public static string[] LinesFromFile(string path, bool loadLatest)
{
string loadpath = path;
if (loadLatest)
{
System.IO.FileInfo fileinfo = HFile.GetFileInfo(path);
System.IO.FileInfo[] fileinfos = fileinfo.Directory.GetFiles(fileinfo.Name + "*");
if (fileinfos.Length != 0)
{
List <string> filepaths = new List <string>();
foreach (System.IO.FileInfo lfileinfo in fileinfos)
{
filepaths.Add(lfileinfo.FullName);
}
filepaths.Sort();
loadpath = filepaths.Last();
}
}
if (HFile.Exists(loadpath) == false)
{
return(null);
}
string[] lines = HFile.ReadAllLines(loadpath);
return(lines);
}
public static Crd FromFile(string path)
{
string[] lines = HFile.ReadAllLines(path);
int? num_elems = null;
List <Atom> elems = null;
foreach (string line in lines)
{
if (line.StartsWith("*"))
{
// comment
continue;
}
// " 358272 EXT"
// " 1 1 TIP3 OH2 -79.8000000000 -20.4000000000 -4.2000000000 BWAT 1 0.0000000000"
// 01234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789
// 0 1 2 3 4 5 6 7 8 9 10 11 12 13
// " %8d %8d %-8s %-8s %18.10f %18.10f %18.10f %-8s %-8d %18.10f"
if (elems == null)
{
// " 358272 EXT"
// 012345678901234
// 0 1
string[] tokens = new string[]
{
line.Substring(0, 10),
line.Substring(10),
};
num_elems = int.Parse(tokens[0]);
HDebug.Exception(tokens[1] == " EXT");
elems = new List <Atom>(num_elems.Value);
}
else
{
elems.Add(new Atom {
line = line
});
}
}
HDebug.Assert(elems.Count == num_elems);
return(new Crd
{
atoms = elems.ToArray(),
});
}
public static 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 Eigenvec FromFile(string filepath)
{
List <List <string> > frameliness;
{
string[] lines = HFile.ReadAllLines(filepath);
frameliness = GroupByFrames(lines);
}
Eigenvec eigvec = new Eigenvec();
eigvec.frames = new List <Frame>();
foreach (List <string> framelines in frameliness)
{
Frame frame = Frame.FromLines(framelines.ToArray());
eigvec.frames.Add(frame);
}
return(eigvec);
}
public static CTesthess Testhess
(string testhesspath
, string xyzpath
, string prmpath
, string keypath //=null
, Dictionary <string, string[]> optOutSource // =null
, Func <int, int, HessMatrix> HessMatrixZeros // =null
)
{
int size;
{
size = Tinker.Xyz.FromFile(xyzpath, false).atoms.Length;
}
{
//bool ComputeAnalyticalHessianMatrix = true;
string command = "";
command += testhesspath; //command += GetProgramPath("testhess.exe");
command += " " + xyzpath;
command += " " + prmpath;
if (keypath != null)
{
command += " -k " + keypath;
}
//command += " " + (ComputeAnalyticalHessianMatrix ? "Y" : "N");
command += " > output.txt";
bool pause = false;
HProcess.StartAsBatchInConsole(null, pause, command);
//int exitcode = HProcess.StartAsBatchSilent(null, null, null, command);
}
var testhess = ReadHess(xyzpath, "output.txt", optOutSource, HessMatrixZeros);
testhess.prm = Prm.FromFile(prmpath);
if (optOutSource != null)
{
optOutSource.Add("output.txt", HFile.ReadAllLines("output.txt"));
}
return(testhess);
}
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 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
});
}
/// 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);
}
public static CTestgrad ReadGrad
(string outputpath
, Dictionary <string, string[]> optOutSource // = null
)
{
string[] lines = HFile.ReadAllLines(outputpath);
if (optOutSource != null)
{
optOutSource.Add("output.txt", lines);
}
#region output.txt
/// ######################################################################
/// ##########################################################################
/// ### ###
/// ### TINKER --- Software Tools for Molecular Design ###
/// ## ##
