/// <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); }