/// <summary>
/// assign data to a table
/// </summary>
private void AssignDomainInterfaceToTable(string pdbId, string chain,
string DomainID1, string DomainID2, ref int dInterfaceId)
{
DataRow domainInterfaceRow =
DomainInterfaceTables.domainInterfaceTables[DomainInterfaceTables.DomainInterfaces].NewRow();
DataRow[] rangeRows = multDomainTable.Select(string.Format("DomainID = '{0}'", DomainID1));
// domainInterfaceRow["DomainRange1"] = rangeRows[0]["DomainRanges"];
string family1 = rangeRows[0]["FamilyCode"].ToString().Trim();
rangeRows = multDomainTable.Select(string.Format("DomainID = '{0}'", DomainID2));
// domainInterfaceRow["DomainRange2"] = rangeRows[0]["DomainRanges"];
string family2 = rangeRows[0]["FamilyCode"].ToString().Trim();
char isReversed = '0';
int relSeqId = DomainClassifier.GetRelSeqId(family1, family2, out isReversed);
domainInterfaceRow["RelSeqID"] = relSeqId;
// domainInterfaceRow["GroupSeqID"] = groupId;
domainInterfaceRow["PdbID"] = pdbId;
domainInterfaceRow["InterfaceID"] = 0;
domainInterfaceRow["DomainInterfaceId"] = dInterfaceId;
domainInterfaceRow["DomainID1"] = DomainID1;
domainInterfaceRow["DomainID2"] = DomainID2;
dInterfaceId++;
// domainInterfaceRow["NumOfSg"] = 1;
// domainInterfaceRow["NumOfSg_Identity"] = 1;
domainInterfaceRow["AsymChain1"] = chain;
domainInterfaceRow["AsymChain2"] = chain;
domainInterfaceRow["IsReversed"] = isReversed;
domainInterfaceRow["SurfaceArea"] = -1;
DomainInterfaceTables.domainInterfaceTables[DomainInterfaceTables.DomainInterfaces].Rows.Add(domainInterfaceRow);
}
/// <summary>
///
/// </summary>
/// <param name="stepNum"></param>
public void BuildDomainInterfaces(int stepNum)
{
InitializeThread();
DomainInterfaceTables.InitializeTables();
ProtCidSettings.progressInfo.Reset();
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Retrieving domain-domain interactions.");
/* ProtCidSettings.progressInfo.progStrQueue.Enqueue("Creating database tables.");
* DomainInterfaceTables.InitializeDbTables();
* ProtCidSettings.progressInfo.progStrQueue.Enqueue("Done.");
*/
switch (stepNum)
{
case 1:
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Detecting domain-domain interactions from cryst chain interfaces.");
DomainClassifier domainClassifier = new DomainClassifier();
domainClassifier.RetrieveDomainInterfaces();
ProtCidSettings.progressInfo.currentOperationIndex++;
// goto case 1;
break;
case 2:
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Write domain interface files.");
DomainInterfaceWriter domainInterfaceWriter = new DomainInterfaceWriter();
domainInterfaceWriter.WriteDomainInterfaceFiles();
// domainInterfaceWriter.UpdateDomainInterfaceFiles();
// domainInterfaceWriter.WriteMultiChainDomainInterfaces();
ProtCidSettings.progressInfo.currentOperationIndex++;
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Calculate SAs of domain interface files.");
DomainInterfaceSA interfaceSa = new DomainInterfaceSA();
// interfaceSa.UpdateDomainInterfaceSAs();
interfaceSa.CalculateDomainInterfaceSAs();
ProtCidSettings.progressInfo.currentOperationIndex++;
// goto case 2;
break;
case 3:
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Comparing domain interfaces.");
PfamDomainInterfaceComp domainComp = new PfamDomainInterfaceComp();
domainComp.CompareDomainInterfaces();
/* domainComp.SynchronizeDomainChainInterfaceComp();
* domainComp.CompareSpecificDomainInterfaces ();
* domainComp.UpdateMultiChainDomainInterfaces();
*/
ProtCidSettings.progressInfo.currentOperationIndex++;
break;
case 4:
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Comparing entry domain interfaces.");
DomainInterfaceBuComp.CrystBuDomainInterfaceComp domainInterfaceComp =
new InterfaceClusterLib.DomainInterfaces.DomainInterfaceBuComp.CrystBuDomainInterfaceComp();
// int[] relSeqIds = {10515 };
// domainInterfaceComp.UpdateCrystBuDomainInterfaceComp(relSeqIds);
domainInterfaceComp.CompareCrystBuDomainInterfaces();
ProtCidSettings.progressInfo.currentOperationIndex++;
break;
case 5:
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Cluster domain interfaces.");
DomainInterfaceCluster interfaceCluster = new DomainInterfaceCluster();
int[] relSeqIds = { 2 };
interfaceCluster.UpdateDomainInterfaceClusters(relSeqIds);
// interfaceCluster.ClusterDomainInterfaces();
// interfaceCluster.ClusterLeftRelations();
break;
// goto case 4;
case 6:
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Print Domain Interface Cluster Info.");