/// ## Version 6.2 February 2013 ##
/// ## ##
/// ## Copyright (c) Jay William Ponder 1990-2013 ##
/// ### All Rights Reserved ###
/// ### ###
/// ##########################################################################
/// ######################################################################
///
///
/// Atoms with an Unusual Number of Attached Atoms :
///
/// Type Atom Name Atom Type Expected Found
///
/// Valence 1496-NR2 69 2 3
/// Valence 2438-FE 107 6 5
///
/// Total Potential Energy : -3753.7592 Kcal/mole
///
/// Potential Energy Breakdown by Individual Components :
///
/// Energy EB EA EBA EUB EAA EOPB
/// Terms EOPD EID EIT ET EPT EBT
/// ETT EV EC ECD ED EM
/// EP ER ES ELF EG EX
///
/// 134.1618 490.7835 0.0000 27.0850 0.0000 0.0000
/// 0.0000 22.5749 0.0000 644.4690 0.0000 0.0000
/// 0.0000 -645.8696 -4426.9638 0.0000 0.0000 0.0000
/// 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
///
/// Cartesian Gradient Breakdown over Individual Atoms :
///
/// Type Atom dE/dX dE/dY dE/dZ Norm
///
/// Anlyt 1 -0.2655 -0.4022 0.3265 0.5821
/// Anlyt 2 -0.0118 0.1880 -0.2657 0.3257
/// Anlyt 3 0.1314 0.0874 -0.0147 0.1585
/// Anlyt 4 0.1543 -0.0348 -0.1401 0.2113
/// Anlyt 5 0.0216 0.4618 0.4205 0.6250
/// Anlyt 6 -0.0560 -0.0821 -0.0337 0.1050
/// ...
/// Anlyt 2510 0.2699 0.2529 0.4340 0.5703
///
/// Total Gradient Norm and RMS Gradient per Atom :
///
/// Anlyt Total Gradient Norm Value 27.5518
///
/// Anlyt RMS Gradient over All Atoms 0.5499
#endregion
double potential = double.NaN;
List <CTestgrad.Anlyt> analyts = new List <CTestgrad.Anlyt>();
CTestgrad.EnrgCmpnt enrgCmpnt = null;
for (int i = 0; i < lines.Length; i++)
{
string line = lines[i];
string[] tokens = line.Split().HRemoveAll("");
if (tokens.Length == 0)
{
continue;
}
int tmpint;
if (tokens[0] == "Anlyt" && int.TryParse(tokens[1], out tmpint))
{
CTestgrad.Anlyt analyt = new CTestgrad.Anlyt();
analyt.id = int.Parse(tokens[1]); //if(int.TryParse(tokens[1], out analyt.id) == false) continue;
analyt.fx = double.Parse(tokens[2]); //if(double.TryParse(tokens[2], out analyt.fx) == false) continue;
analyt.fy = double.Parse(tokens[3]); //if(double.TryParse(tokens[3], out analyt.fy) == false) continue;
analyt.fz = double.Parse(tokens[4]); //if(double.TryParse(tokens[4], out analyt.fz) == false) continue;
analyt.norm = double.Parse(tokens[5]); //if(double.TryParse(tokens[5], out analyt.norm) == false) continue;
analyts.Add(analyt);
continue;
}
if (tokens[0] == "Total" && tokens[1] == "Potential" && tokens[2] == "Energy")
{
double.TryParse(tokens[4], out potential);
continue;
}
if (line.Contains("Potential Energy Breakdown by Individual Components :"))
{
int ii = 1;
if (lines[i + ii].Trim().Length != 0)
{
continue;
}
ii++;
Dictionary <string, int> energy_term_sequence = new Dictionary <string, int>();
while (lines[i + ii].Trim().Length != 0)
{
string[] iitokens = lines[i + ii].Split().HRemoveAll("");
iitokens = iitokens.HRemoveAll("Energy");
iitokens = iitokens.HRemoveAll("Terms");
foreach (string iitoken in iitokens)
{
energy_term_sequence.Add(iitoken, energy_term_sequence.Count);
}
ii++;
}
if (lines[i + ii].Trim().Length != 0)
{
continue;
}
ii++;
List <double> energy_value_sequence = new List <double>();
// find location of toker break
List <int> tokenbreak = new List <int>();
{
int jj = ii;
while (lines[i + jj].Trim().Length != 0)
{
string iiline = lines[i + jj];
string[] iitokens = iiline.Split().HRemoveAll("");
foreach (string iitoken in iitokens)
{
string iitoken2 = iitoken.Substring(0, iitoken.Length - 1) + "@";
HDebug.Assert(iitoken2.Length == iitoken.Length);
