public static void Intxyz(string intpath)
{
string command = "";
command += GetProgramPath("intxyz.exe");
command += " " + intpath;
int exitcode = HProcess.StartAsBatchSilent(null, null, null, command);
}
public static int Run(string command
, string[] commandsNext = null
, List <string> lineStderr = null
, List <string> lineStdout = null
, bool silent_run = true
, bool?pause = null
//, string batPathToCopy = null
)
{
List <string> lines = new List <string>();
{
lines.Add(@"set GMXLIB=C:\Program Files (x86)\Gromacs\share\gromacs\top");
lines.Add(@"set GMXBIN=C:\Program Files (x86)\Gromacs\bin");
lines.Add(@"set GMXDATA=C:\Program Files (x86)\Gromacs\share");
lines.Add(@"set GMXLDLIB=C:\Program Files (x86)\Gromacs\lib");
lines.Add(@"set GMXMAN=C:\Program Files (x86)\Gromacs\share\man");
lines.Add(command);
if (commandsNext != null)
{
lines.AddRange(commandsNext);
}
}
int exitcode;
//bool silent_run = true;
if (silent_run)
{
// int StartAsBatchSilent(string batpath, List<string> lineStdout, List<string> lineStderr, params string[] commands)
//exitcode = HProcess.StartAsBatchSilent(batPathToCopy, lineStdout, lineStderr, lines.ToArray());
exitcode = HProcess.StartAsBatchSilent(null, lineStdout, lineStderr, lines.ToArray());
}
else
{
// int StartAsBatchInConsole(string batpath, bool pause=false, params string[] commands)
//exitcode = HProcess.StartAsBatchInConsole(batPathToCopy, (pause == null || pause == true), lines.ToArray());
exitcode = HProcess.StartAsBatchInConsole(null, (pause == null || pause == true), lines.ToArray());
}
return(exitcode);
}
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,
});
}