DomainClusterStat clusterStat = new DomainClusterStat();
int[] updateRelSeqIds = { 2 };
clusterStat.UpdateDomainClusterInfo(updateRelSeqIds);
// clusterStat.PrintDomainClusterInfo();
// clusterStat.PrintDomainDbSumInfo("PfamDomain");
// clusterStat.AddNumCFsToIPfamInPdbMetaData();
// clusterStat.PrintPartialDomainClusterInfo();
// clusterStat.GetPfamDomainSumInfo();
/* DomainInterfaceStatInfo statInfo = new DomainInterfaceStatInfo();
* // statInfo.PrintPepInteractingHmmSites();
* // statInfo.GetPfamPepInterfaceClusterInfo();
* // statInfo.PrintPepLigandHmmSites ();
* statInfo.PrintPfamDomainRelationInfo();
* // statInfo.GetGenAsymChainDomainInterfaces();*/
break;
// goto case 7;
case 7:
PfamClusterFilesCompress clusterFileCompress = new PfamClusterFilesCompress();
clusterFileCompress.CompressPfamClusterChainInterfaceFiles();
clusterFileCompress.RetrieveCrystInterfaceFilesNotInClusters(true);
DomainSeqFasta seqFasta = new DomainSeqFasta();
seqFasta.PrintClusterDomainSequences();
DomainInterfaceImageGen imageGen = new DomainInterfaceImageGen();
imageGen.GenerateDomainInterfaceImages();
PfamRelNetwork pfamNetWriter = new PfamRelNetwork();
pfamNetWriter.GeneratePfamNetworkGraphmlFiles();
// build the unp-unp interaction table based on pdb domain interfaces
UnpInteractionStr unpInteract = new UnpInteractionStr();
unpInteract.BuildUnpInteractionNetTable();
break;
case 8: // about peptide interfaces
PfamPeptideInterfaces pepInterfaces = new PfamPeptideInterfaces();
pepInterfaceBuilder.BuildPfamPeptideInterfaces();
break;
case 9:
// ligandInteractBuilder.AddClusterInfoToPfamDomainAlign();
ligandInteractBuilder.BuildPfamLigandInteractions();
break;
default:
break;
}
ProtCidSettings.logWriter.Close();
ProtCidSettings.progressInfo.threadFinished = true;
}
/// <summary>
///
/// </summary>
public void UpdateDomainInterfacesDb(string[] updateEntries)
{
Dictionary <int, string[]> updateRelEntryDict = new Dictionary <int, string[]>();
string updateRelEntryFile = "UpdateRelationEntries_missing.txt";
// string updateRelEntryFile = "NoCompRepHomoEntriesRel1.txt";
string line = "";
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Detecting domain-domain interactions from cryst chain interfaces.");
ProtCidSettings.logWriter.WriteLine("Detecting domain-domain interactions from cryst chain interfaces.");
DomainClassifier domainClassifier = new DomainClassifier();
updateRelEntryDict = domainClassifier.UpdateDomainInterfaces(updateEntries);
ProtCidSettings.progressInfo.currentOperationIndex++;
if (updateRelEntryDict.Count == 0)
{
if (File.Exists(updateRelEntryFile))
{
List <string> updateEntryList = new List <string>();
StreamReader dataReader = new StreamReader(updateRelEntryFile);
while ((line = dataReader.ReadLine()) != null)
{
string[] fields = line.Split(' ');
string[] entries = new string[fields.Length - 1];
Array.Copy(fields, 1, entries, 0, entries.Length);
updateRelEntryDict.Add(Convert.ToInt32(fields[0]), entries);
for (int i = 1; i < fields.Length; i++)
{
if (!updateEntryList.Contains(fields[i]))
{
updateEntryList.Add(fields[i]);
}
}
}
dataReader.Close();
if (updateEntries == null)
{
updateEntries = updateEntryList.ToArray();
}
}
}
if (updateRelEntryDict.Count == 0)
{
ProtCidSettings.progressInfo.progStrQueue.Enqueue("No relations need to be updated, program terminated, and return.");
return;
}
List <int> updateRelationList = new List <int>(updateRelEntryDict.Keys);
updateRelationList.Sort();
int[] updateRelSeqIds = updateRelationList.ToArray();
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Updating domain interface files.");
ProtCidSettings.logWriter.WriteLine("Updating domain interface files.");
DomainInterfaceWriter domainInterfaceFileGen = new DomainInterfaceWriter();
domainInterfaceFileGen.UpdateDomainInterfaceFiles(updateRelEntryDict);
// domainInterfaceFileGen.WriteMissingDomainInterfaceFiles();
ProtCidSettings.progressInfo.currentOperationIndex++;
ProtCidSettings.logWriter.Flush();
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Update the surface areas for the domain interfaces.");
ProtCidSettings.logWriter.WriteLine("Update the surfacea areas for the domain interfaces");
DomainInterfaceSA interfaceSa = new DomainInterfaceSA();
interfaceSa.UpdateDomainInterfaceSAs(updateEntries);
// interfaceSa.CalculateDomainInterfaceSAs ();
ProtCidSettings.progressInfo.currentOperationIndex++;
