public static Mode[] GetModes(MatrixByArr hess, string cachepath = null)
{
Vector[] eigvec;
double[] eigval;
if (cachepath != null && HFile.Exists(cachepath))
{
HSerialize.Deserialize(cachepath, null, out eigval, out eigvec);
}
else
{
HDebug.Verify(NumericSolver.Eig(hess, out eigvec, out eigval));
HSerialize.SerializeDepreciated(cachepath, null, eigval, eigvec);
}
List <Mode> modes;
{ // sort by eigenvalues
int[] idx = eigval.HAbs().HIdxSorted();
modes = new List <Mode>(idx.Length);
for (int i = 0; i < eigval.Length; i++)
{
Mode mode = new Mode {
eigval = eigval[idx[i]],
eigvec = eigvec[idx[i]]
};
modes.Add(mode);
}
}
return(modes.ToArray());
}
public static CTestgrad Testgrad(string testgradpath
, Tinker.Xyz xyz
, Tinker.Prm prm
, string tempbase //=null
, string[] keys
, Dictionary <string, string[]> optOutSource // = null
)
{
var tmpdir = HDirectory.CreateTempDirectory(tempbase);
string currpath = HEnvironment.CurrentDirectory;
CTestgrad testgrad;
{
HEnvironment.CurrentDirectory = tmpdir.FullName;
if (testgradpath == null)
{
string resbase = "HTLib2.Bioinfo.HTLib2.Bioinfo.External.Tinker.Resources.tinker_6_2_06.";
HResource.CopyResourceTo <Tinker>(resbase + "testgrad.exe", "testgrad.exe");
testgradpath = "testgrad.exe";
}
xyz.ToFile("test.xyz", false);
prm.ToFile("test.prm");
string keypath = null;
if (keys != null && keys.Length > 0)
{
keypath = "test.key";
HFile.WriteAllLines(keypath, keys);
}
testgrad = TestgradImpl(testgradpath, "test.xyz", "test.prm", keypath, optOutSource);
}
HEnvironment.CurrentDirectory = currpath;
try{ tmpdir.Delete(true); } catch {}
return(testgrad);
}
public static void ToFile(string filepath
, Element[] elements
, bool append //= false
, IList <string> additionalHeaders = null
)
{
List <string> lines = new List <string>();
if (additionalHeaders != null)
{
lines.AddRange(additionalHeaders);
}
lines.Add("MODEL 1 ");
lines.AddRange(elements.ToLines());
lines.Add("ENDMDL ");
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 override bool Read()
{
if (HFile == null)
{
return(false);
}
try {
if (Buffer == null)
{
Buffer = (char[])System.Array.CreateInstance(typeof(System.Char), RecordSize);
}
if (Buffer.Length < RecordSize)
{
Buffer = (char[])System.Array.CreateInstance(typeof(System.Char), RecordSize);
}
if (HFile.ReadBlock(Buffer, 0, RecordSize) != RecordSize)
{
return(false);
}
StrBuilder.Length = 0;
StrBuilder.Append(Buffer);
Record = StrBuilder.ToString();
} catch (System.Exception Excpt) {
Err.Add(Excpt);
return(false);
}
return(true);
}
private void SetTemplates()
{
_ordIssueFuture = Template.TwOrdIssueFuture;
if (_configObj.Market.Contains("TWSE"))
{
_ordIdn = TemplateIdn.TwOrdIdnTwse;
_ordNda = Template.TwOrdAddTwse;
_ordQuoteFuture = Template.TwOrdQuoteFutureTwse;
_ordFm = TemplateFm.TwOrdTwse;
}
else if (_configObj.Market.Contains("GTSM"))
{
_ordIdn = TemplateIdn.TwOrdIdnGtsm;
_ordNda = Template.TwOrdAddGtsm;
_ordQuoteFuture = Template.TwOrdQuoteFutureGtsm;
_ordFm = TemplateFm.TwOrdGtsm;
}
else if (_configObj.Market.Contains("EMG"))
{
_ordIdn = TemplateIdn.TwOrdIdnEmg;
_ordNda = Template.TwOrdAddEmg;
_ordQuoteFuture = Template.TwOrdQuoteFutureEmg;
