public override List <byte> CreateNewProfile(profileNode node, string[] profile)
{
List <byte> newProfile = new List <byte>(profile.Length);
for (int i = 0; i < profile.Length; i++)
{
string state = profile[i];
if (node.ContainsState(state))
{
if (Convert.ToInt32(state, System.Globalization.CultureInfo.InvariantCulture) > 255)
{
state = "255";
}
}
if (node.ContainsState(state))
{
newProfile.Add(node.GetCodedState(node.states[state], true));
}
else
{
ErrorBase.AddErrors("Unknow state " + state + " in " + node.profName + " profile!");
}
}
return(newProfile);
}
public string AddPDB(string fileName, PDBMODE flag, CHAIN_MODE flagChain = CHAIN_MODE.SINGLE)
{
string name = Path.GetFileName(fileName);
if (molDic != null && molDic.ContainsKey(name))
{
return(name);
}
try
{
MolData molD = new MolData(fileName, flag, mode, flagChain);
if ((molD.mol == null || molD.mol.Chains == null || molD.mol.Chains.Count == 0))
{
ErrorBase.AddErrors("PDB reading: file " + fileName + " is removed from consideration it looks that it has wrong format");
return(null);
}
molDic.Add(name, molD);
return(name);
}
catch (IncorrectSideChainException ex)
{
ErrorBase.AddErrors("PDB reading: file " + fileName + " is removed from consideration because\n" + ex.Message);
}
catch (Exception ee)
{
ErrorBase.AddErrors("PDB reading: file " + fileName + " is removed from consideration because\n" + ee.Message);
}
return(null);
}
//Flag true only CA will be readed
public MolData(string fileName, PDBMODE flag, INPUTMODE mode, CHAIN_MODE chainFlag = CHAIN_MODE.SINGLE)
{
using (StreamReader rr = new StreamReader(fileName)) {
switch (mode)
{
case INPUTMODE.PROTEIN:
mol = new Molecule(flag, chainFlag);
break;
case INPUTMODE.RNA:
mol = new MoleculeRNA(flag);
break;
}
bool res = mol.ReadMolecule(rr);
if (!res)
{
return;
}
if (mol.Chains.Count == 0)
{
ErrorBase.AddErrors("Error in reading file: " + fileName + "\nCannot find residues, file will not be considered!");
rr.Close();
return;
}
molLength = mol.Chains[0].chainSequence.Length;
}
//CenterMol();
}
/* public override bool ReadMolecule()
* {
* return this.ReadAtoms(pdbStream);
* }*/
internal override bool ReadAtoms(StreamReader pdbStream)
{
this.atoms = new List <Atom>();
// using (StreamReader pdbReader = new StreamReader(pdbStream))
// {
string pdbLine = pdbStream.ReadLine();
while (pdbLine != null)
{
if (pdbLine.StartsWith("ENDMDL") || pdbLine.StartsWith("TER") || pdbLine.StartsWith("END"))
{
break;
}
if (pdbLine.StartsWith("ATOM"))
{
if (pdbLine.Contains("\t"))
{
ErrorBase.AddErrors("ATOM line containes tab what is not allowed");
return(false);
}
AtomRNA atom = new AtomRNA();
string error = atom.ParseAtomLine(this, pdbLine, flag);
if (error == null)
{
if (flag == PDBMODE.ONLY_P || flag == PDBMODE.ONLY_P_AND_C4)
{
if (atom.AtomName == "P")
{
this.atoms.Add(atom);
}
if (atom.AtomName == "C4*" || atom.AtomName == "C4'")
{
this.atoms.Add(atom);
}
}
else
{
this.atoms.Add(atom);
}
}
else
{
ErrorBase.AddErrors("Error in file: " + ((FileStream)pdbStream.BaseStream).Name + " " + error);
}
}
pdbLine = pdbStream.ReadLine();
}
// }
return(true);
}
public virtual List <byte> CreateNewProfile(profileNode node, string [] profile)
{
List <byte> newProfile = new List <byte>(profile.Length);
for (int i = 0; i < profile.Length; i++)
{
string state = profile[i];
if (node.ContainsState(state))
{
newProfile.Add(node.GetCodedState(node.states[state]));
}
else
{
ErrorBase.AddErrors("Unknow state " + state + " in " + node.profName + " profile!");
