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 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 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 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 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 void SaveCoordsToPdb(string path, Pdb pdb, Vector[] coords)
{
Pdb.Atom[] pdbatoms = pdb.atoms;
Vector[] pdbcoords = new Vector[pdbatoms.Length];
Dictionary <int, int> serial2idx = pdbatoms.ToDictionaryAsSerialToIndex();
for (int ia = 0; ia < size; ia++)
{
Universe.Atom uatom = atoms[ia];
List <Pdb.Atom> patoms = uatom.sources.HSelectByType((Pdb.Atom)null).ToList();
if (patoms.Count >= 1)
{
HDebug.Assert(patoms.Count == 1);
int serial = patoms[0].serial;
int idx = serial2idx[serial];
HDebug.Assert(pdbatoms[idx].serial == serial);
HDebug.Assert(pdbcoords[idx] == null);
pdbcoords[idx] = coords[ia].Clone();
}
else
{
HDebug.Assert();
}
}
for (int i = 0; i < pdbcoords.Length; i++)
{
if (pdbcoords[i] == null)
{
HDebug.Assert(false);
pdbcoords[i] = new double[3] {
double.NaN, double.NaN, double.NaN
};
}
}
pdb.ToFile(path, pdbcoords);
}
public static CPsfgen Psfgen
(IList <Tuple <string, string, Pdb.IAtom[]> > lstSegFileAtoms // segname, filename, pdbatoms
, string tempbase //=null
, string parameters //=null
, string namdversion //="2.8"
, IList <string> infiles
, IList <string> outfiles
, string topology
, IList <string> psfgen_lines = null
, string psfgen_workdir = null
, HOptions options = null
)
{
if (options == null)
{
options = new HOptions((string)null);
}
Dictionary <System.IO.FileInfo, string[]> infile_lines = new Dictionary <System.IO.FileInfo, string[]>();
foreach (string infile in infiles)
{
infile_lines.Add(HFile.GetFileInfo(infile), HFile.ReadAllLines(infile));
}
string currpath = HEnvironment.CurrentDirectory;
System.IO.DirectoryInfo tmpdir = null;
if (psfgen_workdir != null)
{
HEnvironment.CurrentDirectory = psfgen_workdir;
}
else
{
tmpdir = HDirectory.CreateTempDirectory(tempbase);
HEnvironment.CurrentDirectory = tmpdir.FullName;
}
string[] lines = null;
if ((psfgen_lines != null) && (psfgen_lines.Count > 0))
{
lines = psfgen_lines.ToArray();
}
else
{
lines = GetPsfgenLines
(custom_pdbalias: null
, custom_patches: null
);
}
if (topology != null)
{
lines = lines.ToArray().HReplace("$topology$", topology);
}
List <string> psf_lines;
List <string> pdb_lines;
{
{
//foreach(var respath_filename in GetResourcePaths("2.8", "psfgen"))
foreach (var respath_filename in GetResourcePaths(namdversion, "psfgen"))
{
string respath = respath_filename.Item1;
string filename = respath_filename.Item2;
HResource.CopyResourceTo <Tinker>(respath, filename);
}
}
// Dictionary<string, Tuple<string, Pdb.IAtom[]>> segname_filename_pdbatoms = new Dictionary<string, Tuple<string, Pdb.IAtom[]>>();
// //if(pdbs.Length != 1) throw new ArgumentException();
// for(int i=0; i<lstSegFilePdb.Count; i++)
// {
// string segnameprefix = lstSegFilePdb[i].Item1; if( segnameprefix == null) segnameprefix = string.Format("{0:00}", i);
// string filenameprefix = lstSegFilePdb[i].Item2; if(filenameprefix == null) filenameprefix = string.Format("{0:00}", i);
// Pdb pdb = lstSegFilePdb[i].Item3;
// List<Pdb.IAtom> pdb_atoms = new List<Pdb.IAtom>();
// pdb_atoms.AddRange(pdb.atoms);
// pdb_atoms.AddRange(pdb.hetatms);
// char[] chains = pdb_atoms.ListChainID().HToHashSet().ToArray();
//
// HDebug.AssertIf(chains.Length> 1, segnameprefix.Length <= 5);
// HDebug.AssertIf(chains.Length<=1, segnameprefix.Length <= 6);
// foreach(char chain in chains)
// {
// Pdb.IAtom[] chain_atoms = pdb_atoms.SelectByChainID(chain).SelectByAltLoc().ToArray();
// string suffix = null;
// if(('a' <= chain) && (chain <= 'z')) suffix = string.Format("L{0}", chain);
// if(('A' <= chain) && (chain <= 'Z')) suffix = string.Format("U{0}", chain);
// if(('0' <= chain) && (chain <= '9')) suffix = string.Format("N{0}", chain);
// string segname = segnameprefix + ((chains.Length <= 1) ? "" : suffix);
// string filename = filenameprefix + ((chains.Length <= 1) ? "" : suffix);
// segname_filename_pdbatoms.Add(segname, new Tuple<string,Pdb.IAtom[]>(filename, chain_atoms));
// }
// }
foreach (var finfo_line in infile_lines)
{
string inname = finfo_line.Key.Name;
string[] inlines = finfo_line.Value;
HFile.WriteAllLines(inname, inlines);
}
HashSet <string> segnames = new HashSet <string>();
int segindex = 0;
foreach (var seg_file_atoms in lstSegFileAtoms)
{
string segname = seg_file_atoms.Item1;
string filename = seg_file_atoms.Item2;
Pdb.IAtom[] chain_atoms = seg_file_atoms.Item3.SelectByAltLoc().ToArray();
HDebug.Exception(chain_atoms.ListChainID().HToHashSet().Count == 1);
if (segname == null)
{
while (segindex <= 9999)
{
if (segnames.Contains(segindex.ToString()) == false)
{
segname = segindex.ToString();
segnames.Add(segname);
break;
}
segindex++;
}
}
if (filename == null)
{
filename = segname;
}
Pdb.ToFile
(filename + ".pdb"
, chain_atoms.HToType <Pdb.IAtom, Pdb.Element>()
, false
);
for (int i = 0; i < lines.Length; i++)
{
