/// <summary>
/// get the cryst interfaces from the cryst interface files
/// </summary>
/// <param name="pdbId"></param>
/// <param name="pqsBuId"></param>
public InterfaceChains[] GetInterfacesFromFiles(string pdbId, string type)
{
string searchMode = pdbId + "*." + type + ".gz";
string filePath = ProtCidSettings.dirSettings.interfaceFilePath +
"\\" + type + "\\" + pdbId.Substring(1, 2);
List <InterfaceChains> interfaceList = new List <InterfaceChains>();
if (Directory.Exists(filePath))
{
string[] interfaceFiles = Directory.GetFiles(filePath, searchMode);
for (int i = 0; i < interfaceFiles.Length; i++)
{
InterfaceChains crystInterface = new InterfaceChains();
string interfaceFile = ParseHelper.UnZipFile(interfaceFiles[i], ProtCidSettings.tempDir);
ReadInterfaceFromFile(interfaceFile, ref crystInterface, "ALL");
File.Delete(interfaceFile);
if (crystInterface.GetInterfaceResidueDist())
{
interfaceList.Add(crystInterface);
}
}
}
return(interfaceList.ToArray());
}
/// <summary>
///
/// </summary>
/// <param name="buInterfaceDefTable"></param>
/// <param name="biolUnitHash"></param>
/// <returns></returns>
private InterfaceChains[] GetEntryBiolUnitInterfaces(DataTable buInterfaceDefTable, Dictionary <string, AtomInfo[]> biolUnitHash, string buType)
{
string chainSymOpString1 = "";
string chainSymOpString2 = "";
List <InterfaceChains> buInterfaceList = new List <InterfaceChains> ();
foreach (DataRow interfaceDefRow in buInterfaceDefTable.Rows)
{
if (buType == "pqs") // use PQS chains
{
chainSymOpString1 = interfaceDefRow["Chain1"].ToString().TrimEnd();
chainSymOpString2 = interfaceDefRow["Chain2"].ToString().TrimEnd();
}
else
{
chainSymOpString1 = interfaceDefRow["Chain1"].ToString().TrimEnd() + "_" +
interfaceDefRow["SymmetryString1"].ToString().TrimEnd();
chainSymOpString2 = interfaceDefRow["Chain2"].ToString().TrimEnd() + "_" +
interfaceDefRow["SymmetryString2"].ToString().TrimEnd();
}
if (biolUnitHash.ContainsKey(chainSymOpString1) && biolUnitHash.ContainsKey(chainSymOpString2))
{
InterfaceChains buInterface = new InterfaceChains();
buInterface.firstSymOpString = chainSymOpString1;
buInterface.secondSymOpString = chainSymOpString2;
buInterface.interfaceId = Convert.ToInt32(interfaceDefRow["InterfaceID"].ToString());
buInterface.pdbId = interfaceDefRow["PdbID"].ToString();
buInterface.chain1 = (AtomInfo[])biolUnitHash[chainSymOpString1];
buInterface.chain2 = (AtomInfo[])biolUnitHash[chainSymOpString2];
buInterface.GetInterfaceResidueDist();
buInterfaceList.Add(buInterface);
}
}
return(buInterfaceList.ToArray());
}
/// <summary>
///
/// </summary>
/// <param name="srcDir"></param>
/// <param name="pdbId"></param>
/// <param name="interfaceIds"></param>
/// <param name="type"></param>
/// <returns></returns>
public InterfaceChains[] GetInterfacesFromFiles(string srcDir, string pdbId, int[] interfaceIds, string type)
{
List <InterfaceChains> interfaceList = new List <InterfaceChains> ();
if (Directory.Exists(srcDir))
{
foreach (int interfaceId in interfaceIds)
{
string searchMode = pdbId + "_" + interfaceId.ToString() + "." + type + ".gz";
string[] interfaceFiles = Directory.GetFiles(srcDir, searchMode);
if (interfaceFiles.Length > 0)
{
InterfaceChains crystInterface = new InterfaceChains();
crystInterface.pdbId = pdbId;
string interfaceFile = ParseHelper.UnZipFile(interfaceFiles[0], ProtCidSettings.tempDir);
ReadInterfaceFromFile(interfaceFile, ref crystInterface, "ALL");
File.Delete(interfaceFile);
if (crystInterface.GetInterfaceResidueDist())
{
interfaceList.Add(crystInterface);
}
}
}
}
return(interfaceList.ToArray());
}
/// <summary>
/// for h**o-dimer with sequence identity of two monomers > 95%
/// </summary>
/// <param name="inInterface">an interface with two homologous chains, with sequence identity >= 95%</param>
/// <returns></returns>
public double CalculateHomoInterfaceSymmetry(InterfaceChains inInterface, CrcSeqAlignInfo seqAlignInfo)
{
if (inInterface.seqDistHash == null)
{
inInterface.GetInterfaceResidueDist();
}
List <string>[] seqIdPairLists = GetSeqIdPairLists(inInterface.seqDistHash, seqAlignInfo);
List <string> totalSeqPairList = new List <string>(seqIdPairLists[0]);
List <string> sameSeqPairList = new List <string>();
foreach (string seqPair in seqIdPairLists[0])
{
if (seqIdPairLists[1].Contains(seqPair))
{
sameSeqPairList.Add(seqPair);
}
}
foreach (string seqPair in seqIdPairLists[1])
{
if (!totalSeqPairList.Contains(seqPair))
{
totalSeqPairList.Add(seqPair);
