public static string[] LinesFromFile(string path, bool loadLatest)
{
string loadpath = path;
if (loadLatest)
{
System.IO.FileInfo fileinfo = HFile.GetFileInfo(path);
System.IO.FileInfo[] fileinfos = fileinfo.Directory.GetFiles(fileinfo.Name + "*");
if (fileinfos.Length != 0)
{
List <string> filepaths = new List <string>();
foreach (System.IO.FileInfo lfileinfo in fileinfos)
{
filepaths.Add(lfileinfo.FullName);
}
filepaths.Sort();
loadpath = filepaths.Last();
}
}
if (HFile.Exists(loadpath) == false)
{
return(null);
}
string[] lines = HFile.ReadAllLines(loadpath);
return(lines);
}
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 CTesthess ReadHess
(Xyz xyz
, string outputpath
, Dictionary <string, string[]> optOutSource // =null
, Func <int, int, HessMatrix> HessMatrixZeros // =null
)
{
int size = xyz.atoms.Length;
#region format: output.txt
/// ######################################################################
/// ##########################################################################
/// ### ###
/// ### TINKER --- Software Tools for Molecular Design ###
/// ## ##
/// ## Version 6.2 February 2013 ##
/// ## ##
/// ## Copyright (c) Jay William Ponder 1990-2013 ##
/// ### All Rights Reserved ###
/// ### ###
/// ##########################################################################
/// ######################################################################
///
///
/// Atoms with an Unusual Number of Attached Atoms :
///
/// Type Atom Name Atom Type Expected Found
///
/// Valence 1496-NR2 69 2 3
/// Valence 2438-FE 107 6 5
///
/// Diagonal Hessian Elements for Each Atom :
///
/// Atom X Y Z
///
/// 1 1445.9830 1358.3447 1484.8642
/// 2 212.9895 294.4584 604.5062
/// 3 187.1986 751.6727 125.0336
/// 4 813.4799 132.1743 151.5707
/// ...
/// 2507 178.7277 479.7434 243.4103
/// 2508 969.8813 977.2507 1845.6726
/// 2509 390.1648 232.0577 1029.6844
/// 2510 322.3674 337.8749 996.8230
///
/// Sum of Diagonal Hessian Elements : 5209042.9060
///
/// Hessian Matrix written to File : test.hes
#endregion
Tuple <int, double, double, double>[] outDiagHessElems = new Tuple <int, double, double, double> [size];
double?outSumDiagHessElem = null;
string outHessMatFile = null;
string outHessFormat = null;
{
string step = "";
foreach (string _line in HFile.ReadLines(outputpath))
{
string line = _line.Trim();
if (line.Length == 0)
{
continue;
}
if (line.Trim().StartsWith("#"))
{
continue;
}
if (line.Contains(" :"))
{
if (line.Contains("Atoms with an Unusual Number of Attached Atoms"))
{
step = ""; continue;
}
else if (line.Contains("Diagonal Hessian Elements for Each Atom"))
{
step = "hess diagonal"; continue;
}
else if (line.Contains("Sum of Diagonal Hessian Elements"))
{
step = "sum hess diagonal";
}
else if (line.Contains("Hessian Matrix written to File"))
{
step = "full hess file";
}
else if (line.Contains("Hessian Sparse Matrix written to File"))
{
step = "sparse hess file";
}
else if (line.Contains("Select Smaller Size for Sparse Hessian Matrix"))
{
continue;
}
else
{
HDebug.Assert(false);
continue;
}
}
switch (step)
{
case "":
continue;
case "hess diagonal":
{
string[] tokens = line.Split().HRemoveAll("");
if (tokens[0] == "Atom")
{
continue;
}
int Atom = int.Parse(tokens[0]); // ; if( int.TryParse(tokens[0], out Atom) == false) continue;
