/// <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!");
}
