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 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 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 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 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 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 void ToFile(string filepath
, List <Atom> atoms
, List <Vector>[] coordss
, List <double>[] bfactorss
)
{
List <string> lines = new List <string>();
int size = atoms.Count;
for (int iensemble = 0; iensemble < coordss.Length; iensemble++)
{
List <Vector> coords = coordss[iensemble];
List <double> bfactors = bfactorss[iensemble];
HDebug.Assert(size == coords.Count);
//lines.Add("MODEL 1 ");
lines.Add(Pdb.Model.FromModelSerial(iensemble + 1).line);
for (int i = 0; i < size; i++)
{
Atom atom = atoms[i];
{
if (coordss != null)
{
double x = coords[i][0];
double y = coords[i][1];
double z = coords[i][2];
atom = Atom.FromString(atom.GetUpdatedLine(x, y, z));
}
if (bfactors != null)
{
atom = Atom.FromString(atom.GetUpdatedLineTempFactor(bfactors[i]));
}
lines.Add(atom.line);
}
}
lines.Add(Pdb.Endmdl.From().line);
//lines.Add("ENDMDL ");
}
HFile.WriteAllLines(filepath, lines);
}
public static void ElementsToFile(string path, bool saveAsNext, IList <Element> elements)
{
string writepath = path;
if (saveAsNext)
{
int idx = 2;
while (HFile.Exists(writepath))
{
writepath = string.Format("{0}_{1}", path, idx);
idx++;
}
}
List <string> lines = new List <string>();
foreach (Element element in elements)
{
lines.Add(element.line);
}
HFile.WriteAllLines(writepath, lines);
}
public static ONewton Newton(string tinkerpath
, Tinker.Xyz xyz
, Tinker.Xyz.Atom.Format xyz_atoms_format
, Tinker.Prm prm
, string tempbase
, string copytemp // = null
, string param
//, string precondition // = "A" // Precondition via Auto/None/Diag/Block/SSOR/ICCG [A] : A
//, double gradCriterion // = 0.01 // Enter RMS Gradient per Atom Criterion [0.01] : 0.001
, IList <Tinker.Xyz.Atom> atomsToFix // = null
, bool pause // = false
, params string[] keys
)
{
if (HDebug.IsDebuggerAttached && atomsToFix != null)
{
Dictionary <int, Tinker.Xyz.Atom> xyzatoms = xyz.atoms.ToIdDictionary();
foreach (var atom in atomsToFix)
{
HDebug.Assert(object.ReferenceEquals(atom, xyzatoms[atom.Id]));
}
}
Tinker.Xyz minxyz;
string[] minlog;
using (var temp = new HTempDirectory(tempbase, copytemp))
{
temp.EnterTemp();
if (tinkerpath == null)
{
string resbase = "HTLib2.Bioinfo.HTLib2.Bioinfo.External.Tinker.Resources.tinker_6_2_06.";
HResource.CopyResourceTo <Tinker>(resbase + "newton.exe", "newton.exe");
tinkerpath = "newton.exe";
}
xyz.ToFile("prot.xyz", false);
prm.ToFile("prot.prm");
List <string> keylines = new List <string>(keys);
if (atomsToFix != null)
{
foreach (var atom in atomsToFix)
{
Vector coord = atom.Coord;
double force_constant = 10000; // force constant in kcal/Å2 for the harmonic restraint potential
string keyline = string.Format("RESTRAIN-POSITION {0} {1} {2} {3} {4}", atom.Id, coord[0], coord[1], coord[2], force_constant);
keylines.Add(keyline);
}
}
HFile.WriteAllLines("prot.key", keylines);
// Precondition via Auto/None/Diag/Block/SSOR/ICCG [A] : A
// Enter RMS Gradient per Atom Criterion [0.01] : 0.001
//bool pause = false;
string command = tinkerpath;
command += string.Format(" prot.xyz prot.prm");
command += string.Format(" -k prot.key");
command += string.Format(" {0}", param);
HProcess.StartAsBatchInConsole("newton.bat", pause
, "time /t >> prot.log"
, command //+" >> prot.log"
, "time /t >> prot.log"
);
HDebug.Assert(HFile.Exists("prot.xyz_2"));
HDebug.Assert(HFile.Exists("prot.xyz_3") == false);
minxyz = Tinker.Xyz.FromFile("prot.xyz_2", false, xyz_atoms_format);
minlog = HFile.ReadAllLines("prot.log");
temp.QuitTemp();
}
return(new ONewton
{
minxyz = minxyz,
minlog = minlog
});
}
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,
});
}
/// https://www.charmmtutorial.org/index.php/Full_example
public static string[] Hessian
(IEnumerable <string> toplines
, IEnumerable <string> parlines
, IEnumerable <string> psflines
, IEnumerable <string> crdlines
)
{
string tempbase = @"C:\temp\";
string[] mincrdlines;
using (var temp = new HTempDirectory(tempbase, null))
{
temp.EnterTemp();
string topname = "top.rtf"; HFile.WriteAllLines(topname, toplines);
string parname = "par.prm"; HFile.WriteAllLines(parname, parlines);
string psfname = "target.psf"; HFile.WriteAllLines(psfname, psflines);
string crdname = "target.crd"; HFile.WriteAllLines(crdname, crdlines);
string mincrdname = "target-minimized.crd";
string conf_inp = @"* Minimize PDB
* Minimize PDB
*
! read topology and parameter file
read rtf card name top.rtf
read param card name par.prm
! read the psf and coordinate file
read psf card name target.psf
read coor card name target.crd
! set up shake
shake bonh param sele all end
! set up electrostatics, since we're not using PME, set up switching
! electrostatics
nbond inbfrq -1 elec fswitch vdw vswitch cutnb 16. ctofnb 12. ctonnb 10.
