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 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 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 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 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 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 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);
}
