/// <summary>
/// Similarity between two structures
/// which need to be superposed
/// 1. Superpose individual chains of structure1 to
/// inidividual chains of structure2 based on PSIBLAST sequence alignment
/// including renaming the sequence id in second structure
/// 2. apply KLD Q function
/// </summary>
/// <param name="interChains1">structure1</param>
/// <param name="interChains2">structure2</param>
public InterfacePairInfo[] CompareSupStructuresByKldGaussFunc(InterfaceChains[] interfaceChains1, InterfaceChains[] interfaceChains2, DataTable alignInfoTable)
{
List <InterfacePairInfo> interfacesList = new List <InterfacePairInfo> ();
SuperpositionInterfaces supInterfaces = new SuperpositionInterfaces();
supInterfaces.SuperposeInterfaces(interfaceChains2, alignInfoTable);
for (int i = 0; i < interfaceChains1.Length; i++)
{
for (int j = 0; j < interfaceChains2.Length; j++)
{
// Q score
float qScore = (float)qFunc.KLDQFunc_Gauss(interfaceChains1[i], interfaceChains2[j]);
// if (qScore <= AppSettings.parameters.simInteractParam.interfaceSimCutoff)
// {
InterfacePairInfo interfacesInfo = new InterfacePairInfo((InterfaceInfo)interfaceChains1[i], (InterfaceInfo)interfaceChains2[j]);
interfacesInfo.qScore = qScore;
interfacesList.Add(interfacesInfo);
/* }
* else
* {
* // try the other chain order
* interfaceChains2[j].Reverse ();
* float reversedQScore = (float)qFunc.KLDQFunc_Gauss (interfaceChains1[i], interfaceChains2[j]);
* if (reversedQScore < qScore)
* {
* InterfacePairInfo interfacesInfo = new InterfacePairInfo ((InterfaceInfo)interfaceChains1[i], (InterfaceInfo)interfaceChains2[j]);
* interfacesInfo.qScore = reversedQScore;
* interfacesList.Add (interfacesInfo);
* }
* else
* {
* // go back to the original chain order
* interfaceChains2[j].Reverse ();
* InterfacePairInfo interfacesInfo = new InterfacePairInfo ((InterfaceInfo)interfaceChains1[i], (InterfaceInfo)interfaceChains2[j]);
* interfacesInfo.qScore = qScore;
* interfacesList.Add (interfacesInfo);
* }
* }*/
}
}
// change the sequence number back.
supInterfaces.ReverseSupInterfaces(interfaceChains2, alignInfoTable);
return(interfacesList.ToArray());
}
/// <summary>
///
/// </summary>
/// <param name="interfaceChains1"></param>
/// <param name="interfaceChains2"></param>
/// <param name="alignRow"></param>
/// <returns></returns>
public InterfacePairInfo CompareSupStructures(InterfaceChains interface1, InterfaceChains interface2, DataTable alignInfoTable)
{
InterfacePairInfo interfacePairInfo = new InterfacePairInfo((InterfaceInfo)interface1, (InterfaceInfo)interface2);
SuperpositionInterfaces supInterface = new SuperpositionInterfaces();
bool isReverse = false;
double identity = supInterface.SuperposeInterfaces(interface1, interface2, alignInfoTable, isReverse);
// Q score
float qScore = (float)qFunc.WeightQFunc(interface1, interface2);
// change the sequence number back.
supInterface.ReverseSupInterfaces(interface1, interface2, alignInfoTable, isReverse);
if (qScore >= AppSettings.parameters.simInteractParam.interfaceSimCutoff)
{
interfacePairInfo.qScore = qScore;
interfacePairInfo.identity = identity;
interfacePairInfo.isInterface2Reversed = false;
}
else
{
isReverse = true;
double reversedIdentity = supInterface.SuperposeInterfaces(interface1, interface2, alignInfoTable, isReverse);
if (reversedIdentity < AppSettings.parameters.simInteractParam.identityCutoff)
{
reversedIdentity = AppSettings.parameters.simInteractParam.identityCutoff;
}
float reversedQScore = (float)qFunc.WeightQFunc(interface1, interface2);
supInterface.ReverseSupInterfaces(interface1, interface2, alignInfoTable, isReverse);
if (reversedQScore >= qScore)
{
interfacePairInfo.qScore = reversedQScore;
interfacePairInfo.identity = reversedIdentity;
interfacePairInfo.isInterface2Reversed = true;
}
else
{
// go back to the original chain order
// interface2.Reverse ();
interfacePairInfo.qScore = qScore;
interfacePairInfo.identity = identity;
interfacePairInfo.isInterface2Reversed = false;
}
}
return(interfacePairInfo);
}
/// <summary>
///
/// </summary>
/// <param name="interfaceChains1"></param>
/// <param name="interfaceChains2"></param>
/// <param name="alignRow"></param>
/// <returns></returns>
public InterfacePairInfo CompareSupStructuresByKld(InterfaceChains interface1, InterfaceChains interface2, DataTable alignInfoTable)
{
InterfacePairInfo interfacePairInfo = null;
SuperpositionInterfaces supInterfaces = new SuperpositionInterfaces();
supInterfaces.SuperposeInterfaces(interface2, alignInfoTable);
// Q score
float qScore = (float)qFunc.KldQFunc(interface1, interface2);
if (qScore <= AppSettings.parameters.simInteractParam.interfaceSimCutoff)
{
interfacePairInfo = new InterfacePairInfo((InterfaceInfo)interface1, (InterfaceInfo)interface2);
interfacePairInfo.qScore = qScore;
}
// change the sequence number back.
