/// <summary>
/// update domain interfaces for same version of Pfam
/// </summary>
public void UpdateDomainInterfaces()
{
InitializeThread();
ProtCidSettings.logWriter.WriteLine(DateTime.Today.ToShortDateString());
ProtCidSettings.logWriter.WriteLine("Updating Pfam domain interface clusters.");
DomainInterfaceTables.InitializeTables();
ProtCidSettings.progressInfo.Reset();
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Update Pfam domain-domain interface info.");
string[] updateEntries = GetUpdateEntries();
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Update domain interface database");
UpdateDomainInterfacesDb(updateEntries);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Update Pfam-Peptide interactions");
PfamPepInterfaceWriter pepInterfaceWriter = new PfamPepInterfaceWriter();
pepInterfaceBuilder.UpdatePfamPeptideInteractions(updateEntries);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Update Pfam-ligand interactions");
ligandInteractBuilder.UpdatePfamLigandInteractions(updateEntries);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Update peptide-chain comparison");
pepInterfaceBuilder.UpdatePfamPepChainComparison(updateEntries);
ProtCidSettings.logWriter.Close();
ProtCidSettings.progressInfo.threadFinished = true;
}
public void UpdatePfamDomainInterfaceClusters()
{
InitializeThread();
DomainInterfaceTables.InitializeTables();
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Comparing entry domain interfaces.");
// string[] updateEntries = {/* "4yc3",*/ "4y72"};
string[] updateEntries = GetReversedOrderDomainInterfaces();
DomainInterfaceBuComp.CrystBuDomainInterfaceComp domainInterfaceComp =
new InterfaceClusterLib.DomainInterfaces.DomainInterfaceBuComp.CrystBuDomainInterfaceComp();
domainInterfaceComp.UpdateCrystBuDomainInterfaceComp(updateEntries);
/* UnpInteractionStr unpInterInPdb = new UnpInteractionStr();
* unpInterInPdb.UpdateUnpInteractionNetTableFromXml ();
* string[] updateEntries = {"4xr8"};
* unpInterInPdb.UpdateUnpInteractionNetTable(updateEntries);
* PfamDomainInterfaceComp domainComp = new PfamDomainInterfaceComp();
* string[] entries = {"5vam", "6cad", "6b8u"};
* domainComp.SynchronizeDomainChainInterfaceComp(entries);
*/
/* DomainClusterStat clusterStat = new DomainClusterStat();
* int[] relSeqIds = { 14511 };
* clusterStat.PrintDomainClusteStatInfo(relSeqIds);
* // clusterStat.AddMissingRedundantInterfacesToClusterTable ();
*
* int[] updateRelSeqIds = GetUpdateRelSeqIds();
* PfamClusterFilesCompress clusterFileCompress = new PfamClusterFilesCompress();
* clusterFileCompress.UpdateRelationClusterChainInterfaceFiles(updateRelSeqIds);
*
* string[] updateEntries = GetOtherUpdateEntries();
*
* UpdateDomainInterfacesDb(updateEntries);
*
* ProtCidSettings.progressInfo.progStrQueue.Enqueue("Comparing entry domain interfaces.");
* DomainInterfaceBuComp.CrystBuDomainInterfaceComp domainInterfaceComp =
* new InterfaceClusterLib.DomainInterfaces.DomainInterfaceBuComp.CrystBuDomainInterfaceComp();
* domainInterfaceComp.UpdateCrystBuDomainInterfaceComp (updateEntries);
*
* int[] updateRelSeqIds = GetUpdateRelSeqIds ();
* Dictionary<int, string[]> updateRelEntryDict = ReadUpdateRelEntries();
*
* ProtCidSettings.progressInfo.progStrQueue.Enqueue("Updating the comparison of domain interfaces in each relation.");
* ProtCidSettings.logWriter.WriteLine("Updating the comparison of domain interfaces in each relation.");
* PfamDomainInterfaceComp domainComp = new PfamDomainInterfaceComp();
* // domainComp.UpdateEntryDomainInterfaceComp(updateEntries);
* domainComp.UpdateEntryDomainInterfaceComp(updateRelEntryDict);
*
* ProtCidSettings.progressInfo.progStrQueue.Enqueue("Update domain interface clusters.");
* ProtCidSettings.logWriter.WriteLine("Update domain interface clusters.");
* DomainInterfaceCluster domainInterfaceCluster = new DomainInterfaceCluster();
* domainInterfaceCluster.ClusterDomainInterfaces();
* // int[] updateRelSeqIds = domainInterfaceCluster.GetUpdateRelSeqIds();
* // domainInterfaceCluster.UpdateDomainInterfaceClusters(updateRelSeqIds);
*
* ProtCidSettings.progressInfo.progStrQueue.Enqueue("Update Domain Interface Cluster Info.");
* ProtCidSettings.logWriter.WriteLine("Update Domain Interface Cluster Info.");