}
}
return(newProfile);
}
private void PDBSAlign(object o)
{
Params p = (Params)o;
List <string> toRemove = new List <string>();
MAlignment align = new MAlignment(refSeq.Length);
DebugClass.WriteMessage("Started");
foreach (var item in auxFiles[p.k])
{
molDic[item].indexMol = new int[refSeq.Length];
MAlignment.alignSeq alignRes = align.Align(refSeq, molDic[item].mol.Chains[0].chainSequence);
if (alignRes.seq1.Contains('-'))
{
ErrorBase.AddErrors("Reference structure " + refStuctName + " cannot be used as reference to " + item + " structure because after alignment gaps to referense structure must be added what is not allowed");
toRemove.Add(item);
continue;
}
//string ss = align.Align(molDic[refStuctName].mol.Chains[0].chainSequence, molDic[item].mol.Chains[0].chainSequence).seq2;
string ss = alignRes.seq2;
for (int j = 0, count = 0; j < ss.Length; j++)
{
if (ss[j] != '-')
{
molDic[item].indexMol[j] = count++;
}
else
{
molDic[item].indexMol[j] = -1;
}
}
}
DebugClass.WriteMessage("Almost done");
foreach (var item in toRemove)
{
molDic.Remove(item);
}
resetEvents[p.k].Set();
}
public string AddPDB(MemoryStream stream, PDBMODE flag, string modelName)
{
try
{
MolData molD = new MolData();
if (!molD.ReadMolData(stream, flag, modelName))
{
return(null);
}
molDic.Add(modelName, molD);
return(modelName);
}
catch (IncorrectSideChainException ex)
{
ErrorBase.AddErrors("PDB reading: file " + modelName + " is removed from consideration because\n" + ex.Message);
}
return(null);
}
private void CreateResidues()
{
List <Residue> auxRes = new List <Residue>();
List <Atom> localAtoms = new List <Atom>();
//this.residues = new List<Residue>();
Residue residue = null;
foreach (Atom atom in this.atoms)
{
//if (residue == null || atom.ResidueSequenceNumber != residue.ResidueSequenceNumber||
if (residue == null || atom.tabParam[2] != residue.ResidueSequenceNumber ||
atom.tabParam[1] != residue.ChainIdentifier)
//atom.ChainIdentifier != residue.ChainIdentifier)
{
residue = new Residue(this, atom, flag);
auxRes.Add(residue);
}
else
{
bool test = false;
foreach (var item in residue.Atoms)
{
if (atom.AtomName == item.AtomName)
{
ErrorBase.AddErrors("Residue " + residue.ResidueName + " has two the same atoms " + atom.AtomName);
test = true;
}
}
if (!test)
{
residue.Atoms.Add(atom);
}
//residue.AddAtom(atom);
}
atom.tabParam = null;
}
this.residues = new List <Residue>(auxRes);
auxRes = null;
}
public bool ReadMolData(MemoryStream stream, PDBMODE flag, string modelName)
{
StreamReader rr = new StreamReader(stream);
mol = new Molecule(flag);
bool res = mol.ReadMolecule(rr);
if (!res)
{
return(false);
}
if (mol.Chains.Count == 0)
{
ErrorBase.AddErrors("Error in reading file: " + modelName + "\nCannot find residues, file will not be considered!");
return(false);
}
molLength = mol.Chains[0].chainSequence.Length;
return(true);
//CenterMol();
}
public override Dictionary <string, protInfo> GetProfile(profileNode node, string fileName, DCDFile dcd = null)
{
Dictionary <string, protInfo> dic = new Dictionary <string, protInfo>();
currentProgress = 0;
if (!File.Exists(GetProfileFileName(fileName)))
{
throw new Exception("Profile rnaSS does not exists!");
}
string profileName;
if (node.ContainsState("+"))
{
profileName = LWprofile;
}
else
{
profileName = SSprofile;
}
StreamReader wr = new StreamReader(GetProfileFileName(fileName));
List <string> files = GetFileList(fileName);
maxV = files.Count;
Dictionary <string, int> dicFile = new Dictionary <string, int>();