if (lines[i].Contains("$segname$"))
{
string insert = lines[i];
insert = insert.Replace("$segname$", segname);
insert = insert.Replace("$segfilename$", filename);
lines = lines.HInsert(i, insert);
i++;
}
}
}
lines = lines.HRemoveAllContains("$segname$");
HFile.WriteAllLines("prot.inp", lines);
string command0 = string.Format("psfgen < prot.inp");
bool pause = options.Contains("psfgen pause");
HProcess.StartAsBatchInConsole(null, pause, command0);
psf_lines = System.IO.File.ReadLines("prot.psf").ToList();
pdb_lines = System.IO.File.ReadLines("prot.pdb").ToList();
}
HEnvironment.CurrentDirectory = currpath;
if (tmpdir != null)
{
try{ tmpdir.Delete(true); } catch {}
}
return(new CPsfgen
{
psf_lines = psf_lines,
pdb_lines = pdb_lines,
});
}
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 CPdbxyz Pdbxyz
(Pdb pdb
, Tinker.Prm prm
, string tempbase //=null
, string parameters //=null
, string tinkerversion //="6.2.1"
, params string[] keys
)
{
var tmpdir = HDirectory.CreateTempDirectory(tempbase);
string currpath = HEnvironment.CurrentDirectory;
Tinker.Xyz xyz;
string[] seq;
string[] capture;
{
HEnvironment.CurrentDirectory = tmpdir.FullName;
{
foreach (var respath_filename in GetResourcePaths("6.2.1", "pdbxyz"))
{
string respath = respath_filename.Item1;
string filename = respath_filename.Item2;
HResource.CopyResourceTo <Tinker>(respath, filename);
}
}
pdb.ToFile("prot.pdb");
prm.ToFile("prot.prm");
string keypath = null;
if ((keys != null) && (keys.Length > 0))
{
keypath = "prot.key";
HFile.WriteAllLines(keypath, keys);
}
{
//bool ComputeAnalyticalGradientVector = true;
//bool ComputeNumericalGradientVector = false;
//bool OutputBreakdownByGradientComponent = false;
string command = "";
command += "pdbxyz.exe";
command += " prot.pdb";
command += " prot.prm";
if (keypath != null)
{
command += " -k " + keypath;
}
command += " > output.txt";
List <string> errors = new List <string>();
int exitcode = HProcess.StartAsBatchSilent(null, null, errors, command);
capture = HFile.ReadAllLines("output.txt");
capture = capture.HAddRange(errors.ToArray());
xyz = Tinker.Xyz.FromFile("prot.xyz", false);
if (HFile.Exists("prot.seq"))
{
seq = HFile.ReadAllLines("prot.seq");
}
else
{
seq = null;
}
}
}
HEnvironment.CurrentDirectory = currpath;
try{ tmpdir.Delete(true); } catch {}
return(new CPdbxyz
{
xyz = xyz,
seq = seq,
capture = capture,
});
}
public static HessInfoCoarseResiIter GetHessCoarseResiIter
(Hess.HessInfo hessinfo
, Vector[] coords
, FuncGetIdxKeepListRemv GetIdxKeepListRemv
, ILinAlg ila
, double thres_zeroblk = 0.001
, IterOption iteropt = IterOption.Matlab_experimental
, string[] options = null
)
{
bool rediag = true;
HessMatrix H = null;
List <int>[] lstNewIdxRemv = null;
int numca = 0;
double[] reMass = null;
object[] reAtoms = null;
Vector[] reCoords = null;
Tuple <int[], int[][]> idxKeepRemv = null;
//System.Console.WriteLine("begin re-indexing hess");
{
object[] atoms = hessinfo.atoms;
idxKeepRemv = GetIdxKeepListRemv(atoms, coords);
int[] idxKeep = idxKeepRemv.Item1;
int[][] idxsRemv = idxKeepRemv.Item2;
{
List <int> check = new List <int>();
check.AddRange(idxKeep);
foreach (int[] idxRemv in idxsRemv)
{
check.AddRange(idxRemv);
}
check = check.HToHashSet().ToList();
if (check.Count != coords.Length)
{
throw new Exception("the re-index contains the duplicated atoms or the missing atoms");
}
}
List <int> idxs = new List <int>();
idxs.AddRange(idxKeep);
foreach (int[] idxRemv in idxsRemv)
{
idxs.AddRange(idxRemv);
}
HDebug.Assert(idxs.Count == idxs.HToHashSet().Count);
H = hessinfo.hess.ReshapeByAtom(idxs);
numca = idxKeep.Length;
reMass = hessinfo.mass.ToArray().HSelectByIndex(idxs);
reAtoms = hessinfo.atoms.ToArray().HSelectByIndex(idxs);
reCoords = coords.HSelectByIndex(idxs);
int nidx = idxKeep.Length;
lstNewIdxRemv = new List <int> [idxsRemv.Length];
for (int i = 0; i < idxsRemv.Length; i++)
{
lstNewIdxRemv[i] = new List <int>();
foreach (var idx in idxsRemv[i])
{
lstNewIdxRemv[i].Add(nidx);
nidx++;
}
}
HDebug.Assert(nidx == lstNewIdxRemv.Last().Last() + 1);
HDebug.Assert(nidx == idxs.Count);
}
GC.Collect(0);
HDebug.Assert(numca == H.ColBlockSize - lstNewIdxRemv.HListCount().Sum());
//if(bool.Parse("false"))
{
if (bool.Parse("false"))
#region
{
int[] idxKeep = idxKeepRemv.Item1;
int[][] idxsRemv = idxKeepRemv.Item2;
Pdb.Atom[] pdbatoms = hessinfo.atomsAsUniverseAtom.ListPdbAtoms();
Pdb.ToFile(@"C:\temp\coarse-keeps.pdb", pdbatoms.HSelectByIndex(idxKeep), false);
if (HFile.Exists(@"C:\temp\coarse-graining.pdb"))
{
HFile.Delete(@"C:\temp\coarse-graining.pdb");
}
foreach (int[] idxremv in idxsRemv.Reverse())
{
List <Pdb.Element> delatoms = new List <Pdb.Element>();
foreach (int idx in idxremv)
{
if (pdbatoms[idx] == null)
{
continue;
}
string line = pdbatoms[idx].GetUpdatedLine(coords[idx]);
Pdb.Atom delatom = Pdb.Atom.FromString(line);
delatoms.Add(delatom);
}
Pdb.ToFile(@"C:\temp\coarse-graining.pdb", delatoms.ToArray(), true);
}
}
#endregion
if (bool.Parse("false"))
#region
{
// export matrix to matlab, so the matrix can be checked in there.
