public ProteinInterfaceAnalysisResultData(int[] detectedBestStageIndexes, ClusteringFullResultListContainer proteinInterfacesClusteringResult, List <InteractionProteinInterfaceClusteringHierarchyData> interactionProteinInterfaceClusteringHierarchyData, InteractionBetweenProteinInterfacesListContainer interactionsBetweenProteinInterfacesList, List <ProteinInterfaceSequenceAndPositionData> proteinInterfacesSequenceAndPositionDataList) { DetectedBestStageIndexes = detectedBestStageIndexes; ProteinInterfacesClusteringResult = proteinInterfacesClusteringResult; InteractionProteinInterfaceClusteringHierarchyData = interactionProteinInterfaceClusteringHierarchyData; InteractionsBetweenProteinInterfacesList = interactionsBetweenProteinInterfacesList; ProteinInterfacesSequenceAndPositionDataList = proteinInterfacesSequenceAndPositionDataList; }
/// <summary> /// This method returns the total number of interactions an atom has with non-proteinInterfaces in oppoproteinInterface chains. The method /// requires the object returned by the FindInteractionsBetweenProteinInterfaces method. /// </summary> /// <param name="interactionBetweenProteinInterfacesContainer"></param> /// <param name="sourceChainIndex"></param> /// <param name="atomToFind"></param> /// <returns></returns> public static int CountAtomInteractionsOutsideProteinInterface( InteractionBetweenProteinInterfacesListContainer interactionBetweenProteinInterfacesContainer, int sourceChainIndex, ATOM_Record atomToFind ) { int totalInteractionsOutsideProteinInterfaces = interactionBetweenProteinInterfacesContainer.InteractionBetweenNonProteinInterfacesList.Count( a => (a.Atom1.FullProteinInterfaceId.ChainId == sourceChainIndex && a.Atom1.Atom == atomToFind) || (a.Atom2.FullProteinInterfaceId.ChainId == sourceChainIndex && a.Atom2.Atom == atomToFind)); return(totalInteractionsOutsideProteinInterfaces); }
public static List <ATOM_Record> FindAtomInteractingWithOtherProteinInterfaces(ATOM_Record atom, InteractionBetweenProteinInterfacesListContainer interactionBetweenProteinInterfacesContainer, FindAtomInteractingWithAnotherProteinInterfaceOptions findAtomInteractingWithAnotherProteinInterfaceOptions) { if (ParameterValidation.IsAtomNullOrEmpty(atom)) { throw new ArgumentNullException(nameof(atom)); } if (ParameterValidation.IsInteractionBetweenProteinInterfacesListContainerNullOrEmpty(interactionBetweenProteinInterfacesContainer)) { ////////Console.WriteLine("empty"); return(null); } List <InteractionBetweenProteinInterfaces> searchList = null; if (findAtomInteractingWithAnotherProteinInterfaceOptions == FindAtomInteractingWithAnotherProteinInterfaceOptions.FindAtomsInteractingWithOtherProteinInterfaces) { searchList = interactionBetweenProteinInterfacesContainer.InteractionBetweenProteinInterfacesList; } else if (findAtomInteractingWithAnotherProteinInterfaceOptions == FindAtomInteractingWithAnotherProteinInterfaceOptions.FindAtomsInteractingWithNonProteinInterfaces) { searchList = interactionBetweenProteinInterfacesContainer.InteractionBetweenNonProteinInterfacesList; } else { throw new NotImplementedException(); } if (searchList == null) { ////////Console.WriteLine("returning null"); return(null); } var result = new List <ATOM_Record>(); foreach (InteractionBetweenProteinInterfaces interaction in searchList) { if (interaction.Atom1.Atom == atom && interaction.Atom2.Atom != atom) { //return interaction.Atom1.Atom; result.Add(interaction.Atom2.Atom); } if (interaction.Atom1.Atom != atom && interaction.Atom2.Atom == atom) { //return interaction.Atom2.Atom; result.Add(interaction.Atom1.Atom); } } //if (result.Count == 0) //{ // //////Console.WriteLine("returning empty list"); //} return(result); }
/// <summary> /// This method finds interactions between detected proteinInterfaces. It is specific to dimers with exactly two chains. [Chain A /// ProteinInterface Index, Chain B ProteinInterface Index] /// </summary> /// <param name="cancellationToken"></param> /// <param name="pdbFilename"></param> /// <param name="pdbFileChains"></param> /// <param name="chainInteractingAtomLists"></param> /// <param name="fullClusteringResult"></param> /// <param name="proteinInterfacesClusteringResult"></param> /// <param name="detectedFinalStageIndexes"></param> /// <param name="pdbIdChainIdList"></param> /// <returns></returns> public static InteractionBetweenProteinInterfacesListContainer FindInteractionsBetweenAnyProteinInterfaces( CancellationToken cancellationToken, decimal