/// <summary>
/// check the representative interfaces exist in the NMR group
/// </summary>
/// <param name="noCrystFileList"></param>
/// <param name="groupId"></param>
/// <returns></returns>
public InterfaceChains[] GetNmrEntryInterfaces(string[] nmrPdbList)
{
asuInterfacesNonCryst = new AsuInterfaces();
Dictionary <string, InterfaceChains[]> sgEntryInterfacesHash = new Dictionary <string, InterfaceChains[]> ();
CrystInterfaceTables.InitializeTables();
foreach (string pdbId in nmrPdbList)
{
string noCrystFile = Path.Combine(ProtCidSettings.dirSettings.coordXmlPath, pdbId + ".xml.gz");
// unzip xml file
if (!File.Exists(noCrystFile))
{
ProtCidSettings.progressInfo.progStrQueue.Enqueue(string.Format("{0} file not exist. ", noCrystFile));
#if DEBUG
ProtCidSettings.logWriter.WriteLine(string.Format("{0} file not exist. ", noCrystFile));
#endif
continue;
}
try
{
InterfaceChains[] asuInterfaces = null;
asuInterfaces = asuInterfacesNonCryst.GetAsuInterfacesFromXml(noCrystFile);
AddEntityIDsToInterfaces(pdbId, ref asuInterfaces);
if (asuInterfaces != null && asuInterfaces.Length > 0)
{
sgEntryInterfacesHash.Add(pdbId, asuInterfaces);
AssignEntryInterfacesToTable(asuInterfaces, pdbId, "NMR");
}
}
catch (Exception ex)
{
ProtCidSettings.progressInfo.progStrQueue.Enqueue(ex.Message);
#if DEBUG
ProtCidSettings.logWriter.WriteLine(ex.Message);
#endif
}
}
return(null);
}
/// <summary>
///
/// </summary>
/// <param name="pdbId"></param>
/// <param name="isUpdate"></param>
/// <returns></returns>
public InterfaceChains[] FindUniquePfamInterfaces(string pdbId, bool isUpdate)
{
string spaceGroup = GetEntrySpaceGroup(pdbId);
string xmlFile = Path.Combine(ProtCidSettings.dirSettings.coordXmlPath, pdbId + ".xml.gz");
if (!Directory.Exists(ProtCidSettings.tempDir))
{
Directory.CreateDirectory(ProtCidSettings.tempDir);
}
string coordXmlFile = ParseHelper.UnZipFile(xmlFile, ProtCidSettings.tempDir);
InterfaceChains[] entryInterfaces = null;
AsuInterfaces asuInterfacesNonCryst = new AsuInterfaces();
try
{
if (spaceGroup == "NMR")
{
entryInterfaces = asuInterfacesNonCryst.GetAsuInterfacesFromXml(coordXmlFile);
if (entryInterfaces == null)
{
ProtCidSettings.progressInfo.progStrQueue.Enqueue("NMR entry " + pdbId + " is a monomer.");
#if DEBUG
ProtCidSettings.logWriter.WriteLine("NMR entry " + pdbId + " is a monomer.");
ProtCidSettings.logWriter.Flush();
#endif
}
}
else
{
ContactInCrystal contactInCrystal = new ContactInCrystal();
int numOfChainsInUnitCell = contactInCrystal.FindInteractChains(coordXmlFile);
if (numOfChainsInUnitCell > 64)
{
ProtCidSettings.progressInfo.progStrQueue.Enqueue("The number of chains of " + pdbId + " in a unit cell: " + numOfChainsInUnitCell.ToString());
#if DEBUG
ProtCidSettings.logWriter.WriteLine("The number of chains of " + pdbId + " in a unit cell: " + numOfChainsInUnitCell.ToString());
ProtCidSettings.logWriter.Flush();
#endif
}
if (contactInCrystal.InterfaceChainsList == null)
{
ProtCidSettings.progressInfo.progStrQueue.Enqueue("No interfaces exist in entry: " + pdbId);
}
entryInterfaces = contactInCrystal.InterfaceChainsList;
}
}
catch (Exception ex)
{
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Retrieving interfaces from " + pdbId + " errors: " + ex.Message);
#if DEBUG
ProtCidSettings.logWriter.WriteLine("Retrieving interfaces from " + pdbId + " errors: " + ex.Message);