_ordFm = TemplateFm.TwOrdEmg;
}
else
{
throw new Exception("The Market you choose does not exist, please change the configuration and choose an existing one.");
}
}
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 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 void WriteFile(HFile file)
{
WriteEndDirectoriesArray();
WriteStartFilesArray();
JsonFileWriter jsonFileWriter = new JsonFileWriter(Writer);
jsonFileWriter.Write(file);
}
public void ToFile(string filepath)
{
string[] lines = new string[elements.Length];
for (int i = 0; i < elements.Length; i++)
{
lines[i] = elements[i].line;
}
HFile.WriteAllLines(filepath, lines);
}
public JsonFile(HFile file)
{
if (file == null)
{
throw new ArgumentNullException(nameof(file));
}
Name = file.Name;
Hash = file.Hash;
}
public static CTesthess Testhess
(string testhesspath
, Tinker.Xyz xyz
, Tinker.Prm prm
, string tempbase //=null
, string[] keys
, Dictionary <string, string[]> optOutSource // =null
, Func <int, int, HessMatrix> HessMatrixZeros // =null
)
{
var tmpdir = HDirectory.CreateTempDirectory(tempbase);
string currpath = HEnvironment.CurrentDirectory;
CTesthess testhess;
{
HEnvironment.CurrentDirectory = tmpdir.FullName;
if (testhesspath == null)
{
string resbase = "HTLib2.Bioinfo.HTLib2.Bioinfo.External.Tinker.Resources.tinker_6_2_01.";
HResource.CopyResourceTo <Tinker>(resbase + "testhess.exe", "testhess.exe");
testhesspath = "testhess.exe";
}
xyz.ToFile("test.xyz", false);
prm.ToFile("test.prm");
string keypath = null;
if ((keys != null) && (keys.Length > 0))
{
keypath = "test.key";
HFile.WriteAllLines(keypath, keys);
}
testhess = Testhess(testhesspath, "test.xyz", "test.prm", keypath, optOutSource, HessMatrixZeros);
testhess.xyz = xyz;
testhess.prm = prm;
}
HEnvironment.CurrentDirectory = currpath;
try{ tmpdir.Delete(true); } catch {}
string test_eig = "true";
if (test_eig == "false")
{
Vector D;
using (new Matlab.NamedLock(""))
{
Matlab.PutSparseMatrix("testeig.H", testhess.hess.GetMatrixSparse(), 3, 3);
Matlab.Execute("testeig.H = (testeig.H + testeig.H')/2;");
Matlab.Execute("[testeig.V, testeig.D] = eig(full(testeig.H));");
Matlab.Execute("testeig.D = diag(testeig.D);");
D = Matlab.GetVector("testeig.D");
Matlab.Execute("clear testeig;");
}
}
return(testhess);
}
public void Add(HFile file)
{
if (directoryStack.Count == 0)
{
throw new Exception("There is no directory added.");
}
HDirectory topDirectory = directoryStack.Peek();
topDirectory.Files.Add(file);
}
public void Add(HFile file)
{
if (directoryStack.Count == 0)
{
throw new Exception("There is no directory added that can be used as parent for this file.");
}
HDirectory topDirectory = directoryStack.Peek();
topDirectory.Files.Add(file);
}
//public Mode[] ToModesUnnormalized_wrong(double[] masses)
//{
// Mode[] modes = ToModes_wrong();
// Mode[] unmodes = modes.ToModesUnnormalized(masses);
// return unmodes;
//}
public static Vibrate FromFile(string filepath)
{
Vibrate vib;
{
List <string> lines = HFile.ReadLines(filepath).ToList();
vib = FromLines(lines);
}
System.GC.Collect();
return(vib);
}
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);
}