supInterfaces.ReverseSupInterfaces(interface2, alignInfoTable);
return(interfacePairInfo);
}
/// <summary>
/// Similarity between two structures
/// which need to be superposed
/// 1. Superpose individual chains of structure1 to
/// inidividual chains of structure2 based on PSIBLAST sequence alignment
/// including renaming the sequence id in second structure
/// 2. apply Q function
/// </summary>
/// <param name="interChains1">structure1</param>
/// <param name="interChains2">structure2</param>
public InterfacePairInfo[] CompareSupStructures(InterfaceChains[] interfaceChains1, InterfaceChains[] interfaceChains2, DataTable alignInfoTable)
{
List <InterfacePairInfo> interfacesList = new List <InterfacePairInfo>();
double identity = 1.0;
bool isReverse = false;
SuperpositionInterfaces supInterfaces = new SuperpositionInterfaces();
for (int i = 0; i < interfaceChains1.Length; i++)
{
for (int j = 0; j < interfaceChains2.Length; j++)
{
try
{
isReverse = false;
identity = supInterfaces.SuperposeInterfaces
(interfaceChains1[i], interfaceChains2[j], alignInfoTable, isReverse);
if (identity < AppSettings.parameters.simInteractParam.identityCutoff)
{
identity = AppSettings.parameters.simInteractParam.identityCutoff;
}
// Q score
float qScore = (float)qFunc.WeightQFunc(interfaceChains1[i], interfaceChains2[j]);
supInterfaces.ReverseSupInterfaces(interfaceChains1[i], interfaceChains2[j], alignInfoTable, isReverse);
if (qScore >= AppSettings.parameters.simInteractParam.interfaceSimCutoff)
{
InterfacePairInfo interfacesInfo = new InterfacePairInfo((InterfaceInfo)interfaceChains1[i], (InterfaceInfo)interfaceChains2[j]);
interfacesInfo.qScore = qScore;
interfacesInfo.identity = identity;
interfacesInfo.isInterface2Reversed = false;
interfacesList.Add(interfacesInfo);
}
else
{
// try the other chain order
isReverse = true;
double reversedIdentity = supInterfaces.SuperposeInterfaces
(interfaceChains1[i], interfaceChains2[j], alignInfoTable, isReverse);
if (reversedIdentity < AppSettings.parameters.simInteractParam.identityCutoff)
{
reversedIdentity = AppSettings.parameters.simInteractParam.identityCutoff;
}
float reversedQScore = (float)qFunc.WeightQFunc(interfaceChains1[i], interfaceChains2[j]);
supInterfaces.ReverseSupInterfaces(interfaceChains1[i], interfaceChains2[j], alignInfoTable, isReverse);
if (reversedQScore >= qScore &&
reversedQScore > AppSettings.parameters.contactParams.minQScore)
{
InterfacePairInfo interfacesInfo = new InterfacePairInfo((InterfaceInfo)interfaceChains1[i], (InterfaceInfo)interfaceChains2[j]);
interfacesInfo.qScore = reversedQScore;
interfacesInfo.identity = reversedIdentity;
interfacesInfo.isInterface2Reversed = true;
interfacesList.Add(interfacesInfo);
}
else
{
if (qScore > AppSettings.parameters.contactParams.minQScore)
{
InterfacePairInfo interfacesInfo = new InterfacePairInfo((InterfaceInfo)interfaceChains1[i], (InterfaceInfo)interfaceChains2[j]);
interfacesInfo.qScore = qScore;
interfacesInfo.identity = identity;
interfacesInfo.isInterface2Reversed = false;
interfacesList.Add(interfacesInfo);
}
}
}
}
catch (Exception ex)
{
ProtCidSettings.progressInfo.progStrQueue.Enqueue
(interfaceChains1[i].pdbId + " " + interfaceChains2[j].pdbId +
"calculating Q error: " + ex.Message);
}
}
}
return(interfacesList.ToArray());
}