}
}
double jIndex = (double)sameSeqPairList.Count / (double)totalSeqPairList.Count;
return(jIndex);
}
/// <summary>
/// get the cryst interfaces from the cryst interface files
/// </summary>
/// <param name="pdbId"></param>
/// <param name="pqsBuId"></param>
public Dictionary <string, List <InterfaceChains> > GetBuInterfacesFromFiles(string pdbId, string type)
{
Dictionary <string, List <InterfaceChains> > buInterfacesListHash = new Dictionary <string, List <InterfaceChains> >();
string searchMode = pdbId + "*." + type + ".gz";
string fileDir = ProtCidSettings.dirSettings.interfaceFilePath + "\\" + type + "\\" + pdbId.Substring(1, 2);
if (Directory.Exists(fileDir))
{
string[] interfaceFiles = Directory.GetFiles(fileDir, searchMode);
string buId = "";
string justFileName = "";
// InterfaceReader interfaceReader = new InterfaceReader ();
foreach (string interfaceFile in interfaceFiles)
{
justFileName = interfaceFile.Substring(interfaceFile.LastIndexOf("\\") + 1,
interfaceFile.Length - interfaceFile.LastIndexOf("\\") - 1);
buId = justFileName.Substring(4, justFileName.IndexOf("_") - 4);
string unzippedInterfaceFile = ParseHelper.UnZipFile(interfaceFile, ProtCidSettings.tempDir);
InterfaceChains thisInterface = new InterfaceChains();
ReadBuInterfaceFromFile(unzippedInterfaceFile, ref thisInterface, "ALL");
File.Delete(unzippedInterfaceFile);
if (type == "pqs")
{
ConvertPqsResidueNumToPdb(pdbId, ref thisInterface);
}
if (thisInterface.GetInterfaceResidueDist())
{
if (buInterfacesListHash.ContainsKey(buId))
{
buInterfacesListHash[buId].Add(thisInterface);
}
else
{
List <InterfaceChains> interfaceList = new List <InterfaceChains>();
interfaceList.Add(thisInterface);
buInterfacesListHash.Add(buId, interfaceList);
}
}
}
}
return(buInterfacesListHash);
}
/// <summary>
/// get the cryst interfaces from the cryst interface files
/// </summary>
/// <param name="pdbId"></param>
/// <param name="pqsBuId"></param>
public InterfaceChains[] GetBuInterfacesFromFiles(string pdbId, string buId, string type)
{
List <InterfaceChains> interfaceList = new List <InterfaceChains> ();
string searchMode = pdbId + buId + "*." + type + ".gz";
string fileDir = ProtCidSettings.dirSettings.interfaceFilePath + "\\" + type + "\\" + pdbId.Substring(1, 2);
if (Directory.Exists(fileDir))
{
string[] interfaceFiles = Directory.GetFiles(fileDir, searchMode);
foreach (string interfaceFile in interfaceFiles)
{
try
{
InterfaceChains thisInterface = new InterfaceChains();
string decompInterfaceFile = ParseHelper.UnZipFile(interfaceFile, ProtCidSettings.tempDir);
ReadBuInterfaceFromFile(decompInterfaceFile, ref thisInterface, "ALL");
File.Delete(decompInterfaceFile);
if (type == "pqs")
{
string asymChain1 = thisInterface.firstSymOpString.Substring(0, thisInterface.firstSymOpString.IndexOf("_"));
string asymChain2 = thisInterface.secondSymOpString.Substring(0, thisInterface.secondSymOpString.IndexOf("_"));
if (asymChain1 == "-" || asymChain2 == "-")
{
continue;
}
ConvertPqsResidueNumToPdb(pdbId, ref thisInterface);
}
if (thisInterface.GetInterfaceResidueDist())
{
interfaceList.Add(thisInterface);
}
}
catch (Exception ex)
{
ProtCidSettings.progressInfo.progStrQueue.Enqueue
("Errors in retrieving interfaces from " + interfaceFile + ": " + ex.Message);
}
}
}
return(interfaceList.ToArray());
}
/// <summary>
/// for h**o-dimer with sequence identity of two monomers > 95%
/// </summary>
/// <param name="inInterface">an interface with two homologous chains, with sequence identity >= 95%</param>
/// <returns></returns>
public double CalculateHomoInterfaceSymmetry(InterfaceChains inInterface)
{
if (inInterface.seqDistHash == null)
{
inInterface.GetInterfaceResidueDist();
}
List <string> seqIdPairListA = new List <string>();
List <string> seqIdPairListB = new List <string>();
foreach (string seqIdPair in inInterface.seqDistHash.Keys)
{
seqIdPairListA.Add(seqIdPair);
string[] seqIds = seqIdPair.Split('_');
seqIdPairListB.Add(seqIds[1] + "_" + seqIds[0]);
}
List <string> totalSeqPairList = new List <string>(seqIdPairListA);
List <string> sameSeqPairList = new List <string>();
foreach (string seqPair in seqIdPairListA)
{
if (seqIdPairListB.Contains(seqPair))
{
sameSeqPairList.Add(seqPair);
}
}
foreach (string seqPair in seqIdPairListB)
{
if (!totalSeqPairList.Contains(seqPair))
{
totalSeqPairList.Add(seqPair);
}
}
double jIndex = (double)sameSeqPairList.Count / (double)totalSeqPairList.Count;
return(jIndex);
}