foreach (var item in files)
{
string[] aux = item.Split(Path.DirectorySeparatorChar);
if (!dicFile.ContainsKey(aux[aux.Length - 1]))
{
dicFile.Add(aux[aux.Length - 1], 0);
}
}
protInfo info;
string line = wr.ReadLine();
string name = "";
string seq = "";
List <string> profile = new List <string>();
List <byte> newProfile = new List <byte>();
while (line != null)
{
if (line.Contains('>'))
{
if (name.Length > 0)
{
info = new protInfo();
info.sequence = seq;
info.profile = newProfile;
if (dicFile.ContainsKey(name))
{
if (!dic.ContainsKey(name))
{
dic.Add(name, info);
}
else
{
ErrorBase.AddErrors("There are two the same names " + name + " in the profile file " + GetProfileFileName(fileName));
}
}
currentProgress++;
}
name = line.Remove(0, 1);
}
if (line.Contains(SEQprofile))
{
seq = line.Remove(0, SEQprofile.Length);
}
if (line.Contains(profileName))
{
string tmp = line.Remove(0, profileName.Length);
string[] aux;
profile.Clear();
if (tmp.Contains(" "))
{
tmp = tmp.TrimEnd();
aux = tmp.Split(' ');
foreach (var item in aux)
{
profile.Add(item);
}
}
else
{
for (int i = 0; i < tmp.Length; i++)
{
profile.Add(tmp[i].ToString());
}
}
newProfile = new List <byte>();
for (int i = 0; i < profile.Count; i++)
{
if (node.ContainsState(profile[i].ToString()))
{
newProfile.Add(node.GetCodedState(node.states[profile[i].ToString()]));
}
else
if (profile[i].ToString() != "-" && profile[i].ToString() != "X")
{
throw new Exception("Unknow state: " + profile[i].ToString() + " in structure " + name + " in profile " + node.profName + " profile!");
}
else
{
newProfile.Add(0);
}
}
}
line = wr.ReadLine();
}
info = new protInfo();
info.sequence = seq;
info.profile = newProfile;
if (!dic.ContainsKey(name))
{
dic.Add(name, info);
}
else
{
ErrorBase.AddErrors("There are two the same names " + name + " in the profile file " + GetProfileFileName(fileName));
}
wr.Close();
currentProgress = maxV;
return(dic);
}
public override int Run(object processParams)
{
string[] aux;
System.OperatingSystem osinfo = System.Environment.OSVersion;
if (osinfo.VersionString.Contains("Win"))
{
if (!Environment.Is64BitOperatingSystem)
{
this.ex = new Exception("Dssp profile is not working on 32 bit windows system!");
return(0);
}
}
string currentDir = Directory.GetCurrentDirectory();
StreamWriter wr;
wr = new StreamWriter(((ThreadFiles)processParams).fileName);
if (wr == null)
{
this.ex = new Exception("Cannot open file: " + ((ThreadFiles)processParams).fileName);
return(0);
}
List <string> auxFiles = threadingList[((ThreadFiles)processParams).threadNumber];
try
{
foreach (var item in auxFiles)
{
// wrapper.timeSp = 0;
if (!File.Exists(item))
{
ErrorBase.AddErrors("File " + item + "does not exist");
continue;
}
//wrapper.Run(item,item.Length);
//timeSp += wrapper.timeSp;
IntPtr pSS = IntPtr.Zero;
IntPtr pSEQ = IntPtr.Zero;
IntPtr pLW = IntPtr.Zero;
string SS = "";
string SEQ = "";
string LW = "";
int error = 0;
IntPtr ptr = RNAProfiles(item);
int errorNum = 0;
if (errorNum > 0)
{
ErrorBase.AddErrors(item + ": " + RNAViewErrors(error));
continue;
}
pSS = GetSS(ptr);
pLW = GetLW(ptr);
pSEQ = GetSEQ(ptr);
if (pSS == IntPtr.Zero || pLW == IntPtr.Zero || pSEQ == IntPtr.Zero)
{
ErrorBase.AddErrors("Could not create profile for: " + item + " structure");
RNAFree(ptr);
continue;
}
DebugClass.WriteMessage("PDB:" + item);
SS = Marshal.PtrToStringAnsi(pSS);
SEQ = Marshal.PtrToStringAnsi(pSEQ);
LW = Marshal.PtrToStringAnsi(pLW);
aux = item.Split(Path.DirectorySeparatorChar);
