public void OnlyInSnapshot1_is_empty_if_both_snapshotss_contain_one_identical_file_in_same_dir()
{
Snapshot snapshot1 = new Snapshot();
HDirectory hDirectory1 = new HDirectory("Dir1");
hDirectory1.Files.AddRange(new[]
{
new HFile {
Name = "File1", Hash = new byte[] { 0x01, 0x02, 0x03 }
}
});
snapshot1.Directories.AddRange(new[] { hDirectory1 });
Snapshot snapshot2 = new Snapshot();
HDirectory hDirectory2 = new HDirectory("Dir1");
hDirectory2.Files.AddRange(new[]
{
new HFile {
Name = "File1", Hash = new byte[] { 0x01, 0x02, 0x03 }
}
});
snapshot2.Directories.AddRange(new[] { hDirectory2 });
SnapshotComparer comparer = new SnapshotComparer(snapshot1, snapshot2);
comparer.Compare();
Assert.That(comparer.OnlyInSnapshot1, Is.EqualTo(new string[0]));
}
private void CompareChildDirectories(HDirectory directory1, HDirectory directory2, string rootPath)
{
List <HDirectory> subDirectories1 = directory1.Directories.ToList();
List <HDirectory> subDirectories2 = directory2.Directories.ToList();
foreach (HDirectory subDirectory1 in subDirectories1)
{
HDirectory subDirectory2 = subDirectories2.FirstOrDefault(x => x.Name == subDirectory1.Name);
if (subDirectory2 == null)
{
onlyInSnapshot1.Add(rootPath + subDirectory1.Name + "/");
}
else
{
subDirectories2.Remove(subDirectory2);
string rootPath1 = rootPath + subDirectory1.Name + "/";
CompareChildFiles(subDirectory1, subDirectory2, rootPath1);
CompareChildDirectories(subDirectory1, subDirectory2, rootPath1);
}
}
foreach (HDirectory subDirectory2 in subDirectories2)
{
onlyInSnapshot2.Add(rootPath + subDirectory2.Name + "/");
}
}
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 void Add(HDirectory directory)
{
JsonDirectoryWriter topDirectoryWriter = directoryStack.Peek();
JsonDirectoryWriter newDirectoryWriter = topDirectoryWriter.WriteStartDirectory(directory.Name);
newDirectoryWriter.WriteEnd();
}
public JsonDirectory(HDirectory xDirectory)
{
if (xDirectory == null)
{
throw new ArgumentNullException(nameof(xDirectory));
}
Name = xDirectory.Name;
if (xDirectory.Directories == null)
{
Directories = null;
}
else
{
Directories = xDirectory.Directories
.Select(x => new JsonDirectory(x))
.ToList();
}
if (xDirectory.Files == null)
{
Files = null;
}
else
{
Files = xDirectory.Files
.Select(x => new JsonFile(x))
.ToList();
}
}
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 static HItem PlaceInto(this HItem hItem, string parentName)
{
HDirectory parentDirectory = new HDirectory
{
Name = parentName
};
hItem.Parent = parentDirectory;
return(parentDirectory);
}
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 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 AddAndOpen(HDirectory directory)
{
if (directoryStack.Count == 0)
{
directoryStack.Push(jsonSnapshotWriter);
}
else
{
JsonDirectoryWriter topDirectoryWriter = directoryStack.Peek();
JsonDirectoryWriter newDirectoryWriter = topDirectoryWriter.WriteStartDirectory(directory.Name);
directoryStack.Push(newDirectoryWriter);
}
}
public void HavingDirectoryWithMatchingName_WhenChecked_ThenMatches()
{
// pattern: file-or-dir-1
// path: /file-or-dir-1 (dir)
HDirectory hDirectory = new HDirectory
{
Name = "file-or-dir-1"
};
bool actual = blackPath.Matches(hDirectory);
Assert.That(actual, Is.True);
}
private void CompareChildFiles(HDirectory directory1, HDirectory directory2, string rootPath)
{
HItemCollection <HFile> files1 = directory1.Files;
HItemCollection <HFile> files2 = directory2.Files;
List <HFile> onlyInDirectory2 = files2.ToList();
foreach (HFile file1 in files1)
{
List <HFile> file2Matches = files2
.Where(x => x.Name == file1.Name || ByteArrayCompare.AreEqual(x.Hash, file1.Hash))
.ToList();
if (file2Matches.Count == 0)
{
onlyInSnapshot1.Add(rootPath + file1.Name);
}
else
{
foreach (HFile file2 in file2Matches)
{
ItemComparison itemComparison = new ItemComparison
{
RootPath = rootPath,
Item1 = file1,
Item2 = file2
};
