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;
}
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 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]);
//all = all.Trim();
wr.WriteLine(all.Trim());
//wr.WriteLine();
//molDic.CleanMolData();
DebugClass.WriteMessage("Make finished");
}
}
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(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 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);
}
}
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 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 (dirSettings.mode == INPUTMODE.PROTEIN)
{
if (this.GetType() == typeof(ContactProfile))
{
strName = pdbs.AddPDB(item, PDBMODE.ALL_ATOMS);
}
else
{
strName = pdbs.AddPDB(item, PDBMODE.ONLY_CA);
}
}
else
{
strName = pdbs.AddPDB(item, PDBMODE.ONLY_P_AND_C4);
}
if (strName != null)
{
MakeProfiles(strName, pdbs.molDic[strName], wr);
}
Interlocked.Increment(ref currentProgress);
}
}
catch (Exception ex)
{
// wr.Close();
throw new Exception(ex.Message);
}
wr.Close();
currentProgress = maxV;
return(0);
}
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();
* PDBFiles pdbsNew = new PDBFiles();
* //Needed only for CATH
* string []cathFiles=Directory.GetFiles("F:\\CATH");
* Dictionary<string, Dictionary<string, string>> aux = new Dictionary<string, Dictionary<string, string>>();
* foreach(var item in cathFiles)
* {
* if(item.Contains("COMBS"))
* ReadCathFile(item, aux);
* }
*
*
*
* //-----------------------
*
*
* maxV = files.Count;
* bool test=false;
* try
* {
* foreach (var item in aux.Keys)
* {
* string strName;
*
* //if (!test && item.Contains("1vij"))
* test = true;
*
* if (!test)
* continue;
* //strName = pdbs.AddPDB(item, PDBMODE.CA_CB);
* strName = pdbs.AddPDB("F:\\cath_pdb\\"+item, PDBMODE.ONLY_CA,CHAIN_MODE.ALL);
*
* // if(aux.ContainsKey(pdbs.molDic))
*
* if (strName != null)
* {
* if (!aux.ContainsKey(strName))
* Console.WriteLine("UPS");
* List<Chain> toRemove = new List<Chain>();
* chainId.Clear();
* pdbsNew.molDic.Clear();
* MolData mol=new MolData();
* mol.mol = new Molecule();
* pdbsNew.molDic=new Dictionary<string,MolData>();
* pdbsNew.molDic.Add(strName,mol);
* char chStart = '0';
* foreach (var chains in aux[strName].Keys)
* {
* if (!chains.Contains("_"))
* continue;
* Console.WriteLine(chains);
* Chain cc=pdbs.molDic[strName].mol.CuttMoleculeToSEQ(aux[strName][chains], chains.Substring(0, 1)[0]);
* if(cc!=null)
* {
* cc.ChainIdentifier = chStart;
* chainId.Add(chStart, chains);
* chStart++;
* pdbsNew.molDic[strName].mol.Chains.Add(cc);
* }
* }
* if(pdbsNew.molDic[strName].mol.Chains.Count>0)
* MakeProfiles(strName, pdbsNew.molDic[strName], wr);
* }
* pdbs.molDic.Clear();
* currentProgress++;
* }
* }
* catch (Exception ex)
* {
* // wr.Close();
* throw new Exception(ex.Message);
* }
*
* wr.Close();
* currentProgress = maxV;
* return 0;
* }*/
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();
chunk = new float[dirSettings.numberOfCores][, ];
center = new float[dirSettings.numberOfCores][];
for (int i = 0; i < dirSettings.numberOfCores; i++)
{
chunk[i] = new float[fragBagLibrary[0].GetLength(0), fragBagLibrary[0].GetLength(1)];
center[i] = new float[3];
}
maxV = files.Count;
try
{
resetEvents = new ManualResetEvent[dirSettings.numberOfCores];
for (int i = 0; i < dirSettings.numberOfCores; i++)
{
resetEvents[i] = new ManualResetEvent(false);
}
foreach (var item in files)
{
string strName;
//strName = pdbs.AddPDB(item, PDBMODE.CA_CB);
if (dirSettings.mode == INPUTMODE.PROTEIN)
{
strName = pdbs.AddPDB(item, PDBMODE.ONLY_CA, CHAIN_MODE.ALL);
}
else
{
strName = pdbs.AddPDB(item, PDBMODE.ONLY_P, CHAIN_MODE.ALL);
}
// if(aux.ContainsKey(pdbs.molDic))
if (strName != null)
{
MakeProfiles(strName, pdbs.molDic[strName], wr);
}
pdbs.molDic.Clear();
ErrorBase.ClearErrors();
Interlocked.Increment(ref currentProgress);
}
}
catch (Exception ex)
{
// wr.Close();
throw new Exception(ex.Message);
}
wr.Close();
// currentProgress = maxV;
return(0);
}
