/// <summary>
///
/// </summary>
public void BuildPfamPeptideInterfaceClusters()
{
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Retrieve Pfam-Peptide interfaces and cluster interfaces");
ProtCidSettings.logWriter.WriteLine("Retrieve Pfam-Peptide interfaces and cluster interfaces");
// retreive peptide interfaces
PfamPeptideInterfaces pfamPepInterfaces = new PfamPeptideInterfaces();
pfamPepInterfaces.RetrievePfamPeptideInterfaces();
// pfamPepInterfaces.GetPfamPeptideInPdbMetaData();
// write peptide interfaces into PDB format files
PfamPepInterfaceWriter pepInterfaceWriter = new PfamPepInterfaceWriter();
pepInterfaceWriter.GeneratePfamPeptideInterfaceFiles();
// calculate the SA by NACCESS
DomainInterfaceSA pepInterfaceSa = new DomainInterfaceSA();
pepInterfaceSa.domainInterfaceTableName = "PfamPeptideInterfaces";
pepInterfaceSa.CalculateDomainInterfaceSAs();
// common hmm positions
PfamHmmSites commonHmmSites = new PfamHmmSites();
// common hmm positions between peptide interfaces
commonHmmSites.CountPeptideInterfaceHmmSites();
// common hmmm positions between domain and peptide interfaces
// commonHmmSites.CountPfamCommonHmmSites();
// Peptide-peptide RMSD
PeptideInterfaceRmsd pepInterfaceRmsd = new PeptideInterfaceRmsd();
pepInterfaceRmsd.CalculateDomainInterfacePeptideRmsd();
pepInterfaceRmsd.CalculateMissingPfamDomainInterfacePeptideRmsd();
// cluster peptide interfaces, them compress the peptide interfaces into tar files
PeptideInterfaceCluster pepCluster = new PeptideInterfaceCluster();
pepCluster.ClusterPeptideInterfaces();
PeptideInterfaceClusterStat pepClusterStat = new PeptideInterfaceClusterStat();
pepClusterStat.GetPepInterfaceClusterStat();
PepClusterInterfaceCompress pepClusterFileCompress = new PepClusterInterfaceCompress();
pepClusterFileCompress.CompressClusterPeptideInterfaceFiles();
PfamPepSeqFasta pepSeqFasta = new PfamPepSeqFasta();
pepSeqFasta.PrintPfamPeptideClusterSequences();
PfamPepInterfaceFileCompress fileCompress = new PfamPepInterfaceFileCompress();
fileCompress.CompressPfamPeptideInterfaces();
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Clustering peptide interfaces done!");
ProtCidSettings.logWriter.WriteLine("Clustering peptide interfaces done! ");
}
public void UpdateSomePfamPeptideInteractionsDebug()
{
string[] updateEntries = GetMissingPfamPepInterfacesEntries();
// string[] updateEntries = {"4tq1" };
PfamPeptideInterfaces pfamPepInterfaces = new PfamPeptideInterfaces();
Dictionary <string, string[]> updatePfamEntryDict = pfamPepInterfaces.UpdatePfamPeptideInterfaces(updateEntries);
// PeptideInterfaceClusterStat pepClusterStat1 = new PeptideInterfaceClusterStat();
// pepClusterStat1.AddNumCFs();
string[] updatePfamIds = { "MHC_II_alpha" };
ProtCidSettings.logWriter.WriteLine("Update peptide interface clusters");
// cluster peptide interfaces,
PeptideInterfaceCluster pepCluster = new PeptideInterfaceCluster();
pepCluster.UpdatePeptideInterfaceClusters(updatePfamIds);
ProtCidSettings.logWriter.WriteLine("Done!");
ProtCidSettings.logWriter.Flush();
// the pymol sessions for each pfam-peptide interface clusters
ProtCidSettings.logWriter.WriteLine("Compress peptide interface files of clusters");
PepClusterInterfaceCompress pepClusterFileCompress = new PepClusterInterfaceCompress();
pepClusterFileCompress.UpdateClusterPeptideInterfaceFiles(updatePfamIds);
ProtCidSettings.logWriter.WriteLine("Done!");
ProtCidSettings.logWriter.Flush();
ProtCidSettings.logWriter.WriteLine("Sequences for peptide interface clusters");
// the sequences for both pfam domains and peptides
PfamPepSeqFasta pepSeqFasta = new PfamPepSeqFasta();
pepSeqFasta.UpdatePfamPeptideClusterSequences(updatePfamIds);
ProtCidSettings.logWriter.WriteLine("Done!");
ProtCidSettings.logWriter.Flush();
ProtCidSettings.logWriter.WriteLine("Update peptide interface clusters");
// the summary info for the updated pfams
PeptideInterfaceClusterStat pepClusterStat = new PeptideInterfaceClusterStat();
pepClusterStat.UpdatePepInterfaceClusterStat(updatePfamIds);
ProtCidSettings.logWriter.WriteLine("Done!");
ProtCidSettings.logWriter.Flush();
// update pfam-peptide interfaces, align pfam domains, peptides are not aligned
ProtCidSettings.logWriter.WriteLine("Compress all Pfam-peptide interfaces");
PfamPepInterfaceFileCompress fileCompress = new PfamPepInterfaceFileCompress();
fileCompress.UpdatePfamPeptideInterfaces(updatePfamIds);