double X = double.Parse(tokens[1]); // ; if(double.TryParse(tokens[1], out X) == false) continue;
double Y = double.Parse(tokens[2]); // ; if(double.TryParse(tokens[2], out Y) == false) continue;
double Z = double.Parse(tokens[3]); // ; if(double.TryParse(tokens[3], out Z) == false) continue;
HDebug.Assert(outDiagHessElems[Atom - 1] == null);
outDiagHessElems[Atom - 1] = new Tuple <int, double, double, double>(Atom, X, Y, Z);
}
continue;
case "sum hess diagonal":
{
string[] tokens = line.Split().HRemoveAll("");
double sum = double.Parse(tokens.Last()); // if(double.TryParse(tokens.Last(), out sum) == false) continue;
outSumDiagHessElem = sum;
}
step = "";
continue;
case "full hess file": outHessFormat = "full matrix"; goto case "hess file";
case "sparse hess file": outHessFormat = "sparse matrix"; goto case "hess file";
case "hess file":
{
string[] tokens = line.Split().HRemoveAll("");
string outputpath_dir = HFile.GetFileInfo(outputpath).Directory.FullName;
outHessMatFile = outputpath_dir + "\\" + tokens.Last();
}
step = "";
continue;
default:
HDebug.Assert(false);
step = "";
continue;
}
}
}
#region Format: test.hes
/// Diagonal Hessian Elements (3 per Atom)
///
/// 1445.9830 1358.3447 1484.8642 212.9895 294.4584 604.5062
/// 187.1986 751.6727 125.0336 813.4799 132.1743 151.5707
/// 1167.7472 1188.3459 1162.5475 268.8291 498.0188 143.2438
/// ...
/// Off-diagonal Hessian Elements for Atom 1 X
/// 23.0878 14.6380 -214.0545 96.9308 -186.7740 -205.1460
/// -208.7035 -28.9630 -788.9124 39.6748 126.4491 -190.5074
/// ...
/// Off-diagonal Hessian Elements for Atom 1 Y
/// -64.1616 97.2697 -292.3813 264.1922 -184.4701 -728.8687
/// -109.9103 15.4168 -152.5717 -11.7733 18.8369 -188.4875
/// ...
/// Off-diagonal Hessian Elements for Atom 1 Z
/// -155.9409 219.8782 -610.0622 -10.0041 -62.8209 -156.1112
/// 77.0829 -14.2127 -166.0525 53.1834 -97.4207 -347.9315
/// ...
/// Off-diagonal Hessian Elements for Atom 2 X
/// -106.5166 185.8395 19.7546 -10.0094 25.8072 -8.1335
/// 35.8501 -64.8320 3.8761 -13.8893 9.4266 0.1312
/// ...
///
/// ...
///
/// Off-diagonal Hessian Elements for Atom 2508 X
/// 488.4590 -69.2721 -338.4824 -155.1656 253.3732 -297.4214
/// -164.8301 -191.3769
/// Off-diagonal Hessian Elements for Atom 2508 Y
/// 74.0161 -149.1060 -273.4863 176.4975 -170.6527 -341.1639
/// -263.6141
/// Off-diagonal Hessian Elements for Atom 2508 Z
/// 304.9942 223.7496 -851.3028 -242.9481 -310.7953 -821.2532
/// Off-diagonal Hessian Elements for Atom 2509 X
/// 198.4498 -331.6530 78.8172 17.3909 -30.0512
/// Off-diagonal Hessian Elements for Atom 2509 Y
/// -227.5916 25.7235 74.5131 -53.2690
/// Off-diagonal Hessian Elements for Atom 2509 Z
/// 46.7873 20.7615 -168.0704
/// Off-diagonal Hessian Elements for Atom 2510 X
/// 252.6853 247.2963
/// Off-diagonal Hessian Elements for Atom 2510 Y
/// 343.6797
#endregion
HessMatrix hess;
{
if (HessMatrixZeros != null)
{
hess = HessMatrixZeros(size * 3, size * 3);
}
else
{
switch (outHessFormat)
{
case "full matrix": hess = HessMatrixDense.ZerosDense(size * 3, size * 3); break;
case "sparse matrix": hess = HessMatrixSparse.ZerosSparse(size * 3, size * 3); break;
default: hess = null; break;
}
}
//HDebug.SetEpsilon(hess);
string step = "";
int diagidx = -1;
int offidx1 = -1;