maxAtomInterationDistance, string pdbFilename, Dictionary<string, List<string>> pdbIdChainIdList, ProteinChainListContainer pdbFileChains, ProteinChainListContainer chainInteractingAtomLists, ClusteringFullResultListContainer fullClusteringResult, ClusteringFullResultListContainer proteinInterfacesClusteringResult, int[] detectedFinalStageIndexes) { if (string.IsNullOrWhiteSpace(pdbFilename)) { throw new ArgumentOutOfRangeException(nameof(pdbFilename)); } if (!File.Exists(pdbFilename)) { throw new FileNotFoundException("File not found", pdbFilename); } if (ParameterValidation.IsProteinChainListContainerNullOrEmpty(chainInteractingAtomLists)) { throw new ArgumentOutOfRangeException(nameof(chainInteractingAtomLists)); } if (ParameterValidation.IsClusteringFullResultListContainerNullOrEmpty(fullClusteringResult)) { throw new ArgumentOutOfRangeException(nameof(fullClusteringResult)); } if (ParameterValidation.IsClusteringFullResultListContainerNullOrEmpty(proteinInterfacesClusteringResult)) { throw new ArgumentOutOfRangeException(nameof(proteinInterfacesClusteringResult)); } if (ParameterValidation.IsIntArrayNullOrEmpty(detectedFinalStageIndexes)) { throw new ArgumentOutOfRangeException(nameof(detectedFinalStageIndexes)); } string proteinId = ProteinDataBankFileOperations.PdbIdFromPdbFilename(pdbFilename); var interactionBetweenProteinInterfacesListContainer = new InteractionBetweenProteinInterfacesListContainer(); List<AtomPair> interactionList; if (pdbFileChains != null && pdbFileChains.ChainList != null && pdbFileChains.ChainList.Count > 0) { interactionList = SearchInteractions.FindInteractions(cancellationToken, maxAtomInterationDistance, proteinId, pdbIdChainIdList, pdbFileChains); //, false, -1, pdbFileChains); } else { interactionList = SearchInteractions.FindInteractions(cancellationToken, maxAtomInterationDistance, pdbFilename, pdbIdChainIdList); } var interactionInsideProteinInterfaceArray = new bool[interactionList.Count]; ////////Console.WriteLine(""); ////////Console.WriteLine(""); ////////Console.WriteLine("------------------ START ------------------"); //int c = 0; for (int chainIndexA = 0; chainIndexA < proteinInterfacesClusteringResult.ChainList.Count; chainIndexA++) { for (int chainIndexB = 0; chainIndexB < proteinInterfacesClusteringResult.ChainList.Count; chainIndexB++) { if (chainIndexA == chainIndexB || chainIndexB < chainIndexA) { continue; } List<ClusteringFullResultListContainer.Chain.Stage.Cluster> proteinInterfaceListA = proteinInterfacesClusteringResult.ChainList[chainIndexA].StageList[detectedFinalStageIndexes[chainIndexA]].ClusterList; List<ClusteringFullResultListContainer.Chain.Stage.Cluster> proteinInterfaceListB = proteinInterfacesClusteringResult.ChainList[chainIndexB].StageList[detectedFinalStageIndexes[chainIndexB]].ClusterList; int realProteinInterfaceIndexA = -1; for (int proteinInterfaceIndexA = 0; proteinInterfaceIndexA < proteinInterfaceListA.Count; proteinInterfaceIndexA++) { int realProteinInterfaceIndexB = -1; List<int> proteinInterfaceMemberIndexListA = proteinInterfaceListA[proteinInterfaceIndexA].AtomIndexList; List<ATOM_Record> proteinInterfaceAtomListA = proteinInterfaceMemberIndexListA.Select(proteinInterfaceMemberIndexA => chainInteractingAtomLists.ChainList[chainIndexA].AtomList[proteinInterfaceMemberIndexA]).ToList(); proteinInterfaceAtomListA = proteinInterfaceAtomListA.OrderBy(a => ProteinDataBankFileOperations.NullableTryParseInt32(a.resSeq.FieldValue)).ToList(); if (proteinInterfaceAtomListA.Count > 0) { realProteinInterfaceIndexA++; } else { continue; } for (int proteinInterfaceIndexB = 0; proteinInterfaceIndexB < proteinInterfaceListB.Count; proteinInterfaceIndexB++) { List<int> proteinInterfaceMemberIndexListB = proteinInterfaceListB[proteinInterfaceIndexB].AtomIndexList; List<ATOM_Record> proteinInterfaceAtomListB = proteinInterfaceMemberIndexListB.Select(proteinInterfaceMemberIndexB => chainInteractingAtomLists.ChainList[chainIndexB].AtomList[proteinInterfaceMemberIndexB]).ToList(); proteinInterfaceAtomListB = proteinInterfaceAtomListB.OrderBy(b => ProteinDataBankFileOperations.NullableTryParseInt32(b.resSeq.FieldValue)).ToList(); if (proteinInterfaceAtomListB.Count > 0) { realProteinInterfaceIndexB++; } else { continue; } for (int proteinInterfaceAtomListIndexA = 0; proteinInterfaceAtomListIndexA < proteinInterfaceAtomListA.Count; proteinInterfaceAtomListIndexA++) { ATOM_Record atomA = proteinInterfaceAtomListA[proteinInterfaceAtomListIndexA]; for (int proteinInterfaceAtomListIndexB = 0; proteinInterfaceAtomListIndexB < proteinInterfaceAtomListB.Count; proteinInterfaceAtomListIndexB++) { ATOM_Record atomB = proteinInterfaceAtomListB[proteinInterfaceAtomListIndexB]; //c++; ////////Console.WriteLine(c.ToString().PadLeft(5) + // " Chain " + chainIndexA + " (" + proteinInterfaceListA.Count(a => a.AtomIndexList.Count > 0) + " proteinInterfaces) ProteinInterface " + realProteinInterfaceIndexA + " (" + proteinInterfaceAtomListA.Count + " atoms) <--->" + // " Chain " + chainIndexB + " (" + proteinInterfaceListB.Count(a => a.AtomIndexList.Count > 0) + " proteinInterfaces) ProteinInterface " + realProteinInterfaceIndexB + " (" + proteinInterfaceAtomListB.Count + " atoms) --->" + // " chainID " + atomA.chainID.FieldValue + " resName " + atomA.resName.FieldValue + " resSeq " + atomA.resSeq.FieldValue + " <--->" + // " chainID " + atomB.chainID.FieldValue + " resName " + atomB.resName.FieldValue + " resSeq " + atomB.resSeq.FieldValue); for (int interactionIndex = 0; interactionIndex < interactionList.Count; interactionIndex++) { AtomPair interaction = interactionList[interactionIndex]; if ((interaction.Atom1 == atomA && interaction.Atom2 == atomB) || (interaction.Atom1 == atomB && interaction.Atom2 == atomA)) { interactionInsideProteinInterfaceArray[interactionIndex] = true; var interactionBetweenProteinInterfaces = new InteractionBetweenProteinInterfaces(); interactionBetweenProteinInterfacesListContainer.InteractionBetweenProteinInterfacesList.Add(interactionBetweenProteinInterfaces); interactionBetweenProteinInterfaces.Atom1.Atom = atomA; interactionBetweenProteinInterfaces.Atom1.FullProteinInterfaceId.ProteinId = proteinId; interactionBetweenProteinInterfaces.Atom1.FullProteinInterfaceId.ChainId = chainIndexA; interactionBetweenProteinInterfaces.Atom1.FullProteinInterfaceId.ProteinInterfaceId = realProteinInterfaceIndexA; interactionBetweenProteinInterfaces.Atom2.Atom = atomB; interactionBetweenProteinInterfaces.Atom2.FullProteinInterfaceId.ProteinId = proteinId; interactionBetweenProteinInterfaces.Atom2.FullProteinInterfaceId.ChainId = chainIndexB; interactionBetweenProteinInterfaces.Atom2.FullProteinInterfaceId.ProteinInterfaceId = realProteinInterfaceIndexB; } } } } } } } } for (int interactionIndex = 0; interactionIndex < interactionInsideProteinInterfaceArray.Length; interactionIndex++) { bool interactionInsideProteinInterface = interactionInsideProteinInterfaceArray[interactionIndex]; if (!interactionInsideProteinInterface) { var interactionBetweenNonProteinInterfaces = new InteractionBetweenProteinInterfaces(); interactionBetweenProteinInterfacesListContainer.InteractionBetweenNonProteinInterfacesList.Add(interactionBetweenNonProteinInterfaces); interactionBetweenNonProteinInterfaces.Atom1.Atom = interactionList[interactionIndex].Atom1; interactionBetweenNonProteinInterfaces.Atom1.FullProteinInterfaceId.ProteinId = proteinId; interactionBetweenNonProteinInterfaces.Atom1.FullProteinInterfaceId.ChainId = interactionList[interactionIndex].Atom1FullProteinInterfaceId.ChainId; interactionBetweenNonProteinInterfaces.Atom1.FullProteinInterfaceId.ProteinInterfaceId = -1; interactionBetweenNonProteinInterfaces.Atom2.Atom = interactionList[interactionIndex].Atom2; interactionBetweenNonProteinInterfaces.Atom2.FullProteinInterfaceId.ProteinId = proteinId; interactionBetweenNonProteinInterfaces.Atom2.FullProteinInterfaceId.ChainId = interactionList[interactionIndex].Atom2FullProteinInterfaceId.ChainId; interactionBetweenNonProteinInterfaces.Atom2.FullProteinInterfaceId.ProteinInterfaceId = -1; } } ////////Console.WriteLine("------------------ END ------------------"); // ensure sorted order interactionBetweenProteinInterfacesListContainer.InteractionBetweenProteinInterfacesList = interactionBetweenProteinInterfacesListContainer.InteractionBetweenProteinInterfacesList .OrderBy(a => a.Atom1.FullProteinInterfaceId.ChainId) .ThenBy(a => a.Atom1.FullProteinInterfaceId.ProteinInterfaceId) .ThenBy(a => ProteinDataBankFileOperations.NullableTryParseInt32(a.Atom1.Atom.resSeq.FieldValue)) .ThenBy(a => a.Atom2.FullProteinInterfaceId.ChainId) .ThenBy(a => a.Atom2.FullProteinInterfaceId.ProteinInterfaceId) .ThenBy(a => ProteinDataBankFileOperations.NullableTryParseInt32(a.Atom2.Atom.resSeq.FieldValue)) .ToList(); interactionBetweenProteinInterfacesListContainer.InteractionBetweenNonProteinInterfacesList = interactionBetweenProteinInterfacesListContainer.InteractionBetweenNonProteinInterfacesList .OrderBy(a => a.Atom1.FullProteinInterfaceId.ChainId) .ThenBy(a => a.Atom1.FullProteinInterfaceId.ProteinInterfaceId) .ThenBy(a => ProteinDataBankFileOperations.NullableTryParseInt32(a.Atom1.Atom.resSeq.FieldValue)) .ThenBy(a => a.Atom2.FullProteinInterfaceId.ChainId) .ThenBy(a => a.Atom2.FullProteinInterfaceId.ProteinInterfaceId) .ThenBy(a => ProteinDataBankFileOperations.NullableTryParseInt32(a.Atom2.Atom.resSeq.FieldValue)) .ToList(); // remove duplicates (as the list is sorted, duplicates will always be together in the list) for (int index = interactionBetweenProteinInterfacesListContainer.InteractionBetweenProteinInterfacesList.Count - 1; index > 0; index--) { InteractionBetweenProteinInterfaces lastInteractionBetweenProteinInterfaces = interactionBetweenProteinInterfacesListContainer.InteractionBetweenProteinInterfacesList[index - 1]; InteractionBetweenProteinInterfaces thisInteractionBetweenProteinInterfaces = interactionBetweenProteinInterfacesListContainer.InteractionBetweenProteinInterfacesList[index]; if (lastInteractionBetweenProteinInterfaces == null || thisInteractionBetweenProteinInterfaces == null) { continue; } if (thisInteractionBetweenProteinInterfaces.Atom1.FullProteinInterfaceId.ProteinId == lastInteractionBetweenProteinInterfaces.Atom1.FullProteinInterfaceId.ProteinId && thisInteractionBetweenProteinInterfaces.Atom1.FullProteinInterfaceId.ChainId == lastInteractionBetweenProteinInterfaces.Atom1.FullProteinInterfaceId.ChainId && thisInteractionBetweenProteinInterfaces.Atom1.FullProteinInterfaceId.ProteinInterfaceId == lastInteractionBetweenProteinInterfaces.Atom1.FullProteinInterfaceId.ProteinInterfaceId && thisInteractionBetweenProteinInterfaces.Atom1.Atom == lastInteractionBetweenProteinInterfaces.Atom1.Atom && thisInteractionBetweenProteinInterfaces.Atom2.FullProteinInterfaceId.ProteinId == lastInteractionBetweenProteinInterfaces.Atom2.FullProteinInterfaceId.ProteinId && thisInteractionBetweenProteinInterfaces.Atom2.FullProteinInterfaceId.ChainId == lastInteractionBetweenProteinInterfaces.Atom2.FullProteinInterfaceId.ChainId && thisInteractionBetweenProteinInterfaces.Atom2.FullProteinInterfaceId.ProteinInterfaceId == lastInteractionBetweenProteinInterfaces.Atom2.FullProteinInterfaceId.ProteinInterfaceId && thisInteractionBetweenProteinInterfaces.Atom2.Atom == lastInteractionBetweenProteinInterfaces.Atom2.Atom) { interactionBetweenProteinInterfacesListContainer.InteractionBetweenProteinInterfacesList.RemoveAt(index - 1); //////Console.WriteLine("removed duplicate"); } } for (int index = interactionBetweenProteinInterfacesListContainer.InteractionBetweenNonProteinInterfacesList.Count - 1; index > 0; index--) { InteractionBetweenProteinInterfaces lastInteractionBetweenProteinInterfaces = interactionBetweenProteinInterfacesListContainer.InteractionBetweenNonProteinInterfacesList[index - 1]; InteractionBetweenProteinInterfaces thisInteractionBetweenProteinInterfaces = interactionBetweenProteinInterfacesListContainer.InteractionBetweenNonProteinInterfacesList[index]; if (lastInteractionBetweenProteinInterfaces == null || thisInteractionBetweenProteinInterfaces == null) { continue; } if (thisInteractionBetweenProteinInterfaces.Atom1.FullProteinInterfaceId.ProteinId == lastInteractionBetweenProteinInterfaces.Atom1.FullProteinInterfaceId.ProteinId && thisInteractionBetweenProteinInterfaces.Atom1.FullProteinInterfaceId.ChainId == lastInteractionBetweenProteinInterfaces.Atom1.FullProteinInterfaceId.ChainId && thisInteractionBetweenProteinInterfaces.Atom1.FullProteinInterfaceId.ProteinInterfaceId == lastInteractionBetweenProteinInterfaces.Atom1.FullProteinInterfaceId.ProteinInterfaceId && thisInteractionBetweenProteinInterfaces.Atom1.Atom == lastInteractionBetweenProteinInterfaces.Atom1.Atom && thisInteractionBetweenProteinInterfaces.Atom2.FullProteinInterfaceId.ProteinId == lastInteractionBetweenProteinInterfaces.Atom2.FullProteinInterfaceId.ProteinId && thisInteractionBetweenProteinInterfaces.Atom2.FullProteinInterfaceId.ChainId == lastInteractionBetweenProteinInterfaces.Atom2.FullProteinInterfaceId.ChainId && thisInteractionBetweenProteinInterfaces.Atom2.FullProteinInterfaceId.ProteinInterfaceId == lastInteractionBetweenProteinInterfaces.Atom2.FullProteinInterfaceId.ProteinInterfaceId && thisInteractionBetweenProteinInterfaces.Atom2.Atom == lastInteractionBetweenProteinInterfaces.Atom2.Atom) { interactionBetweenProteinInterfacesListContainer.InteractionBetweenNonProteinInterfacesList.RemoveAt(index - 1); //////Console.WriteLine("removed duplicate"); } } return interactionBetweenProteinInterfacesListContainer; }