energy
coor copy comp
! mini sd nstep 100
! mini abnr nstep 1000 nprint 10000 tolg 0.0000
! ! mini abnr nstep 1000 nprint 100 tolg 0.01
! ! mini abnr nstep 10000000 nprint 100 tolg 0.00
! ! mini abnr nstep 1000000 nprint 100 tolg 10.00 ! target-min-step1-tolg-10_00.crd
! ! mini abnr nstep 1000000 nprint 100 tolg 1.00 ! target-min-step2-tolg-1_00.crd
! ! mini abnr nstep 1000000 nprint 100 tolg 0.10
! ! mini sd nstep 10000 ! target-min-step3-sd10000.crd
! ! mini abnr nstep 1000000 nprint 100 tolg 0.01 ! target-min-step4-tolg-0_01.crd
! ! mini abnr nstep 10000 nprint 100 tolg 0.0001 ! target-min-step5-tolg-0_0001.crd
! ! mini abnr nstep 10000 nprint 100 tolg 0.000001 ! target-min-step6-tolg-0_000001.crd
! ! mini abnr nstep 10000 nprint 100 tolg 0.000000 ! target-min-step7-tolg-0_000000.crd
!
!
! coor rms
!
! ioform extended
!
! write coor card name target-minimized.crd
! * Initial minimization, no PME.
! *
! VIBRAN NMOD 20 ATOM FSWITCH rdie eps 4.0 VDW VSHIFT cutnb 13.0 ctofnb 12.0 CTONNB 8.0
!
! DIMB ITERations 500 TOLErance 0.04 PARDim 200 IUNMode 21 DWIN
!
! WRITe SECOnd-derivatives card
! BOMLEV -2
! VIBRAN
! DIAG ENTRopy
! VIBRan NMODes 500
! DIAG
! print norm vector dipole
!mini abnr nstep 100 nprint 100 tolg 0.000000 ! target-min-step7-tolg-0_000000.crd
BOMLEV -2
open unit 1 write form name " + " \"second.dat\" " + @"
REDUce CMPAct
vibran
!diag
write second card unit 1
close unit 1
!calc natom3 ?NATOM *3
!vibran nmode @natom3
!diag
!print norm
!bomlev - 2
!VIBRan NMOD 300
!DIAGonalize
!https://www.charmm.org/charmm/documentation/by-version/c42b1/params/doc/vibran/
stop
";
conf_inp = conf_inp.Replace("$$topname$$", topname)
.Replace("$$parname$$", parname)
.Replace("$$psfname$$", psfname)
.Replace("$$crdname$$", crdname)
.Replace("$$mincrdname$$", mincrdname)
;
HFile.WriteAllText("conf.inp", conf_inp);
System.Console.WriteLine("Run the following command at " + temp + " :");
System.Console.WriteLine(" $ charmm < conf.inp");
System.Console.WriteLine(" or $ mpd&");
System.Console.WriteLine(" $ mpirun -n 38 charmm_M < conf.inp");
System.Console.WriteLine("Then, copy second.dat to " + temp);
while (true)
{
bool next = HConsole.ReadValue <bool>("Ready for next? ", false, null, false, true);
if (next)
{
if (HFile.ExistsAll(mincrdname))
{
mincrdlines = HFile.ReadAllLines(mincrdname);
/// second.dat has the following format
///
/// num-atoms
/// pot-energy
/// atom1-xforce atom1-yforce atom1-zforce
/// atom2-xforce atom2-yforce atom2-zforce
/// ...
