/* public InterfacesComp(double uniqueCutoff)
* {
* this.uniqueCutoff = uniqueCutoff;
* }
*/
#region Interfaces within one structure
/// <summary>
/// get q scores within a crystal
/// </summary>
/// <param name="interChains">input: all pairwise interactive chains</param>
/// return: an array of unique pairwise interfaces and their q scores
public InterfacePairInfo[] CompareInterfacesWithinCrystal(ref InterfaceChains[] interfaceChains)
{
List <InterfacePairInfo> interfacesList = new List <InterfacePairInfo> ();
// pairwise compare two interfaces
for (int i = 0; i < interfaceChains.Length - 1; i++)
{
for (int j = i + 1; j < interfaceChains.Length; j++)
{
// get q scores for each interaction chains: Q_weight
float qScore = (float)qFunc.WeightQFunc(interfaceChains[i], interfaceChains[j]);
if (qScore < AppSettings.parameters.simInteractParam.uniqueInterfaceCutoff)
{
interfaceChains[j].Reverse();
float reversedQScore = (float)qFunc.WeightQFunc(interfaceChains[i], interfaceChains[j]);
if (reversedQScore > qScore)
{
qScore = reversedQScore;
}
else
{
interfaceChains[j].Reverse();
}
}
InterfacePairInfo interfacesInfo = new InterfacePairInfo((InterfaceInfo)interfaceChains[i],
(InterfaceInfo)interfaceChains[j]);
interfacesInfo.qScore = qScore;
interfacesList.Add(interfacesInfo);
}
}
// return an array of interface info
return(interfacesList.ToArray());
}
/// <summary>
/// pairwise interfaces comparisons between two crystal structures
/// </summary>
/// <param name="interChains1">interactive chains and interfaces</param>
/// <param name="interChains2">interactive chains and </param>
public InterfacePairInfo[] CompareInterfacesBetweenCrystals(InterfaceChains[] interChains1, InterfaceChains[] interChains2)
{
List <InterfacePairInfo> interfacesList = new List <InterfacePairInfo> ();
for (int i = 0; i < interChains1.Length; i++)
{
for (int j = 0; j < interChains2.Length; j++)
{
// get q scores for each interaction chains: Q_weight
float qScore = (float)qFunc.WeightQFunc(interChains1[i], interChains2[j]);
if (qScore < AppSettings.parameters.simInteractParam.interfaceSimCutoff)
{
interChains2[j].Reverse();
float reversedQScore = (float)qFunc.WeightQFunc(interChains1[i], interChains2[j]);
if (qScore < reversedQScore)
{
qScore = reversedQScore;
}
else
{
interChains2[j].Reverse();
}
}
if (qScore >= 0.0)
{
InterfacePairInfo interfacesInfo = new InterfacePairInfo((InterfaceInfo)interChains1[i], (InterfaceInfo)interChains2[j]);
interfacesInfo.qScore = qScore;
interfacesList.Add(interfacesInfo);
}
}
}
return(interfacesList.ToArray());
}
/// <summary>
/// compare one pair interactive chains with a list of interactive chains
/// if no similar interfaces, return true
/// otherwise return false
/// </summary>
/// <param name="interChains"></param>
/// <param name="interChainsList"></param>
/// <returns></returns>
public bool IsInterfaceUnique(InterfaceChains interChains, List <InterfaceChains> interChainsList)
{
// pairwise compare two interfaces
for (int i = 0; i < interChainsList.Count; i++)
{
// get q scores for each interaction chains: Q_weight
float qScore = (float)qFunc.WeightQFunc(interChains, interChainsList[i]);
InterfacePairInfo interfacesInfo = new InterfacePairInfo((InterfaceInfo)interChains, (InterfaceInfo)interChainsList[i]);
interfacesInfo.qScore = qScore;
if (qScore >= AppSettings.parameters.simInteractParam.interfaceSimCutoff)
{
return(false);
}
}
return(true);
}
/// <summary>
/// get q scores within a crystal
/// </summary>
/// <param name="interChains">input: all pairwise interactive chains
/// output: unique pairwise interactive chains</param>
/// return: an array of pairwise interfaces and their q scores
public InterfacePairInfo[] FindUniqueInterfacesWithinCrystal(ref InterfaceChains[] interChains)
{
List <InterfacePairInfo> interfacesCompList = new List <InterfacePairInfo> ();
List <int> uniqueInterChainsIdList = new List <int> ();
// initialize the unique interchains list
for (int i = 0; i < interChains.Length; i++)
{
uniqueInterChainsIdList.Add(i + 1);
}
// pairwise compare two interfaces
for (int i = 0; i < interChains.Length - 1; i++)
{
// should have similar structure to a structure
if (!uniqueInterChainsIdList.Contains(i + 1))
{
continue;
}
for (int j = i + 1; j < interChains.Length; j++)
{
// should have similar structures
if (!uniqueInterChainsIdList.Contains(j + 1))
{
continue;
}
// get q scores for each interaction chains: Q_weight
float qScore = (float)qFunc.WeightQFunc(interChains[i], interChains[j]);
if (qScore < AppSettings.parameters.simInteractParam.uniqueInterfaceCutoff)
{
interChains[j].Reverse();
float reversedQScore = (float)qFunc.WeightQFunc(interChains[i], interChains[j]);
if (reversedQScore > qScore)
{
qScore = reversedQScore;
}
else
{
interChains[j].Reverse();
}
}
InterfacePairInfo interfacesInfo = new InterfacePairInfo((InterfaceInfo)interChains[i], (InterfaceInfo)interChains[j]);
interfacesInfo.qScore = qScore;
// remove same interfaces with Qscore >= cutoff and with same asymmetric chains
if (qScore > AppSettings.parameters.simInteractParam.uniqueInterfaceCutoff &&
AreAsymChainsSame(interChains[i], interChains[j]) > -1)
{
interfacesInfo.sameAsym = true;
uniqueInterChainsIdList.Remove(j + 1);
}
interfacesCompList.Add(interfacesInfo);
}
}
// keep unique interfaces
InterfaceChains[] uniqueInterChains = new InterfaceChains [uniqueInterChainsIdList.Count];
for (int i = 0; i < uniqueInterChainsIdList.Count; i++)
{
uniqueInterChains[i] = interChains[uniqueInterChainsIdList[i] - 1];
}
interChains = uniqueInterChains;
// return an array of interface info
return(interfacesCompList.ToArray());
}
/// <summary>
/// remove the interface pair from the interfaces list
/// </summary>
/// <param name="interfacePairList"></param>
/// <param name="interfaceInfo"></param>
private void RemoveInterfacePairInfo(ref List <InterfacePairInfo> interfacePairList, InterfacePairInfo interfaceInfo)
{
int removedIndex = -1;
bool interfaceFound = false;
foreach (InterfacePairInfo interfacePair in interfacePairList)
{
removedIndex++;
if (interfacePair.interfaceInfo1.interfaceId == interfaceInfo.interfaceInfo1.interfaceId &&
interfacePair.interfaceInfo2.interfaceId == interfaceInfo.interfaceInfo2.interfaceId)
{
interfaceFound = true;
break;
}
}
if (interfaceFound)
{
interfacePairList.RemoveAt(removedIndex);
}
}