Ejemplo n.º 1
0
        /// <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();
        }
Ejemplo n.º 2
0
        /// <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);
        }