bool sameName = file1.Name == file2.Name;
bool sameContent = ByteArrayCompare.AreEqual(file1.Hash, file2.Hash);
if (!sameName && sameContent)
{
differentNames.Add(itemComparison);
}
if (sameName && !sameContent)
{
differentContent.Add(itemComparison);
}
onlyInDirectory2.Remove(file2);
}
}
}
foreach (HFile file2 in onlyInDirectory2)
{
onlyInSnapshot2.Add(rootPath + file2.Name);
}
}
public void Add(HDirectory directory)
{
if (directoryStack.Count == 0)
{
Snapshot.Name = directory.Name;
Snapshot.Files.AddRange(directory.Files);
Snapshot.Directories.AddRange(directory.Directories);
Snapshot.Error = directory.Error;
}
else
{
HDirectory topDirectory = directoryStack.Peek();
topDirectory.Directories.Add(directory);
}
}
private static void DisplayDirectory(HDirectory hDirectory, int index)
{
string indent = new string(' ', index);
foreach (HDirectory subdirectory in hDirectory.Directories)
{
Console.WriteLine(indent + subdirectory.Name);
DisplayDirectory(subdirectory, index + 1);
}
foreach (HFile xFile in hDirectory.Files)
{
Console.WriteLine(indent + xFile.Name);
}
}
private static void DisplayDirectory(HDirectory hDirectory, int index)
{
string indent = new(' ', index * 2);
foreach (HDirectory xSubdirectory in hDirectory.Directories)
{
Console.WriteLine(indent + xSubdirectory.Name);
DisplayDirectory(xSubdirectory, index + 1);
}
foreach (HFile xFile in hDirectory.Files)
{
Console.Write(indent + xFile.Name);
CustomConsole.WriteLine(ConsoleColor.DarkGray, " [" + xFile.Hash + "]");
}
}
private void SaveDirectory(JsonAnalysisExport jsonAnalysisExport, HDirectory directory)
{
jsonAnalysisExport.AddAndOpen(directory);
foreach (HDirectory subDirectory in directory.Directories)
{
SaveDirectory(jsonAnalysisExport, subDirectory);
}
foreach (HFile file in directory.Files)
{
jsonAnalysisExport.Add(file);
}
jsonAnalysisExport.CloseDirectory();
}
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);
}
public void HavingDirectoryWithMatchingNamePlacedInPath_WhenChecked_ThenMatches()
{
// pattern: item-1/
// path: /dir-2/item-1 (dir)
HDirectory hDirectory = new HDirectory
{
Name = "item-1",
Parent = new HDirectory
{
Name = "dir-2"
}
};
bool actual = blackPath.Matches(hDirectory);
Assert.That(actual, Is.True);
}
public static JDirectory ToJDirectory(this HDirectory directory)
{
if (directory == null)
{
throw new ArgumentNullException(nameof(directory));
}
return(new JDirectory
{
Name = directory.Name,
Directories = directory.Directories?
.Select(x => x.ToJDirectory())
.ToList(),
Files = directory.Files?
.Select(x => x.ToJFile())
.ToList()
});
}
public void HavingDirectoryWithMatchingNamePlacedInPath_WhenChecked_ThenDoesNotMatch()
{
// pattern: /file-or-dir-1
// path: /dir-2/file-or-dir-1 (dir)
HDirectory hDirectory = new HDirectory
{
Name = "file-or-dir-1",
Parent = new HDirectory
{
Name = "dir-2"
}
};
bool actual = blackPath.Matches(hDirectory);
Assert.That(actual, Is.False);
}
private static void Read(ICollection <Tuple <string, HFile> > files, HDirectory hDirectory, string parentPath)
{
if (hDirectory.Files != null)
{
foreach (HFile xFile in hDirectory.Files)
{
string filePath = Path.Combine(parentPath, xFile.Name);
files.Add(new Tuple <string, HFile>(filePath, xFile));
}
}
if (hDirectory.Directories != null)
{
foreach (HDirectory xSubDirectory in hDirectory.Directories)
{
string subdirectoryPath = Path.Combine(parentPath, xSubDirectory.Name);
Read(files, xSubDirectory, subdirectoryPath);
}
}
}
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);
}
public static HDirectory ToHDirectory(this JDirectory jDirectory)
{
HDirectory directory = new HDirectory
{
Name = jDirectory.Name
};
List <HDirectory> directories = jDirectory.GetHDirectories();
if (directories != null)
{
directory.Directories.AddRange(directories);
}
List <HFile> files = jDirectory.GetHFiles();
if (files != null)
{
directory.Files.AddRange(files);
}
return(directory);