int[] idxca = HEnum.HEnumCount(numca).ToArray();
int[] idxoth = HEnum.HEnumFromTo(numca, coords.Length - 1).ToArray();
Matlab.Register(@"C:\temp\");
Matlab.PutSparseMatrix("H", H.GetMatrixSparse(), 3, 3);
Matlab.Execute("figure; spy(H)");
Matlab.Clear();
}
#endregion
if (bool.Parse("false"))
#region
{
HDirectory.CreateDirectory(@"K:\temp\$coarse-graining\");
{ // export original hessian matrix
List <int> cs = new List <int>();
List <int> rs = new List <int>();
foreach (ValueTuple <int, int, MatrixByArr> bc_br_bval in hessinfo.hess.EnumBlocks())
{
cs.Add(bc_br_bval.Item1);
rs.Add(bc_br_bval.Item2);
}
Matlab.Clear();
Matlab.PutVector("cs", cs.ToArray());
Matlab.PutVector("rs", rs.ToArray());
Matlab.Execute("hess = sparse(cs+1, rs+1, ones(size(cs)));");
Matlab.Execute("hess = float(hess);");
Matlab.Execute("figure; spy(hess)");
Matlab.Execute("cs = int32(cs+1);");
Matlab.Execute("rs = int32(rs+1);");
Matlab.Execute(@"save('K:\temp\$coarse-graining\hess-original.mat', 'cs', 'rs', '-v6');");
Matlab.Clear();
}
{ // export reshuffled hessian matrix
List <int> cs = new List <int>();
List <int> rs = new List <int>();
foreach (ValueTuple <int, int, MatrixByArr> bc_br_bval in H.EnumBlocks())
{
cs.Add(bc_br_bval.Item1);
rs.Add(bc_br_bval.Item2);
}
Matlab.Clear();
Matlab.PutVector("cs", cs.ToArray());
Matlab.PutVector("rs", rs.ToArray());
Matlab.Execute("H = sparse(cs+1, rs+1, ones(size(cs)));");
Matlab.Execute("H = float(H);");
Matlab.Execute("figure; spy(H)");
Matlab.Execute("cs = int32(cs+1);");
Matlab.Execute("rs = int32(rs+1);");
Matlab.Execute(@"save('K:\temp\$coarse-graining\hess-reshuffled.mat', 'cs', 'rs', '-v6');");
Matlab.Clear();
}
}
#endregion
if (bool.Parse("false"))
#region
{
int[] idxca = HEnum.HEnumCount(numca).ToArray();
int[] idxoth = HEnum.HEnumFromTo(numca, coords.Length - 1).ToArray();
HessMatrix A = H.SubMatrixByAtoms(false, idxca, idxca);
HessMatrix B = H.SubMatrixByAtoms(false, idxca, idxoth);
HessMatrix C = H.SubMatrixByAtoms(false, idxoth, idxca);
HessMatrix D = H.SubMatrixByAtoms(false, idxoth, idxoth);
Matlab.Clear();
Matlab.PutSparseMatrix("A", A.GetMatrixSparse(), 3, 3);
Matlab.PutSparseMatrix("B", B.GetMatrixSparse(), 3, 3);
Matlab.PutSparseMatrix("C", C.GetMatrixSparse(), 3, 3);
Matlab.PutSparseMatrix("D", D.GetMatrixSparse(), 3, 3);
Matlab.Clear();
}
#endregion
}
List <HessCoarseResiIterInfo> iterinfos = null;
{
object[] atoms = reAtoms; // reAtoms.HToType(null as Universe.Atom[]);
CGetHessCoarseResiIterImpl info = null;
switch (iteropt)
{
case IterOption.ILinAlg_20150329: info = GetHessCoarseResiIterImpl_ILinAlg_20150329(H, lstNewIdxRemv, thres_zeroblk, ila, false); break;
case IterOption.ILinAlg: info = GetHessCoarseResiIterImpl_ILinAlg(H, lstNewIdxRemv, thres_zeroblk, ila, false); break;
case IterOption.Matlab: info = GetHessCoarseResiIterImpl_Matlab(atoms, H, lstNewIdxRemv, thres_zeroblk, ila, false, options); break;
case IterOption.Matlab_experimental: info = GetHessCoarseResiIterImpl_Matlab_experimental(atoms, H, lstNewIdxRemv, thres_zeroblk, ila, false, options); break;
case IterOption.Matlab_IterLowerTri: info = GetHessCoarseResiIterImpl_Matlab_IterLowerTri(atoms, H, lstNewIdxRemv, thres_zeroblk, ila, false, options); break;
case IterOption.LinAlg_IterLowerTri: info = GetHessCoarseResiIterImpl_LinAlg_IterLowerTri.Do(atoms, H, lstNewIdxRemv, thres_zeroblk, ila, false, options); break;
}
;
H = info.H;
iterinfos = info.iterinfos;
}
//{
// var info = GetHessCoarseResiIterImpl_Matlab(H, lstNewIdxRemv, thres_zeroblk);
// H = info.H;
//}
GC.Collect(0);
if (HDebug.IsDebuggerAttached)
{
int nidx = 0;
int[] ikeep = idxKeepRemv.Item1;
foreach (int idx in ikeep)
{
bool equal = object.ReferenceEquals(hessinfo.atoms[idx], reAtoms[nidx]);
if (equal == false)
{
HDebug.Assert(false);
}
HDebug.Assert(equal);
nidx++;
}
}
if (rediag)
{
H = H.CorrectHessDiag();
}
//System.Console.WriteLine("finish fixing diag");