/// atomn-xforce atomn-yforce atomn-zforce
/// upper- or lower-diag elem 1
/// upper- or lower-diag elem 2
/// ....
/// upper- or lower-diag elem 3n*3n/2
/// atom1-xcoord atom1-ycoord atom1-zcoord
/// atom2-xcoord atom2-ycoord atom2-zcoord
/// ...
/// atomn-xcoord atomn-ycoord atomn-zcoord
///
break;
}
System.Console.WriteLine("DO, copy target.psf and target.crd to " + temp);
}
}
temp.QuitTemp();
}
return(mincrdlines);
}
/// https://www.charmmtutorial.org/index.php/Full_example
public static string[] MinimizeCrd
(IEnumerable <string> toplines
, IEnumerable <string> parlines
, IEnumerable <string> psflines
, IEnumerable <string> crdlines
, string conf_inp_mini
)
{
string tempbase = @"C:\temp\";
if (conf_inp_mini == null)
{
conf_inp_mini = @"
mini sd nstep 100
mini abnr nstep 1000 nprint 10000 tolg 0.0001
! mini abnr nstep 1000 nprint 100 tolg 0.01
! mini abnr nstep 10000000 nprint 100 tolg 0.00
! mini abnr nstep 1000000 nprint 100 tolg 10.00 ! target-min-step1-tolg-10_00.crd
! mini abnr nstep 1000000 nprint 100 tolg 1.00 ! target-min-step2-tolg-1_00.crd
! mini abnr nstep 1000000 nprint 100 tolg 0.10
! mini sd nstep 10000 ! target-min-step3-sd10000.crd
! mini abnr nstep 1000000 nprint 100 tolg 0.01 ! target-min-step4-tolg-0_01.crd
! mini abnr nstep 10000 nprint 100 tolg 0.0001 ! target-min-step5-tolg-0_0001.crd
! mini abnr nstep 10000 nprint 100 tolg 0.000001 ! target-min-step6-tolg-0_000001.crd
! mini abnr nstep 10000 nprint 100 tolg 0.000000 ! target-min-step7-tolg-0_000000.crd
";
}
string[] mincrdlines;
using (var temp = new HTempDirectory(tempbase, null))
{
temp.EnterTemp();
string topname = "top.rtf"; HFile.WriteAllLines(topname, toplines);
string parname = "par.prm"; HFile.WriteAllLines(parname, parlines);
string psfname = "target.psf"; HFile.WriteAllLines(psfname, psflines);
string crdname = "target.crd"; HFile.WriteAllLines(crdname, crdlines);
string mincrdname = "target-minimized.crd";
string conf_inp = @"* Minimize PDB
*
! read topology and parameter file
read rtf card name $$topname$$
read param card name $$parname$$
! read the psf and coordinate file
read psf card name $$psfname$$
read coor card name $$crdname$$
! set up shake
shake bonh param sele all end
! set up electrostatics, since we're not using PME, set up switching
! electrostatics
nbond inbfrq -1 elec fswitch vdw vswitch cutnb 16. ctofnb 12. ctonnb 10.
energy
coor copy comp
" + conf_inp_mini + @"
coor rms
ioform extended
write coor card name $$mincrdname$$
* Initial minimization, no PME.