public static Pdb FromPdbidCache(string pdbid, string cachepath)
{
Pdb pdb;
if (HFile.Exists(cachepath))
{
pdb = FromPdbid(pdbid);
pdb.ToFile(cachepath);
}
pdb = FromFile(cachepath);
return(pdb);
}
public void Write(HFile file)
{
Writer.WriteStartObject();
Writer.WritePropertyName("n");
Writer.WriteValue(file.Name);
Writer.WritePropertyName("h");
Writer.WriteValue(file.Hash);
Writer.WriteEndObject();
}
private IEnumerable <FilePair> GeneratePairs(IReadOnlyList <HFile> filesLeft, IReadOnlyList <HFile> filesRight)
{
for (int i = 0; i < filesLeft.Count; i++)
{
HFile fileLeft = filesLeft[i];
for (int j = 0; j < filesRight.Count; j++)
{
HFile fileRight = filesRight[j];
yield return(new FilePair(fileLeft, fileRight, CheckFilesExistence));
}
}
}
public static void CopyPdb(string pathbase, params string[] pdbids)
{
if (pathbase.EndsWith("\\") == false)
{
pathbase += "\\";
}
foreach (string pdbid in pdbids)
{
string pdbpath = pathbase + pdbid.ToUpper() + ".pdb";
List <string> pdblines = GetPdbLines(pdbid);
HFile.WriteAllLines(pdbpath, pdblines);
}
}
public static void WriteMdp(string mdppath
, string integrator // = "steep"
, double emtol // = 5 // Stop minimization when the maximum force < 1.0 kJ/mol/nm
, double emstep = 0.01 // Energy step size
, long nsteps = 500000 // Maximum number of (minimization) steps to perform
// Parameters describing how to find the neighbors of each atom and how to calculate the interactions
, int nstlist = 1 // Frequency to update the neighbor list and long range forces
, string ns_type = "grid" // Method to determine neighbor list (simple, grid)
, double rlist = 1.0 // Cut-off for making neighbor list (short range forces) ; htna 1.0-1.2
, string coulombtype = "Shift"
, double rcoulomb = 1.0
, double rcoulomb_switch = 0.0
, string vdwtype = "Shift"
, double rvdw = 1.0
, double rvdw_switch = 0.0
)
{
string[] lines = new string[]
{
"; Parameters describing what to do, when to stop and what to save ",
"integrator = $$integrator$$ ",
"emtol = $$emtol$$ ; Stop minimization when the maximum force < 1.0 kJ/mol/nm ",
"emstep = $$emstep$$ ; Energy step size ",
"nsteps = $$nsteps$$ ; Maximum number of (minimization) steps to perform ",
" ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions",
"nstlist = $$nstlist$$ ; Frequency to update the neighbor list and long range forces ",
"ns_type = $$ns_type$$ ; Method to determine neighbor list (simple, grid) ",
"rlist = $$rlist$$ ; Cut-off for making neighbor list (short range forces) ; htna 1.0-1.2 ",
"coulombtype = $$coulombtype$$ ",
"rcoulomb = $$rcoulomb$$ ",
"rcoulomb_switch = $$rcoulomb_switch$$ ",
"vdwtype = $$vdwtype$$ ",
"rvdw = $$rvdw$$ ",
"rvdw_switch = $$rvdw_switch$$ ",
}
.HReplace("$$integrator$$ ", integrator)
.HReplace("$$emtol$$ ", emtol)
.HReplace("$$emstep$$ ", emstep)
.HReplace("$$nsteps$$ ", nsteps)
.HReplace("$$nstlist$$ ", nstlist)
.HReplace("$$ns_type$$ ", ns_type)
.HReplace("$$rlist$$ ", rlist)
.HReplace("$$coulombtype$$ ", coulombtype)
.HReplace("$$rcoulomb$$ ", rcoulomb)
.HReplace("$$rcoulomb_switch$$", rcoulomb_switch)
.HReplace("$$vdwtype$$ ", vdwtype)
.HReplace("$$rvdw$$ ", rvdw)
.HReplace("$$rvdw_switch$$ ", rvdw_switch)
;