HDebug.Assert(iitoken2.Last() == '@');
iiline = iiline.Replace(iitoken, iitoken2);
}
for (int idx = 0; idx < iiline.Length; idx++)
{
if (iiline[idx] == '@')
{
tokenbreak.Add(idx);
}
}
jj++;
}
tokenbreak.Add(-1);
tokenbreak = tokenbreak.HToHashSet()
.ToList()
.HSort()
.ToList()
;
}
while (lines[i + ii].Trim().Length != 0)
{
string iiline = lines[i + ii];
//string[] iitokens = iiline.Split().HRemoveAll("");
List <string> iitokens = new List <string>();
{
string iiline2 = "";
for (int jj = 0; jj < tokenbreak.Count - 1; jj++)
{
int idx0 = tokenbreak[jj] + 1;
int idx1 = tokenbreak[jj + 1];
if (idx1 >= iiline.Length)
{
break;
}
int leng = idx1 - idx0 + 1;
iitokens.Add(iiline.Substring(idx0, leng));
iiline2 += iitokens[jj];
}
HDebug.Assert(iiline == iiline2);
}
foreach (string iitoken in iitokens)
{
if (iitoken.Contains("*"))
{
/// Handle "**********"
//// Energy EB EA EBA EUB
//// Terms EAA EOPB EOPD EID
//// EIT ET EPT EBT
//// EAT ETT EV EC
//// ECD ED EM EP
//// ER ES ELF EG
//// EX
////
//// 56384.95472959 41770.94471911 0.00000000 0.00000000
//// 0.00000000 0.00000000 0.00000000 0.00000000
//// 0.00000000 0.00000000 0.00000000 0.00000000
//// 0.00000000 0.00000000 232979.82170784****************
//// 0.00000000 0.00000000 0.00000000 0.00000000
//// 0.00000000 0.00000000 0.00000000 0.00000000
//// 0.00000000
if (iitoken.StartsWith("*"))
{
HDebug.Assert(iitoken.EndsWith("*"));
energy_value_sequence.Add(double.NaN);
}
else
{
HDebug.Assert(iitoken.EndsWith("*"));
string liitoken = iitoken.Replace("*", "");
energy_value_sequence.Add(double.Parse(liitoken));
energy_value_sequence.Add(double.NaN);
}
}
else
{
energy_value_sequence.Add(double.Parse(iitoken));
}
}
ii++;
}
if (lines[i + ii].Trim().Length != 0)
{
continue;
}
ii++;
if (energy_term_sequence.Count != energy_value_sequence.Count)
{
continue;
}
#region format
///0 1 2 3 4 5 6 7 |8
///01234567890123456789012345678901234567890123456789012345678901234567890123456789|0
///
/// Potential Energy Breakdown by Individual Components :
///
/// Energy EB EA EBA EUB EAA EOPB
/// Terms EOPD EID EIT ET EPT EBT
/// ETT EV EC ECD ED EM
/// EP ER ES ELF EG EX
///
/// 134.0512 490.5575 0.0000 27.1282 0.0000 0.0000
/// 0.0000 22.6363 0.0000 775.1337 0.0000 0.0000
/// 0.0000************ -4039.6760 0.0000 0.0000 0.0000
/// 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
///
///0 1 2 3 4 5 6 7 |8
///01234567890123456789012345678901234567890123456789012345678901234567890123456789|0
///
/// Potential Energy Breakdown by Individual Components :
///
/// Energy EB EA EBA EUB
/// Terms EAA EOPB EOPD EID
/// EIT ET EPT EBT
/// ETT EV EC ECD
/// ED EM EP ER
/// ES ELF EG EX
///
/// 1827.83562614 115.54269101 0.00000000 139.97155716
/// 0.00000000 0.00000000 0.00000000 6.08959854
/// 0.00000000 176.68828153 0.00000000 0.00000000
/// 0.00000000 0.00000000 0.00000000 0.00000000
/// 0.00000000 0.00000000 0.00000000 0.00000000
/// 0.00000000 0.00000000 0.00000000 0.00000000
#endregion
CTestgrad.EnrgCmpnt ec = new CTestgrad.EnrgCmpnt();
if (energy_term_sequence.ContainsKey("EB"))
{
ec.EB = energy_value_sequence[energy_term_sequence["EB"]];
}
if (energy_term_sequence.ContainsKey("EA"))
{
ec.EA = energy_value_sequence[energy_term_sequence["EA"]];
}
if (energy_term_sequence.ContainsKey("EBA"))
{
ec.EBA = energy_value_sequence[energy_term_sequence["EBA"]];
}
if (energy_term_sequence.ContainsKey("EUB"))
{
ec.EUB = energy_value_sequence[energy_term_sequence["EUB"]];
}
if (energy_term_sequence.ContainsKey("EAA"))
{
ec.EAA = energy_value_sequence[energy_term_sequence["EAA"]];
}
if (energy_term_sequence.ContainsKey("EOPB"))
