public static Top FromPdb(string pdbpath
, string ff = "charmm27"
, string water = "none"
, HPack <Pdb> optout_confout = null
)
{
Top top;
FileInfo pdbinfo = new FileInfo(pdbpath);
string currdir = HEnvironment.CurrentDirectory;
DirectoryInfo temproot = HDirectory.CreateTempDirectory();
HEnvironment.CurrentDirectory = temproot.FullName;
{
HFile.Copy(pdbinfo.FullName, "protein.pdb");
RunPdb2gmx(f: "protein.pdb"
, o: "confout.pdb"
, p: "topol.top"
, q: "clean.pdb"
, ff: ff
, water: water
, merge: "all"
, lineStderr: null
, lineStdout: null
);
top = Top.FromFile("topol.top");
if (optout_confout != null)
{
optout_confout.value = Pdb.FromFile("confout.pdb");
}
}
HEnvironment.CurrentDirectory = currdir;
Thread.Sleep(100);
try{ temproot.Delete(true); } catch (Exception) {}
return(top);
}
public static 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;
}
