Example #1
0
        public void BuildClanDomainInterfaces(int step)
        {
            ProtCidSettings.dataType = "pfam";
            DomainInterfaceBuilder.InitializeThread();

            DomainInterfaceTables.InitializeTables();
            ProtCidSettings.progressInfo.Reset();
            ProtCidSettings.progressInfo.progStrQueue.Enqueue("Retrieving domain-domain interactions.");

            switch (step)
            {
            case 1:
                ClanDomainInterfaceComp domainInterfaceComp = new ClanDomainInterfaceComp();
                int relSeqId1 = 11619;
                int relSeqId2 = 11642;
                int clanSeqId = 398;
                domainInterfaceComp.CompareRepDomainInterfaces2PfamRelations(clanSeqId, relSeqId1, relSeqId2);
                break;

            case 2:
                ClanDomainInterfaceCluster clanInterfaceCluster = new ClanDomainInterfaceCluster();
                clanInterfaceCluster.ClusterSuperDomainInterfaces();
                break;

            case 3:     // output coordinate domain interfaces for each cluster
                break;

            default:
                break;
            }
        }
Example #2
0
        private void uniProtToolStripMenuItem_Click(object sender, EventArgs e)
        {
            DomainInterfaceBuilder.InitializeThread();
            UnpInteractionStr unpDomainInter = new UnpInteractionStr();

            unpDomainInter.BuildUnpInteractionNetTable();
        }
Example #3
0
        /// <summary>
        ///
        /// </summary>
        public void ClusterUserDefinedGroupDomainInterfaces()
        {
            ProtCidSettings.dataType = "pfam";
            DomainInterfaceBuilder.InitializeThread();

            DomainInterfaceTables.InitializeTables();
            ProtCidSettings.progressInfo.Reset();
            ProtCidSettings.progressInfo.progStrQueue.Enqueue("Retrieving domain-domain interactions for user-defined group.");

            // structure alignments between representative domains from PFAMs in a group
            int groupSeqId = 100000;

            /*     Hashtable groupPfamHash = new Hashtable();
             *     string[] groupPfams = { "Integrase_Zn", "zf-H2C2" };
             *     groupPfamHash.Add(groupSeqId, groupPfams);
             *
             *     PfamLib.DomainAlign.PfamDomainAlign domainAlign = new PfamLib.DomainAlign.PfamDomainAlign();
             *     domainAlign.AlignPfamDomainsForUserDefinedGroups(groupPfamHash);
             */
            // calcuate the Q score between two different relations
            groupSeqId = 100000;
            Dictionary <int, int[]> groupRelationHash = new Dictionary <int, int[]> ();
            List <int> relSeqIdList = new List <int> ();

            relSeqIdList.Add(7956);
            relSeqIdList.Add(15374);
            int[] relSeqIds = new int[relSeqIdList.Count];
            relSeqIdList.CopyTo(relSeqIds);
            groupRelationHash.Add(groupSeqId, relSeqIds);

            groupSeqId++;
            relSeqIdList = new List <int> ();
            relSeqIdList.Add(7954);
            relSeqIdList.Add(15481);
            relSeqIds = new int[relSeqIdList.Count];
            relSeqIdList.CopyTo(relSeqIds);
            groupRelationHash.Add(groupSeqId, relSeqIds);

            Dictionary <string, string> pfamClanHash = new Dictionary <string, string> ();

            pfamClanHash.Add("Integrase_Zn", "Zn_N");
            pfamClanHash.Add("zf-H2C2", "Zn_N");

            ClanDomainInterfaceComp domainInterfaceComp = new ClanDomainInterfaceComp();

            domainInterfaceComp.CompareRepDomainInterfaces2PfamRelations(groupRelationHash, pfamClanHash);
        }
Example #4
0
        /// <summary>
        ///
        /// </summary>
        /// <param name="updateEntries"></param>
        public void UpdatePfamLigandInteractions(string[] updateEntries)
        {
            DomainInterfaceBuilder.InitializeThread();

