/*
* Function:
* 1. constant function
* y = 1 if x > 0 and x <= 5;
* 2. Gaussian distribution function
* y = (area / (sigma * sqrt(PI / 2))) * exp(-2 * ((x - mean) / sigma)^2) if x > 5
* */
/// <summary>
/// Q Score from KLD
/// </summary>
/// <param name="interface1"></param>
/// <param name="interface2"></param>
/// <returns></returns>
public double KLDQFunc_Gauss(InterfaceChains interface1, InterfaceChains interface2)
{
bool needReversed = false;
// string[] allResiduePairs = GetCommonResiduePairs (interface1, interface2, out needReversed);
string[] allResiduePairs = GetAllResiduePairs(interface1, interface2, out needReversed);
// no common residue pairs
if (needReversed)
{
interface2.Reverse();
allResiduePairs = GetAllResiduePairs(interface1, interface2);
}
Dictionary <string, double> probDistHash1 = null;
Dictionary <string, double> probDistHash2 = null;
double propSum1 = GetProbDistHash(interface1, allResiduePairs, ref probDistHash1, "GAUSS");
double propSum2 = GetProbDistHash(interface2, allResiduePairs, ref probDistHash2, "GAUSS");
double qScore = GetSimScoreForDistributions(probDistHash1, probDistHash2);
// reverse back to original order
if (needReversed)
{
interface2.Reverse();
}
return(qScore);
}
/// <summary>
/// compare two interfaces
/// </summary>
/// <param name="interChains"></param>
/// <param name="interChainsList"></param>
/// <returns></returns>
public bool AreChainInterfacesSame(InterfaceChains interface1, InterfaceChains interface2)
{
// get q scores for the interaction chains: Q_weight
float qScore = (float)qFunc.WeightQFunc(interface1, interface2);
if (qScore >= AppSettings.parameters.simInteractParam.uniqueInterfaceCutoff)
{
return(true);
}
else
{
interface2.Reverse();
qScore = (float)qFunc.WeightQFunc(interface1, interface2);
if (qScore >= AppSettings.parameters.simInteractParam.uniqueInterfaceCutoff)
{
return(true);
}
else
{
// reverse it back
interface2.Reverse();
return(false);
}
}
}
/// <summary>
/// compare two interfaces
/// if no similar interfaces, return true
/// otherwise return false
/// </summary>
/// <param name="interChains"></param>
/// <param name="interChainsList"></param>
/// <returns></returns>
public bool AreInterfacesSame(InterfaceChains interface1, InterfaceChains interface2)
{
// compare two interfaces,
// if different asymmetric chains, then not same
int asymChainCompResult = AreAsymChainsSame(interface1, interface2);
if (asymChainCompResult < 0)
{
return(false);
}
else if (asymChainCompResult == 1) // reversed same
{
interface2.Reverse(); // match the asymmetric chains to interface1
}
// get q scores for the interaction chains: Q_weight
float qScore = (float)qFunc.WeightQFunc(interface1, interface2);
if (qScore >= AppSettings.parameters.simInteractParam.uniqueInterfaceCutoff)
{
return(true);
}
else
{
interface2.Reverse();
qScore = (float)qFunc.WeightQFunc(interface1, interface2);
if (qScore >= AppSettings.parameters.simInteractParam.uniqueInterfaceCutoff)
{
return(true);
}
else
{
// reverse it back
if (asymChainCompResult != 1)
{
interface2.Reverse();
}
return(false);
}
}
}
/// <summary>
/// superpose interfaces based on psiblast alignment
/// </summary>
/// <param name="interChains2"></param>
/// <param name="alignInfoTable"></param>
public double SuperposeInterfaces(InterfaceChains interface1,
InterfaceChains interface2, DataTable alignInfoTable, bool isReverse)
{
DataRow alignRow = null;
DataRow alignRow2 = null;
double identity = 100.0;
if (isReverse)
{
interface2.Reverse();
}
int entityId11 = interface1.entityId1;
AtomInfo[] chain21 = interface2.chain1;
int entityId21 = interface2.entityId1;
int entityId12 = interface1.entityId2;
AtomInfo[] chain22 = interface2.chain2;
int entityId22 = interface2.entityId2;
alignRow = GetAlignRow(alignInfoTable, entityId11, entityId21);
if (alignRow != null)
{
identity = Convert.ToDouble(alignRow["Identity"].ToString());
SuperposeChain(chain21, alignRow);
}
if (entityId21 == entityId22 && entityId11 == entityId12)
{
SuperposeChain(chain22, alignRow);
interface2.seqDistHash =
SuperposeInterface(interface2.seqDistHash, alignRow);
}
else
{
alignRow2 = GetAlignRow(alignInfoTable, entityId12, entityId22);
if (alignRow2 != null)
{
if (identity > Convert.ToDouble(alignRow2["Identity"].ToString()))
{
identity = Convert.ToDouble(alignRow2["Identity"].ToString());
}
SuperposeChain(chain22, alignRow2);
}
interface2.seqDistHash =
SuperposeInterface(interface2.seqDistHash, alignRow, alignRow2);
}
// reset the hashtable for residue and its bb atoms.
interface2.ResetSeqResidueHash();
return(identity);
}
/// <summary>
/// reverse the residue sequence id after interface comparing
/// </summary>
/// <param name="interChains2"></param>
/// <param name="alignInfoTable"></param>
public void ReverseSupInterfaces(InterfaceChains interface1, InterfaceChains interface2,
DataTable alignInfoTable, bool isReverse)
{
DataRow alignRow = null;
DataRow alignRow2 = null;
int entityId11 = interface1.entityId1;
AtomInfo[] chain21 = interface2.chain1;
int entityId21 = interface2.entityId1;
int entityId12 = interface1.entityId2;
AtomInfo[] chain22 = interface2.chain2;
int entityId22 = interface2.entityId2;
alignRow = GetAlignRow(alignInfoTable, entityId11, entityId21);
if (alignRow != null)
{
ReverseSupChain(chain21, alignRow);
}
if (entityId21 == entityId22 && entityId11 == entityId12)
{
ReverseSupChain(chain22, alignRow);
interface2.seqDistHash =
ReverseSupInterface(interface2.seqDistHash, alignRow);
}
else
{
alignRow2 = GetAlignRow(alignInfoTable, entityId12, entityId22);
if (alignRow2 != null)
{
ReverseSupChain(chain22, alignRow2);
interface2.seqDistHash =
ReverseSupInterface(interface2.seqDistHash, alignRow, alignRow2);
}
}
if (isReverse)
{
interface2.Reverse();
}
interface2.ClearSeqResidueHash();
}
