/// <summary> /// superpose one chain, then calculate RMSD between chain and peptide /// </summary> public void ComparePeptideChainInterfaces() { ProtCidSettings.progressInfo.progStrQueue.Enqueue("Superpose chains, then calculate peptide and chain RMSD"); ProtCidSettings.logWriter.WriteLine("Superpose chains, then calculate peptide and chain RMSD"); PfamChainInterfaceHmmSites pepChainHmmSiteComp = new PfamChainInterfaceHmmSites(); // common hmm positions between peptide and chain interfaces pepChainHmmSiteComp.CountPfamPepChainInterfaceHmmSites(); // pepChainHmmSiteComp.CountPfamMissingChainInterfaceHmmSites("Pkinase", 18047); // pepChainHmmSiteComp.CountPfamMissingChainInterfaceHmmSites(); // pepChainHmmSiteComp.RemovePeptideChainHmmSitesComp(); // peptide-chain RMSD PeptideChainInterfaceRmsd pepChainRmsd = new PeptideChainInterfaceRmsd(); // pepChainRmsd.CalculateClusterPeptideChainInterfaceRmsd(); pepChainRmsd.CalculatePeptideChainRmsd(); // pepChainRmsd.ImportPepChainRmsdIntoDb(); // PepClusterInterfaceCompress pepInterfaceCompress = new PepClusterInterfaceCompress (); // pepInterfaceCompress.CompressClusterPeptidChainInterfacesFiles(); // pepCluster.FindChainInterfacesNotIn(); // pepCluster.CompressPepChainInterfaces();*/ ProtCidSettings.progressInfo.progStrQueue.Enqueue("RMSD between peptide and chain done!"); ProtCidSettings.logWriter.WriteLine("RMSD between peptide and chain done!"); }
/// <summary> /// /// </summary> /// <param name="updateEntries"></param> public void UpdatePfamPepChainComparison(string[] updateEntries) { PfamChainInterfaceHmmSites pepChainHmmSites = new PfamChainInterfaceHmmSites(); pepChainHmmSites.UpdateCountPfamChainInterfaceHmmSites(updateEntries); PeptideChainInterfaceRmsd pepChainRmsd = new PeptideChainInterfaceRmsd(); pepChainRmsd.UpdateCalculatePeptideChainRmsd(updateEntries); // pepChainRmsd.CalculatePeptideChainRmsd (); PepClusterInterfaceCompress pepInterfaceCompress = new PepClusterInterfaceCompress(); pepInterfaceCompress.CompressClusterPeptidChainInterfacesFiles(); }