public static bool IsProteinAtomListContainerNullOrEmpty(ProteinAtomListContainer proteinAtomListContainer)
{
if (proteinAtomListContainer == null || proteinAtomListContainer.AtomList == null || proteinAtomListContainer.AtomList.Count == 0)
{
return(true);
}
return(false);
}
public static ProteinChainListContainer AtomPairListToUnpairedAtomLists(List <AtomPair> atomPairList, bool distinct = false)
{
var proteinChainSequenceListContainer = new ProteinChainListContainer {
ChainList = new List <ProteinAtomListContainer>()
};
ProteinAtomListContainer atoms1 = GetListOfAtomFromAtomPair(atomPairList, 1, distinct);
proteinChainSequenceListContainer.ChainList.Add(atoms1);
ProteinAtomListContainer atoms2 = GetListOfAtomFromAtomPair(atomPairList, 2, distinct);
proteinChainSequenceListContainer.ChainList.Add(atoms2);
return(proteinChainSequenceListContainer);
}
/// <summary>
/// This method splits a List of AtomPair into separate chains.
/// </summary>
/// <param name="atomPairList"></param>
/// <param name="atomNumberInPair"></param>
/// <param name="distinct"></param>
/// <returns></returns>
private static ProteinAtomListContainer GetListOfAtomFromAtomPair(List <AtomPair> atomPairList, int atomNumberInPair, bool distinct = false)
{
if (atomNumberInPair != 1 && atomNumberInPair != 2)
{
throw new ArgumentOutOfRangeException(nameof(atomNumberInPair));
}
if (atomPairList == null || atomPairList.Count <= 0)
{
//return null;
throw new ArgumentOutOfRangeException(nameof(atomPairList));
}
var result = new ProteinAtomListContainer();
for (int index = 0; index < atomPairList.Count; index++)
{
AtomPair atomPair = atomPairList[index];
if (atomNumberInPair == 1)
{
result.AtomList.Add(atomPair.Atom1);
}
else if (atomNumberInPair == 2)
{
result.AtomList.Add(atomPair.Atom2);
}
}
if (distinct)
{
result.AtomList = result.AtomList.Distinct().ToList();
}
return(result);
}
/// <summary>
/// Removes groups from the cluster which do not meet the proteinInterface definition criteria. Also provides a count of proteinInterfaces per
/// stage.
/// </summary>
/// <param name="proteinId"></param>
/// <param name="chainInteractingAtomLists"></param>
/// <param name="fullClusteringResult"></param>
/// <param name="chainStageProteinInterfaceCount"></param>
/// <param name="clusteringProteinInterfaceDensityDetectionOptions"></param>
/// <param name="minimumProteinInterfaceAlphas"></param>
/// <param name="maximumProteinInterfaceAlphas"></param>
/// <param name="minimumProteinInterfaceDensity"></param>
/// <param name="maximumProteinInterfaceDensity"></param>
/// <returns></returns>
public static ClusteringFullResultListContainer DetectProteinInterfaces(
string proteinId,
ProteinChainListContainer chainInteractingAtomLists,
ClusteringFullResultListContainer fullClusteringResult,
out List <List <int> > chainStageProteinInterfaceCount,
ClusteringProteinInterfaceDensityDetectionOptions clusteringProteinInterfaceDensityDetectionOptions,// = ClusteringProteinInterfaceDensityDetectionOptions.ResidueSequenceIndex,
decimal minimumProteinInterfaceDensity,
decimal maximumProteinInterfaceDensity = -1,
int minimumProteinInterfaceAlphas = 4,
int maximumProteinInterfaceAlphas = -1
)
{
if (ParameterValidation.IsProteinChainListContainerNullOrEmpty(chainInteractingAtomLists))
{
throw new ArgumentOutOfRangeException(nameof(chainInteractingAtomLists));
}
if (ParameterValidation.IsClusteringFullResultListContainerNullOrEmpty(fullClusteringResult))
{
throw new ArgumentOutOfRangeException(nameof(fullClusteringResult));
}
//var resultChainsStagesGroupsMembers = new List<List<List<List<int>>>>();
var resultChainsStagesGroupsMembers = new ClusteringFullResultListContainer();
chainStageProteinInterfaceCount = new List <List <int> >();
for (int chainIndex = 0; chainIndex < fullClusteringResult.ChainList.Count; chainIndex++)
{
//var thisChain = new List<List<List<int>>>();
var thisChain = new ClusteringFullResultListContainer.Chain();
resultChainsStagesGroupsMembers.ChainList.Add(thisChain);
var chainProteinInterfacesCount = new List <int>();
chainStageProteinInterfaceCount.Add(chainProteinInterfacesCount);
// Check every stage to see which has the lowest and highest number of suspected interaction proteinInterfaces.