*
stop
";
conf_inp = conf_inp.Replace("$$topname$$", topname)
.Replace("$$parname$$", parname)
.Replace("$$psfname$$", psfname)
.Replace("$$crdname$$", crdname)
.Replace("$$mincrdname$$", mincrdname)
;
HFile.WriteAllText("conf.inp", conf_inp);
System.Console.WriteLine("Run the following command at " + temp + " :");
System.Console.WriteLine(" $ charmm < conf.inp");
System.Console.WriteLine(" or $ mpd&");
System.Console.WriteLine(" $ mpirun -n 38 charmm_M < conf.inp");
System.Console.WriteLine("Then, copy target-minimized.crd to " + temp);
while (true)
{
bool next = HConsole.ReadValue <bool>("Ready for next? ", false, null, false, true);
if (next)
{
if (HFile.ExistsAll(mincrdname))
{
mincrdlines = HFile.ReadAllLines(mincrdname);
break;
}
System.Console.WriteLine("DO, copy target.psf and target.crd to " + temp);
}
}
temp.QuitTemp();
}
return(mincrdlines);
}
public static SPsfCrd BuildPsfCrd
(IEnumerable <string> toplines
, IEnumerable <string> parlines
, IEnumerable <string> pdblines
)
{
string tempbase = @"C:\temp\";
SPsfCrd psfcrd;
using (var temp = new HTempDirectory(tempbase, null))
{
temp.EnterTemp();
string topname = "top.rtf"; HFile.WriteAllLines(topname, toplines);
string parname = "par.prm"; HFile.WriteAllLines(parname, parlines);
string tgtname = "target"; HFile.WriteAllLines(tgtname + ".pdb", pdblines);
string Setup_inp = @"* Run Segment Through CHARMM
*
! read topology and parameter files
read rtf card name $$topname$$
read para card name $$parname$$
! Read sequence from the PDB coordinate file
open unit 1 card read name $$tgtname$$.pdb
read sequ pdb unit 1
! now generate the PSF and also the IC table (SETU keyword)
generate setu a-pro first NTER last CTER
rewind unit 1
! set bomlev to -1 to avois sying on lack of hydrogen coordinates
bomlev -1
read coor pdb unit 1
! them put bomlev back up to 0
bomlev 0
close unit 1
! prints out number of atoms that still have undefined coordinates.
define test select segid a-pro .and. ( .not. hydrogen ) .and. ( .not. init ) show end
ic para
ic fill preserve
ic build
hbuild sele all end
! write out the protein structure file (psf) and
! the coordinate file in pdb and crd format.
write psf card name $$tgtname$$.psf
* PSF
*
write coor card name $$tgtname$$.crd
* Coords
*
stop
"
.Replace("$$topname$$", topname)
.Replace("$$parname$$", parname)
.Replace("$$tgtname$$", tgtname);
HFile.WriteAllText("Setup.inp", Setup_inp);
System.Console.WriteLine("Run the following command at " + temp + " :");
System.Console.WriteLine(" $ charmm < Setup.inp");
System.Console.WriteLine(" or $ mpd&");
System.Console.WriteLine(" $ mpirun -n 38 charmm_M < Setup.inp");
System.Console.WriteLine("Then, copy target.psf and target.crd to " + temp);
while (true)
{
bool next = HConsole.ReadValue <bool>("Ready for next? ", false, null, false, true);
if (next)
{
if (HFile.ExistsAll("target.crd", "target.psf"))
{
string[] crdlines = HFile.ReadAllLines("target.crd");
string[] psflines = HFile.ReadAllLines("target.psf");
psfcrd = new SPsfCrd
{
crdlines = crdlines,
psflines = psflines,
};
break;
}
System.Console.WriteLine("DO, copy target.psf and target.crd to " + temp);
}
}
temp.QuitTemp();
}
return(psfcrd);
}
public static void ToFile(string filepath
, IList <Atom> atoms
, IList <Vector> coords = null
, IList <MatrixByArr> anisous = null
, double?anisouScale = null
, IList <double> bfactors = null
, bool append = false
, IList <string> headers = null
, int?modelidx = null
)
{
List <string> lines = new List <string>();
int size = atoms.Count;
if (coords != null)
{
HDebug.Assert(size == coords.Count);
}
if (anisous != null)
{
HDebug.Assert(size == anisous.Count);
}
//if(anisouScale != null) Debug.Assert(size == anisouScale.Count);
if (headers != null)
{
lines.AddRange(headers);
}
{
// 1 2 3 4 5 6 7 8
// 12345678901234567890123456789012345678901234567890123456789012345678901234567890
// "MODEL 1 "
string line = "MODEL 1 ";
if (modelidx != null)
{
line.Replace("1", modelidx.Value.ToString());
}
line = line.Substring(0, 80);
lines.Add(line);
}
for (int i = 0; i < size; i++)
{