* DomainClusterStat clusterStat = new DomainClusterStat();
* // clusterStat.PrintDomainDbSumInfo("PfamDomain");
* clusterStat.PrintDomainClusterInfo();
*
* // clusterStat.UpdateDomainClusterInfo(updateRelSeqIds);
*
* ProtCidSettings.progressInfo.progStrQueue.Enqueue("Update cluster file compressing.");
* PfamClusterFilesCompress clusterFileCompress = new PfamClusterFilesCompress();
* clusterFileCompress.UpdateRelationClusterChainInterfaceFiles(updateRelSeqIds);
*
* ProtCidSettings.progressInfo.progStrQueue.Enqueue("Update domain cluster interface images.");
* ProtCidSettings.logWriter.WriteLine("Update domain cluster interface images");
* DomainInterfaceImageGen imageGen = new DomainInterfaceImageGen();
* // imageGen.GenerateDomainInterfaceImages();
* imageGen.UpdateDomainInterfaceImages(updateRelSeqIds);
*
* DomainSeqFasta seqFasta = new DomainSeqFasta();
* seqFasta.PrintClusterDomainSequences();
* // seqFasta.UpdateClusterDomainSequences(updateRelSeqIds); */
}
/// <summary>
///
/// </summary>
/// <param name="stepNum"></param>
public void BuildDomainInterfaces(int stepNum)
{
InitializeThread();
DomainInterfaceTables.InitializeTables();
ProtCidSettings.progressInfo.Reset();
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Retrieving domain-domain interactions.");
/* ProtCidSettings.progressInfo.progStrQueue.Enqueue("Creating database tables.");
* DomainInterfaceTables.InitializeDbTables();
* ProtCidSettings.progressInfo.progStrQueue.Enqueue("Done.");
*/
switch (stepNum)
{
case 1:
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Detecting domain-domain interactions from cryst chain interfaces.");
DomainClassifier domainClassifier = new DomainClassifier();
domainClassifier.RetrieveDomainInterfaces();
ProtCidSettings.progressInfo.currentOperationIndex++;
// goto case 1;
break;
case 2:
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Write domain interface files.");
DomainInterfaceWriter domainInterfaceWriter = new DomainInterfaceWriter();
domainInterfaceWriter.WriteDomainInterfaceFiles();
// domainInterfaceWriter.UpdateDomainInterfaceFiles();
// domainInterfaceWriter.WriteMultiChainDomainInterfaces();
ProtCidSettings.progressInfo.currentOperationIndex++;
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Calculate SAs of domain interface files.");
DomainInterfaceSA interfaceSa = new DomainInterfaceSA();
// interfaceSa.UpdateDomainInterfaceSAs();
interfaceSa.CalculateDomainInterfaceSAs();
ProtCidSettings.progressInfo.currentOperationIndex++;
// goto case 2;
break;
case 3:
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Comparing domain interfaces.");
PfamDomainInterfaceComp domainComp = new PfamDomainInterfaceComp();
domainComp.CompareDomainInterfaces();
/* domainComp.SynchronizeDomainChainInterfaceComp();
* domainComp.CompareSpecificDomainInterfaces ();
* domainComp.UpdateMultiChainDomainInterfaces();
*/
ProtCidSettings.progressInfo.currentOperationIndex++;
break;
case 4:
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Comparing entry domain interfaces.");
DomainInterfaceBuComp.CrystBuDomainInterfaceComp domainInterfaceComp =
new InterfaceClusterLib.DomainInterfaces.DomainInterfaceBuComp.CrystBuDomainInterfaceComp();
// int[] relSeqIds = {10515 };
// domainInterfaceComp.UpdateCrystBuDomainInterfaceComp(relSeqIds);
domainInterfaceComp.CompareCrystBuDomainInterfaces();
ProtCidSettings.progressInfo.currentOperationIndex++;
break;
case 5:
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Cluster domain interfaces.");
DomainInterfaceCluster interfaceCluster = new DomainInterfaceCluster();
int[] relSeqIds = { 2 };
interfaceCluster.UpdateDomainInterfaceClusters(relSeqIds);
// interfaceCluster.ClusterDomainInterfaces();
// interfaceCluster.ClusterLeftRelations();
break;
// goto case 4;
case 6:
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Print Domain Interface Cluster Info.");
DomainClusterStat clusterStat = new DomainClusterStat();
int[] updateRelSeqIds = { 2 };
clusterStat.UpdateDomainClusterInfo(updateRelSeqIds);
// clusterStat.PrintDomainClusterInfo();
// clusterStat.PrintDomainDbSumInfo("PfamDomain");
// clusterStat.AddNumCFsToIPfamInPdbMetaData();
// clusterStat.PrintPartialDomainClusterInfo();
// clusterStat.GetPfamDomainSumInfo();
/* DomainInterfaceStatInfo statInfo = new DomainInterfaceStatInfo();
