/// <summary>
/// This method finds chemical interaction bonds between atoms on separate chains.
/// </summary>
/// <param name="cancellationToken"></param>
/// <param name="pdbFilename">The filename of the PDB file to parse for chemical interactions.</param>
/// <param name="pdbIdChainIdList"></param>
/// <param name="breakWhenFirstInteractionFound"></param>
/// <param name="totalThreads"></param>
/// <returns>Returns a list of atom pairs which are close enough in distance to have chemical interactions.</returns>
public static List <AtomPair> FindInteractions(CancellationToken cancellationToken, decimal maxAtomInterationDistance /*= 8.0m*/, string pdbFilename, Dictionary <string, List <string> > pdbIdChainIdList, bool breakWhenFirstInteractionFound = false, int totalThreads = -1, bool sort = true, int requiredChains = -1)
{
if (ParameterValidation.IsLoadFilenameInvalid(pdbFilename)) // && ParameterValidation.IsProteinChainListContainerNullOrEmpty(pdbFileChains))
{
throw new ArgumentOutOfRangeException(nameof(pdbFilename));
}
string proteinId = ProteinDataBankFileOperations.PdbIdFromPdbFilename(pdbFilename);
bool useCache = false;
if (useCache && !string.IsNullOrWhiteSpace(proteinId))
{
var cachedInteractions = InteractionsCache.LoadPdbInteractionCache(proteinId, requiredChains);
if (cachedInteractions != null)
{
return(cachedInteractions);
}
}
var chainIdList = pdbIdChainIdList != null ? (proteinId != null && pdbIdChainIdList.ContainsKey(proteinId) ? pdbIdChainIdList[proteinId].ToArray() : null) : null;
ProteinChainListContainer proteinFileChains = ProteinDataBankFileOperations.PdbAtomicChains(pdbFilename, chainIdList, requiredChains, requiredChains, true);
List <AtomPair> atomPairList = FindInteractions(cancellationToken, maxAtomInterationDistance, proteinId, pdbIdChainIdList, proteinFileChains, breakWhenFirstInteractionFound, totalThreads, sort, requiredChains);
if (atomPairList == null)
{
// only save if null, otherwise, already saved in other method
atomPairList = new List <AtomPair>();
if (useCache)
{
InteractionsCache.SavePdbInteractionCache(proteinId, atomPairList, requiredChains);
}
}
return(atomPairList);
}
/// <summary>
///
/// </summary>
/// <param name="cancellationToken"></param>
/// <param name="pdbFilename"></param>
/// <param name="pdbIdChainIdList"></param>
/// <param name="pdbFileChains"></param>
/// <param name="singularAaToAaInteractions"></param>
/// <param name="fullClusteringResult"></param>
/// <returns></returns>
public static ProteinInterfaceAnalysisResultData AnalyseProteinInterfaces(
CancellationToken cancellationToken,
decimal maxAtomInterationDistance,
decimal minimumProteinInterfaceDensity,
string pdbFilename,
Dictionary <string, List <string> > pdbIdChainIdList,
ProteinChainListContainer pdbFileChains,
ProteinChainListContainer singularAaToAaInteractions,
ClusteringFullResultListContainer fullClusteringResult)
{
if (ParameterValidation.IsLoadFilenameInvalid(pdbFilename))
{
throw new ArgumentOutOfRangeException(nameof(pdbFilename));
}
if (ParameterValidation.IsProteinChainListContainerNullOrEmpty(singularAaToAaInteractions))
{
throw new ArgumentOutOfRangeException(nameof(singularAaToAaInteractions));
}
if (ParameterValidation.IsClusteringFullResultListContainerNullOrEmpty(fullClusteringResult))
{
throw new ArgumentOutOfRangeException(nameof(fullClusteringResult));
}
string proteinId = ProteinDataBankFileOperations.PdbIdFromPdbFilename(pdbFilename);
List <List <int> > chainStageProteinInterfaceCount;
// Find how many proteinInterfaces at each stage.
ClusteringFullResultListContainer proteinInterfacesClusteringResult = DetectProteinInterfaces(proteinId, singularAaToAaInteractions, fullClusteringResult, out chainStageProteinInterfaceCount, ClusteringProteinInterfaceDensityDetectionOptions.ResidueSequenceIndex, minimumProteinInterfaceDensity);
// Find the last stage having required number of proteinInterfaces.
int[] detectedBestClusterStagesIndexes = ProteinInterfaceTreeOptimalStageDetection.FindFinalProteinInterfaceStageIndexes(singularAaToAaInteractions, fullClusteringResult, proteinInterfacesClusteringResult, chainStageProteinInterfaceCount);
int totalChains = singularAaToAaInteractions.ChainList.Count;
var interactionProteinInterfaceClusteringHierarchyDataList = new List <InteractionProteinInterfaceClusteringHierarchyData>();
int[] numberProteinInterfacesPerChain = FindNumberProteinInterfacesPerChain(proteinInterfacesClusteringResult, detectedBestClusterStagesIndexes);
for (int chainIndex = 0; chainIndex < totalChains; chainIndex++)
{
int stageIndex = detectedBestClusterStagesIndexes[chainIndex];
string chainIdLetter = SpreadsheetFileHandler.AlphabetLetterRollOver(chainIndex);
var interactionProteinInterfaceClusteringHierarchyData = new InteractionProteinInterfaceClusteringHierarchyData(proteinId, chainIdLetter, numberProteinInterfacesPerChain[chainIndex], stageIndex + 1, fullClusteringResult.ChainList[chainIndex].StageList.Count);
interactionProteinInterfaceClusteringHierarchyDataList.Add(interactionProteinInterfaceClusteringHierarchyData);
}
InteractionBetweenProteinInterfacesListContainer interactionBetweenProteinInterfacesContainer = CrossProteinInterfaceInteractions.FindInteractionsBetweenAnyProteinInterfaces(cancellationToken, maxAtomInterationDistance, pdbFilename, pdbIdChainIdList, pdbFileChains, singularAaToAaInteractions, fullClusteringResult, proteinInterfacesClusteringResult, detectedBestClusterStagesIndexes);
List <ProteinInterfaceSequenceAndPositionData> analyseProteinInterfacesSequenceAndPositionData = AnalyseProteinInterfacesSequenceAndPositionData(pdbFilename, pdbIdChainIdList, pdbFileChains, singularAaToAaInteractions, proteinInterfacesClusteringResult, detectedBestClusterStagesIndexes, interactionBetweenProteinInterfacesContainer);
var result = new ProteinInterfaceAnalysisResultData(
detectedBestClusterStagesIndexes,
proteinInterfacesClusteringResult,
interactionProteinInterfaceClusteringHierarchyDataList,
interactionBetweenProteinInterfacesContainer,
analyseProteinInterfacesSequenceAndPositionData
);
return(result);
}