}
public HDirectory ToHDirectory()
{
HDirectory directory = new HDirectory
{
Name = Name
};
List <HDirectory> directories = GetHDirectories();
if (directories != null)
{
directory.Directories.AddRange(directories);
}
List <HFile> files = GetHFiles();
if (files != null)
{
directory.Files.AddRange(files);
}
return(directory);
}
public void OnlyInSnapshot1_contains_the_name_of_the_file_if_only_snapshot1_has_one_file_in_dir()
{
Snapshot snapshot1 = new Snapshot();
HDirectory hDirectory1 = new HDirectory("Dir1");
hDirectory1.Files.AddRange(new[]
{
new HFile {
Name = "File1", Hash = new byte[] { 0x01, 0x02, 0x03 }
}
});
snapshot1.Directories.AddRange(new[] { hDirectory1 });
Snapshot snapshot2 = new Snapshot();
HDirectory hDirectory2 = new HDirectory("Dir1");
snapshot2.Directories.AddRange(new[] { hDirectory2 });
SnapshotComparer comparer = new SnapshotComparer(snapshot1, snapshot2);
comparer.Compare();
Assert.That(comparer.OnlyInSnapshot1, Is.EqualTo(new[] { "/Dir1/File1" }));
}
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 CNamd2 Namd2
(IList <string> pdb_lines
, IList <string> psf_lines
, IList <string> prm_lines
, string tempbase // = null
, string namd2version // = "2.8"
, string option // = "+p3"
, IList <string> infiles = null
, IList <string> outfiles = null
, IList <string> conf_lines = null
)
{
string[] lines = null;
if ((conf_lines != null) && (conf_lines.Count > 0))
{
lines = conf_lines.ToArray();
}
else
{
// http://www.msg.ucsf.edu/local/programs/Vega/pages/tu_namdmin.htm
lines = new string[]
{ "numsteps 10000 " // minimization steps
//{ "numsteps 1000 " // minimization steps
, "minimization on "
, "dielectric 1.0 "
, "coordinates prot.pdb " // coordinate file
, "outputname output " // output file: prot.coor
, "outputEnergies 1000 "
, "binaryoutput no "
, "DCDFreq 1000 "
, "restartFreq 1000 "
, "structure prot.psf " // psf file
, "paraTypeCharmm on "
, "parameters prot.prm " // parameter file
//, "parameters par_all22_vega.inp "
, "exclude scaled1-4 "
, "1-4scaling 1.0 "
, "switching on "
, "switchdist 8.0 "
, "cutoff 22.0 " //, "cutoff 12.0 "
, "pairlistdist 23.5 " //, "pairlistdist 13.5 "
, "margin 0.0 "
, "stepspercycle 20 "
, "fixedAtoms on " // fix atoms
, "fixedAtomsCol O " // select fixing atoms from O
};
}
var tmpdir = HDirectory.CreateTempDirectory(tempbase);
string currpath = HEnvironment.CurrentDirectory;
HEnvironment.CurrentDirectory = tmpdir.FullName;
string[] coor_lines = null;
double coor_rmsd = double.NaN;
{
{
//foreach(var respath_filename in GetResourcePaths("2.8", "psfgen"))
foreach (var respath_filename in GetResourcePaths(namd2version, "namd2"))
{
string respath = respath_filename.Item1;
string filename = respath_filename.Item2;
HResource.CopyResourceTo <Tinker>(respath, filename);
}
}
Vector[] coords0 = Pdb.FromLines(pdb_lines).atoms.ListCoord().ToArray();
System.IO.File.WriteAllLines("prot.pdb", pdb_lines);
System.IO.File.WriteAllLines("prot.psf", psf_lines);
System.IO.File.WriteAllLines("prot.prm", prm_lines);
System.IO.File.WriteAllLines("prot.conf", lines);
if (option == null)
{
option = "";
}
string command = string.Format("namd2 {0} prot.conf", option);
HProcess.StartAsBatchInConsole(null, false, command);
if (HFile.Exists("output.coor"))
{
coor_lines = HFile.ReadAllLines("output.coor");
Vector[] coords1 = Pdb.FromLines(coor_lines).atoms.ListCoord().ToArray();
Vector[] coords1x = Align.MinRMSD.Align(coords0, coords1);
coor_rmsd = Align.MinRMSD.GetRMSD(coords0, coords1x);
}
}
HEnvironment.CurrentDirectory = currpath;
try{ tmpdir.Delete(true); } catch {}
if (coor_lines == null)
{
return(null);
}
return(new CNamd2
{
coor_lines = coor_lines,
coor_rmsd = coor_rmsd,
});
}
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 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 void AddAndOpen(HDirectory directory)
{
Add(directory);
directoryStack.Push(directory);
}