* // statInfo.PrintPepInteractingHmmSites();
* // statInfo.GetPfamPepInterfaceClusterInfo();
* // statInfo.PrintPepLigandHmmSites ();
* statInfo.PrintPfamDomainRelationInfo();
* // statInfo.GetGenAsymChainDomainInterfaces();*/
break;
// goto case 7;
case 7:
PfamClusterFilesCompress clusterFileCompress = new PfamClusterFilesCompress();
clusterFileCompress.CompressPfamClusterChainInterfaceFiles();
clusterFileCompress.RetrieveCrystInterfaceFilesNotInClusters(true);
DomainSeqFasta seqFasta = new DomainSeqFasta();
seqFasta.PrintClusterDomainSequences();
DomainInterfaceImageGen imageGen = new DomainInterfaceImageGen();
imageGen.GenerateDomainInterfaceImages();
PfamRelNetwork pfamNetWriter = new PfamRelNetwork();
pfamNetWriter.GeneratePfamNetworkGraphmlFiles();
// build the unp-unp interaction table based on pdb domain interfaces
UnpInteractionStr unpInteract = new UnpInteractionStr();
unpInteract.BuildUnpInteractionNetTable();
break;
case 8: // about peptide interfaces
PfamPeptideInterfaces pepInterfaces = new PfamPeptideInterfaces();
pepInterfaceBuilder.BuildPfamPeptideInterfaces();
break;
case 9:
// ligandInteractBuilder.AddClusterInfoToPfamDomainAlign();
ligandInteractBuilder.BuildPfamLigandInteractions();
break;
default:
break;
}
ProtCidSettings.logWriter.Close();
ProtCidSettings.progressInfo.threadFinished = true;
}
/// <summary>
///
/// </summary>
public void UpdateDomainInterfaces(int step)
{
InitializeThread();
ProtCidSettings.logWriter.WriteLine(DateTime.Today.ToShortDateString());
ProtCidSettings.logWriter.WriteLine("Updating Pfam domain interface clusters.");
DomainInterfaceTables.InitializeTables();
ProtCidSettings.progressInfo.Reset();
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Update Pfam domain-domain interface info.");
// string[] updateEntries = GetUpdateEntries();
// for update peptide/ligands
// string[] updateEntries = GetOtherUpdateEntries(@"D:\Qifang\ProjectData\DbProjectData\PDB\updateEntries_ligandsDif.txt");
// string[] updateEntries = GetOtherUpdateEntries(@"D:\Qifang\ProjectData\DbProjectData\PDB\MissingChainPepEntries.txt");
// string[] updateEntries = GetMissingDomainInterfaceEntries();
string[] updateEntries = { "2gs0" };
switch (step)
{
case 1:
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Update domain interface database");
UpdateDomainInterfacesDb(updateEntries);
/* int[] updateRelSeqIds = { 10348 };
* PfamClusterFilesCompress clusterFileCompress = new PfamClusterFilesCompress();
* clusterFileCompress.UpdateRelationClusterChainInterfaceFiles(updateRelSeqIds);
* string updateRelEntryFile = "UpdateRelationEntries.txt";
* UpdateDomainInterfacesDb(updateRelEntryFile);
* //
* // updateEntries = GetOtherUpdateEntries();
* updateEntries = new string[1];
* updateEntries[0] = "3mtj";
* DomainInterfaceBuComp.CrystBuDomainInterfaceComp domainInterfaceComp =
* new InterfaceClusterLib.DomainInterfaces.DomainInterfaceBuComp.CrystBuDomainInterfaceComp();
* domainInterfaceComp.UpdateCrystBuDomainInterfaceComp(updateEntries);
* DomainClusterStat clusterStat = new DomainClusterStat();
* clusterStat.UpdateBACompInfo();
* DomainSeqFasta seqFasta = new DomainSeqFasta();
* int[] updateRelSeqIds = { 2986};
* seqFasta.UpdateClusterDomainSequences(updateRelSeqIds);*/
break;
case 2:
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Update Pfam-Peptide interactions");
// pepInterfaceBuilder.UpdatePfamPeptideInteractions(updateEntries);
pepInterfaceBuilder.UpdateSomePfamPeptideInteractionsDebug();
break;
case 3:
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Update Pfam-ligand interactions");
ligandInteractBuilder.UpdatePfamLigandInteractions(updateEntries);
/* ligandInteractBuilder.DebugPfamLigandInteractions();
* ligandInteractBuilder.UpdatePfamLigandInteractions(updateDnaEntries, updateEntries);
* PfamDomainFileCompress domainCompress = new PfamDomainFileCompress();
* domainCompress.CompressPfamDomainFiles ();*/
ProtCidSettings.logWriter.Flush();
break;
case 4:
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Update peptide-chain comparison");
pepInterfaceBuilder.UpdatePfamPepChainComparison(updateEntries);
break;
default:
break;
}
ProtCidSettings.logWriter.Close();
ProtCidSettings.progressInfo.threadFinished = true;
}