ProtCidSettings.logWriter.Flush();
#endif
}
finally
{
if (File.Exists(coordXmlFile))
{
File.Delete(coordXmlFile);
}
}
return(entryInterfaces);
}
/// <summary>
/// find unique interfaces in a crystal
/// </summary>
/// <param name="xmlFile"></param>
/// <returns></returns>
public void FindUniqueInterfaces(string repEntry, string[] pdbIdList)
{
CrystInterfaceTables.InitializeTables();
asuInterfacesNonCryst = new AsuInterfaces();
List <string> entryList = new List <string> (pdbIdList);
entryList.Insert(0, repEntry);
if (!Directory.Exists(ProtCidSettings.tempDir))
{
Directory.CreateDirectory(ProtCidSettings.tempDir);
}
ProtCidSettings.progressInfo.ResetCurrentProgressInfo();
ProtCidSettings.progressInfo.currentOperationLabel = "Computing Interfaces.";
ProtCidSettings.progressInfo.totalStepNum = entryList.Count;
ProtCidSettings.progressInfo.totalOperationNum = entryList.Count;
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Computing interfaces from crystal structures.");
Dictionary <string, InterfaceChains[]> entryInterfacesHash = new Dictionary <string, InterfaceChains[]> ();
Dictionary <string, string> entrySgHash = GetEntrySgAsu(entryList);
foreach (string pdbId in entryList)
{
ProtCidSettings.progressInfo.currentFileName = pdbId;
ProtCidSettings.progressInfo.currentOperationNum++;
ProtCidSettings.progressInfo.currentStepNum++;
InterfaceChains[] entryInterfaces = null;
string xmlFile = Path.Combine(ProtCidSettings.dirSettings.coordXmlPath, pdbId + ".xml.gz");
string coordXmlFile = ParseHelper.UnZipFile(xmlFile, ProtCidSettings.tempDir);
try
{
if ((string)entrySgHash[pdbId] == "NMR")
{
entryInterfaces = asuInterfacesNonCryst.GetAsuInterfacesFromXml(coordXmlFile);
}
else
{
ContactInCrystal contactInCrystal = new ContactInCrystal();
int numOfChainsInUnitCell = contactInCrystal.FindInteractChains(coordXmlFile);
if (numOfChainsInUnitCell > 64)
{
ProtCidSettings.progressInfo.progStrQueue.Enqueue("The number of chains of " + pdbId + " in a unit cell: " + numOfChainsInUnitCell.ToString());
}
if (contactInCrystal.InterfaceChainsList == null)
{
continue;
}
entryInterfaces = contactInCrystal.InterfaceChainsList;
}
AssignEntryInterfacesToTable(entryInterfaces, pdbId, (string)entrySgHash[pdbId]);
entryInterfacesHash.Add(pdbId, entryInterfaces);
string deleteString = string.Format("Delete From CrystEntryInterfaces Where PdbID = '{0}'", pdbId);
ProtCidSettings.protcidQuery.Query(deleteString);
dbInsert.InsertDataIntoDBtables
(ProtCidSettings.protcidDbConnection, CrystInterfaceTables.crystInterfaceTables[CrystInterfaceTables.CrystEntryInterfaces]);
CrystInterfaceTables.crystInterfaceTables[CrystInterfaceTables.CrystEntryInterfaces].Clear();
}
catch (Exception ex)
{
if (ex.Message.ToLower().IndexOf("no protein chains") < -1 &&
ex.Message.ToLower().IndexOf("no symmetry operators") < -1)
{
ProtCidSettings.progressInfo.progStrQueue.Enqueue(pdbId + ": " + ex.Message);
#if DEBUG
ProtCidSettings.logWriter.WriteLine(pdbId + ": " + ex.Message);
#endif
}
}
finally
{
if (File.Exists(coordXmlFile))
{
File.Delete(coordXmlFile);
}
}
}
Directory.Delete(ProtCidSettings.tempDir, true);
// compare interfaces between representative entry and its homology entries
// save data into db
crystInterfaceComp.CompareRepHomoEntryInterfacesInGroup(repEntry, pdbIdList, entryInterfacesHash);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Done!");
