/// <summary>
///
/// </summary>
/// <param name="pdbId"></param>
public void WriteDomainDnaRnaInterfaceFiles(string pdbId)
{
string queryString = string.Format("Select * From PfamDnaRnas Where PdbID = '{0}';", pdbId);
DataTable pfamDnaRnaTable = ProtCidSettings.protcidQuery.Query(queryString);
int[] chainDomainIds = GetEntryChainDomainIds(pfamDnaRnaTable);
queryString = string.Format("Select PdbID, AsymID, PolymerStatus, PolymerType From AsymUnit Where PdbID = '{0}';", pdbId);
DataTable entryAsuTable = ProtCidSettings.pdbfamQuery.Query(queryString);
Dictionary <string, List <string> > buDomainWithMaxHmmHash = new Dictionary <string, List <string> > ();
foreach (int chainDomainId in chainDomainIds)
{
SelectDomainDnaRnaInterfaces(chainDomainId, pfamDnaRnaTable, ref buDomainWithMaxHmmHash);
}
List <string> buIdList = new List <string> (buDomainWithMaxHmmHash.Keys);
string[] buIds = new string[buIdList.Count];
buIdList.CopyTo(buIds);
Dictionary <string, Dictionary <string, AtomInfo[]> > entryBuHash = buGenerator.BuildPdbBus(pdbId, buIds, true);
EntryCrystal thisEntryCrystal = buGenerator.ReadEntryCrystalFromXml(pdbId);
string domainFile = "";
string chainId = "";
string chainSymOp = "";
foreach (string buId in buDomainWithMaxHmmHash.Keys)
{
List <string> domainSymOpList = buDomainWithMaxHmmHash[buId];
string[][] nonProtChainSymOps = GetAllNonProtChainSymOps(pdbId, buId, entryAsuTable);
string[] dnaRnaChainSymOps = nonProtChainSymOps[0];
string[] ligandChainSymOps = nonProtChainSymOps[1];
if (dnaRnaChainSymOps.Length == 0)
{
continue;
}
foreach (string domainSymOp in domainSymOpList)
{
// string[] dnaRnaChains = GetInteractingDnaRnaChainSymOps(pdbId, buId, domainSymOp, pfamDnaRnaTable);
string[] domainSymOpFields = SeparateDomainFields(domainSymOp);
chainId = GetDomainChainId(pdbId, buId, Convert.ToInt32(domainSymOpFields[0]), domainSymOpFields[1], pfamDnaRnaTable);
chainSymOp = chainId + "_" + domainSymOpFields[1];
domainFile = Path.Combine(pfamDnaRnaDir, pdbId + domainSymOpFields[0] + ".pfam");
// WriteDomainDnaRnaInterfaceFiles(pdbId, buId, chainSymOp, dnaRnaChains, buHash, thisEntryCrystal, domainFile);
try
{
WriteDomainDnaRnaInterfaceFiles(pdbId, buId, chainSymOp, dnaRnaChainSymOps, ligandChainSymOps, entryBuHash[buId], thisEntryCrystal, domainFile);
}
catch (Exception ex)
{
ProtCidSettings.logWriter.WriteLine(pdbId + " " + domainSymOp + " domain-DNA/RNA interface error: " + ex.Message);
ProtCidSettings.logWriter.Flush();
}
}
}
}
/// <summary>
///
/// </summary>
/// <param name="pdbId"></param>
/// <returns></returns>
public Dictionary <string, Dictionary <string, AtomInfo[]> > GetPdbBiolUnits(string pdbId, string[] nonMonomerBUs)
{
PdbBuGenerator pdbBuBuilder = new PdbBuGenerator();
string zippedXmlFile = Path.Combine(ProtCidSettings.dirSettings.coordXmlPath, pdbId + ".xml.gz");
string xmlFile = ParseHelper.UnZipFile(zippedXmlFile, ProtCidSettings.tempDir);
// Hashtable pdbBiolUnits = pdbBuBuilder.BuildPdbBusFromCoordFile(xmlFile, nonMonomerBUs, "ALL");
Dictionary <string, Dictionary <string, AtomInfo[]> > pdbBiolUnits = pdbBuBuilder.BuildPdbBus(pdbId, nonMonomerBUs, false);
if (pdbBiolUnits.Count == 0)
{
if (IsEntryNmrStructure(pdbId))
{
Dictionary <string, Dictionary <string, AtomInfo[]> > asymUnitHash = GetAsymUnit(pdbId);
// the BuID is set to be 1 for NMR structure
// the NMR biological unit is same as asymunit
pdbBiolUnits.Add("1", asymUnitHash["0"]);
}
}
File.Delete(xmlFile);
return(pdbBiolUnits);
}
/// <summary>
///
/// </summary>
/// <param name="pdbId"></param>
/// <param name="chainDnaRnaTable"></param>
public void RetrieveChainDnaRnaInteractions(string pdbId)
{
string[][] protDnaRnaChains = GetProtDnaRnaChains(pdbId);
string[] protChains = protDnaRnaChains[0];
string[] dnaRnaChains = protDnaRnaChains[1];
if (protChains.Length == 0 || dnaRnaChains.Length == 0)
{
return;
}
string[] protDnaRnaBuIds = GetBiolAssembliesWithBothChains(pdbId, protChains, dnaRnaChains);
Dictionary <string, Dictionary <string, AtomInfo[]> > protDnaRnaBuHash = buGenerator.BuildPdbBus(pdbId, protDnaRnaBuIds, true);
// protein chain - DNA/RNA interactios from biological assemblies in the PDB
foreach (string buId in protDnaRnaBuIds)
{
Dictionary <string, AtomInfo[]> buHash = protDnaRnaBuHash[buId];
RetrieveProtDnaRnaInteractions(pdbId, buId, buHash, protChains, dnaRnaChains);
}
// retrieve protein-DNA/RNA interactions
RetrieveChainDnaRnaInteractionsInAsu(pdbId, protChains, dnaRnaChains);
}