for (int stageIndex = 0; stageIndex < fullClusteringResult.ChainList[chainIndex].StageList.Count; stageIndex++)
{
//var thisStage = new List<List<int>>();
var thisStage = new ClusteringFullResultListContainer.Chain.Stage();
thisChain.StageList.Add(thisStage);
int proteinInterfacesAtThisStage = 0;
// For every group, check if they have enough members (carbon alpha atoms) to meet the requirements of being an interaction proteinInterface.
for (int groupIndex = 0; groupIndex < fullClusteringResult.ChainList[chainIndex].StageList[stageIndex].ClusterList.Count; groupIndex++)
{
//var thisGroup = new List<int>();
var thisGroup = new ClusteringFullResultListContainer.Chain.Stage.Cluster();
thisStage.ClusterList.Add(thisGroup);
int groupTotalCarbonAlphas = fullClusteringResult.ChainList[chainIndex].StageList[stageIndex].ClusterList[groupIndex].AtomIndexList.Count;
if (((minimumProteinInterfaceAlphas > -1) && (groupTotalCarbonAlphas < minimumProteinInterfaceAlphas)) || ((maximumProteinInterfaceAlphas > -1) && groupTotalCarbonAlphas > maximumProteinInterfaceAlphas))
{
continue;
}
//var interactingGroup = clusters.ChainList[chainIndex].StageList[stageIndex].ClusterList[groupIndex].Select(member => chainInteractingAtomLists.ChainList[chainIndex].AtomList[member]).ToList();
var interactingGroup = new ProteinAtomListContainer
{
AtomList = fullClusteringResult.ChainList[chainIndex].StageList[stageIndex].ClusterList[groupIndex].AtomIndexList.Select(member => chainInteractingAtomLists.ChainList[chainIndex].AtomList[member]).ToList()
};
decimal totalProteinInterfaceLength;
switch (clusteringProteinInterfaceDensityDetectionOptions)
{
case ClusteringProteinInterfaceDensityDetectionOptions.ResidueSequenceIndex:
totalProteinInterfaceLength = Clustering.FindProteinInterfaceDistanceFromResidueSequenceIndex(interactingGroup);
break;
case ClusteringProteinInterfaceDensityDetectionOptions.ShortestRoutePath:
decimal bestPathDistance;
Clustering.BruteForceTravellingSalesmanProblemSolver(interactingGroup, out bestPathDistance);
totalProteinInterfaceLength = bestPathDistance;
break;
case ClusteringProteinInterfaceDensityDetectionOptions.LongestDistanceBetweenInteractions:
decimal longestDistance;
Clustering.FindLongestDistanceBetweenNodes(interactingGroup, out longestDistance);
totalProteinInterfaceLength = longestDistance;
break;
default:
throw new ArgumentOutOfRangeException();
}
// The length is the maximum distance between any two values/points or the total distance between them.
decimal interactionProteinInterfaceDensity = Math.Round((groupTotalCarbonAlphas / totalProteinInterfaceLength) * 100, 0);
if (((minimumProteinInterfaceDensity <= -1) || (interactionProteinInterfaceDensity >= minimumProteinInterfaceDensity)) && ((maximumProteinInterfaceDensity <= -1) || (interactionProteinInterfaceDensity <= maximumProteinInterfaceDensity)))
{
proteinInterfacesAtThisStage++;
//stageTotalProteinInterfaces[chainIndex].StageList[stageIndex]++;
for (int memberIndex = 0; memberIndex < fullClusteringResult.ChainList[chainIndex].StageList[stageIndex].ClusterList[groupIndex].AtomIndexList.Count; memberIndex++)
{
int thisMember = fullClusteringResult.ChainList[chainIndex].StageList[stageIndex].ClusterList[groupIndex].AtomIndexList[memberIndex];
thisGroup.AtomIndexList.Add(thisMember);
}
if (proteinInterfacesAtThisStage >= 4)
{
////////Console.WriteLine(proteinInterfacesAtThisStage);
}
}
}
chainProteinInterfacesCount.Add(proteinInterfacesAtThisStage);
}
}
return(resultChainsStagesGroupsMembers);
}
