/// <summary>
/// compare two domain interfaces
/// </summary>
/// <param name="domainInterface1"></param>
/// <param name="domainInterface2"></param>
/// <returns></returns>
public DomainInterfacePairInfo CompareEntryDomainInterfaces(DomainInterface domainInterface1,
DomainInterface domainInterface2)
{
double qScore = qFunc.WeightQFunc(domainInterface1, domainInterface2);
bool interfaceReversed = false;
if (qScore < AppSettings.parameters.simInteractParam.interfaceSimCutoff &&
domainInterface1.familyCode1 == domainInterface2.familyCode2)
{
domainInterface2.Reverse();
double reversedQScore = qFunc.WeightQFunc(domainInterface1, domainInterface2);
if (qScore < reversedQScore)
{
qScore = reversedQScore;
interfaceReversed = true;
}
else
{
domainInterface2.Reverse();
}
}
DomainInterfacePairInfo interfacePairInfo = new DomainInterfacePairInfo
(new DomainInterfaceInfo(domainInterface1), new DomainInterfaceInfo(domainInterface2));
interfacePairInfo.qScore = qScore;
interfacePairInfo.isInterface2Reversed = interfaceReversed;
return(interfacePairInfo);
}
/// <summary>
/// compare two domain interfaces of same entry
/// </summary>
/// <param name="domainInterfaces1"></param>
/// <param name="domainInterfaces2"></param>
public DomainInterfacePairInfo[] CompareEntryDomainInterfaces(DomainInterface[] domainInterfaces1, DomainInterface[] domainInterfaces2)
{
Dictionary <string, long[]> familyDomainHash = GetFamilyDomainHash(domainInterfaces1, domainInterfaces2);
DataTable domainAlignInfoTable = GetDomainAlignmentTable(familyDomainHash);
List <DomainInterfacePairInfo> interfaceCompList = new List <DomainInterfacePairInfo>();
foreach (DomainInterface domainInterface1 in domainInterfaces1)
{
foreach (DomainInterface domainInterface2 in domainInterfaces2)
{
try
{
DomainInterfacePairInfo compInfo =
CompareTwoDomainInterfaces(domainInterface1, domainInterface2, domainAlignInfoTable);
if (compInfo != null && // compInfo.qScore > -1)
compInfo.qScore >= AppSettings.parameters.contactParams.minQScore)
{
interfaceCompList.Add(compInfo);
}
}
catch (Exception ex)
{
nonAlignDomainWriter.WriteLine(domainInterface1.pdbId + " " + domainInterface1.domainInterfaceId +
" " + domainInterface2.pdbId + " " + domainInterface2.domainInterfaceId + " : " + ex.Message);
}
}
}
nonAlignDomainWriter.Flush();
DomainInterfacePairInfo[] pairCompInfos = new DomainInterfacePairInfo[interfaceCompList.Count];
interfaceCompList.CopyTo(pairCompInfos);
return(pairCompInfos);
}
/// <summary>
/// compare domain interfaces for one entry
/// </summary>
/// <param name="domainInterfaces1"></param>
/// <param name="domainInterfaces2"></param>
public DomainInterfacePairInfo[] CompareEntryDomainInterfaces(DomainInterface[] domainInterfaces)
{
Dictionary <string, long[]> familyDomainHash = GetFamilyDomainHash(domainInterfaces);
DataTable domainAlignInfoTable = GetDomainAlignmentTable(familyDomainHash);
List <DomainInterfacePairInfo> interfaceCompList = new List <DomainInterfacePairInfo> ();
foreach (DomainInterface domainInterface1 in domainInterfaces)
{
foreach (DomainInterface domainInterface2 in domainInterfaces)
{
if (domainInterface1.domainInterfaceId != domainInterface2.domainInterfaceId)
{
if (!IsDomainInterfaceAlignmentExist(domainInterface1, domainInterface2, domainAlignInfoTable))
{
nonAlignDomainWriter.WriteLine(domainInterface1.pdbId + " " + domainInterface1.domainInterfaceId + " " +
domainInterface1.domainId1 + " " + domainInterface1.domainId2 + " " +
" " + domainInterface2.pdbId + " " + domainInterface2.domainInterfaceId + " " +
domainInterface2.domainId1 + " " + domainInterface2.domainId2);
continue;
}
DomainInterfacePairInfo compInfo =
CompareTwoDomainInterfaces(domainInterface1, domainInterface2, domainAlignInfoTable);
if (compInfo != null && compInfo.qScore > -1)
// compInfo.qScore >= AppSettings.parameters.contactParams.minQScore)
{
interfaceCompList.Add(compInfo);
}
}
}
}
nonAlignDomainWriter.Flush();
return(interfaceCompList.ToArray());
}
/// <summary>
/// same domain interfaces means two domain interfaces with same domain id components
/// and Q score >= unique interface q score which is defined to 0.90
/// </summary>
/// <param name="domainInterface1"></param>
/// <param name="domainInterface2"></param>
/// <returns></returns>
public bool AreSameDomainInterfaces(DomainInterface domainInterface1, DomainInterface domainInterface2)
{
DomainInterfacePairInfo pairInfo =
CompareEntryDomainInterfaces(domainInterface1, domainInterface2);
if (pairInfo.qScore >= AppSettings.parameters.simInteractParam.uniqueInterfaceCutoff &&
AreDomainInterfacesSameDomainIds(domainInterface1, domainInterface2))
