private DistanceMeasure CreateMeasureForDCD(DCDFile dcd, DistanceMeasures measure, PDB.PDBMODE atoms, bool jury1d, string alignFileName,
string profileName = null, string refJuryProfile = null)
{
DistanceMeasure dist=null;
switch (measure)
{
case DistanceMeasures.HAMMING:
if (refJuryProfile == null || !jury1d)
throw new Exception("Sorry but for jury measure you have to define 1djury profile to find reference structure");
else
dist = new JuryDistance(dcd, alignFileName, true, profileName, refJuryProfile);
break;
case DistanceMeasures.RMSD:
dist = new Rmsd(dcd, alignFileName, jury1d, atoms, refJuryProfile);
break;
case DistanceMeasures.MAXSUB:
dist = new MaxSub(dcd, alignFileName, jury1d, refJuryProfile);
break;
case DistanceMeasures.GDT_TS:
dist = new GDT_TS(dcd, alignFileName, jury1d, refJuryProfile);
break;
}
dist.InitMeasure();
return dist;
}
private DistanceMeasure CreateMeasure(string processName, string dirName,DistanceMeasures measure,PDB.PDBMODE atoms,bool jury1d,string alignFileName,
string profileName=null,string refJuryProfile=null)
{
DistanceMeasure dist=null;
switch(measure)
{
case DistanceMeasures.HAMMING:
if (alignFileName != null)
dist = new JuryDistance(alignFileName, jury1d, profileName, refJuryProfile);
else
dist = new JuryDistance(dirName, alignFileName, jury1d, profileName, refJuryProfile);
break;
case DistanceMeasures.COSINE:
if (alignFileName != null)
dist = new CosineDistance(alignFileName, jury1d, profileName, refJuryProfile);
else
dist = new CosineDistance(dirName, alignFileName, jury1d, profileName, refJuryProfile);
break;
case DistanceMeasures.RMSD:
if (dirName == null)
throw new Exception("RMSD and MAXSUB measures cannot be used for aligned profiles!");
dist = new Rmsd(dirName, alignFileName, jury1d, atoms, refJuryProfile);
break;
case DistanceMeasures.MAXSUB:
if (dirName == null)
throw new Exception("RMSD and MAXSUB measures cannot be used for aligned profiles!");
dist = new MaxSub(dirName, alignFileName, jury1d, refJuryProfile);
break;
case DistanceMeasures.GDT_TS:
if (dirName == null)
throw new Exception("RMSD and MAXSUB measures cannot be used for aligned profiles!");
dist = new GDT_TS(dirName, alignFileName, jury1d, refJuryProfile);
break;
}
return dist;
}
private void SaveAll()
{
DistanceMeasure dist=null;
Settings set = new Settings();
set.Load();
string[] files;
if (set.extension.Length > 0)
files = Directory.GetFiles(directory, set.extension);
else
files = Directory.GetFiles(directory);
List<string> fileList = new List<string>(2);
StreamWriter r = new StreamWriter(saveFile);
maxV = files.Length;
foreach (var item in files)
{
fileList.Clear();
fileList.Add(item);
fileList.Add(markStructure);
switch (distanceControl1.distDef)
{
case DistanceMeasures.HAMMING:
dist = new JuryDistance(fileList, null, false, distanceControl1.profileName, distanceControl1.referenceProfile);
break;
case DistanceMeasures.RMSD:
dist = new Rmsd(fileList, null, false, distanceControl1.CAtoms, null);
break;
case DistanceMeasures.MAXSUB:
dist = new MaxSub(fileList, null, false, null);
break;
case DistanceMeasures.GDT_TS:
dist = new GDT_TS(fileList, null, false, null);
break;
}
dist.InitMeasure();
try
{
int val = dist.GetDistance(Path.GetFileName(fileList[1]), Path.GetFileName(fileList[0]));
currentV++;
if (val < int.MaxValue)
r.WriteLine(fileList[0] + " " + (double)val / 100);
else
r.WriteLine(fileList[0] + " NaN");
}
catch (Exception ex)
{
exc = ex;
}
}
r.Close();
currentV = maxV;
}
