/// <summary>
/// Perform sequence alignment on the chains of each protein to see if it is a homodimer.
/// </summary>
/// <returns></returns>
public static DimerSequenceTypeCategories <ISequence> SplitDimerTypes(CancellationToken cancellationToken, List <ISequence> sequences, decimal minimumHeterodimerSimilarityRequired = 30.0m, decimal minimumHomodimerSimiliarityRequired = 90.0m, ProgressActionSet progressActionSet = null, int totalThreads = -1)
{
if (sequences == null || sequences.Count == 0)
{
throw new ArgumentOutOfRangeException(nameof(sequences));
}
if (progressActionSet == null)
{
throw new ArgumentNullException(nameof(progressActionSet));
}
var splitDimers = SplitDimersHomoHetero(cancellationToken, sequences, minimumHeterodimerSimilarityRequired, minimumHomodimerSimiliarityRequired, progressActionSet, totalThreads);
var heterodimers = new List <ISequence>(sequences);
var homodimers = new List <ISequence>(sequences);
var homologydimers = new List <ISequence>(sequences);
heterodimers = RemoveSequences(cancellationToken, heterodimers, splitDimers.HeteroDimerPdbIdList, RemoveSequencesOptions.RemoveSequencesNotInList);
homodimers = RemoveSequences(cancellationToken, homodimers, splitDimers.HomoDimerPdbIdList, RemoveSequencesOptions.RemoveSequencesNotInList);
homologydimers = RemoveSequences(cancellationToken, homologydimers, splitDimers.HomologyDimerPdbIdList, RemoveSequencesOptions.RemoveSequencesNotInList);
var result = new DimerSequenceTypeCategories <ISequence>()
{
HomoDimerPdbIdList = homodimers,
HeteroDimerPdbIdList = heterodimers,
HomologyDimerPdbIdList = homologydimers,
};
return(result);
}
/// <summary>
/// Perform sequence alignment on the chains of each protein to see if it is a homodimer or heterodimer
/// </summary>
/// <returns></returns>
public static DimerSequenceTypeCategories <string> SplitDimersHomoHetero(CancellationToken cancellationToken, List <ISequence> sequences, decimal minimumHeterodimerSimilarityRequired = 30.0m, decimal minimumHomodimerSimiliarityRequired = 90.0m, ProgressActionSet progressActionSet = null, int totalThreads = -1)
{
if (sequences == null || sequences.Count == 0)
{
throw new ArgumentOutOfRangeException(nameof(sequences));
}
if (progressActionSet == null)
{
throw new ArgumentNullException(nameof(progressActionSet));
}
var workDivision = new WorkDivision <DimerSequenceTypeCategories <string> >(sequences.Count, totalThreads);
ProgressActionSet.StartAction(sequences.Count, progressActionSet);
for (int threadIndex = 0; threadIndex < workDivision.ThreadCount; threadIndex++)
{
int localThreadIndex = threadIndex;
Task <DimerSequenceTypeCategories <string> > task = Task.Run(() =>
{
var taskResult = new DimerSequenceTypeCategories <string>();
for (int sequencesIndexA = workDivision.ThreadFirstIndex[localThreadIndex]; sequencesIndexA <= workDivision.ThreadLastIndex[localThreadIndex]; sequencesIndexA++)
{
if (cancellationToken.IsCancellationRequested)
{
break;
}
string proteinIdA = SequenceIdSplit.SequenceIdToPdbIdAndChainId(sequences[sequencesIndexA].ID).PdbId;
for (int sequencesIndexB = 0; sequencesIndexB < sequences.Count; sequencesIndexB++)
{
if (cancellationToken.IsCancellationRequested)
{
break;
}
// Don't align the same sequence index. Skip calculating indexes already calculated. Perform alignment operation if protein id is the same.
var proteinIdB = SequenceIdSplit.SequenceIdToPdbIdAndChainId(sequences[sequencesIndexB].ID).PdbId;
if (sequencesIndexA == sequencesIndexB || sequencesIndexB < sequencesIndexA || proteinIdA != proteinIdB)
{
continue;
}
var dimerType = FindDimerType(sequences[sequencesIndexA], sequences[sequencesIndexB], minimumHeterodimerSimilarityRequired, minimumHomodimerSimiliarityRequired);
if (dimerType == DimerType.HeteroDimer)
{
taskResult.HeteroDimerPdbIdList.Add(proteinIdA);
}
else if (dimerType == DimerType.HomoDimer)
{
taskResult.HomoDimerPdbIdList.Add(proteinIdA);
}
else if (dimerType == DimerType.HomologyDimer)
{
taskResult.HomologyDimerPdbIdList.Add(proteinIdA);
}
}
workDivision.IncrementItemsCompleted(1);
ProgressActionSet.ProgressAction(1, progressActionSet);
ProgressActionSet.EstimatedTimeRemainingAction(workDivision.StartTicks, workDivision.ItemsCompleted, workDivision.ItemsToProcess, progressActionSet);
}
return(taskResult);
}, cancellationToken);
workDivision.TaskList.Add(task);
}
workDivision.WaitAllTasks();
var dimerSequenceTypeCategories = new DimerSequenceTypeCategories <string>();
foreach (var task in workDivision.TaskList.Where(t => t != null && t.IsCompleted && !t.IsFaulted && !t.IsCanceled && t.Result != null))
{
dimerSequenceTypeCategories.HeteroDimerPdbIdList.AddRange(task.Result.HeteroDimerPdbIdList);
dimerSequenceTypeCategories.HomoDimerPdbIdList.AddRange(task.Result.HomoDimerPdbIdList);
dimerSequenceTypeCategories.HomologyDimerPdbIdList.AddRange(task.Result.HomologyDimerPdbIdList);
}
dimerSequenceTypeCategories.HeteroDimerPdbIdList = dimerSequenceTypeCategories.HeteroDimerPdbIdList.Distinct().ToList();
dimerSequenceTypeCategories.HomoDimerPdbIdList = dimerSequenceTypeCategories.HomoDimerPdbIdList.Distinct().ToList();
dimerSequenceTypeCategories.HomologyDimerPdbIdList = dimerSequenceTypeCategories.HomologyDimerPdbIdList.Distinct().ToList();
return(dimerSequenceTypeCategories);
}
