protected void InitMeasure(DCDFile dcd, string alignFile, bool flag, PDBMODE allAtoms, string refJuryProfile = null)
{
base.InitMeasure(dcd, alignFile, flag, refJuryProfile);
DCDReader readDCD = new DCDReader(dcd);
pdbs = new PDBFiles();
readDCD.DCDPrepareReading(dcd.dcdFile, dcd.pdbFile);
int counter = 0;
bool cont = true;
do
{
MemoryStream mStream = new MemoryStream();
StreamWriter wStream = new StreamWriter(mStream);
cont = readDCD.ReadAndSavePDB(wStream);
string name = "Model" + counter++;
mStream.Position = 0;
pdbs.AddPDB(mStream, allAtoms, name);
}while(cont);
readDCD.FinishDCDReading();
pdbs.FindReferenceSeq();
pdbs.MakeAlignment(alignFile);
structNames = CheckAvailableStructures();
atomDic = pdbs.MakeAllAtomsDic();
}
protected void InitMeasure(string dirName, string alignFile, bool flag, PDBMODE allAtoms, string refJuryProfile = null)
{
base.InitMeasure(dirName, alignFile, flag, refJuryProfile);
pdbs = new PDBFiles();
string[] files;
if (dirSettings.extension == null)
{
files = Directory.GetFiles(dirName);
}
else
{
files = Directory.GetFiles(dirName, dirSettings.extension);
}
if (files.Length == 0)
{
throw new Exception("In selected directory " + dirName + " there are no files with extesion " + dirSettings.extension);
}
maxV = files.Length;
string refSeqFile = dirName + ".ref";
pdbs.ReadRefSeq(refSeqFile);
currentV = 0;
pdbs.AddPDB(files, allAtoms, ref currentV);
if (pdbs.molDic.Keys.Count == 0)
{
throw new Exception("Non pdb files correctly read");
}
pdbs.FindReferenceSeq();
pdbs.MakeAlignment(alignFile);
structNames = CheckAvailableStructures();
order = true;
atomDic = pdbs.MakeAllAtomsDic();
}
protected void InitMeasure(List <string> fileNames, string alignFile, bool flag, PDBMODE allAtoms, string refJuryProfile = null)
{
base.InitMeasure(fileNames, alignFile, flag, refJuryProfile);
dirSettings.Load();
pdbs = new PDBFiles();
maxV = fileNames.Count;
currentV = 0;
pdbs.AddPDB(fileNames, allAtoms, ref currentV);
if (pdbs.molDic.Keys.Count == 0)
{
throw new Exception("Unable to read pdb data!!");
}
pdbs.FindReferenceSeq();
if (pdbs.molDic.Count == 0)
{
throw new Exception("All pdb structures have been removed. No Data!");
}
pdbs.MakeAlignment(null);
structNames = CheckAvailableStructures();
order = true;
atomDic = pdbs.MakeAllAtomsDic();
}
