/// <summary>
/// rebuild the interfaces from XML coordinate file and the interface definition
/// </summary>
/// <param name="pdbId"></param>
/// <param name="type"></param>
/// <returns></returns>
public InterfaceChains[] GetCrystInterfacesFromXmlFile(string pdbId, string type)
{
ContactInCrystal crystInterfaceRetriever = new ContactInCrystal();
string queryString = string.Format("Select Distinct * From CrystEntryInterfaces " +
" Where PdbID = '{0}';", pdbId);
DataTable interfaceDefTable = ProtCidSettings.protcidQuery.Query(queryString);
Dictionary <int, string> interfaceDefHash = GetInterfaceDefHash(interfaceDefTable);
string xmlFile = Path.Combine(ProtCidSettings.dirSettings.coordXmlPath, pdbId + ".xml.gz");
string coordXmlFile = ParseHelper.UnZipFile(xmlFile, ProtCidSettings.tempDir);
bool interfaceExist = false;
try
{
crystInterfaceRetriever.FindInteractChains(coordXmlFile, interfaceDefHash, out interfaceExist);
SetInterfaceEntities(crystInterfaceRetriever.InterfaceChainsList, interfaceDefTable);
}
catch
{
return(null);
}
finally
{
File.Delete(coordXmlFile);
}
return(crystInterfaceRetriever.InterfaceChainsList);
}
/// <summary>
/// interfaces in crystal structures
/// </summary>
/// <param name="pdbId"></param>
/// <param name="interfaceExist"></param>
/// <returns></returns>
private InterfaceChains[] GetCrystInterfacesFromDb(string pdbId)
{
string xmlFile = Path.Combine(ProtCidSettings.dirSettings.coordXmlPath, pdbId + ".xml.gz");
if (!File.Exists(xmlFile))
{
return(null);
}
string coordXmlFile = ParseHelper.UnZipFile(xmlFile, ProtCidSettings.tempDir);
Dictionary <int, string> interfaceDefHash = null;
Dictionary <int, string> interfaceEntityInfoHash = null;
bool interfaceExist = true;
GetCrystInterfaceDef(pdbId, ref interfaceDefHash, ref interfaceEntityInfoHash);
contactInCrystal.FindInteractChains(coordXmlFile, interfaceDefHash, interfaceEntityInfoHash, out interfaceExist);
if (!interfaceExist)
{
return(null);
}
File.Delete(coordXmlFile);
return(contactInCrystal.InterfaceChainsList);
}
/// <summary>
///
/// </summary>
/// <param name="pdbId"></param>
/// <param name="interfaceIds"></param>
/// <param name="type"></param>
/// <returns></returns>
public InterfaceChains[] GetCrystInterfacesFromXmlFile(string pdbId, int[] interfaceIds, string type)
{
ContactInCrystal crystInterfaceRetriever = new ContactInCrystal();
string queryString = string.Format("Select Distinct * From CrystEntryInterfaces " +
" Where PdbID = '{0}';", pdbId);
DataTable interfaceDefTable = ProtCidSettings.protcidQuery.Query(queryString);
if (interfaceDefTable.Rows.Count == 0)
{
return(null);
}
Dictionary <int, string> interfaceDefHash = GetInterfaceDefHash(interfaceDefTable, interfaceIds);
string xmlFile = Path.Combine(ProtCidSettings.dirSettings.coordXmlPath, pdbId + ".xml.gz");
string coordXmlFile = ParseHelper.UnZipFile(xmlFile, ProtCidSettings.tempDir);
bool interfaceExist = false;
crystInterfaceRetriever.FindInteractChains(coordXmlFile, interfaceDefHash, out interfaceExist);
/* InterfaceChains[] chainInterfaces = new InterfaceChains[interfaceIds.Length];
* int count = 0;
* foreach (int interfaceId in interfaceIds)
* {
* foreach (InterfaceChains crystInterface in crystInterfaceRetriever.InterfaceChainsList)
* {
* if (crystInterface.interfaceId == interfaceId)
