/// <summary>
///
/// </summary>
/// <param name="domainRow"></param>
/// <param name="pfamCode1"></param>
/// <param name="pfamCode2"></param>
/// <param name="chainInterfaces"></param>
/// <returns></returns>
private DomainInterface GetInterChainDomainInterface(DataRow domainInterfaceRow, string pfamCode1, string pfamCode2, InterfaceChains[] chainInterfaces)
{
string pdbId = domainInterfaceRow["PdbID"].ToString();
DomainInterface domainInterface = new DomainInterface();
int domainInterfaceId = Convert.ToInt32(domainInterfaceRow["DomainInterfaceID"].ToString());
string interfacePfam1 = "";
string interfacePfam2 = "";
Range[] domainRanges1 = GetDomainRange(pdbId, Convert.ToInt64(domainInterfaceRow["DomainID1"].ToString()), out interfacePfam1);
Range[] domainRanges2 = GetDomainRange(pdbId, Convert.ToInt64(domainInterfaceRow["DomainID2"].ToString()), out interfacePfam2);
int chainInterfaceId = Convert.ToInt32(domainInterfaceRow["InterfaceID"].ToString());
if (chainInterfaceId > 0) // inter-chain domain interface
{
InterfaceChains chainInterface = GetChainInterface(chainInterfaces, chainInterfaceId);
if (chainInterface != null)
{
domainInterface = GetDomainInterface(chainInterface, domainRanges1, domainRanges2);
}
}
if (domainInterface != null)
{
/* if (domainInterfaceRow["IsReversed"].ToString() == "1")
* {
* domainInterface.familyCode1 = pfamCode2;
* domainInterface.familyCode2 = pfamCode1;
* }
* else
* {
* domainInterface.familyCode1 = pfamCode1;
* domainInterface.familyCode2 = pfamCode2;
* }*/
domainInterface.domainInterfaceId = domainInterfaceId;
domainInterface.pdbId = pdbId;
domainInterface.interfaceId = chainInterfaceId;
domainInterface.domainId1 = Convert.ToInt64(domainInterfaceRow["DomainID1"].ToString());
domainInterface.domainId2 = Convert.ToInt64(domainInterfaceRow["DomainID2"].ToString());
domainInterface.familyCode1 = interfacePfam1;
domainInterface.familyCode2 = interfacePfam2;
// if the domain interface chain order is different from the pfam ids defined for the relation
// then reverse the interface chains
if (interfacePfam1 == pfamCode2 && interfacePfam2 == pfamCode1)
{
domainInterface.Reverse();
}
}
return(domainInterface);
}
/// <summary>
///
/// </summary>
/// <param name="pdbId"></param>
/// <param name="relSeqId"></param>
/// <param name="type"></param>
/// <returns></returns>
public DomainInterface[] GetInterChainDomainInterfaces(string pdbId, int relSeqId, string type)
{
string queryString = string.Format("Select * From {0}DomainInterfaces " +
" Where RelSeqID = {1} AND PdbID = '{2}' AND InterfaceID > 0;", ProtCidSettings.dataType, relSeqId, pdbId);
DataTable domainInterfaceTable = ProtCidSettings.protcidQuery.Query(queryString);
queryString = string.Format("Select * From {0}DomainFamilyRelation Where RelSeqId = {1};",
ProtCidSettings.dataType, relSeqId);
DataTable domainSeqIdTable = ProtCidSettings.protcidQuery.Query(queryString);
string family1 = domainSeqIdTable.Rows[0]["FamilyCode1"].ToString().Trim();
string family2 = domainSeqIdTable.Rows[0]["FamilyCode2"].ToString().Trim();
int[] chainInterfaceIds = GetInterChainInterfaceIDs(relSeqId, pdbId);
InterfaceChains[] chainInterfaces = GetCrystInterfaces(pdbId, chainInterfaceIds, type);
List <DomainInterface> domainInterfaceList = new List <DomainInterface> ();
Range[] domainRanges1 = null;
Range[] domainRanges2 = null;
int chainInterfaceId = -1;
int domainInterfaceId = -1;
string interfacePfam1 = "";
string interfacePfam2 = "";
bool isReversedChains = false;
foreach (DataRow domainRow in domainInterfaceTable.Rows)
{
isReversedChains = false;
DomainInterface domainInterface = new DomainInterface();
domainInterfaceId = Convert.ToInt32(domainRow["DomainInterfaceID"].ToString());
domainRanges1 = GetDomainRange(pdbId, Convert.ToInt64(domainRow["DomainID1"].ToString()), out interfacePfam1);
domainRanges2 = GetDomainRange(pdbId, Convert.ToInt64(domainRow["DomainID2"].ToString()), out interfacePfam2);
chainInterfaceId = Convert.ToInt32(domainRow["InterfaceID"].ToString());
InterfaceChains chainInterface = GetChainInterface(chainInterfaces, chainInterfaceId);
if (chainInterface == null)
{
continue;
}
// domain interface chains are in the different order of the corresponding chain interface chains
if (domainRow["IsReversed"].ToString() == "1")
{
isReversedChains = true;
domainInterface = GetDomainInterface(chainInterface, domainRanges2, domainRanges1, isReversedChains);
}
else
{
domainInterface = GetDomainInterface(chainInterface, domainRanges1, domainRanges2);
}
domainInterface.domainInterfaceId = domainInterfaceId;
domainInterface.pdbId = pdbId;
domainInterface.interfaceId = chainInterfaceId;
domainInterface.domainId1 = Convert.ToInt64(domainRow["DomainID1"].ToString());
domainInterface.domainId2 = Convert.ToInt64(domainRow["DomainID2"].ToString());
domainInterface.familyCode1 = interfacePfam1;
domainInterface.familyCode2 = interfacePfam2;
if (family2 != family1 && interfacePfam1 == family2 && interfacePfam2 == family1)
{
domainInterface.Reverse();
}
domainInterfaceList.Add(domainInterface);
}
return(domainInterfaceList.ToArray());
}