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 Rmsd(List <string> fileNames, string alignFile, bool flag, PDBMODE allAtoms, string refJuryProfile = null)
: base(fileNames, alignFile, flag, refJuryProfile)
{
dirSettings.Load();
pdbs = new PDBFiles();
pdbs.AddPDB(fileNames, allAtoms);
pdbs.FindReferenceSeq();
pdbs.MakeAlignment(null);
opt = new Optimization();
structNames = CheckAvailableStructures();
order = true;
}
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();
}
public Rmsd(string dirName, string alignFile, bool flag, PDBMODE allAtoms, string refJuryProfile = null) : base(dirName, alignFile, flag, refJuryProfile)
{
dirSettings.Load();
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);
}
string refSeqFile = dirName + ".ref";
pdbs.ReadRefSeq(refSeqFile);
pdbs.AddPDB(files, allAtoms);
if (pdbs.molDic.Keys.Count == 0)
{
throw new Exception("Non pdb files correctly read");
}
pdbs.FindReferenceSeq();
pdbs.MakeAlignment(alignFile);
opt = new Optimization();
structNames = CheckAvailableStructures();
order = true;
}
public Rmsd(string dirName,string alignFile,bool flag,PDBMODE allAtoms,string refJuryProfile=null):base(dirName,alignFile,flag,refJuryProfile)
{
dirSettings.Load();
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);
string refSeqFile = dirName + ".ref";
pdbs.ReadRefSeq(refSeqFile);
pdbs.AddPDB(files, allAtoms);
if (pdbs.molDic.Keys.Count == 0)
throw new Exception("Non pdb files correctly read");
pdbs.FindReferenceSeq();
pdbs.MakeAlignment(alignFile);
opt=new Optimization();
structNames = CheckAvailableStructures();
order = true;
}
public Rmsd(List <string> fileNames, string alignFile, bool flag, PDBMODE allAtoms,string refJuryProfile=null)
: base(fileNames, alignFile, flag,refJuryProfile)
{
dirSettings.Load();
pdbs = new PDBFiles();
pdbs.AddPDB(fileNames, allAtoms);
pdbs.FindReferenceSeq();
pdbs.MakeAlignment(null);
opt = new Optimization();
structNames = CheckAvailableStructures();
order = true;
}
public override void RunThreads(string fileName)
{
List <string> files = CheckFile(fileName);
if (files.Count == 0)
{
return;
}
//Task[] runnigTask = new Task[threadNumbers];
//Task startProg;
maxV = files.Count * 2;
ReadPdbs(files);
if (pdbs.molDic.Count == 0)
{
return;
}
string aux = Path.GetDirectoryName(files[0]).TrimEnd(Path.DirectorySeparatorChar);
string refSeqFile = aux + ".ref";
if (File.Exists(refSeqFile))
{
pdbs.ReadRefSeq(refSeqFile);
}
else
{
pdbs.FindReferenceSeq();
}
pdbs.MakeAlignment(null);
if (contOne == null)
{
string molDicKey = "";
foreach (var item in pdbs.molDic.Keys)
{
molDicKey = item;
break;
}
int len = pdbs.molDic[molDicKey].indexMol.Length;
contOne = new int[len * (len + 1) / 2];
contact = new byte[threadNumbers][];
contactToString = new char [threadNumbers][];
for (int i = 0; i < threadNumbers; i++)
{
contact[i] = new byte [len * (len + 1) / 2];
contactToString[i] = new char [len * (len + 1)];
}
for (int i = 0; i < contOne.Length; i++)
{
contOne[i] = 0;
}
for (int i = 0; i < threadNumbers; i++)
{
for (int j = 0; j < contOne.Length; j++)
{
contact[i][j] = 0;
}
}
}
auxFiles = new List <string> [threadNumbers];
List <string> allFiles = new List <string>(pdbs.molDic.Keys);
for (int i = 0; i < threadNumbers; i++)
{
auxFiles[i] = new List <string>((i + 1) * pdbs.molDic.Count / threadNumbers - i * pdbs.molDic.Count / threadNumbers);
for (int j = i * allFiles.Count / threadNumbers; j < (i + 1) * allFiles.Count / threadNumbers; j++)
{
auxFiles[i].Add(files[j]);
}
}
for (int i = 0; i < threadNumbers; i++)
{
Params p = new Params();
p.fileName = fileName;
p.k = i;
resetEvents[p.k] = new ManualResetEvent(false);
ThreadPool.QueueUserWorkItem(new WaitCallback(RunMakeProfiles), (object)p);
}
for (int i = 0; i < threadNumbers; i++)
{
resetEvents[i].WaitOne();
}
//JoinFiles(fileName);
CuttProfiles(fileName);
currentProgress = maxV;
}