* {
* chainInterfaces[count] = crystInterface;
* count++;
* }
* }
* }*/
File.Delete(coordXmlFile);
SetInterfaceEntities(crystInterfaceRetriever.InterfaceChainsList, interfaceDefTable);
return(crystInterfaceRetriever.InterfaceChainsList);
// return chainInterfaces;
}
/// <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 xmlFile, string sg_asu, ref InterfaceChains[] uniqueEntryinterfaces)
{
string pdbId = xmlFile.Substring(xmlFile.LastIndexOf("\\") + 1, 4);
string coordXmlFile = ParseHelper.UnZipFile(xmlFile, ProtCidSettings.tempDir);;
string queryString = string.Format("Select * From CrystEntryInterfaces Where PdbID = '{0}';", pdbId);
DataTable crystInterfaceTable = ProtCidSettings.protcidQuery.Query(queryString);
Dictionary <int, string> interfaceDefHash = new Dictionary <int, string> ();
Dictionary <int, string> interfaceEntityInfoHash = new Dictionary <int, string> ();
if (crystInterfaceTable.Rows.Count > 0)
{
// build cryst interfaces based on database info
foreach (DataRow dRow in crystInterfaceTable.Rows)
{
string symOpString1 = dRow["AsymChain1"].ToString().Trim() + "_" +
dRow["SymmetryString1"].ToString().Trim();
string symOpString2 = dRow["AsymChain2"].ToString().Trim() + "_" +
dRow["SymmetryString2"].ToString().Trim();
if (!interfaceDefHash.ContainsKey(Convert.ToInt32(dRow["InterfaceId"].ToString())))
{
interfaceDefHash.Add(Convert.ToInt32(dRow["InterfaceId"].ToString()),
symOpString1 + ";" + symOpString2);
interfaceEntityInfoHash.Add(Convert.ToInt32(dRow["InterfaceId"].ToString()),
dRow["EntityID1"].ToString() + "_" + dRow["EntityID2"].ToString());
}
}
}
try
{
ContactInCrystal contactInCrystal = new ContactInCrystal();
if (interfaceDefHash.Count > 0) // interfaces defined in db
{
bool interfaceExist = true;
contactInCrystal.FindInteractChains(coordXmlFile, interfaceDefHash, interfaceEntityInfoHash, out interfaceExist);
if (interfaceExist)
{
uniqueEntryinterfaces = contactInCrystal.InterfaceChainsList;
foreach (InterfaceChains interfaceChains in uniqueEntryinterfaces)
{
DataRow[] interfaceDefRows = crystInterfaceTable.Select
(string.Format("InterfaceId = '{0}'", interfaceChains.interfaceId));
interfaceChains.entityId1 = Convert.ToInt32(interfaceDefRows[0]["EntityID1"].ToString());
interfaceChains.entityId2 = Convert.ToInt32(interfaceDefRows[0]["EntityID2"].ToString());
}
}
}
else // no interface definition in db, retrieve interfaces from coordinate file
{
int numOfChainsInUnitCell = contactInCrystal.FindInteractChains(coordXmlFile);
if (numOfChainsInUnitCell > 64)
{
#if DEBUG
ProtCidSettings.logWriter.WriteLine("The number of chains of " + pdbId + " in a unit cell: " + numOfChainsInUnitCell.ToString());
#endif
}
if (contactInCrystal.InterfaceChainsList != null)
{
uniqueEntryinterfaces = contactInCrystal.InterfaceChainsList;
AssignEntryInterfacesToTable(uniqueEntryinterfaces, pdbId, sg_asu);
AssignEntryInterfaceCompToTable(pdbId, uniqueEntryinterfaces);
}
}
}
catch (Exception ex)
{
if (ex.Message.ToLower().IndexOf("no protein chains") < -1 &&
ex.Message.ToLower().IndexOf("no symmetry operators") < -1)
{
throw new Exception(pdbId + ": " + ex);
}
}
finally
{
if (File.Exists(coordXmlFile))
{
File.Delete(coordXmlFile);
}
}
}
/// <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;
}