Atom atom = atoms[i];
if (atom == null)
{
continue;
}
{
if (coords != null)
{
double x = coords[i][0];
double y = coords[i][1];
double z = coords[i][2];
atom = Atom.FromString(atom.GetUpdatedLine(x, y, z));
}
if (bfactors != null)
{
atom = Atom.FromString(atom.GetUpdatedLineTempFactor(bfactors[i]));
}
lines.Add(atom.line);
}
{
if (anisous != null)
{
MatrixByArr U = anisous[i];
if (anisouScale != null)
{
U = U * anisouScale.Value;
}
Anisou anisou = Anisou.FromAtom(atom, U.ToArray().HToInt());
string line = anisou.line; //anisou.GetUpdatedU(anisous[i])
lines.Add(line);
}
}
}
lines.Add("ENDMDL ");
//int idx = 0;
//foreach(Element element in elements)
//{
// string line = element.line;
// if(typeof(Atom).IsInstanceOfType(element))
// {
// double x = coords[idx][0];
// double y = coords[idx][1];
// double z = coords[idx][2];
// Atom atom = (Atom)element;
// line = atom.GetUpdatedLine(x, y, z);
// idx++;
// }
// lines.Add(line);
//}
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 void ToFile(string filepath, IList <Vector> coords = null, IList <double> bfactors = null, IList <MatrixByArr> anisous = null, double anisous_scale = 1, bool append = false)
{
List <string> lines = new List <string>();
if (coords == null)
{
coords = this.atoms.ListCoord();
}
//Debug.Assert(atoms.Length == coords.Count);
int idx = 0;
foreach (Element element in elements)
{
//string line = element.line;
if (typeof(Atom).IsInstanceOfType(element))
{
double x = coords[idx][0];
double y = coords[idx][1];
double z = coords[idx][2];
Atom atom = (Atom)element;
atom = Atom.FromString(atom.GetUpdatedLine(x, y, z));
if (bfactors != null)
{
atom = Atom.FromString(atom.GetUpdatedLineTempFactor(bfactors[idx]));
}
lines.Add(atom.line);
if (anisous != null)
{
MatrixByArr anisoui = anisous[idx] * anisous_scale;
int[,] U = new int[3, 3] {
{ (int)anisoui[0, 0], (int)anisoui[0, 1], (int)anisoui[0, 2], },
{ (int)anisoui[1, 0], (int)anisoui[1, 1], (int)anisoui[1, 2], },
{ (int)anisoui[2, 0], (int)anisoui[2, 1], (int)anisoui[2, 2], },
};
Anisou anisou = Anisou.FromAtom(atom, U);
lines.Add(anisou.line);
}
idx++;
}
else if (typeof(Anisou).IsInstanceOfType(element) && anisous != null)
{
// skip because it is handled in the "Atom" part
}
else
{
lines.Add(element.line);
}
}
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 void ToFile(string filepath)
{
string[] lines = ToLines();
HFile.WriteAllLines(filepath, 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 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 OMinimize Minimize(string minimizepath
, Tinker.Xyz xyz
, Tinker.Xyz.Atom.Format xyz_atoms_format
, Tinker.Prm prm
, string tempbase
, string copytemp // = null
, string param
, IList <Tinker.Xyz.Atom> atomsToFix // = null
, bool pause // = false
, params string[] keys
)
{
if (HDebug.IsDebuggerAttached && atomsToFix != null)
{
Dictionary <int, Tinker.Xyz.Atom> xyzatoms = xyz.atoms.ToIdDictionary();
foreach (var atom in atomsToFix)
{
HDebug.Assert(object.ReferenceEquals(atom, xyzatoms[atom.Id]));
}
}
Tinker.Xyz minxyz;
string[] minlog;
using (var temp = new HTempDirectory(tempbase, copytemp))
{
temp.EnterTemp();
xyz.ToFile("prot.xyz", false);
prm.ToFile("prot.prm");
List <string> keylines = new List <string>();
//if(grdmin != null)
//{
// string keyline = string.Format("GRDMIN {0}", grdmin.Value);
// keylines.Add(keyline);
//}
if (atomsToFix != null)
{
foreach (var atom in atomsToFix)
{
Vector coord = atom.Coord;
double force_constant = 10000; // force constant in kcal/Å2 for the harmonic restraint potential
string keyline = string.Format("RESTRAIN-POSITION {0} {1} {2} {3} {4}", atom.Id, coord[0], coord[1], coord[2], force_constant);
keylines.Add(keyline);
}
}
if (keys != null)
{
keylines.AddRange(keys);
}
HFile.WriteAllLines("prot.key", keylines);
// Enter RMS Gradient per Atom Criterion [0.01] :
string command = minimizepath;
command += " prot.xyz prot.prm";
command += " -k prot.key < param.txt";
HFile.WriteAllLines("param.txt", param.HSplit());
//command += string.Format(" >> prot.log");