/*
 *          ProtCidSettings.progressInfo.progStrQueue.Enqueue("Update Pfam-DNA/RNA interactions info");
 *          ProtCidSettings.logWriter.WriteLine("Update Pfam-DNA/RNA interactions info");
 *          PfamDnaRnaInteractions pfamDnaInteract = new PfamDnaRnaInteractions();
 *          string[] updateDnaRnaEntries = null;
 *          updateDnaRnaEntries = pfamDnaInteract.GetUpdateEntriesWithDnaRna(updateEntries);
 *          pfamDnaInteract.UpdatePfamDnaRnaInteractions(updateDnaRnaEntries);
 *
 *          ProtCidSettings.progressInfo.progStrQueue.Enqueue("Update Pfam-ligands interactions info");
 *          ProtCidSettings.logWriter.WriteLine("Update Pfam-ligands interactions info");
 *          PfamLigandInteractions pfamLigands = new PfamLigandInteractions();
 *          pfamLigands.UpdateLigandsInPdb(updateEntries);
 *          pfamLigands.UpdatePfamLigandInteractions(updateEntries);
 *          pfamLigands.UpdatePfamLigandInteractionSumInfo(updateEntries);
 *          pfamLigands.UpdateLigandInteractingPfamsSumInfo(updateEntries);
 *
 *          ProtCidSettings.logWriter.WriteLine("Update Pfam-DNA/RNA interface files");
 *          PfamDnaRnaFileCompress dnaRnaFileCompress = new PfamDnaRnaFileCompress();
 *          dnaRnaFileCompress.UpdateDomainDnaRnaFiles(updateDnaRnaEntries);
 *
 *          ProtCidSettings.logWriter.WriteLine("Update Pfam-ligands the number of common Pfam HMM positions");
 *          LigandComPfamHmm ligandComHmmCal = new LigandComPfamHmm();
 *          Dictionary<string, List<string>> updatePfamEntryListDict = ligandComHmmCal.UpdateLigandsComPfamHmmPos(updateEntries);
 * //         Dictionary<string, List<string>> updatePfamEntryListDict = ligandComHmmCal.GetUpdatePfams(updateEntries);
 *
 *          ProtCidSettings.logWriter.WriteLine("Update Pfam-ligands clusters");
 *          PfamLigandClusterHmm ligandClusters = new PfamLigandClusterHmm();
 *          ligandClusters.UpdatePfamLigandsByPfamHmm(updatePfamEntryListDict);
 */
            ProtCidSettings.logWriter.WriteLine("Update compressing Pfam-ligands domain interface files. Pfam_ID.tar.gz: Pfam domain aligned (one Pfam - ligands)");
            PfamDomainFileCompress domainFileCompress = new PfamDomainFileCompress();

            domainFileCompress.UpdatePfamDomainFiles(updateEntries);

            ProtCidSettings.logWriter.WriteLine("Update ligand-Pfam domain interface files. Ligand.tar.gz (one ligand - Pfams) ");
            PfamLigandFileCompress ligandFileCompress = new PfamLigandFileCompress();

            ligandFileCompress.UpdateLigandPfamDomainFilesFromPdb(updateEntries);

            ProtCidSettings.logWriter.WriteLine("Pfam-ligand update is done!");
            ProtCidSettings.logWriter.Flush();
        }
Example #5
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();
        }
Example #6
0
        public void DebugPfamLigandInteractions()
        {
            DomainInterfaceBuilder.InitializeThread();

            /*           LigandComPfamHmm comPfamHmm = new LigandComPfamHmm();
             *         string pfamId = "T-box";
             *         comPfamHmm.CalculatePfamLigandComHmmPos (pfamId);
             *
             *         PfamLigandClusterHmm ligandClusters = new PfamLigandClusterHmm();
             * //           pfamId = "1-cysPrx_C";
             *         ligandClusters.ClusterPfamLigandsByPfamHmm(pfamId, false);
             * //          ligandClusters.ClusterPfamLigandsByPfamHmm();
             *
             *         PfamDomainFileCompress domainFileCompress = new PfamDomainFileCompress();
             * //           domainFileCompress.CompressPfamDomainFiles();
             * //            pfamId = "40S_S4_C"; // 40S_S4_C
             *         domainFileCompress.CompilePfamDomainWithLigandFiles(pfamId, null);*/

            PfamLigandFileCompress ligandFileCompress = new PfamLigandFileCompress();
            string ligandId = "DNA";

            ligandFileCompress.CompressDomainDnaRnaFiles(ligandId);
            ligandFileCompress.CompressLigandPfamDomainFilesFromPdb();
        }
Example #7
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);
        }