfo.FullName, "protein.pdb");
RunPdb2gmx(f: "protein.pdb"
, o: "confout.pdb"
, p: "topol.top"
, q: "clean.pdb"
, ff: ff
, water: water
, merge: "all"
, lineStderr: null
, lineStdout: null
);
top = Top.FromFile("topol.top");
if (optout_confout != null)
{
optout_confout.value = Pdb.FromFile("confout.pdb");
}
}
HEnvironment.CurrentDirectory = currdir;
Thread.Sleep(100);
try{ temproot.Delete(true); } catch (Exception) {}
return(top);
}