return(new HessInfoCoarseResiIter
{
hess = H,
mass = reMass.HSelectCount(numca),
atoms = reAtoms.HSelectCount(numca),
coords = reCoords.HSelectCount(numca),
numZeroEigval = 6,
iterinfos = iterinfos,
});
}
public static void SelfTest(string rootpath, string[] args)
{
//{
// Pdb pdb = Pdb.FromFile(rootpath + @"\Sample\1a6g.pdb");
// HTLib2.Bioinfo.Universe.Build(pdb);
//}
GetPotential_SelfTest(rootpath, args);
Universe univ = null;
string sample = null;
//sample = "1a6g_autopsf.unfolded";
//sample = "1a6g_autopsf";
switch (sample)
{
case "alanin":
{
List <ForceField.IForceField> frcflds = ForceField.GetMindyForceFields();
double k = 0.0001;
double threshold = 0.001;
//int iter = univ.Minimize_ConjugateGradient_v0(frcflds, k, threshold);
int randomPurturb = 0; // no random purturbation
bool[] atomsMovable = null; // update all atoms
int iter_conjgrad;
{
Namd.Psf psf = Namd.Psf.FromFile(rootpath + @"\Sample\alanin.psf");
Pdb pdb = Pdb.FromFile(rootpath + @"\Sample\alanin.pdb");
Namd.Prm prm = Namd.Prm.FromFileXPlor(rootpath + @"\Sample\alanin.params", new TextLogger());
univ = Universe.Build(psf, prm, pdb, false);
//frcflds = new List<ForceField.IForceField>();
//frcflds.Add(new ForceField.MindyBond());
//frcflds.Add(new ForceField.MindyAngle());
//frcflds.Add(new ForceField.MindyDihedral());
//frcflds.Add(new ForceField.MindyImproper());
//frcflds.Add(new ForceField.MindyNonbondedLennardJones());
//frcflds.Add(new ForceField.MindyNonbondedElectrostatic());
//iter_conjgrad = univ.Minimize_ConjugateGradient_v1(0, frcflds, k, 0.1, null, threshold, randomPurturb, atomsMovable, new MinimizeLogger_PrintEnergyForceMag(), null, null);
//frcflds = new List<ForceField.IForceField>();
//frcflds.Add(new ForceField.MindyBond());
//frcflds.Add(new ForceField.MindyAngle());
//frcflds.Add(new ForceField.MindyImproper());
//frcflds.Add(new ForceField.MindyNonbondedLennardJones());
//frcflds.Add(new ForceField.MindyNonbondedElectrostatic());
//iter_conjgrad = univ.Minimize_ConjugateGradient_v1(0, frcflds, k*0.1, 0.1, null, threshold, randomPurturb, atomsMovable, new MinimizeLogger_PrintEnergyForceMag(), null, null);
frcflds = new List <ForceField.IForceField>();
if (HDebug.False)
{
frcflds.Add(new ForceField.MindyBond());
}
else
{
frcflds.Add(new ForceField.PwBond());
}
if (HDebug.False)
{
frcflds.Add(new ForceField.MindyAngle());
}
else
{
frcflds.Add(new ForceField.PwAngle());
}
frcflds.Add(new ForceField.MindyDihedral());
if (HDebug.False)
{
frcflds.Add(new ForceField.MindyImproper());
}
else
{
frcflds.Add(new ForceField.PwImproper());
}
if (HDebug.False)
{
frcflds.Add(new ForceField.MindyNonbondedElectrostatic());
}
else
{
frcflds.Add(new ForceField.PwElec());
}
if (HDebug.False)
{
frcflds.Add(new ForceField.MindyNonbondedLennardJones());
}
else
{
frcflds.Add(new ForceField.PwVdw());
}
univ.LoadCoords(@"D:\xxxx.coords");
iter_conjgrad = univ.Minimize_ConjugateGradient_v1(0, frcflds, k, 0.01, null, threshold, randomPurturb, atomsMovable, new MinimizeLogger_PrintEnergyForceMag(), null, null);
univ.SaveCoords(@"D:\xxxx.coords");
System.Console.WriteLine("=======================================================================");
System.Console.WriteLine("=======================================================================");
System.Console.WriteLine("=======================================================================");
}
{
//Psf psf = Psf.FromFile(rootpath + @"\Sample\alanin.psf");
//Pdb pdb = Pdb.FromFile(rootpath + @"\Sample\alanin.pdb");
//Prm prm = Prm.FromFileXPlor(rootpath + @"\Sample\alanin.params", new TextLogger());
//univ = Universe.Build(psf, prm, pdb);
//frcflds = new List<ForceField.IForceField>();
//if(true) frcflds.Add(new ForceField.MindyBond()); else frcflds.Add(new ForceField.PwBond());
//if(true) frcflds.Add(new ForceField.MindyAngle()); else frcflds.Add(new ForceField.PwAngle());
