/// <summary>
///
/// </summary>
/// <param name="domainInterfaceId"></param>
/// <param name="domainInterfaceTable"></param>
/// <param name="pdbpfamTable"></param>
/// <param name="chainAtomsHash"></param>
/// <returns></returns>
private DomainInterface ReadIntraDomainInterfaceFromChain(int domainInterfaceId, DataTable domainInterfaceTable,
DataTable pdbpfamTable, Dictionary <string, ChainAtoms> chainAtomsHash)
{
DomainInterface domainInterface = new DomainInterface();
DataRow[] domainInterfaceRows = domainInterfaceTable.Select(string.Format("DomainInterfaceID = '{0}'", domainInterfaceId));
if (domainInterfaceRows.Length > 0)
{
long domainId1 = Convert.ToInt64(domainInterfaceRows[0]["DomainID1"].ToString());
long domainId2 = Convert.ToInt64(domainInterfaceRows[0]["DomainID2"].ToString());
string asymChain = domainInterfaceRows[0]["AsymChain1"].ToString().TrimEnd();
if (chainAtomsHash.ContainsKey(asymChain))
{
ChainAtoms chain = chainAtomsHash[asymChain];
Range[] domainRanges1 = GetDomainRange(pdbpfamTable, domainId1);
Range[] domainRanges2 = GetDomainRange(pdbpfamTable, domainId2);
domainInterface.domainInterfaceId = domainInterfaceId;
domainInterface.firstSymOpString = asymChain + "_1_555";
domainInterface.secondSymOpString = asymChain + "_1_555";
domainInterface.domainId1 = domainId1;
domainInterface.domainId2 = domainId2;
domainInterface.chain1 = GetDomainAtoms(chain.CartnAtoms, domainRanges1);
domainInterface.chain2 = GetDomainAtoms(chain.CartnAtoms, domainRanges2);
domainInterface.GetInterfaceResidueDist();
}
}
return(domainInterface);
}
/// <summary>
/// a list of domain interfaces for the input domainInterfaceIds
/// </summary>
/// <param name="srcDir"></param>
/// <param name="pdbId"></param>
/// <param name="domainInterfaceIds"></param>
/// <param name="type"></param>
/// <returns></returns>
public DomainInterface[] GetDomainInterfacesFromFiles(string srcDir, string pdbId, int[] domainInterfaceIds, string type)
{
DataTable pfamDomainTable = GetEntryPfamDomainTable(pdbId);
long domainId = 0;
List <DomainInterface> domainInterfaceList = new List <DomainInterface> ();
srcDir = Path.Combine(srcDir, pdbId.Substring(1, 2));
string gzDomainInterfaceFile = "";
string domainInterfaceFile = "";
string remark = "";
if (Directory.Exists(srcDir))
{
foreach (int dInterfaceId in domainInterfaceIds)
{
gzDomainInterfaceFile = Path.Combine(srcDir, pdbId + "_d" + dInterfaceId.ToString() + "." + type + ".gz");
if (File.Exists(gzDomainInterfaceFile))
{
InterfaceChains crystInterface = new InterfaceChains();
domainInterfaceFile = ParseHelper.UnZipFile(gzDomainInterfaceFile, ProtCidSettings.tempDir);
remark = ReadInterfaceChainsFromFile(domainInterfaceFile, ref crystInterface);
DomainInterface domainInterface = new DomainInterface(crystInterface);
domainInterface.pdbId = pdbId;
domainInterface.remark = remark;
domainInterface.domainInterfaceId = GetDomainInterfaceId(domainInterfaceFile);
string[] domainChainStrings = GetDomainChainStrings(remark);
domainId = Convert.ToInt64(domainChainStrings[0].Substring(0, domainChainStrings[0].IndexOf("_")));
domainInterface.domainId1 = domainId;
domainInterface.familyCode1 = GetPfamId(domainId, pfamDomainTable);
domainId = Convert.ToInt64(domainChainStrings[1].Substring(0, domainChainStrings[1].IndexOf("_")));
domainInterface.domainId2 = domainId;
domainInterface.familyCode2 = GetPfamId(domainId, pfamDomainTable);
File.Delete(domainInterfaceFile);
if (domainInterface.GetInterfaceResidueDist())
{
domainInterfaceList.Add(domainInterface);
}
}
}
}
return(domainInterfaceList.ToArray());
}
/// <summary>