HFile.WriteAllLines(mdppath, lines);
}
public static string[] ReadAllLines(params string[] filepaths)
{
List <string> lines = new List <string>();
foreach (string path in filepaths)
{
foreach (string line in HFile.HEnumAllLines(path))
{
lines.Add(line);
}
}
return(lines.ToArray());
}
public void HavingFileWithMatchingName_WhenChecked_ThenMatches()
{
// pattern: file-or-dir-1
// path: /file-or-dir-1 (file)
HFile hFile = new HFile
{
Name = "file-or-dir-1"
};
bool actual = blackPath.Matches(hFile);
Assert.That(actual, Is.True);
}
public void HavingFileWithMatchingName_WhenChecked_ThenDoesNotMatch()
{
// pattern: item-1/
// path: /item-1 (file)
HFile hFile = new HFile
{
Name = "item-1"
};
bool actual = blackPath.Matches(hFile);
Assert.That(actual, Is.False);
}
public static JFile ToJFile(this HFile file)
{
if (file == null)
{
throw new ArgumentNullException(nameof(file));
}
return(new JFile
{
Name = file.Name,
Size = file.Size,
Hash = file.Hash,
LastModifiedTime = file.LastModifiedTime
});
}
public static Crd FromFile(string path)
{
string[] lines = HFile.ReadAllLines(path);
int? num_elems = null;
List <Atom> elems = null;
foreach (string line in lines)
{
if (line.StartsWith("*"))
{
// comment
continue;
}
// " 358272 EXT"
// " 1 1 TIP3 OH2 -79.8000000000 -20.4000000000 -4.2000000000 BWAT 1 0.0000000000"
// 01234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789
// 0 1 2 3 4 5 6 7 8 9 10 11 12 13
// " %8d %8d %-8s %-8s %18.10f %18.10f %18.10f %-8s %-8d %18.10f"
if (elems == null)
{
// " 358272 EXT"
// 012345678901234
// 0 1
string[] tokens = new string[]
{
line.Substring(0, 10),
line.Substring(10),
};
num_elems = int.Parse(tokens[0]);
HDebug.Exception(tokens[1] == " EXT");
elems = new List <Atom>(num_elems.Value);
}
else
{
elems.Add(new Atom {
line = line
});
}
}
HDebug.Assert(elems.Count == num_elems);
return(new Crd
{
atoms = elems.ToArray(),
});
}
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 WriteImport(string pypath, bool append = false)
{
StreamWriter file;
if (append)
{
file = HFile.AppendText(pypath);
}
else
{
file = HFile.CreateText(pypath);
}
file.WriteLine("from pymol.cgo import *");
file.WriteLine("from pymol import cmd");
file.Close();
}
private void SetTemplates()
{
_ordIdn = TemplateIdn.TwOrdDrop;
if (_configObj.Market.ToLower().Contains("twse"))
{
_ordNda = Template.TwOrdDropTwse;
}
else if (_configObj.Market.ToLower().Contains("gtsm"))
{
_ordNda = Template.TwOrdDropGtsm;
}
else
{
_ordNda = Template.TwOrdDropEmg;
}
}
public static void WriteBlank(string pmlpath
, bool append
)
{
StreamWriter file;
if (append)
{
file = HFile.AppendText(pmlpath);
}
else
{
file = HFile.CreateText(pmlpath);
}
file.Close();
}
public static Xyz Intxyz(string intpath, string tempbase = null)
{
string[] intlines = HFile.ReadAllLines(intpath);
Xyz xyz;
var tmpdir = HDirectory.CreateTempDirectory(tempbase);
string currpath = HEnvironment.CurrentDirectory;
{
HEnvironment.CurrentDirectory = tmpdir.FullName;
HFile.WriteAllLines("test.int", intlines);
Intxyz("test.int");
xyz = Xyz.FromFile("test.xyz", true);
}
HEnvironment.CurrentDirectory = currpath;
try{ tmpdir.Delete(true); } catch {}
return(xyz);
}