//frcflds.Add(new ForceField.MindyDihedral());
//if(true) frcflds.Add(new ForceField.MindyImproper()); else frcflds.Add(new ForceField.PwImproper());
//if(true) frcflds.Add(new ForceField.MindyNonbondedElectrostatic()); else frcflds.Add(new ForceField.PwElec());
//if(true) frcflds.Add(new ForceField.MindyNonbondedLennardJones()); else frcflds.Add(new ForceField.PwVdw());
univ.atoms[0].Coord += new Vector(0.1, 0.1, 0.1);
//iter_conjgrad = univ.Minimize_ConjugateGradient_v1(0, frcflds, k, 0.001, null, threshold, randomPurturb, atomsMovable, new MinimizeLogger_PrintEnergyForceMag(), null, null);
iter_conjgrad = univ.Minimize_ConjugateGradient_AtomwiseUpdate(frcflds,
threshold: threshold,
k: k,
max_atom_movement: 0.001,
max_iteration: null,
atomsMovable: atomsMovable,
logger: new MinimizeLogger_PrintEnergyForceMag()
);
}
k = 0.0005;
HDebug.Assert(false);
//int iter_stepdsnt = univ.Minimize_SteepestDescent(frcflds, k, threshold, System.Console.Error);
}
break;
case "1a6g_autopsf":
{
Namd.Psf psf = Namd.Psf.FromFile(rootpath + @"\Sample\1a6g_autopsf.psf");
Pdb pdb = Pdb.FromFile(rootpath + @"\Sample\1a6g_autopsf.pdb");
Namd.Prm prm = Namd.Prm.FromFile(rootpath + @"\Sample\1a6g_autopsf.prm", new TextLogger());
univ = Universe.Build(psf, prm, pdb, false);
List <ForceField.IForceField> frcflds = ForceField.GetMindyForceFields();
double threshold = 0.001;
string minimize_ver = "v1";
switch (minimize_ver)
{
//case "v2":
// {
// double atom_max_move = 0.03;
// int iter_conjgrad = univ.Minimize_ConjugateGradient_v2(frcflds, atom_max_move, threshold, System.Console.Error);
// break;
// }
case "v1":
{
double k = 0.0001;
int randomPurturb = 0; // no random purturbation
bool[] atomsMovable = null; // update all atoms
int iter_conjgrad = univ.Minimize_ConjugateGradient_v1(0, frcflds, k, 0.1, null, threshold, randomPurturb, atomsMovable, new MinimizeLogger_PrintEnergyForceMag(), null, null);
break;
}
default:
goto case "v1";
}
//atom_max_move = 0.03;
//int iter_stepdsnt = univ.Minimize_SteepestDescent(frcflds, atom_max_move, threshold, System.Console.Error);
}
break;
case "1a6g_autopsf.unfolded":
{
Namd.Psf psf = Namd.Psf.FromFile(rootpath + @"\Sample\1a6g_autopsf.psf");
Pdb pdb = Pdb.FromFile(rootpath + @"\Sample\1a6g_autopsf.pdb");
{
Random rand = new Random(1);
List <Vector> coords = pdb.atoms.ListCoord();
for (int i = 0; i < coords.Count; i++)
{
double x = i * 0.1 + rand.NextDouble() * 0.01;
double y = i * 0.1 + rand.NextDouble() * 0.01;
double z = i * 0.1 + rand.NextDouble() * 0.01;
coords[i] = new Vector(x, y, z);
}
pdb.ToFile(rootpath + @"\Sample\1a6g_autopsf.unfolded.pdb", coords);
pdb = Pdb.FromFile(rootpath + @"\Sample\1a6g_autopsf.unfolded.pdb");
}
Namd.Prm prm = Namd.Prm.FromFile(rootpath + @"\Sample\1a6g_autopsf.prm", new TextLogger());
univ = Universe.Build(psf, prm, pdb, false);
List <ForceField.IForceField> frcflds = ForceField.GetMindyForceFields();
double threshold = 0.01;
string minimize_ver = "v1";
switch (minimize_ver)
{
//case "v2":
// {
// double atom_max_move = 0.1;
// int iter_conjgrad = univ.Minimize_ConjugateGradient_v2(frcflds, atom_max_move, threshold, System.Console.Error);
// break;
// }
case "v1":
{
double k = 0.0001;
int randomPurturb = 100;
bool[] atomsMovable = null; // updates all atoms
int iter_conjgrad = univ.Minimize_ConjugateGradient_v1(0, frcflds, k, 0.1, null, threshold, randomPurturb, atomsMovable, new MinimizeLogger_PrintEnergyForceMag(), null, null);
break;
}
default:
goto case "v1";
}
//atom_max_move = 0.03;
//int iter_stepdsnt = univ.Minimize_SteepestDescent(frcflds, atom_max_move, threshold, System.Console.Error);
}
break;
default:
goto case "alanin";
}
}
public static Vector[] MinimizeLBfgs(IList <Pdb.Atom> atoms
, IList <Vector> coords = null
, string ff = null // -ff string select Force field, interactive by default. Use -h for information.
// "charmm27", ...