ProtCidSettings.logWriter.WriteLine("Update pfam-peptide data done!");
ProtCidSettings.logWriter.Flush();
}
/// <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>
/// <param name="updateEntries"></param>
public void UpdatePfamPeptideInteractions(string[] updateEntries)
{
// retreive peptide interfaces
PfamPeptideInterfaces pfamPepInterfaces = new PfamPeptideInterfaces();
ProtCidSettings.logWriter.WriteLine("Update Pfam-peptide interfaces");
ProtCidSettings.logWriter.WriteLine("#entries=" + updateEntries.Length);
ProtCidSettings.logWriter.Flush();
Dictionary <string, string[]> updatePfamEntryDict = pfamPepInterfaces.UpdatePfamPeptideInterfaces(updateEntries);
// Dictionary<string, string[]> updatePfamEntryDict = ReadUpdatePfamPepEntryHash();
List <string> updatePfamIdList = new List <string>(updatePfamEntryDict.Keys);
updatePfamIdList.Sort();
string[] updatePfamIds = new string[updatePfamIdList.Count];
updatePfamIdList.CopyTo(updatePfamIds);
string[] updatePepEntries = GetUpdateEntriesFromHash(updatePfamEntryDict);
ProtCidSettings.logWriter.WriteLine("Update Pfam-peptide in pdb meta data.");
pfamPepInterfaces.UpdatePfamPeptideInPdbMetaData(updatePfamIds);
ProtCidSettings.logWriter.WriteLine("Done!");
ProtCidSettings.logWriter.Flush();
ProtCidSettings.logWriter.WriteLine("Update Pfam-peptide coordinate interface files.");
// write peptide interfaces into PDB format files
PfamPepInterfaceWriter pepInterfaceWriter = new PfamPepInterfaceWriter();
pepInterfaceWriter.UpdatePfamPeptideInterfaceFiles(updatePepEntries);
// pepInterfaceWriter.WriteDomainPeptideInterfaceFiles();
ProtCidSettings.logWriter.WriteLine("Done!");
ProtCidSettings.logWriter.Flush();
// calculate the SA by NACCESS
ProtCidSettings.logWriter.WriteLine("Update surface areas of pfam-peptide interfaces.");
DomainInterfaceSA pepInterfaceSa = new DomainInterfaceSA();
pepInterfaceSa.domainInterfaceTableName = "PfamPeptideInterfaces";
pepInterfaceSa.UpdateDomainInterfaceSAs(updatePepEntries);
ProtCidSettings.logWriter.WriteLine("Done!");
ProtCidSettings.logWriter.Flush();
ProtCidSettings.logWriter.WriteLine("Update peptide interface hmm sites");
// common hmm positions
PfamHmmSites commonHmmSites = new PfamHmmSites();
// common hmm positions between peptide interfaces
commonHmmSites.UpdatePeptideInterfaceHmmSites(updatePepEntries);
ProtCidSettings.logWriter.WriteLine("Done!");
ProtCidSettings.logWriter.Flush();
// Peptide-peptide RMSD
ProtCidSettings.logWriter.WriteLine("Update peptide RMSDs");
PeptideInterfaceRmsd pepInterfaceRmsd = new PeptideInterfaceRmsd();
pepInterfaceRmsd.UpdateDomainInterfacePeptideRmsd(updatePfamEntryDict);
ProtCidSettings.logWriter.Flush();
ProtCidSettings.logWriter.WriteLine("Update peptide interface clusters");
// cluster peptide interfaces,
PeptideInterfaceCluster pepCluster = new PeptideInterfaceCluster();
pepCluster.UpdatePeptideInterfaceClusters(updatePfamIds);
ProtCidSettings.logWriter.WriteLine("Done!");
ProtCidSettings.logWriter.Flush();
// the pymol sessions for each pfam-peptide interface clusters
ProtCidSettings.logWriter.WriteLine("Compress peptide interface files of clusters");
PepClusterInterfaceCompress pepClusterFileCompress = new PepClusterInterfaceCompress();
pepClusterFileCompress.UpdateClusterPeptideInterfaceFiles(updatePfamIds);
ProtCidSettings.logWriter.WriteLine("Done!");
ProtCidSettings.logWriter.Flush();
ProtCidSettings.logWriter.WriteLine("Sequences for peptide interface clusters");
// the sequences for both pfam domains and peptides
PfamPepSeqFasta pepSeqFasta = new PfamPepSeqFasta();
pepSeqFasta.UpdatePfamPeptideClusterSequences(updatePfamIds);
ProtCidSettings.logWriter.WriteLine("Done!");
ProtCidSettings.logWriter.Flush();
ProtCidSettings.logWriter.WriteLine("Update peptide interface clusters");
// the summary info for the updated pfams
PeptideInterfaceClusterStat pepClusterStat = new PeptideInterfaceClusterStat();
pepClusterStat.UpdatePepInterfaceClusterStat(updatePfamIds);
ProtCidSettings.logWriter.WriteLine("Done!");
ProtCidSettings.logWriter.Flush();
// update pfam-peptide interfaces, align pfam domains, peptides are not aligned
ProtCidSettings.logWriter.WriteLine("Compress all Pfam-peptide interfaces");
PfamPepInterfaceFileCompress fileCompress = new PfamPepInterfaceFileCompress();
fileCompress.UpdatePfamPeptideInterfaces(updatePfamIds);
ProtCidSettings.logWriter.WriteLine("Update pfam-peptide data done!");
ProtCidSettings.logWriter.Flush();
}
