/// <summary>
/// the intra-chain domain interfaces from chains of the ASU
/// </summary>
/// <param name="relSeqId"></param>
/// <param name="pdbId"></param>
/// <returns></returns>
private Dictionary <int, DomainInterfaceComponent> GetIntraChainDomainInterfaceContents(int relSeqId, string pdbId)
{
// int asuRelSeqId = ConvertRelSeqID(relSeqId, BuCompBuilder.BuType, "asu");
string queryString = string.Format("Select * From AsuIntraDomainInterfaces " +
" Where RelSeqID = {0} AND PdbID = '{1}';", relSeqId, pdbId);
DataTable intraChainDomainInterfaceTable = dbQuery.Query(ProtCidSettings.buCompConnection, queryString);
Dictionary <int, DomainInterfaceComponent> domainInterfaceHash = new Dictionary <int, DomainInterfaceComponent> ();
if (intraChainDomainInterfaceTable.Rows.Count > 0)
{
string[] familyCodes = GetRelationFamilyCodes(relSeqId);
int domainInterfaceId = -1;
int chainInterfaceId = 0;
string asymChain = "";
Dictionary <long, Range[]> domainRangeHash = new Dictionary <long, Range[]> ();
string isReversed = "";
foreach (DataRow domainInterfaceRow in intraChainDomainInterfaceTable.Rows)
{
domainInterfaceId = Convert.ToInt32(domainInterfaceRow["DomainInterfaceID"].ToString());
asymChain = domainInterfaceRow["AsymChain"].ToString().TrimEnd();
DomainInterfaceComponent domainInterfaceContent = new DomainInterfaceComponent();
domainInterfaceContent.chainSymOpString1 = asymChain + "_1_555";
domainInterfaceContent.chainSymOpString2 = asymChain + "_1_555";
Range[] domainRange1 = GetDomainRange(pdbId, Convert.ToInt64(domainInterfaceRow["DomainID1"].ToString()), ref domainRangeHash);
if (domainRange1 == null)
{
continue;
}
Range[] domainRange2 = GetDomainRange(pdbId, Convert.ToInt64(domainInterfaceRow["DomainID2"].ToString()), ref domainRangeHash);
if (domainRange2 == null)
{
continue;
}
domainInterfaceContent.domainRange1 = domainRange1;
domainInterfaceContent.domainRange2 = domainRange2;
domainInterfaceContent.chainInterfaceId = chainInterfaceId;
domainInterfaceContent.domainId1 = Convert.ToInt64(domainInterfaceRow["DomainID1"].ToString());
domainInterfaceContent.domainId2 = Convert.ToInt64(domainInterfaceRow["DomainID2"].ToString());
isReversed = domainInterfaceRow["IsReversed"].ToString();
if (isReversed == "1")
{
domainInterfaceContent.familyCode1 = familyCodes[1];
domainInterfaceContent.familyCode2 = familyCodes[0];
}
else
{
domainInterfaceContent.familyCode1 = familyCodes[0];
domainInterfaceContent.familyCode2 = familyCodes[1];
}
domainInterfaceHash.Add(domainInterfaceId, domainInterfaceContent);
}
}
return(domainInterfaceHash);
}
/// <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());
}
/// <summary>
///
/// </summary>
/// <param name="relSeqId"></param>
/// <param name="pdbId"></param>
/// <param name="domainInterfaceTable"></param>
/// <returns></returns>
private Dictionary <string, Dictionary <int, DomainInterfaceComponent> > GetDomainInterfaceContents(int relSeqId, string pdbId, DataTable domainInterfaceTable)
{
string[] familyCodes = GetRelationFamilyCodes(relSeqId);
Dictionary <string, Dictionary <int, DomainInterfaceComponent> > buDomainInterfaceHash = new Dictionary <string, Dictionary <int, DomainInterfaceComponent> > ();
string buId = "";
int domainInterfaceId = -1;
int chainInterfaceId = -1;
Dictionary <long, Range[]> domainRangeHash = new Dictionary <long, Range[]> ();
string isReversed = "";
foreach (DataRow domainInterfaceRow in domainInterfaceTable.Rows)
{
buId = domainInterfaceRow["BuID"].ToString().TrimEnd();
domainInterfaceId = Convert.ToInt32(domainInterfaceRow["DomainInterfaceID"].ToString());
chainInterfaceId = Convert.ToInt32(domainInterfaceRow["InterfaceID"].ToString());
string[] chainSymOpStrings = GetChainInterfaceChainComponent(pdbId, buId, chainInterfaceId);
if (chainSymOpStrings == null)
{
continue;
}
DomainInterfaceComponent domainInterfaceContent = new DomainInterfaceComponent();
domainInterfaceContent.chainSymOpString1 = chainSymOpStrings[0];
domainInterfaceContent.chainSymOpString2 = chainSymOpStrings[1];
Range[] domainRange1 = GetDomainRange(pdbId, Convert.ToInt64(domainInterfaceRow["DomainID1"].ToString()), ref domainRangeHash);
if (domainRange1 == null)
{
continue;
}
Range[] domainRange2 = GetDomainRange(pdbId, Convert.ToInt64(domainInterfaceRow["DomainID2"].ToString()), ref domainRangeHash);
if (domainRange2 == null)
{
continue;
}
domainInterfaceContent.domainRange1 = domainRange1;
domainInterfaceContent.domainRange2 = domainRange2;
domainInterfaceContent.chainInterfaceId = chainInterfaceId;
domainInterfaceContent.domainId1 = Convert.ToInt64(domainInterfaceRow["DomainID1"].ToString());
domainInterfaceContent.domainId2 = Convert.ToInt64(domainInterfaceRow["DomainID2"].ToString());
isReversed = domainInterfaceRow["IsReversed"].ToString();
if (isReversed == "1")
{
domainInterfaceContent.familyCode1 = familyCodes[1];
domainInterfaceContent.familyCode2 = familyCodes[0];
}
else
{
domainInterfaceContent.familyCode1 = familyCodes[0];
domainInterfaceContent.familyCode2 = familyCodes[1];
}
if (buDomainInterfaceHash.ContainsKey(buId))
{
buDomainInterfaceHash[buId].Add(domainInterfaceId, domainInterfaceContent);
}
else
{
Dictionary <int, DomainInterfaceComponent> domainInterfaceHash = new Dictionary <int, DomainInterfaceComponent> ();
domainInterfaceHash.Add(domainInterfaceId, domainInterfaceContent);
buDomainInterfaceHash.Add(buId, domainInterfaceHash);
}
}
return(buDomainInterfaceHash);
}