, string water = null // -water enum select Water model to use: select, none, spc, spce, tip3p, tip4p or tip5p
, double mdp_emtol = 0.001 // the minimization is converged when the maximum force is smaller than this value
, double mdp_emstep = 0.001 // initial step-size
)
{
Vector[] confout;
{
string currdir = HEnvironment.CurrentDirectory;
System.IO.DirectoryInfo temproot = HDirectory.CreateTempDirectory();
HEnvironment.CurrentDirectory = temproot.FullName;
{
if (coords != null)
{
HDebug.Assert(atoms.Count == coords.Count);
}
Pdb.ToFile("conf.pdb", atoms, coords: coords
, headers: new string[] { "CRYST1 " }
);
HFile.WriteAllLines("grompp-nm.mdp"
, new string[] { "; Parameters describing what to do, when to stop and what to save "
, "integrator = l-bfgs "
, "emtol = 0.001 "
, "emstep = 0.001 ; Energy step size "
, "nsteps = 5000000000 ; Maximum number of (minimization) steps to perform "
, " ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions "
, "nstlist = 1 ; Frequency to update the neighbor list and long range forces "
, "ns_type = grid ; Method to determine neighbor list (simple, grid) "
, "rlist = 1.0 ; Cut-off for making neighbor list (short range forces) ; htna 1.0-1.2 "
, "coulombtype = Shift "
, "rcoulomb = 1.0 "
, "rcoulomb_switch = 0.7 "
, "vdwtype = Shift "
, "rvdw = 1.0 "
, "rvdw_switch = 0.7 "
//," "
//," "
//,"nstxout = 1; (100) [steps] frequency to write coordinates to output trajectory file, the last coordinates are always written"
//,"nstvout = 1; (100) [steps] frequency to write velocities to output trajectory, the last velocities are always written "
//,"nstfout = 1; ( 0) [steps] frequency to write forces to output trajectory. "
});
RunPdb2gmx(f: "conf.pdb"
, o: "confout.pdb"
, p: "topol.top"
, i: "posre.itp"
, n: "clean.ndx"
, q: "clean.pdb"
, ff: "charmm27"
, water: "none"
, merge: "all"
, lineStderr: null
, lineStdout: null
);
RunGrompp(f: "grompp-nm.mdp"
, p: "topol.top"
, o: "topol-nm.tpr"
, c: "confout.pdb"
, lineStderr: null
, lineStdout: null
);
RunMdrun(s: "topol-nm.tpr"
, c: "confout.pdb"
, o: "traj.trr"
, g: "md.log"
//, mtx:"hessian.mtx"
//, pf:"pullf.xvg"
//, px:"pullx.xvg"
//, nt:"3"
, lineStderr: null
, lineStdout: null
);
Pdb pdbout = Pdb.FromFile("confout.pdb");
confout = pdbout.atoms.ListCoord().ToArray();
}
HEnvironment.CurrentDirectory = currdir;
Thread.Sleep(100);
try{ temproot.Delete(true); } catch (Exception) {}
}
HDebug.Assert(confout.Length == atoms.Count);
return(confout);
}
public static CPsfgenExt PsfgenExt
(IList <Tuple <string, string, Pdb.IAtom[]> > lstSegFileAtoms
, string[] toplines
, string[] parlines
, Pdb alignto
, string[] psfgen_lines
, IList <string> minimize_conf_lines = null
, HOptions options = null
)
{
if (options == null)
{
options = new HOptions((string)null);
}
string tempbase = @"C:\temp\";
string psfgen_workdir = null;
string topname = "prot.top";
string parname = "prot.par";
List <string> psf_lines = null;
List <string> pdb_lines = null;
using (var temp = new HTempDirectory(tempbase, null))
{
temp.EnterTemp();
HFile.WriteAllLines(topname, toplines);
HFile.WriteAllLines(parname, parlines);
if ((HFile.Exists("prot.pdb") == false) || (HFile.Exists("prot.psf") == false))
{
var psfgen = Namd.RunPsfgen
(lstSegFileAtoms, tempbase, null, "2.10"
, new string[] { topname }
, new string[] {}
, topname
, psfgen_lines: psfgen_lines
, psfgen_workdir: psfgen_workdir
, options: options
);
psf_lines = psfgen.psf_lines;
pdb_lines = psfgen.pdb_lines;
if (alignto != null)
{
HDebug.Exception("check!!!");
////////////////////////////
Pdb prot = Pdb.FromLines(pdb_lines);
prot = PsfgenExt_AlignTo(prot, alignto);
pdb_lines = prot.ToLines().ToList();
}
HFile.WriteAllLines("prot.pdb", pdb_lines);
HFile.WriteAllLines("prot.psf", psf_lines);
}
if (options.Contains("nomin") == false)
{
if ((HFile.Exists("protmin.coor") == false) || (HFile.Exists("protmin.pdb") == false))
{
List <string> psfgen_pdb_lines = System.IO.File.ReadLines("prot.pdb").ToList();
List <string> psfgen_psf_lines = System.IO.File.ReadLines("prot.psf").ToList();
List <string> prm_lines = System.IO.File.ReadLines(parname).ToList();
string Namd2_opt = null;
if (options.HSelectStartsWith("minimize option:").Length >= 1)
{
Namd2_opt = options.HSelectStartsWith("minimize option:").First().Replace("minimize option:", "");
}
var minpdb = Namd.Run.Namd2
(psfgen_pdb_lines
, psfgen_psf_lines
, prm_lines
, tempbase
, "2.10"
, ((Namd2_opt == null) ? "+p3" : Namd2_opt)
, conf_lines: minimize_conf_lines
);
HFile.WriteAllLines("protmin.coor", minpdb.coor_lines);
Pdb prot0 = Pdb.FromLines(psfgen_pdb_lines);
Pdb prot1 = Pdb.FromLines(minpdb.coor_lines);
HDebug.Exception(prot0.atoms.Length == prot1.atoms.Length);
HDebug.Exception(prot0.elements.Length == prot1.elements.Length);
// update conformation to minimized conformation