if (SS != null && SS.Length > 0)
{
wr.WriteLine(">" + aux[aux.Length - 1]);
wr.WriteLine(SSprofile + SS);
wr.WriteLine(LWprofile + LW);
wr.WriteLine(SEQprofile + SEQ);
}
RNAFree(ptr);
Interlocked.Increment(ref currentProgress);
}
wr.Close();
}
catch (Exception ex)
{
this.ex = ex;
}
//currentV = maxV;
Directory.SetCurrentDirectory(currentDir);
return(0);
}
public override int Run(object processParams)
{
string[] aux;
System.OperatingSystem osinfo = System.Environment.OSVersion;
if (osinfo.VersionString.Contains("Win"))
{
if (!Environment.Is64BitOperatingSystem)
{
this.ex = new Exception("Dssp profile is not working on 32 bit windows system!");
return(0);
}
}
StreamWriter wr;
wr = new StreamWriter((( ThreadFiles)processParams).fileName);
if (wr == null)
{
this.ex = new Exception("Cannot open file: " + ((ThreadFiles)processParams).fileName);
return(0);
}
List <string> auxFiles = threadingList[(( ThreadFiles)processParams).threadNumber];
try
{
foreach (var item in auxFiles)
{
// wrapper.timeSp = 0;
if (!File.Exists(item))
{
ErrorBase.AddErrors("File " + item + "does not exist");
continue;
}
//wrapper.Run(item,item.Length);
//timeSp += wrapper.timeSp;
IntPtr dsspExt = IntPtr.Zero;
IntPtr pSS = IntPtr.Zero;
IntPtr pSA = IntPtr.Zero;
IntPtr pSEQ = IntPtr.Zero;
string SS = "";
string SA = "";
string SEQ = "";
int error = 0;
dsspExt = PrepProtein();
DebugClass.WriteMessage("PDB:" + item);
error = ReadProt(item, dsspExt);
if (error == 0)
{
pSS = GetSS(dsspExt);
pSA = GetSA(dsspExt);
pSEQ = GetSEQ(dsspExt);
SS = Marshal.PtrToStringAnsi(pSS);
SA = Marshal.PtrToStringAnsi(pSA);
SEQ = Marshal.PtrToStringAnsi(pSEQ);
aux = item.Split(Path.DirectorySeparatorChar);
if (SS != null && SS.Length > 0)
{
wr.WriteLine(">" + aux[aux.Length - 1]);
wr.WriteLine(SSprofile + SS);
wr.WriteLine(SAprofile + ConvertSAProfile(SA, SEQ));
//wr.WriteLine(PSIprofile + wrapper.PSI);
//wr.WriteLine(PHIprofile + wrapper.PHI);
wr.WriteLine(SEQprofile + SEQ);
}
}
else
{
ErrorBase.AddErrors(item + ": " + DSSPErrors(error));
}
if (dsspExt != IntPtr.Zero)
{
DisposeMProtein(dsspExt);
}
if (pSS != IntPtr.Zero)
{
DisposeBuffor(pSS);
}
if (pSA != IntPtr.Zero)
{
DisposeBuffor(pSA);
}
if (pSEQ != IntPtr.Zero)
{
DisposeBuffor(pSEQ);
}
Interlocked.Increment(ref currentProgress);
}
wr.Close();
}
catch (Exception ex)
{
this.ex = ex;
}
//currentV = maxV;
return(0);
}
public override Dictionary <string, protInfo> GetProfile(profileNode node, string listFile, DCDFile dcd = null)
{
Dictionary <string, protInfo> dic = null;
StreamReader wr;
DebugClass.WriteMessage("start reading file" + listFile);
string useFile = listFile;
List <string> names = GetFileList(listFile);
if (names == null)
{
DebugClass.WriteMessage("After GetFileList null");
}
else
{
DebugClass.WriteMessage("After GetFileList " + names.Count);
}
maxV = names.Count;
Dictionary <string, int> dicNames = new Dictionary <string, int>(names.Count);
foreach (var item in names)
{
string[] aux = item.Split(Path.DirectorySeparatorChar);
if (!dicNames.ContainsKey(aux[aux.Length - 1]))
{
dicNames.Add(aux[aux.Length - 1], 0);
}
}
DebugClass.WriteMessage("After loop");
string[] dotFlag = names[0].Split('|');
bool flag = false;
if (dotFlag.Length == 2)
{
flag = true;
}
DebugClass.WriteMessage("Before profile");
if (dcd == null)
{
wr = new StreamReader(GetProfileFileName(listFile));
}
else
{
wr = new StreamReader(GetProfileFileName(dcd));
}
DebugClass.WriteMessage("start ddd reading");
protInfo info;