{
ec.EOPB = energy_value_sequence[energy_term_sequence["EOPB"]];
}
if (energy_term_sequence.ContainsKey("EOPD"))
{
ec.EOPD = energy_value_sequence[energy_term_sequence["EOPD"]];
}
if (energy_term_sequence.ContainsKey("EID"))
{
ec.EID = energy_value_sequence[energy_term_sequence["EID"]];
}
if (energy_term_sequence.ContainsKey("EIT"))
{
ec.EIT = energy_value_sequence[energy_term_sequence["EIT"]];
}
if (energy_term_sequence.ContainsKey("ET"))
{
ec.ET = energy_value_sequence[energy_term_sequence["ET"]];
}
if (energy_term_sequence.ContainsKey("EPT"))
{
ec.EPT = energy_value_sequence[energy_term_sequence["EPT"]];
}
if (energy_term_sequence.ContainsKey("EBT"))
{
ec.EBT = energy_value_sequence[energy_term_sequence["EBT"]];
}
if (energy_term_sequence.ContainsKey("ETT"))
{
ec.ETT = energy_value_sequence[energy_term_sequence["ETT"]];
}
if (energy_term_sequence.ContainsKey("EV"))
{
ec.EV = energy_value_sequence[energy_term_sequence["EV"]];
}
if (energy_term_sequence.ContainsKey("EC"))
{
ec.EC = energy_value_sequence[energy_term_sequence["EC"]];
}
if (energy_term_sequence.ContainsKey("ECD"))
{
ec.ECD = energy_value_sequence[energy_term_sequence["ECD"]];
}
if (energy_term_sequence.ContainsKey("ED"))
{
ec.ED = energy_value_sequence[energy_term_sequence["ED"]];
}
if (energy_term_sequence.ContainsKey("EM"))
{
ec.EM = energy_value_sequence[energy_term_sequence["EM"]];
}
if (energy_term_sequence.ContainsKey("EP"))
{
ec.EP = energy_value_sequence[energy_term_sequence["EP"]];
}
if (energy_term_sequence.ContainsKey("ER"))
{
ec.ER = energy_value_sequence[energy_term_sequence["ER"]];
}
if (energy_term_sequence.ContainsKey("ES"))
{
ec.ES = energy_value_sequence[energy_term_sequence["ES"]];
}
if (energy_term_sequence.ContainsKey("ELF"))
{
ec.ELF = energy_value_sequence[energy_term_sequence["ELF"]];
}
if (energy_term_sequence.ContainsKey("EG"))
{
ec.EG = energy_value_sequence[energy_term_sequence["EG"]];
}
if (energy_term_sequence.ContainsKey("EX"))
{
ec.EX = energy_value_sequence[energy_term_sequence["EX"]];
}
enrgCmpnt = ec;
}
}
return(new CTestgrad {
potential = potential, enrgCmpnt = enrgCmpnt, anlyts = analyts.ToArray()
});
}
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 FileGro FromFile(string filepath)
{
string[] lines = HFile.ReadAllLines(filepath);
return(FromLines(lines));
}
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 Top FromFile(string path, List <string> defines)
{
List <string> lines = new List <string>(HFile.ReadAllLines(path));
List <LineElement> elements = new List <LineElement>();
//List<Tuple<string,List<LineElement>>> elementgroup = new List<Tuple<string, List<LineElement>>>();
//Dictionary<int,Atom> atoms = new Dictionary<int, Atom>();
//List<Bond> bonds = new List<Bond>();
//List<Pair> pairs = new List<Pair>();
//List<Angle> angles = new List<Angle>();
string type = null;
while (lines.Count > 0)
//for(int i=0; i<lines.Length; i++)
{
string line = lines[0];
lines.RemoveAt(0);
//LineElement element = new LineElement(lines[i]);
string typei = LineElement.GetType(line);
if (typei != null)
{
type = typei;
//elementgroup.Add(new Tuple<string, List<LineElement>>(type, new List<LineElement>()));
continue;
}
{
line = line.Trim();
if (line.EndsWith("\\"))
{
while (lines.Count > 0)
{
line = line + "\n" + lines[0].Trim();
lines.RemoveAt(0);
if (line.EndsWith("\\") == false)
{
break;
}
}
//line = "";
//for(; i<lines.Length; i++)
//{
// string lline = lines[i].Trim();
// line = line + lline + "\n";
// if(lline.EndsWith("\\") == false)
// break;
//}
}
line = (line.IndexOf(';') == -1) ? line.Trim() : line.Substring(0, line.IndexOf(';')).Trim();