for (int i = 0; i < prot0.elements.Length; i++)
{
if (prot0.elements[i].GetType() != prot1.elements[i].GetType())
{
throw new HException("prot0.elements[i].GetType() != prot1.elements[i].GetType()");
}
if ((prot0.elements[i] is Pdb.IAtom) == false)
{
continue;
}
Pdb.IAtom iatom0 = prot0.elements[i] as Pdb.IAtom;
Pdb.IAtom iatom1 = prot1.elements[i] as Pdb.IAtom;
Vector coord0 = iatom0.coord;
Vector coord1 = iatom1.coord;
double dist = (coord0 - coord1).Dist;
if (iatom0.occupancy != 0)
{
if (dist != 0)
{
throw new HException("iatom0.coord - iatom1.coord != 0");
}
}
if (dist != 0)
{
if (iatom0 is Pdb.Atom)
{
string nline0 = (iatom0 as Pdb.Atom).GetUpdatedLine(coord1);
Pdb.Atom natom0 = Pdb.Atom.FromString(nline0);
prot0.elements[i] = natom0;
continue;
}
if (iatom0 is Pdb.Hetatm)
{
string nline0 = (iatom0 as Pdb.Hetatm).GetUpdatedLine(coord1);
Pdb.Hetatm natom0 = Pdb.Hetatm.FromString(nline0);
prot0.elements[i] = natom0;
continue;
}
}
}
if ((prot0.elements[0] is Pdb.Remark) && (prot1.elements[0] is Pdb.Remark))
{
prot0.elements[0] = Pdb.Remark.FromString(prot1.elements[0].line);
}
prot0.ToFile("protmin.pdb");
pdb_lines = System.IO.File.ReadLines("protmin.pdb").ToList();
}
}
//{
// Pdb confpdb = GetConfPdb(options);
// var psf = Namd.Psf.FromFile("prot.psf");
// var prm = Namd.Prm.FromFile(parname);
// List<string> log = new List<string>();
// Universe univ = Universe.BuilderNamd.Build(psf, prm, confpdb, true, new TextLogger(log));
// return univ;
//}
temp.QuitTemp();
}
return(new CPsfgenExt
{
psflines = psf_lines,
pdblines = pdb_lines,
});
}
public static MixHessInfo GetHessMixModel(Universe univ, IList <Vector> coords, ILinAlg la
, IList <ResInfo> lstResAllAtom, FnGetHess GetHess, out string errmsg
, bool bGetIntmInfo, string strBkbnReso
)
{
FnGetHess lGetHess = delegate(Universe luniv, IList <Vector> lcoords, int[] lidxAll, int[] lidxBuffer, int[] lidxCoarse, int[] idxBackbone)
{
// double check if all three indices are disjoint
HDebug.Assert(lidxAll.HUnion().Length == lidxAll.Length);
HDebug.Assert(lidxBuffer.HUnion().Length == lidxBuffer.Length);
HDebug.Assert(lidxCoarse.HUnion().Length == lidxCoarse.Length);
HDebug.Assert(lidxAll.HListCommonT(lidxBuffer).Count == 0);
HDebug.Assert(lidxBuffer.HListCommonT(lidxCoarse).Count == 0);
HDebug.Assert(lidxCoarse.HListCommonT(lidxAll).Count == 0);
if (HDebug.IsDebuggerAttached)
{
foreach (int idx in lidxAll)
{
HDebug.Assert(lcoords[idx] != null);
}
foreach (int idx in lidxBuffer)
{
HDebug.Assert(lcoords[idx] != null);
}
foreach (int idx in lidxCoarse)
{
HDebug.Assert(lcoords[idx] != null);
}
}
var hessinfo = GetHess(luniv, lcoords, lidxAll, lidxBuffer, lidxCoarse, idxBackbone);
return(hessinfo);
};
bool bVerifySteps = false; // HDebug.IsDebuggerAttached;
Vector bfactorFull = null;
if (bVerifySteps && HDebug.IsDebuggerAttached)
{
int[] idxAll = HEnum.HEnumCount(coords.Count).ToArray();
var hessinfo = lGetHess(univ, coords, idxAll, new int[0], new int[0], new int[0]);
var modes = hessinfo.GetModesMassReduced();
var modesPosZero = modes.SeparateTolerants();
HDebug.Assert(modesPosZero.Item2.Length == 6);
bfactorFull = modesPosZero.Item1.GetBFactor().ToArray();
}
IList <Pdb.Atom> pdbatoms = univ.atoms.ListPdbAtoms();
ResInfo[] resinfos = pdbatoms.ListResInfo(true);
int[] idxCa; // idxs of Ca atoms
int[] idxBkbn; // idxs of backbone atoms
int[] idxSele; // idxs of all atoms of lstResAllAtom (selected)
int[] idxCntk; // idxs of all atoms contacting idxSele
{
string[] nameBkbn;
switch (strBkbnReso)
{
case "NCaC": nameBkbn = new string[] { "N", "CA", "C" }; break;
case "NCaC-O": nameBkbn = new string[] { "N", "CA", "C", "O" }; break;
case "NCaC-OHn": nameBkbn = new string[] { "N", "CA", "C", "O", "HN" }; break;
case "NCaC-O-Ha": nameBkbn = new string[] { "N", "CA", "C", "O", "HA" }; break;
case "NCaC-OHn-HaCb": nameBkbn = new string[] { "N", "CA", "C", "O", "HN", "HA", "CB" }; break;
default: throw new NotImplementedException();
}
idxCa = univ.atoms.ListPdbAtoms().IdxByName(true, "CA");
//idxBkbn = univ.atoms.ListPdbAtoms().IdxByName(true, "N", "CA", "C", "O", "HA");
idxBkbn = univ.atoms.ListPdbAtoms().IdxByName(true, nameBkbn);
idxSele = resinfos.HIdxEqual(ResInfo.Equals, lstResAllAtom.ToArray());
Vector[] coordSele = coords.HSelectByIndex(idxSele);
int[] idxCtof = coords.HIdxWithinCutoff(4.5, coordSele);
ResInfo[] resCtof = resinfos.HSelectByIndex(idxCtof);
resCtof = resCtof.HUnion(); // remove redundant residues
resCtof = resCtof.HRemoveAll(lstResAllAtom.ToArray()).ToArray(); // remove active site residues
idxCntk = resinfos.HIdxEqual(ResInfo.Equals, resCtof);
bool plot = false;
if (plot)
#region verify by plotting
{
Pdb.ToFile(@"C:\temp\mix.pdb", pdbatoms, coords);
Pymol.Py.CgoOld.WriteBlank(@"C:\temp\mix.py", false);