ProtCidSettings.logWriter.Flush();
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Updating the comparison of domain interfaces in each relation.");
ProtCidSettings.logWriter.WriteLine("Updating the comparison of domain interfaces in each relation.");
PfamDomainInterfaceComp domainComp = new PfamDomainInterfaceComp();
domainComp.UpdateEntryDomainInterfaceComp(updateRelEntryDict);
// domainComp.SynchronizeDomainChainInterfaceComp(updateEntries);
// domainComp.CompareRepHomoEntryDomainInterfaces();
ProtCidSettings.progressInfo.currentOperationIndex++;
ProtCidSettings.logWriter.Flush();
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Updating the comparison between cryst and BU entry domain interfaces.");
ProtCidSettings.logWriter.WriteLine("Updating the comparison between cryst and BU entry domain interfaces.");
DomainInterfaceBuComp.CrystBuDomainInterfaceComp domainInterfaceComp =
new InterfaceClusterLib.DomainInterfaces.DomainInterfaceBuComp.CrystBuDomainInterfaceComp();
domainInterfaceComp.UpdateCrystBuDomainInterfaceComp(updateEntries);
// string[] buUpdateEntries = GetOtherUpdateEntries(@"D:\Qifang\ProjectData\DbProjectData\PDB\newls-pdb_bucomp.txt");
// domainInterfaceComp.UpdateCrystBuDomainInterfaceComp(buUpdateEntries);
ProtCidSettings.progressInfo.currentOperationIndex++;
ProtCidSettings.logWriter.Flush();
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Update domain interface clusters.");
ProtCidSettings.logWriter.WriteLine("Update domain interface clusters.");
DomainInterfaceCluster domainInterfaceCluster = new DomainInterfaceCluster();
domainInterfaceCluster.UpdateDomainInterfaceClusters(updateRelSeqIds);
ProtCidSettings.logWriter.Flush();
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Update Domain Interface Cluster Info.");
ProtCidSettings.logWriter.WriteLine("Update Domain Interface Cluster Info.");
DomainClusterStat clusterStat = new DomainClusterStat();
clusterStat.UpdateDomainClusterInfo(updateRelEntryDict);
ProtCidSettings.logWriter.Flush();
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Update cluster file compressing.");
ProtCidSettings.logWriter.WriteLine("Update compressing cluster interface files.");
PfamClusterFilesCompress clusterFileCompress = new PfamClusterFilesCompress();
clusterFileCompress.UpdateRelationClusterChainInterfaceFiles(updateRelSeqIds);
ProtCidSettings.logWriter.WriteLine("Copy interfaces not in any clusters");
clusterFileCompress.UpdateCrystInterfaceFilesNotInClusters(updateRelSeqIds, true);
ProtCidSettings.logWriter.Flush();
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Update domain cluster interface images.");
ProtCidSettings.logWriter.WriteLine("Update domain cluster interface images");
DomainInterfaceImageGen imageGen = new DomainInterfaceImageGen();
imageGen.UpdateDomainInterfaceImages(updateRelSeqIds);
ProtCidSettings.logWriter.Flush();
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Update domain cluster sequence files.");
ProtCidSettings.logWriter.WriteLine("Update domain cluster sequence files.");
DomainSeqFasta seqFasta = new DomainSeqFasta();
seqFasta.UpdateClusterDomainSequences(updateRelSeqIds);
ProtCidSettings.logWriter.Flush();
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Update Pfam-Pfam network files.");
ProtCidSettings.logWriter.WriteLine("Update Pfam-Pfam network files.");
PfamRelNetwork pfamNetWriter = new PfamRelNetwork();
pfamNetWriter.UpdatePfamNetworkGraphmlFiles(updateEntries);
ProtCidSettings.logWriter.Flush();
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Update Uniprot-uniprot domain interactions.");
ProtCidSettings.logWriter.WriteLine("Update Uniprot-uniprot domain interactions.");
// build the unp-unp interaction table based on pdb domain interfaces
UnpInteractionStr unpInteract = new UnpInteractionStr();
unpInteract.UpdateUnpInteractionNetTable(updateEntries);
ProtCidSettings.logWriter.Flush();
// update the domain alignment pymol session files
// move the code after clustering ligands on May 2, 2017, so the cluster info can be included in the Pfam-ligands file
/* ProtCidSettings.progressInfo.progStrQueue.Enqueue("Update compiling domain alignment pymol sessions");
* PfamDomainFileCompress domainFileCompress = new PfamDomainFileCompress();
* domainFileCompress.UpdatePfamDomainFiles(updateEntries);*/
ProtCidSettings.logWriter.WriteLine("Done!");
ProtCidSettings.logWriter.Flush();
}
