public Rmsd(DCDFile dcd, string alignFile, bool flag, PDBMODE allAtoms, string refJuryProfile = null)
: base(dcd, alignFile, flag, refJuryProfile)
{
DCDReader readDCD = new DCDReader(dcd);
dirSettings.Load();
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);
if (pdbs is ErrorBase)
{
AddErrors(pdbs.errors);
}
opt = new Optimization();
structNames = CheckAvailableStructures();
order = true;
}
public Rmsd(DCDFile dcd, string alignFile, bool flag, PDBMODE allAtoms, string refJuryProfile = null)
: base(dcd, alignFile, flag, refJuryProfile)
{
DCDReader readDCD = new DCDReader(dcd);
dirSettings.Load();
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);
if(pdbs is ErrorBase)
AddErrors(pdbs.errors);
opt = new Optimization();
structNames = CheckAvailableStructures();
order = true;
}
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();
}
public override void Run(DCDFile dcd)
{
DCDReader dcdReader = new DCDReader(null);
string modelName = null;
int counter = 0;
string fileName;
StreamWriter wr;
PDBFiles pdbs = new PDBFiles();
Dictionary <string, int> modelList = null;
fileName = GetProfileFileName(dcd);
if (File.Exists(fileName))
{
modelList = CheckFile(dcd);
wr = File.AppendText(fileName);
}
else
{
wr = new StreamWriter(fileName);
}
if (wr == null)
{
throw new Exception("Cannot open file: " + fileName);
}
dcdReader.DCDPrepareReading(dcd.dcdFile, dcd.pdbFile);
bool cont = true;
do
{
MemoryStream mStream = new MemoryStream();
StreamWriter write = new StreamWriter(mStream);
cont = dcdReader.ReadAndSavePDB(write);
modelName = "Model" + counter++;
if (modelList == null || modelList.ContainsKey(modelName))
{
continue;
}
mStream.Position = 0;
if (this.GetType() == typeof(ContactProfile))
{
pdbs.AddPDB(mStream, PDBMODE.ALL_ATOMS, modelName);
}
else
{
pdbs.AddPDB(mStream, PDBMODE.ONLY_CA, modelName);
}
if (pdbs.molDic.ContainsKey(modelName))
{
MakeProfiles(modelName, pdbs.molDic[modelName], wr);
}
}while (cont);
dcdReader.FinishDCDReading();
wr.Close();
}