Pymol.Py.CgoOld.WriteSphere(@"C:\temp\mix.py", "Ca", coords.HSelectByIndex(idxCa).HRemoveAllNull(), 0.3);
Pymol.Py.CgoOld.WriteSphere(@"C:\temp\mix.py", "backbone", coords.HSelectByIndex(idxBkbn).HRemoveAllNull(), 0.3);
Pymol.Py.CgoOld.WriteSphere(@"C:\temp\mix.py", "active", coordSele.HRemoveAllNull()
, 0.3
, red: 1, green: 0, blue: 0);
Pymol.Py.CgoOld.WriteSphere(@"C:\temp\mix.py", "connect", coords.HSelectByIndex(idxCntk).HRemoveAllNull()
, 0.3
, red: 0, green: 0, blue: 1);
HFile.WriteAllLines(@"C:\temp\mix.pml", new string[]
{
"load mix.pdb",
"run mix.py",
"reset",
});
}
#endregion
}
//idxBkbn = HEnum.HSequence(coords.Count).ToArray();
int[] idxFull = idxSele.HUnionWith(idxCntk).HUnionWith(idxBkbn);
Vector[] coordsFull = coords.HCopyIdx(idxFull, null);
var hessinfoFull = lGetHess(univ, coordsFull
, idxAll: idxSele
, idxBuffer: idxCntk.HRemoveAll(idxSele)
, idxCoarse: idxBkbn.HRemoveAll(idxSele).HRemoveAll(idxCntk)
, idxBackbone: idxBkbn
);
HDebug.Assert(hessinfoFull.hess.IsComputable() == false);
//{
// var modes = hessinfoFull.GetModesMassReduced(false, la);
// var modesPosZero = modes.SeparateTolerants();
// Vector bf = modesPosZero.Item1.GetBFactor().ToArray();
// Vector nma = ext as Vector;
// double corr = BFactor.Corr(bf, nma);
//}
var hessinfoSub = hessinfoFull.GetSubHessInfo(idxFull);
HDebug.Assert(hessinfoSub.hess.IsComputable() == true);
if (HDebug.IsDebuggerAttached)
{
Mode[] lmodes = hessinfoSub.GetModesMassReduced();
if (lmodes.SeparateTolerants().Item2.Length != 6)
{
HDebug.Assert(false);
//throw new Exception();
}
}
if (bVerifySteps && HDebug.IsDebuggerAttached)
{
var modes = hessinfoSub.GetModesMassReduced();
var modesPosZero = modes.SeparateTolerants();
Vector bf0 = modesPosZero.Item1.GetBFactor().ToArray();
Vector bf = new double[coords.Count]; bf.SetValue(double.NaN);
for (int i = 0; i < idxFull.Length; i++)
{
bf[idxFull[i]] = bf0[i];
}
int[] idxCax = idxCa.HRemoveAll(idxSele).HRemoveAll(idxCntk);
double corr = HBioinfo.BFactor.Corr(bf, bfactorFull, idxFull);
double corrCa = HBioinfo.BFactor.Corr(bf, bfactorFull, idxCa);
double corrCax = HBioinfo.BFactor.Corr(bf, bfactorFull, idxCax);
double corrBkbn = HBioinfo.BFactor.Corr(bf, bfactorFull, idxBkbn);
double corrSele = HBioinfo.BFactor.Corr(bf, bfactorFull, idxSele);
double corrCntk = HBioinfo.BFactor.Corr(bf, bfactorFull, idxCntk);
}
int[] idxMix;
{
Universe.Atom[] mixAtoms = hessinfoSub.atoms.HToType <object, Universe.Atom>();
Pdb.Atom[] mixPdbAtoms = mixAtoms.ListPdbAtoms();
ResInfo[] mixResinfos = mixPdbAtoms.ListResInfo(true);
int[] mixIdxCa = mixPdbAtoms.IdxByName(true, "CA");
int[] mixIdxSele = mixResinfos.HIdxEqual(ResInfo.Equals, lstResAllAtom.ToArray());
idxMix = mixIdxCa.HUnionWith(mixIdxSele).HSort();
}
HessMatrix hessMix = Hess.GetHessCoarseBlkmat(hessinfoSub.hess, idxMix, la);
if (hessMix.IsComputable() == false)
{
// hessSub (=hessinfoSub.hess) is computable, but hessMix become in-computable.
// This happens when 1. hessSub=[A,B;C,D] has more then 6 zero eigenvalues,
// 2. the D matrix become singular,
// 3. inv(D) is incomputable
// 4. "A - B inv(D) C" becomes incomputable.
errmsg = "hess(Sele,Cntk,Bkbn)->hess(Sele,Ca) becomes incomputable";
return(null);
}
MixHessInfo hessinfoMix = new MixHessInfo
{
hess = hessMix,
mass = hessinfoSub.mass.ToArray().HSelectByIndex(idxMix),
atoms = hessinfoSub.atoms.ToArray().HSelectByIndex(idxMix),
coords = hessinfoSub.coords.ToArray().HSelectByIndex(idxMix),
numZeroEigval = 6,
};
if (bGetIntmInfo)
{
hessinfoMix.intmHessinfoAllMidBkbn = hessinfoSub;
hessinfoMix.intmAtomCa = univ.atoms.ToArray().HSelectByIndex(idxCa);
hessinfoMix.intmAtomAll = univ.atoms.ToArray().HSelectByIndex(idxSele);
hessinfoMix.intmAtomMid = univ.atoms.ToArray().HSelectByIndex(idxCntk);
hessinfoMix.intmAtomBkbn = univ.atoms.ToArray().HSelectByIndex(idxBkbn);
}
if (HDebug.IsDebuggerAttached)
{
Mode[] lmodes = hessinfoMix.GetModesMassReduced();
if (lmodes.SeparateTolerants().Item2.Length != 6)
{
throw new Exception();
}
}
if (bVerifySteps && HDebug.IsDebuggerAttached)
{
var modes = hessinfoMix.GetModesMassReduced();
var modesPosZero = modes.SeparateTolerants();
Vector bf0 = modesPosZero.Item1.GetBFactor().ToArray();
Vector bf = new double[coords.Count]; bf.SetValue(double.NaN);
for (int i = 0; i < idxMix.Length; i++)
{
bf[idxFull[idxMix[i]]] = bf0[i];
}
int[] idxCax = idxCa.HRemoveAll(idxSele).HRemoveAll(idxCntk);
double corr = HBioinfo.BFactor.Corr(bf, bfactorFull, true);
double corrCa = HBioinfo.BFactor.Corr(bf, bfactorFull, idxCa);
double corrCax = HBioinfo.BFactor.Corr(bf, bfactorFull, idxCax);
double corrBkbn = HBioinfo.BFactor.Corr(bf, bfactorFull, idxBkbn);
double corrSele = HBioinfo.BFactor.Corr(bf, bfactorFull, idxSele);
double corrCntk = HBioinfo.BFactor.Corr(bf, bfactorFull, idxCntk);
}
errmsg = null;
return(hessinfoMix);
}