if (line.Length == 0)
{
continue;
}
if (line[0] == '*')
{
continue;
}
if (line.StartsWith("#define"))
{
string define = line.Replace("#define", "").Trim();
defines.Add(define);
continue;
}
if (line.StartsWith("#include"))
{
string includepath;
{
includepath = line.Replace("#include", "").Trim().Replace("\"", "").Trim();
if (HFile.Exists(includepath) == false)
{
includepath = @"C:\Program Files (x86)\Gromacs\share\gromacs\top\"
+ line.Replace("#include", "").Trim().Replace("\"", "").Trim();
}
if (HFile.Exists(includepath) == false)
{
includepath = HDirectory.GetParent(path).FullName + "\\" //path.Substring(0, path.LastIndexOf('/')+1)
+ line.Replace("#include", "").Trim().Replace("\"", "").Trim();
}
HDebug.Assert(HFile.Exists(includepath));
}
Top includetop = FromFile(includepath, defines);
elements.AddRange(includetop.elements);
type = null;
continue;
}
if (line.StartsWith("#ifdef"))
{
FromFile_ifdef(defines, lines, line);
continue;
}
if (line.StartsWith("#"))
{
HDebug.Assert(false);
}
if (type == "moleculetype")
{
LineElement element = new Moleculetype(line, path); elements.Add(element); continue;
}
if (type == "atoms")
{
LineElement element = new Atom(line, path); elements.Add(element); continue;
}
if (type == "bonds")
{
LineElement element = new Bond(line, path); elements.Add(element); continue;
}
if (type == "pairs")
{
LineElement element = new Pair(line, path); elements.Add(element); continue;
}
if (type == "angles")
{
LineElement element = new Angle(line, path); elements.Add(element); continue;
}
if (type == "dihedrals")
{
LineElement element = new Dihedral(line, path); elements.Add(element); continue;
}
if (type == "cmap")
{
LineElement element = new Cmap(line, path); elements.Add(element); continue;
}
if (type == "position_restraints")
{
LineElement element = new Position_restraints(line, path); elements.Add(element); continue;
}
if (type == "system")
{
LineElement element = new System(line, path); elements.Add(element); continue;
}
if (type == "molecules")
{
LineElement element = new Molecules(line, path); elements.Add(element); continue;
}
if (type == "defaults")
{
LineElement element = new Defaults(line, path); elements.Add(element); continue;
}
if (type == "atomtypes")
{
LineElement element = new Atomtypes(line, path); elements.Add(element); continue;
}
if (type == "pairtypes")
{
LineElement element = new Pairtypes(line, path); elements.Add(element); continue;
}
if (type == "bondtypes")
{
LineElement element = new Bondtypes(line, path); elements.Add(element); continue;
}
if (type == "constrainttypes")
{
LineElement element = new Constrainttypes(line, path); elements.Add(element); continue;
}
if (type == "angletypes")
{
LineElement element = new Angletypes(line, path); elements.Add(element); continue;
}
if (type == "dihedraltypes")
{
LineElement element = new Dihedraltypes(line, path); elements.Add(element); continue;
}
if (type == "implicit_genborn_params")
{
LineElement element = new Implicit_genborn_params(line, path); elements.Add(element); continue;
}
if (type == "cmaptypes")
{
LineElement element = new Cmaptypes(line, path); elements.Add(element); continue;
}
if (type == "settles")
{
LineElement element = new Settles(line, path); elements.Add(element); continue;
}
if (type == "exclusions")
{
LineElement element = new Exclusions(line, path); elements.Add(element); continue;
}
HDebug.Assert(false);
}
}
Top top = new Top();
top.elements = elements.ToArray();
return(top);
}
/// 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);
}
/// 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);
}