/// <summary>
///
/// </summary>
public void BuildPfamLigandInteractions()
{
DomainInterfaceBuilder.InitializeThread();
PfamDnaRnaInteractions pfamDnaInteract = new PfamDnaRnaInteractions();
pfamDnaInteract.RetrievePfamDnaRnaInteractions();
PfamLigandInteractions pfamLigandInteract = new PfamLigandInteractions();
pfamLigandInteract.GetLigandsInPdb();
pfamLigandInteract.RetrievePfamLigandInteractions();
pfamLigandInteract.GetPfamLigandInteractionSumInfo();
pfamLigandInteract.PrintLigandInteractingPfamsSumInfo();
PfamDnaRnaFileCompress dnaRnaFileCompress = new PfamDnaRnaFileCompress();
dnaRnaFileCompress.WriteDomainDnaRnaFiles();
// LigandComAtomsPfam ligandComAtomCal = new LigandComAtomsPfam();
// ligandComAtomCal.CalculateOverlapLigandAtomsInPfam();
LigandComPfamHmm comPfamHmm = new LigandComPfamHmm();
comPfamHmm.CalculateLigandsComPfamHmmPos();
PfamLigandClusterHmm ligandClusters = new PfamLigandClusterHmm();
ligandClusters.ClusterPfamLigandsByPfamHmm();
// need add ligand clusters to the domain tar.gz files
// move the operation here on April 28, 2017
PfamDomainFileCompress domainFileCompress = new PfamDomainFileCompress();
domainFileCompress.CompressPfamDomainFiles();
PfamLigandFileCompress ligandFileCompress = new PfamLigandFileCompress();
ligandFileCompress.CompressLigandPfamDomainFilesFromPdb();
}
/// <summary>
///
/// </summary>
/// <param name="updateEntries"></param>
public void UpdatePfamLigandInteractions(string[] updateDnaRnaEntries, string[] updateEntries)
{
DomainInterfaceBuilder.InitializeThread();
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Update Pfam-DNA/RNA interactions info");
PfamDnaRnaInteractions pfamDnaInteract = new PfamDnaRnaInteractions();
// pfamDnaInteract.UpdatePfamDnaRnaInteractions(updateDnaRnaEntries);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Update Pfam-ligands interactions info");
PfamLigandInteractions pfamLigands = new PfamLigandInteractions();
// pfamLigands.UpdateLigandsInPdb(updateEntries);
pfamLigands.UpdatePfamLigandInteractions(updateEntries);
pfamLigands.UpdatePfamLigandInteractionSumInfo(updateEntries);
pfamLigands.UpdateLigandInteractingPfamsSumInfo(updateEntries);
PfamDnaRnaFileCompress dnaRnaFileCompress = new PfamDnaRnaFileCompress();
dnaRnaFileCompress.UpdateDomainDnaRnaFiles(updateDnaRnaEntries);
LigandComPfamHmm ligandComHmmCal = new LigandComPfamHmm();
Dictionary <string, List <string> > updatePfamEntryListDict = ligandComHmmCal.UpdateLigandsComPfamHmmPos(updateEntries);
PfamLigandClusterHmm ligandClusters = new PfamLigandClusterHmm();
ligandClusters.UpdatePfamLigandsByPfamHmm(updatePfamEntryListDict);
PfamDomainFileCompress domainFileCompress = new PfamDomainFileCompress();
domainFileCompress.UpdatePfamDomainFiles(updateEntries);
PfamLigandFileCompress ligandFileCompress = new PfamLigandFileCompress();
ligandFileCompress.UpdateLigandPfamDomainFilesFromPdb(updateEntries);
}