ProtCidSettings.progressInfo.threadFinished = true;
}
/// <summary>
/// find unique interfaces in a crystal
/// </summary>
/// <param name="xmlFile"></param>
/// <returns></returns>
public void FindUniqueInterfacesFromAsu(string[] pdbIdList)
{
CrystInterfaceTables.InitializeTables();
#if DEBUG
StreamWriter interfaceDataWriter = new StreamWriter("CrystEntryInterfaces.txt", true);
StreamWriter entryInterfaceCompDataWriter = new StreamWriter("EntryInterfaceComp.txt", true);
StreamWriter logWriter = new StreamWriter("EntryInterfaceRetrievalLog.txt", true);
#endif
if (!Directory.Exists(ProtCidSettings.tempDir))
{
Directory.CreateDirectory(ProtCidSettings.tempDir);
}
ProtCidSettings.progressInfo.ResetCurrentProgressInfo();
ProtCidSettings.progressInfo.currentOperationLabel = "Computing Interfaces.";
ProtCidSettings.progressInfo.totalStepNum = pdbIdList.Length;
ProtCidSettings.progressInfo.totalOperationNum = pdbIdList.Length;
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Computing interfaces from crystal structures.");
// Hashtable entrySgHash = GetEntrySgAsu(new ArrayList(pdbIdList));
InterfaceChains[] entryInterfaces = null;
AsuInterfaces asuInterfacesNonCryst = new AsuInterfaces();
string spaceGroup = "";
foreach (string pdbId in pdbIdList)
{
ProtCidSettings.progressInfo.currentFileName = pdbId;
ProtCidSettings.progressInfo.currentOperationNum++;
ProtCidSettings.progressInfo.currentStepNum++;
spaceGroup = GetEntrySpaceGroup(pdbId);
string xmlFile = Path.Combine(ProtCidSettings.dirSettings.coordXmlPath, pdbId + ".xml.gz");
string coordXmlFile = ParseHelper.UnZipFile(xmlFile, ProtCidSettings.tempDir);
try
{
entryInterfaces = asuInterfacesNonCryst.GetAsuInterfacesFromXml(coordXmlFile);
if (entryInterfaces == null)
{
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Entry " + pdbId + " is a monomer.");
#if DEBUG
logWriter.WriteLine("Entry " + pdbId + " is a monomer.");
logWriter.Flush();
#endif
continue;
}
AssignEntryInterfacesToTable(entryInterfaces, pdbId, spaceGroup);
AssignEntryInterfaceCompToTable(pdbId, entryInterfaces);
dbInsert.InsertDataIntoDBtables
(ProtCidSettings.protcidDbConnection, CrystInterfaceTables.crystInterfaceTables[CrystInterfaceTables.CrystEntryInterfaces]);
dbInsert.InsertDataIntoDBtables
(ProtCidSettings.protcidDbConnection, CrystInterfaceTables.crystInterfaceTables[CrystInterfaceTables.EntryInterfaceComp]);
#if DEBUG
WriteDataToFiles(interfaceDataWriter, entryInterfaceCompDataWriter);
#endif
CrystInterfaceTables.crystInterfaceTables[CrystInterfaceTables.CrystEntryInterfaces].Clear();
CrystInterfaceTables.crystInterfaceTables[CrystInterfaceTables.EntryInterfaceComp].Clear();
}
catch (Exception ex)
{
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Retrieving interfaces from " + pdbId + " errors: " + ex.Message);
#if DEBUG
logWriter.WriteLine("Retrieving interfaces from " + pdbId + " errors: " + ex.Message);
logWriter.Flush();
#endif
}
finally
{
if (File.Exists(coordXmlFile))
{
File.Delete(coordXmlFile);
}
}
}
try
{
Directory.Delete(ProtCidSettings.tempDir, true);
}
catch { }
#if DEBUG
interfaceDataWriter.Close();
entryInterfaceCompDataWriter.Close();
logWriter.Close();
#endif
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Done!");
ProtCidSettings.progressInfo.threadFinished = true;
}