string line = wr.ReadLine();
string name = "";
string seq = "";
List <string> profile;;
List <byte> newProfile = null;
string profileName;
if (node.ContainsState("H"))
{
profileName = ssProfile;
}
else
{
profileName = contactProfile;
}
//Check number of elements in file
int lineLength = 0;
while (line != null)
{
if (lineLength < line.Length)
{
lineLength = line.Length;
}
line = wr.ReadLine();
}
wr.BaseStream.Position = 0;
wr.DiscardBufferedData();
profile = new List <string>(lineLength);
dic = new Dictionary <string, protInfo>(names.Count);
line = wr.ReadLine();
string remName = "";
DebugClass.WriteMessage("Starrrrr");
while (line != null)
{
if (line[0] == '>')
{
if (name.Length > 0)
{
if (dicNames.ContainsKey(name))
{
info = new protInfo();
info.sequence = seq;
info.profile = newProfile;
//string newName = line;
//newName = newName.Remove(0, 1);
if (!dic.ContainsKey(remName))
{
dic.Add(remName, info);
}
else
{
ErrorBase.AddErrors("!!In the generated profile file structure " + remName + " exists more then once!!!\nOnly the first profile will be considered!");
}
currentProgress++;
}
}
name = line.Remove(0, 1);
remName = name;
if (name.Contains("|") && !flag)
{
string[] tmp = name.Split('|');
name = tmp[0];
}
}
if (dicNames.ContainsKey(name))
{
if (line.Contains(SEQprofile))
{
seq = line.Remove(0, SEQprofile.Length);
}
else
if (line.Contains(profileName))
{
//StringBuilder tmp = new StringBuilder(line);
line = line.Remove(0, profileName.Length);
//tmp = tmp.Remove(0, profileName.Length);
//StringBuilder tmp = new StringBuilder (line.Remove(0, profileName.Length));
string[] aux;
if (line.Contains(' '))
{
aux = line.Split(' ');
}
else
{
aux = new string[line.Length];
for (int i = 0; i < line.Length; i++)
{
aux[i] = line[i].ToString();
}
}
newProfile = CreateNewProfile(node, aux);
}
}
line = wr.ReadLine();
}
if (dicNames.ContainsKey(name))
{
info = new protInfo();
info.sequence = seq;
info.profile = newProfile;
dic.Add(remName, info);
}
wr.Close();
DebugClass.WriteMessage("Reading finished");
return(dic);
}
internal virtual bool ReadAtoms(StreamReader pdbStream)
{
List <Atom> auxList = new List <Atom>();
//using (StreamReader pdbReader = new StreamReader(pdbStream))
//{
string pdbLine = pdbStream.ReadLine();
while (pdbLine != null)
{
if (pdbLine.StartsWith("ENDMDL") /*|| pdbLine.StartsWith("TER") */ || pdbLine.StartsWith("END"))
{
break;
}
if (flagChain == CHAIN_MODE.SINGLE)
{
if (pdbLine.StartsWith("TER"))
{
break;
}
}
if (pdbLine.StartsWith("ATOM") || pdbLine.StartsWith("HETATM"))
{
if (pdbLine.Contains("\t"))
{
ErrorBase.AddErrors("Error in file: " + ((FileStream)pdbStream.BaseStream).Name + " " + "ATOM line containes tab what is not allowed");
return(false);
}
Atom atom = new Atom();
string error = atom.ParseAtomLine(this, pdbLine, flag);
if (error == null)
{
//Check if the atom already exists!!
if (flag == PDBMODE.ONLY_CA || flag == PDBMODE.CA_CB || flag == PDBMODE.ONLY_CB || flag == PDBMODE.ONLY_SEQ)
{
if (flag == PDBMODE.ONLY_CA || flag == PDBMODE.CA_CB || flag == PDBMODE.ONLY_SEQ)
{
if (atom.AtomName == "CA")
{
auxList.Add(atom);
}
}
if (flag == PDBMODE.ONLY_CB || flag == PDBMODE.CA_CB) //|| (atom.ResidueName=='G' && flag==PDBMODE.ONLY_CA))
{
if (atom.AtomName == "CB")
{
auxList.Add(atom);
}
}
}
else
{
auxList.Add(atom);
}
}
else
{
ErrorBase.AddErrors("Error in file: " + ((FileStream)pdbStream.BaseStream).Name + " " + error);
}
}
pdbLine = pdbStream.ReadLine();
}
this.atoms = new List <Atom>(auxList);
// }
return(true);
}