{
return(true);
}
return(false);
}
/// <summary>
/// compare two domain interfaces
/// </summary>
/// <param name="domainInterfaces1"></param>
/// <param name="domainInterfaces2"></param>
public DomainInterfacePairInfo CompareDomainInterfaces(DomainInterface domainInterface1, DomainInterface domainInterface2)
{
Dictionary <string, long[]> familyDomainHash = GetFamilyDomainHash(domainInterface1, domainInterface2);
DataTable domainAlignmentTable = GetDomainAlignmentTable(familyDomainHash);
/* if (domainAlignInfoTable == null || domainAlignInfoTable.Rows.Count == 0)
* {
* return null;
* }*/
DomainInterfacePairInfo compInfo =
CompareTwoDomainInterfaces(domainInterface1, domainInterface2, domainAlignmentTable);
domainAlignmentTable.Clear();
return(compInfo);
}
/// <summary>
/// compare two domain interfaces
/// </summary>
/// <param name="domainInterface1"></param>
/// <param name="domainInterface2"></param>
/// <param name="domainAlignInfoTable"></param>
/// <returns></returns>
public DomainInterfacePairInfo CompareTwoDomainInterfaces(DomainInterface domainInterface1,
DomainInterface domainInterface2, DataTable domainAlignInfoTable)
{
DomainInterface domainInterface2Copy = new DomainInterface(domainInterface2, true); // keep a deep copy
double identity = supDomainInterface.SuperposeDomainInterfaces(domainInterface1, domainInterface2Copy, domainAlignInfoTable);
double qScore = qFunc.WeightQFunc(domainInterface1, domainInterface2Copy);
// domainInterface2 = domainInterface2Copy; // shadow copy
// supDomainInterface.ReverseSupDomainInterfaces(domainInterface1, domainInterface2, domainAlignInfoTable);
bool interfaceReversed = false;
if (qScore < AppSettings.parameters.simInteractParam.interfaceSimCutoff &&
domainInterface1.familyCode1 == domainInterface2.familyCode2)
{
domainInterface2Copy = new DomainInterface(domainInterface2, true);
domainInterface2Copy.Reverse();
// keep deep copy
double reversedIdentity =
supDomainInterface.SuperposeDomainInterfaces(domainInterface1, domainInterface2Copy, domainAlignInfoTable);
double reversedQScore = qFunc.WeightQFunc(domainInterface1, domainInterface2Copy);
// domainInterface2 = domainInterface2Copy;
// supDomainInterface.ReverseSupDomainInterfaces(domainInterface1, domainInterface2, domainAlignInfoTable);
if (qScore < reversedQScore)
{
qScore = reversedQScore;
identity = reversedIdentity;
interfaceReversed = true;
}
}
DomainInterfacePairInfo interfacePairInfo = new DomainInterfacePairInfo
(new DomainInterfaceInfo(domainInterface1), new DomainInterfaceInfo(domainInterface2));
interfacePairInfo.qScore = qScore;
if (identity <= 0)
{
interfacePairInfo.identity = -1.0;
}
else
{
interfacePairInfo.identity = identity;
}
interfacePairInfo.isInterface2Reversed = interfaceReversed;
return(interfacePairInfo);
}
/// <summary>
/// compare two domain interfaces
/// </summary>
/// <param name="domainInterfaces1"></param>
/// <param name="domainInterfaces2"></param>
public DomainInterfacePairInfo[] CompareDifRelationDomainInterfaces(DomainInterface[] domainInterfaces1, DomainInterface[] domainInterfaces2)
{
Dictionary <string, long[]> familyDomainHash1 = GetFamilyDomainHash(domainInterfaces1);
Dictionary <string, long[]> familyDomainHash2 = GetFamilyDomainHash(domainInterfaces2);
DataTable domainAlignInfoTable = GetDomainAlignmentTable(familyDomainHash1, familyDomainHash2);
List <DomainInterfacePairInfo> interfaceCompList = new List <DomainInterfacePairInfo> ();
foreach (DomainInterface domainInterface1 in domainInterfaces1)
{
foreach (DomainInterface domainInterface2 in domainInterfaces2)
{
if (!IsDomainInterfaceAlignmentExist(domainInterface1, domainInterface2, domainAlignInfoTable))
{
nonAlignDomainWriter.WriteLine(domainInterface1.pdbId + " " + domainInterface1.domainInterfaceId + " " +
domainInterface1.domainId1 + " " + domainInterface1.domainId2 + " " +
" " + domainInterface2.pdbId + " " + domainInterface2.domainInterfaceId + " " +
domainInterface2.domainId1 + " " + domainInterface2.domainId2);
// continue;
}
try
{
DomainInterfacePairInfo compInfo =
CompareTwoDomainInterfaces(domainInterface1, domainInterface2, domainAlignInfoTable);
if (compInfo != null && // compInfo.qScore > -1)
compInfo.qScore >= AppSettings.parameters.contactParams.minQScore)
{
interfaceCompList.Add(compInfo);
}
}
catch (Exception ex)
{
nonAlignDomainWriter.WriteLine(domainInterface1.pdbId + " " + domainInterface1.domainInterfaceId +
" " + domainInterface2.pdbId + " " + domainInterface2.domainInterfaceId + " : " + ex.Message);
}
}
}
nonAlignDomainWriter.Flush();
return(interfaceCompList.ToArray());
}