int offidx2 = -1;
/// string[] lines = HFile.ReadAllLines(outHessMatFile);
/// GC.WaitForFullGCComplete();
/// object[] tokenss = new object[lines.Length];
///
/// Parallel.For(0, lines.Length, delegate(int i)
/// //for(int i=0; i<lines.Length; i++)
/// {
/// string line = lines[i];
/// string[] stokens = line.Trim().Split().RemoveAll("");
/// if(stokens.Length != 0)
/// {
/// double[] dtokens = new double[stokens.Length];
/// for(int j=0; j<stokens.Length; j++)
/// if(double.TryParse(stokens[j], out dtokens[j]) == false)
/// {
/// tokenss[i] = stokens;
/// goto endfor;
/// }
/// tokenss[i] = dtokens;
/// }
/// endfor: ;
/// });
/// System.IO.StreamReader matreader = HFile.OpenText(outHessMatFile);
/// while(matreader.EndOfStream == false)
/// for(int i=0; i<lines.Length; i++)
/// foreach(string line in lines)
foreach (string line in HFile.HEnumAllLines(outHessMatFile))
{
/// string line = lines[i];
/// string line = matreader.ReadLine();
string[] tokens = line.Trim().Split().HRemoveAll("");
if (tokens.Length == 0)
{
continue;
}
/// if(tokenss[i] == null)
/// continue;
/// string[] stokens = (tokenss[i] as string[]);
if (tokens[0] == "Diagonal" && tokens[1] == "Hessian" && tokens[2] == "Elements")
{
step = "Diagonal"; diagidx = 0; continue;
}
if (tokens[0] == "Off-diagonal" && tokens[1] == "Hessian" && tokens[2] == "Elements")
{
step = "Off-diagonal"; offidx1++; offidx2 = offidx1 + 1; continue;
}
if (tokens[0] == "Off-diagonal" && tokens[1] == "sparse" && tokens[2] == "Hessian" &&
tokens[3] == "Indexes/Elements" && tokens[4] == "for" && tokens[5] == "Atom")
{
step = "Off-diagonal sparse";
offidx1 = (int.Parse(tokens[6]) - 1) * 3;
switch (tokens[7])
{
case "X": break;
case "Y": offidx1 += 1; break;
case "Z": offidx1 += 2; break;
default: throw new HException();
}
continue;
}
/// double[] dtokens = (tokenss[i] as double[]);
/// tokens = new string[20];
/// for(int i=0; i*12<line.Length; i++)
/// tokens[i] = line.Substring(i*12, 12).Trim();
/// tokens = tokens.HRemoveAll("").ToArray();
/// tokens = tokens.HRemoveAll(null).ToArray();
switch (step)
{
case "Diagonal":
{
/// foreach(double val in dtokens)
foreach (string token in tokens)
{
HDebug.Assert(token.Last() != ' ');
double val = double.Parse(token);
HDebug.Assert(hess[diagidx, diagidx] == 0);
hess[diagidx, diagidx] = val;
diagidx++;
}
}
continue;
case "Off-diagonal":
{
/// foreach(double val in dtokens)
foreach (string token in tokens)
{
HDebug.Assert(token.Last() != ' ');
//double val = double.Parse(token);
double val;
bool succ = double.TryParse(token, out val);
if (succ == false)
{
HDebug.Assert(false);
goto case "exception 0";
}
if (size < 3000)
{
HDebug.Assert(hess[offidx1, offidx2] == 0);
HDebug.Assert(hess[offidx2, offidx1] == 0);
}
if (val != 0)
{
hess[offidx1, offidx2] = val;
hess[offidx2, offidx1] = val;
}
offidx2++;
}
}
continue;
case "Off-diagonal sparse":
{
HDebug.Assert(tokens.Length % 2 == 0);
for (int i = 0; i < tokens.Length; i += 2)
{
HDebug.Assert(tokens[i].Last() != ' ');
HDebug.Assert(tokens[i + 1].Last() != ' ');
//double val = double.Parse(token);
double val;
bool succ = true;
succ &= int.TryParse(tokens[i], out offidx2); offidx2--;
succ &= double.TryParse(tokens[i + 1], out val);
if (succ == false)
{
HDebug.Assert(false);