/// get the cryst interfaces from the cryst interface files
/// </summary>
/// <param name="pdbId"></param>
/// <param name="pqsBuId"></param>
public DomainInterface[] GetDomainInterfacesFromFiles(string srcDir, string pdbId, string type)
{
DataTable pfamDomainTable = GetEntryPfamDomainTable(pdbId);
long domainId = 0;
string searchMode = pdbId + "*." + type + ".gz";
List <DomainInterface> domainInterfaceList = new List <DomainInterface> ();
if (Directory.Exists(srcDir))
{
string[] interfaceFiles = Directory.GetFiles(Path.Combine(srcDir, pdbId.Substring(1, 2)), searchMode);
string remark = "";
for (int i = 0; i < interfaceFiles.Length; i++)
{
InterfaceChains crystInterface = new InterfaceChains();
string domainInterfaceFile = ParseHelper.UnZipFile(interfaceFiles[i], ProtCidSettings.tempDir);
remark = ReadInterfaceChainsFromFile(domainInterfaceFile, ref crystInterface);
DomainInterface domainInterface = new DomainInterface(crystInterface);
domainInterface.pdbId = pdbId;
domainInterface.remark = remark;
domainInterface.domainInterfaceId = GetDomainInterfaceId(domainInterfaceFile);
string[] domainChainStrings = GetDomainChainStrings(remark);
domainId = Convert.ToInt64(domainChainStrings[0].Substring(0, domainChainStrings[0].IndexOf("_")));
domainInterface.domainId1 = domainId;
domainInterface.familyCode1 = GetPfamId(domainId, pfamDomainTable);
domainId = Convert.ToInt64(domainChainStrings[1].Substring(0, domainChainStrings[1].IndexOf("_")));
domainInterface.domainId2 = domainId;
domainInterface.familyCode2 = GetPfamId(domainId, pfamDomainTable);
File.Delete(domainInterfaceFile);
if (domainInterface.GetInterfaceResidueDist())
{
domainInterfaceList.Add(domainInterface);
}
}
}
return(domainInterfaceList.ToArray());
}
/// <summary>
/// domain-domain interactions with the relation in the BU
/// </summary>
/// <param name="domainInterfacesHash">domain interfaces for the BU</param>
/// <param name="biolUnitHash">the chains and atoms for the BU</param>
/// <returns>the domain-domain interfaces in the BU</returns>
private DomainInterface[] GetDomainInterfaces(Dictionary <int, DomainInterfaceComponent> domainInterfacesHash, Dictionary <string, AtomInfo[]> biolUnitHash)
{
List <DomainInterface> domainInterfaceList = new List <DomainInterface> ();
foreach (int domainInterfaceId in domainInterfacesHash.Keys)
{
DomainInterfaceComponent component = (DomainInterfaceComponent)domainInterfacesHash[domainInterfaceId];
AtomInfo[] domainAtoms1 = null;
AtomInfo[] domainAtoms2 = null;
foreach (string chainSymOpString in biolUnitHash.Keys)
{
if (component.chainSymOpString1 == chainSymOpString)
{
domainAtoms1 = GetDomainAtoms((AtomInfo[])biolUnitHash[chainSymOpString],
component.domainRange1);
}
if (component.chainSymOpString2 == chainSymOpString)
{
domainAtoms2 = GetDomainAtoms((AtomInfo[])biolUnitHash[chainSymOpString],
component.domainRange2);
}
}
DomainInterface domainInterface = new DomainInterface();
domainInterface.domainInterfaceId = domainInterfaceId;
domainInterface.interfaceId = component.chainInterfaceId;
domainInterface.chain1 = domainAtoms1;
domainInterface.chain2 = domainAtoms2;
domainInterface.firstSymOpString = component.chainSymOpString1;
domainInterface.secondSymOpString = component.chainSymOpString2;
domainInterface.domainId1 = component.domainId1;
domainInterface.domainId2 = component.domainId2;
domainInterface.familyCode1 = component.familyCode1;
domainInterface.familyCode2 = component.familyCode2;
domainInterface.GetInterfaceResidueDist();
domainInterfaceList.Add(domainInterface);
}
return(domainInterfaceList.ToArray());
}