void PrepareSift()
{
pdbs = new PDBFiles();
maxV = listFiles.Count * 2+1;
foreach (var item in listFiles)
{
string[] aux = item.Split('\\');
// if (!fileList.ContainsKey(aux[aux.Length-1]))
// continue;
string strName;
strName = pdbs.AddPDB(item, PDBMODE.ALL_ATOMS);
if (strName != null)
{
pdbs.molDic[strName].CreateSideChainContactMap(11.0f, true);
pdbs.molDic[strName].CleanMolData();
}
currentV++;
}
step = (double)(stop - start) / binNumber;
for (double i = start; i < stop; i += step)
binLen.Add(i + step);
}
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 ReadPdbs(List <string> structures)
{
try
{
pdbs = new PDBFiles();
foreach (var item in structures)
{
pdbs.AddPDB(item, PDBMODE.ONLY_SEQ);
currentProgress++;
}
// pdbs.AddPDB(structures, PDBMODE.ONLY_CA,ref currentV);
//pdbs.AddPDB(structures, PDBMODE.ONLY_SEQ, ref currentV);
}
catch (Exception ex)
{
throw new Exception(ex.Message);
}
}
public ClusterOutput RunSift(string dirName)
{
Options opt=new Options();
opt.ReadDefaultFile();
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);
listFiles = new List<string>(files.Length);
foreach(var item in files)
listFiles.Add(item);
return Shape();
}
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();
}
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();
}
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();
}
public override int Run(object processParams)
{
Dictionary<int, List<int>> contacts= new Dictionary<int, List<int>>();
string fileName = ((ThreadFiles)(processParams)).fileName;
List<string> files = threadingList[((ThreadFiles)(processParams)).threadNumber];// CheckFile(listFile);
if (files.Count == 0)
return 0;
StreamWriter wr;
if (File.Exists(fileName))
wr = File.AppendText(fileName);
else
wr = new StreamWriter(fileName);
if (wr == null)
throw new Exception("Cannot open file: " + fileName);
PDBFiles pdbs = new PDBFiles();
string refSeqFile = ((ThreadFiles)(processParams)) + ".ref";
pdbs.ReadRefSeq(refSeqFile);
maxV = files.Count;
try
{
foreach (var item in files)
{
string strName;
//strName = pdbs.AddPDB(item, PDBMODE.CA_CB);
if (this.GetType() == typeof(ContactProfile))
strName = pdbs.AddPDB(item, PDBMODE.ALL_ATOMS);
else
strName = pdbs.AddPDB(item, PDBMODE.ONLY_CA);
if(strName!=null)
MakeProfiles(strName,pdbs.molDic[strName], wr);
currentProgress++;
}
}
catch (Exception ex)
{
// wr.Close();
throw new Exception(ex.Message);
}
wr.Close();
currentProgress = maxV;
return 0;
}
protected void MakeProfiles(string strName,MolData molDic,StreamWriter wr,int k)
{
if (molDic != null)
{
PDBFiles pdb = new PDBFiles();
pdb.AddPDB(strName, PDBMODE.ONLY_CA);
DebugClass.WriteMessage("Make Started");
//int []contact=pdbs.molDic[strName].CreateFullContactMap(8.5f);
//molDic.CreateFullContactMap(9.5f,contact[k]);//correct
List<string> cc=new List<string>(pdb.molDic.Keys);
pdb.molDic[cc[0]].indexMol = molDic.indexMol;
GenerateContactMap(pdb.molDic[cc[0]],k);
//pdb.molDic[cc[0]].CreateFullContactMap(8.5f, contact[k]);
//molDic.CreateFullContactMap(8.5f,contact[k]);
//pdbs.molDic[strName].CreateContactMap(9.5f, "CB");
for (int i = 0; i < contact[k].Length; i++)
if (contact[k][i] == 1)
contOne[i]++;
int j = 0;
for (int i = 0; i < contact[k].Length - 1; i++)
{
if (contact[k][i] == 1)
contactToString[k][j++] = '1';
else
contactToString[k][j++] = '0';
contactToString[k][j++] = ' ';
}
if (contact[k][contact[k].Length - 1] == 1)
contactToString[k][j] = '1';
else
contactToString[k][j] = '0';
string all = new string(contactToString[k], 0, j);
wr.WriteLine(">" + cc[0]);
//for (int i = 0; i < contact[k].Length-1; i++)
// wr.Write(contact[k][i]+" ");
//wr.Write(contact[k][contact.Length-1]);
wr.WriteLine(all);
//wr.WriteLine();
//molDic.CleanMolData();
DebugClass.WriteMessage("Make finished");
}
}