goto case "exception 0";
}
if (size < 3000)
{
HDebug.Assert(hess[offidx1, offidx2] == 0);
HDebug.Assert(hess[offidx2, offidx1] == 0);
}
if (val != 0)
{
hess[offidx1, offidx2] = val;
hess[offidx2, offidx1] = val;
}
}
}
continue;
default:
HDebug.Assert(false);
goto case "exception 1";
case "exception 0":
throw new HException("incomplete hessian file (0)");
case "exception 1":
throw new HException("incomplete hessian file (1)");
}
throw new HException("incomplete hessian file (2)");
}
/// matreader.Close();
if (HDebug.IsDebuggerAttached && size < 3000)
{
//for(int c=0; c<size*3; c++)
// for(int r=0; r<size*3; r++)
// if(hess[c, r] == double.Epsilon)
// throw new Exception("incomplete hessian file (3)");
//
//for(int c=0; c<size*3; c++)
//{
// double sum = 0;
// double max = double.NegativeInfinity;
// for(int r=0; r<size*3; r++)
// {
// max = Math.Max(max, hess[c, r]);
// sum += hess[c, r];
// HDebug.Assert(hess[c, r] != double.Epsilon);
// }
// HDebug.Assert(Math.Abs(sum) < max/1000);
// HDebug.AssertTolerance(0.1, sum);
//}
Hess.CheckHessDiag(hess, 0.1, null);
for (int i = 0; i < size; i++)
{
HDebug.Assert(outDiagHessElems[i].Item1 == i + 1);
HDebug.AssertTolerance(0.000001, outDiagHessElems[i].Item2 - hess[i * 3 + 0, i * 3 + 0]);
HDebug.AssertTolerance(0.000001, outDiagHessElems[i].Item3 - hess[i * 3 + 1, i * 3 + 1]);
HDebug.AssertTolerance(0.000001, outDiagHessElems[i].Item4 - hess[i * 3 + 2, i * 3 + 2]);
}
}
}
if (optOutSource != null)
{
optOutSource.Add("test.hes", HFile.HEnumAllLines(outHessMatFile).ToArray());
}
return(new CTesthess
{
hess = hess,
xyz = xyz,
});
}
public static void SavePse(string psepath
, bool cartoon
, bool line
, string pngpath // null if not save png
, params string[] pdbpaths)
{
string currpath = HEnvironment.CurrentDirectory;
HEnvironment.CurrentDirectory = HFile.GetFileInfo(psepath).Directory.FullName;
{
Random rand = new Random();
string psename = HFile.GetFileInfo(psepath).Name;
int count = pdbpaths.Length;
string[] pdblnames = new string[count];
string[] pdblpaths = new string[count];
for (int i = 0; i < count; i++)
{
var info = HFile.GetFileInfo(pdbpaths[i]);
pdblnames[i] = info.Name.Replace(".pdb", "").Replace(".PDB", "");
pdblpaths[i] = psepath + info.Name + rand.NextInt(99999).ToString(".rnd00000") + ".pdb";
HFile.Copy(pdbpaths[i], pdblpaths[i]);
}
string pmlpath = psepath + rand.NextInt(99999).ToString(".rnd00000") + ".pml";
List <string> pmltext = new List <string>();
for (int i = 0; i < count; i++)
{
pmltext.Add("load $$path$$, $$name$$;".Replace("$$path$$", pdblpaths[i]).Replace("$$name$$", pdblnames[i]));
}
if (cartoon)
{
pmltext.Add("show cartoon;");
}
else
{
pmltext.Add("hide cartoon");
}
if (line)
{
pmltext.Add("show lines;");
}
else
{
pmltext.Add("hide lines");
}
pmltext.Add("reset;");
pmltext.Add("save $$psepath$$;".Replace("$$psepath$$", psepath));
if (pngpath != null)
{
pmltext.Add("png $$pngpath$$;".Replace("$$pngpath$$", pngpath));
}
pmltext.Add("quit;");
HFile.WriteAllLines(pmlpath, pmltext);
System.Diagnostics.Process pymol;
pymol = System.Diagnostics.Process.Start(@"C:\Program Files (x86)\PyMOL\PyMOL\PymolWin.exe", pmlpath);
pymol.WaitForExit();
for (int i = 0; i < count; i++)
{
HFile.Delete(pdblpaths[i]);
}
HFile.Delete(pmlpath);
}
HEnvironment.CurrentDirectory = currpath;
}