HProcess.StartAsBatchInConsole("minimize.bat", pause
, "time /t >> prot.log"
, command
, "time /t >> prot.log"
);
HDebug.Assert(HFile.Exists("prot.xyz_2"));
HDebug.Assert(HFile.Exists("prot.xyz_3") == false);
minxyz = Tinker.Xyz.FromFile("prot.xyz_2", false, xyz.atoms_format);
minlog = HFile.ReadAllLines("prot.log");
temp.QuitTemp();
}
return(new OMinimize
{
minxyz = minxyz,
minlog = minlog
});
}
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;
}
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 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);
}
/// https://www.charmmtutorial.org/index.php/Full_example
public static SPsfCrd Solvate
(IEnumerable <string> toplines
, IEnumerable <string> parlines
, IEnumerable <string> psflines_prot
, IEnumerable <string> crdlines_prot
, IEnumerable <string> crdlines_water
)
{
string tempbase = @"C:\temp\";
SPsfCrd psfcrd;
using (var temp = new HTempDirectory(tempbase, null))
{
temp.EnterTemp();
string topname = "top.rtf"; HFile.WriteAllLines(topname, toplines);
string parname = "par.prm"; HFile.WriteAllLines(parname, parlines);
string psfname_prot = "prot.psf"; HFile.WriteAllLines(psfname_prot, psflines_prot);
string crdname_prot = "prot.crd"; HFile.WriteAllLines(crdname_prot, crdlines_prot);
string crdname_water = "water.crd"; HFile.WriteAllLines(crdname_water, crdlines_water);
string psfname_protwater = "protwater.psf";
string crdname_protwater = "protwater.crd";
string conf_inp = @"* Run Segment Through CHARMM
*
! read topology and parameter files
read rtf card name $$topname$$
read para card name $$parname$$
! read the psf and coordinate file
read psf card name $$psfname_prot$$
read coor card name $$crdname_prot$$
! Read in water sequence
read sequence tip3 46656
! Generate new segment for the water
generate bwat noangle nodihedral
! Read the water PDB coordinates and append them to the protein
read coor card append name $$crdname_water$$
! Delete waters which overlap with protein
delete atom sort -
select .byres. (segid bwat .AND. type oh2 .and. -
((.not. (segid bwat .OR. hydrogen)) .around. 2.5)) end
! set headstr = rhdo with a crystal dimension of @greatervalue
set headstr = test xxx
! we want to do a quick-and-dirty minimization to remove bad contacts. Therefore, we should
! set up shake and the non-bond parameters again.
shake bonh param sele all end
nbond inbfrq -1 elec fswitch vdw vswitch cutnb 16. ctofnb 12. ctonnb 10.
mini sd nstep 100 nprint 1 tolgrd 100.0
! use Expanded I/O format
ioform extended
! since we've changed the structure by adding waters, we need to write out a new PSF
write psf card name $$psfname_protwater$$
* new_1cbn-18126-1-solv.psf
* solvation: @headstr
*
write coor card name $$crdname_protwater$$
* new_1cbn-18126-1-solv.crd
* solvation: @headstr
*
stop
".Replace("$$topname$$", topname)
.Replace("$$parname$$", parname)
.Replace("$$psfname_prot$$", psfname_prot)
.Replace("$$crdname_prot$$", crdname_prot)
.Replace("$$crdname_water$$", crdname_water)
.Replace("$$psfname_protwater$$", psfname_protwater)
.Replace("$$crdname_protwater$$", crdname_protwater)
;
HFile.WriteAllText("conf.inp", conf_inp);
System.Console.WriteLine("Run the following command at " + temp + " :");
System.Console.WriteLine(" $ charmm < conf.inp");
System.Console.WriteLine(" or $ mpd&");
System.Console.WriteLine(" $ mpirun -n 38 charmm_M < conf.inp");
System.Console.WriteLine("Then, copy " + psfname_protwater + " and " + crdname_protwater + " to " + temp);
while (true)
{
bool next = HConsole.ReadValue <bool>("Ready for next? ", false, null, false, true);
if (next)
{
if (HFile.ExistsAll(psfname_protwater, crdname_protwater))
{
string[] psflines_protwater = HFile.ReadAllLines(psfname_protwater);
string[] crdlines_protwater = HFile.ReadAllLines(crdname_protwater);
psfcrd = new SPsfCrd
{
psflines = psflines_protwater,
crdlines = crdlines_protwater,
};
break;
}
System.Console.WriteLine("DO, copy " + psfname_protwater + " and " + crdname_protwater + " to " + temp);
}
}
temp.QuitTemp();
}
return(psfcrd);
}
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);
}
