/// <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="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();
}