/// <summary> /// Load proteinInterface data from the PDB file based on a list of already detected proteinInterfaces. /// The detected proteinInterfaces may be missing data such as other atoms or residues which are also in the proteinInterface but were not /// directly interacting. /// The positions and lengths of the proteinInterfaces are also calculated. /// </summary> /// <param name="pdbFilename"></param> /// <param name="pdbFileChains"></param> /// <param name="singularAaToAaInteractions"></param> /// <param name="proteinInterfacesClusteringResult"></param> /// <param name="detectedBestStages"></param> /// <param name="interactionBetweenProteinInterfacesContainer"></param> /// <returns></returns> public static List <ProteinInterfaceSequenceAndPositionData> AnalyseProteinInterfacesSequenceAndPositionData( string pdbFilename, Dictionary <string, List <string> > pdbIdChainIdList, ProteinChainListContainer pdbFileChains, ProteinChainListContainer singularAaToAaInteractions, ClusteringFullResultListContainer proteinInterfacesClusteringResult, int[] detectedBestStages, InteractionBetweenProteinInterfacesListContainer interactionBetweenProteinInterfacesContainer) { if (string.IsNullOrWhiteSpace(pdbFilename)) { throw new ArgumentOutOfRangeException(nameof(pdbFilename)); } if (!File.Exists(pdbFilename)) { throw new FileNotFoundException("File not found", pdbFilename); } if (ParameterValidation.IsProteinChainListContainerNullOrEmpty(singularAaToAaInteractions)) { throw new ArgumentOutOfRangeException(nameof(singularAaToAaInteractions)); } if (ParameterValidation.IsClusteringFullResultListContainerNullOrEmpty(proteinInterfacesClusteringResult)) { throw new ArgumentOutOfRangeException(nameof(proteinInterfacesClusteringResult)); } if (ParameterValidation.IsIntArrayNullOrEmpty(detectedBestStages)) { throw new ArgumentOutOfRangeException(nameof(detectedBestStages)); } // ProteinInterfaces are clusters with non-proteinInterfaces removed. var result = new List <ProteinInterfaceSequenceAndPositionData>(); string proteinId = ProteinDataBankFileOperations.PdbIdFromPdbFilename(pdbFilename); int totalChains = proteinInterfacesClusteringResult.ChainList.Count; for (int chainIndex = 0; chainIndex < totalChains; chainIndex++) { int stageIndex = detectedBestStages[chainIndex]; string chainIdLetter = SpreadsheetFileHandler.AlphabetLetterRollOver(chainIndex); List <ClusteringFullResultListContainer.Chain.Stage.Cluster> proteinInterfaceList = proteinInterfacesClusteringResult.ChainList[chainIndex].StageList[stageIndex].ClusterList; List <ClusteringFullResultListContainer.Chain.Stage.Cluster> nonEmptyProteinInterfaceList = proteinInterfaceList.Where(a => a != null && a.AtomIndexList != null && a.AtomIndexList.Count > 0).ToList(); // loop through each proteinInterface for (int proteinInterfaceIndex = 0; proteinInterfaceIndex < nonEmptyProteinInterfaceList.Count; proteinInterfaceIndex++) { ClusteringFullResultListContainer.Chain.Stage.Cluster proteinInterface = nonEmptyProteinInterfaceList[proteinInterfaceIndex]; // Find min and max residue sequence index value in the proteinInterface MinMax proteinInterfaceResidueSequenceIndexes = MinMaxResidueSequenceIndex(proteinInterface, singularAaToAaInteractions, chainIndex); int proteinInterfaceLength = CalculateProteinInterfaceLength(proteinInterfaceResidueSequenceIndexes.Min, proteinInterfaceResidueSequenceIndexes.Max); string proteinInterfaceIdLetter = SpreadsheetFileHandler.AlphabetLetterRollOver(proteinInterfaceIndex); var proteinInterfacePositionData = new ProteinInterfaceSequenceAndPositionData { FullProteinInterfaceId = new FullProteinInterfaceId(proteinId, chainIndex, proteinInterfaceIndex, proteinInterfaceResidueSequenceIndexes.Min, proteinInterfaceResidueSequenceIndexes.Max), ChainIdLetter = chainIdLetter, ProteinInterfaceIdLetter = proteinInterfaceIdLetter, StartPosition = proteinInterfaceResidueSequenceIndexes.Min, EndPosition = proteinInterfaceResidueSequenceIndexes.Max, ProteinInterfaceLength = CalculateProteinInterfaceLength(proteinInterfaceResidueSequenceIndexes.Min, proteinInterfaceResidueSequenceIndexes.Max) }; proteinInterfacePositionData.AminoAcidSequenceAllResidueSequenceIndexes = new ProteinInterfaceAminoAcidMetaData[proteinInterfacePositionData.ProteinInterfaceLength]; proteinInterfacePositionData.AminoAcidSequenceAll1L = ""; proteinInterfacePositionData.AminoAcidSequenceInteractionsAll1L = ""; proteinInterfacePositionData.AminoAcidSequenceInteractionsInsideProteinInterfacesOnly1L = ""; proteinInterfacePositionData.AminoAcidSequenceInteractionsNone1L = ""; proteinInterfacePositionData.AminoAcidSequenceInteractionsOutsideProteinInterfacesOnly1L = ""; proteinInterfacePositionData.AminoAcidSequenceAll3L = ""; proteinInterfacePositionData.AminoAcidSequenceInteractionsAll3L = ""; proteinInterfacePositionData.AminoAcidSequenceInteractionsInsideProteinInterfacesOnly3L = ""; proteinInterfacePositionData.AminoAcidSequenceInteractionsNone3L = ""; proteinInterfacePositionData.AminoAcidSequenceInteractionsOutsideProteinInterfacesOnly3L = ""; //int foundAtomCount = 0; const string placeholder1L = "_"; const string placeholder3L = "___"; for (int residueSequenceIndex = proteinInterfaceResidueSequenceIndexes.Min; residueSequenceIndex <= proteinInterfaceResidueSequenceIndexes.Max; residueSequenceIndex++) { /* questions * 1. does this reside interact with another reside which is also part of a proteinInterface? * 2. if not, does this reside interact at all? */ var proteinInterfaceAminoAcidMetaData = new ProteinInterfaceAminoAcidMetaData(); proteinInterfacePositionData.AminoAcidSequenceAllResidueSequenceIndexes[proteinInterfacePositionData.AminoAcidSequenceAll1L.Length] = proteinInterfaceAminoAcidMetaData; ATOM_Record foundAtomInsidePdbFile = AtomSearchMethods.FindAtomInsidePdbFileChain(pdbFileChains, chainIndex, residueSequenceIndex); if (foundAtomInsidePdbFile == null) { // Non-CA atom is loaded here in case of missing CA atom to find the AA code for the resSeq index var chainIdList = pdbIdChainIdList != null ? (pdbIdChainIdList.ContainsKey(proteinId) ? pdbIdChainIdList[proteinId].ToArray() : null) : null; ProteinChainListContainer pdbFileChains2 = ProteinDataBankFileOperations.PdbAtomicChains(pdbFilename, chainIdList, -1, -1, false); foundAtomInsidePdbFile = AtomSearchMethods.FindAtomInsidePdbFileChain(pdbFileChains2, chainIndex, residueSequenceIndex); } proteinInterfaceAminoAcidMetaData.PdbResidueSequenceIndex = residueSequenceIndex; proteinInterfaceAminoAcidMetaData.ArrayMemberIndex = pdbFileChains.ChainList[chainIndex].AtomList.IndexOf(foundAtomInsidePdbFile); proteinInterfaceAminoAcidMetaData.OppoproteinInterfaceInteractions = new bool[proteinInterfaceLength]; if (foundAtomInsidePdbFile != null) { proteinInterfacePositionData.AminoAcidSequenceAll1L += AminoAcidConversions.AminoAcidNameToCode1L(foundAtomInsidePdbFile.resName.FieldValue); proteinInterfacePositionData.AminoAcidSequenceAll3L += foundAtomInsidePdbFile.resName.FieldValue.PadRight(3, '_'); } else { proteinInterfacePositionData.AminoAcidSequenceAll1L += placeholder1L; proteinInterfacePositionData.AminoAcidSequenceInteractionsAll1L += placeholder1L; proteinInterfacePositionData.AminoAcidSequenceInteractionsInsideProteinInterfacesOnly1L += placeholder1L; proteinInterfacePositionData.AminoAcidSequenceInteractionsOutsideProteinInterfacesOnly1L += placeholder1L; proteinInterfacePositionData.AminoAcidSequenceInteractionsNone1L += placeholder1L; proteinInterfacePositionData.AminoAcidSequenceAll3L += placeholder3L; proteinInterfacePositionData.AminoAcidSequenceInteractionsAll3L += placeholder3L; proteinInterfacePositionData.AminoAcidSequenceInteractionsInsideProteinInterfacesOnly3L += placeholder3L; proteinInterfacePositionData.AminoAcidSequenceInteractionsOutsideProteinInterfacesOnly3L += placeholder3L; proteinInterfacePositionData.AminoAcidSequenceInteractionsNone3L += placeholder3L; proteinInterfaceAminoAcidMetaData.ProteinInterfaceInteractionType = ProteinInterfaceInteractionType.NoInteractionFound; proteinInterfaceAminoAcidMetaData.NonProteinInterfaceInteractionResidueNames1L += placeholder1L; proteinInterfaceAminoAcidMetaData.NonProteinInterfaceInteractionResidueNames3L += placeholder3L; continue; } List <ATOM_Record> foundAtomInteractingWithAnotherProteinInterface = AtomSearchMethods.FindAtomInteractingWithOtherProteinInterfaces(foundAtomInsidePdbFile, interactionBetweenProteinInterfacesContainer, FindAtomInteractingWithAnotherProteinInterfaceOptions.FindAtomsInteractingWithOtherProteinInterfaces); List <ATOM_Record> foundAtomInteractingWithNonProteinInterface = AtomSearchMethods.FindAtomInteractingWithOtherProteinInterfaces(foundAtomInsidePdbFile, interactionBetweenProteinInterfacesContainer, FindAtomInteractingWithAnotherProteinInterfaceOptions.FindAtomsInteractingWithNonProteinInterfaces); proteinInterfaceAminoAcidMetaData.OppoproteinInterfaceInteractions = AminoAcidInteractionVector(singularAaToAaInteractions, proteinInterfacesClusteringResult, detectedBestStages, interactionBetweenProteinInterfacesContainer, chainIndex, proteinInterfaceIndex, residueSequenceIndex); proteinInterfaceAminoAcidMetaData.ResidueName1L = AminoAcidConversions.AminoAcidNameToCode1L(foundAtomInsidePdbFile.resName.FieldValue); proteinInterfaceAminoAcidMetaData.ResidueName3L = foundAtomInsidePdbFile.resName.FieldValue.PadRight(3, '_'); if (foundAtomInteractingWithAnotherProteinInterface != null) { foreach (ATOM_Record atom in foundAtomInteractingWithAnotherProteinInterface) { proteinInterfaceAminoAcidMetaData.ProteinInterfaceInteractionResidueNames1L += AminoAcidConversions.AminoAcidNameToCode1L(atom.resName.FieldValue); proteinInterfaceAminoAcidMetaData.ProteinInterfaceInteractionResidueNames3L += atom.resName.FieldValue.PadRight(3, '_'); } } if (foundAtomInteractingWithNonProteinInterface != null) { foreach (ATOM_Record atom in foundAtomInteractingWithNonProteinInterface) { proteinInterfaceAminoAcidMetaData.NonProteinInterfaceInteractionResidueNames1L += AminoAcidConversions.AminoAcidNameToCode1L(atom.resName.FieldValue); proteinInterfaceAminoAcidMetaData.NonProteinInterfaceInteractionResidueNames3L += atom.resName.FieldValue.PadRight(3, '_'); } } if (foundAtomInteractingWithAnotherProteinInterface != null && foundAtomInteractingWithAnotherProteinInterface.Count > 0) { proteinInterfacePositionData.AminoAcidSequenceInteractionsAll1L += AminoAcidConversions.AminoAcidNameToCode1L(foundAtomInsidePdbFile.resName.FieldValue); proteinInterfacePositionData.AminoAcidSequenceInteractionsInsideProteinInterfacesOnly1L += AminoAcidConversions.AminoAcidNameToCode1L(foundAtomInsidePdbFile.resName.FieldValue); proteinInterfacePositionData.AminoAcidSequenceInteractionsOutsideProteinInterfacesOnly1L += placeholder1L; proteinInterfacePositionData.AminoAcidSequenceInteractionsNone1L += placeholder1L; proteinInterfacePositionData.AminoAcidSequenceInteractionsAll3L += foundAtomInsidePdbFile.resName.FieldValue.PadRight(3, '_'); proteinInterfacePositionData.AminoAcidSequenceInteractionsInsideProteinInterfacesOnly3L += foundAtomInsidePdbFile.resName.FieldValue.PadRight(3, '_'); proteinInterfacePositionData.AminoAcidSequenceInteractionsOutsideProteinInterfacesOnly3L += placeholder3L; proteinInterfacePositionData.AminoAcidSequenceInteractionsNone3L += placeholder3L; proteinInterfaceAminoAcidMetaData.ProteinInterfaceInteractionType = ProteinInterfaceInteractionType.InteractionWithAnotherProteinInterface; if (foundAtomInteractingWithNonProteinInterface != null && foundAtomInteractingWithNonProteinInterface.Count > 0) { proteinInterfaceAminoAcidMetaData.ProteinInterfaceInteractionType |= ProteinInterfaceInteractionType.InteractionWithNonProteinInterface; } } else if (foundAtomInteractingWithNonProteinInterface != null && foundAtomInteractingWithNonProteinInterface.Count > 0) { proteinInterfacePositionData.AminoAcidSequenceInteractionsAll1L += AminoAcidConversions.AminoAcidNameToCode1L(foundAtomInsidePdbFile.resName.FieldValue); proteinInterfacePositionData.AminoAcidSequenceInteractionsInsideProteinInterfacesOnly1L += placeholder1L; proteinInterfacePositionData.AminoAcidSequenceInteractionsOutsideProteinInterfacesOnly1L += AminoAcidConversions.AminoAcidNameToCode1L(foundAtomInsidePdbFile.resName.FieldValue); proteinInterfacePositionData.AminoAcidSequenceInteractionsNone1L += placeholder1L; proteinInterfacePositionData.AminoAcidSequenceInteractionsAll3L += foundAtomInsidePdbFile.resName.FieldValue.PadRight(3, '_'); proteinInterfacePositionData.AminoAcidSequenceInteractionsInsideProteinInterfacesOnly3L += placeholder3L; proteinInterfacePositionData.AminoAcidSequenceInteractionsOutsideProteinInterfacesOnly3L += foundAtomInsidePdbFile.resName.FieldValue.PadRight(3, '_'); proteinInterfacePositionData.AminoAcidSequenceInteractionsNone3L += placeholder3L; proteinInterfaceAminoAcidMetaData.ProteinInterfaceInteractionType = ProteinInterfaceInteractionType.InteractionWithNonProteinInterface; } else { proteinInterfacePositionData.AminoAcidSequenceInteractionsAll1L += placeholder1L; proteinInterfacePositionData.AminoAcidSequenceInteractionsInsideProteinInterfacesOnly1L += placeholder1L; proteinInterfacePositionData.AminoAcidSequenceInteractionsOutsideProteinInterfacesOnly1L += placeholder1L; proteinInterfacePositionData.AminoAcidSequenceInteractionsNone1L += AminoAcidConversions.AminoAcidNameToCode1L(foundAtomInsidePdbFile.resName.FieldValue); proteinInterfacePositionData.AminoAcidSequenceInteractionsAll3L += placeholder3L; proteinInterfacePositionData.AminoAcidSequenceInteractionsInsideProteinInterfacesOnly3L += placeholder3L; proteinInterfacePositionData.AminoAcidSequenceInteractionsOutsideProteinInterfacesOnly3L += placeholder3L; proteinInterfacePositionData.AminoAcidSequenceInteractionsNone3L += foundAtomInsidePdbFile.resName.FieldValue.PadRight(3, '_'); proteinInterfaceAminoAcidMetaData.ProteinInterfaceInteractionType = ProteinInterfaceInteractionType.NoInteractionFound; } } result.Add(proteinInterfacePositionData); } } return(result); }
/// <summary> /// This method returns an array showing whether an amino acid has an interaction with any amino acids in a proteinInterface of /// another chain /// </summary> /// <returns></returns> public static bool[] AminoAcidInteractionVector( ProteinChainListContainer singularAaToAaInteractions, ClusteringFullResultListContainer proteinInterfacesClusteringResult, int[] detectedBestStages, InteractionBetweenProteinInterfacesListContainer interactionsBetweenProteinInterfacesContainer, //int proteinInterfaceLength, int sourceChainIndex, int sourceProteinInterfaceIndex, int sourceResidueIndex ) { // find the largest proteinInterface to make vector the same size int maxProteinInterfaceLength = 0; for (int chainIndex = 0; chainIndex < proteinInterfacesClusteringResult.ChainList.Count; chainIndex++) { List <ClusteringFullResultListContainer.Chain.Stage.Cluster> proteinInterfaceList = proteinInterfacesClusteringResult.ChainList[chainIndex].StageList[detectedBestStages[chainIndex]].ClusterList; List <ClusteringFullResultListContainer.Chain.Stage.Cluster> nonEmptyProteinInterfaceList = proteinInterfaceList.Where(a => a != null && a.AtomIndexList != null && a.AtomIndexList.Count > 0).ToList(); for (int proteinInterfaceIndex = 0; proteinInterfaceIndex < nonEmptyProteinInterfaceList.Count; proteinInterfaceIndex++) { ClusteringFullResultListContainer.Chain.Stage.Cluster proteinInterface = nonEmptyProteinInterfaceList[proteinInterfaceIndex]; if (proteinInterface.AtomIndexList == null || proteinInterface.AtomIndexList.Count == 0) { continue; } int length = FindProteinInterfaceLength(singularAaToAaInteractions, proteinInterfacesClusteringResult, detectedBestStages, chainIndex, proteinInterfaceIndex); if (length > maxProteinInterfaceLength) { maxProteinInterfaceLength = length; } } } // find interactions matching the current chain id and proteinInterface id and res id... res id is different from resSeq in the pdb var result = new bool[maxProteinInterfaceLength]; List <InteractionBetweenProteinInterfaces> matchingInteractions = interactionsBetweenProteinInterfacesContainer.InteractionBetweenProteinInterfacesList.Where(a => (a.Atom1.FullProteinInterfaceId.ChainId == sourceChainIndex && a.Atom1.FullProteinInterfaceId.ProteinInterfaceId == sourceProteinInterfaceIndex) || (a.Atom2.FullProteinInterfaceId.ChainId == sourceChainIndex && a.Atom2.FullProteinInterfaceId.ProteinInterfaceId == sourceProteinInterfaceIndex)).ToList(); if (matchingInteractions.Count == 0) { return(result); } foreach (InteractionBetweenProteinInterfaces interaction in matchingInteractions) { if (interaction.Atom1.FullProteinInterfaceId.ChainId == sourceChainIndex && interaction.Atom1.FullProteinInterfaceId.ProteinInterfaceId == sourceProteinInterfaceIndex && ProteinDataBankFileOperations.NullableTryParseInt32(interaction.Atom1.Atom.resSeq.FieldValue) == sourceResidueIndex) { // where in the proteinInterface oppoproteinInterface proteinInterface is Atom2? int index = AtomIndexPositionInProteinInterface(singularAaToAaInteractions, proteinInterfacesClusteringResult, detectedBestStages, interaction.Atom2.FullProteinInterfaceId.ChainId, interaction.Atom2.FullProteinInterfaceId.ProteinInterfaceId, interaction.Atom2.Atom); result[index] = true; } else if (interaction.Atom2.FullProteinInterfaceId.ChainId == sourceChainIndex && interaction.Atom2.FullProteinInterfaceId.ProteinInterfaceId == sourceProteinInterfaceIndex && ProteinDataBankFileOperations.NullableTryParseInt32(interaction.Atom2.Atom.resSeq.FieldValue) == sourceResidueIndex) { int index = AtomIndexPositionInProteinInterface(singularAaToAaInteractions, proteinInterfacesClusteringResult, detectedBestStages, interaction.Atom1.FullProteinInterfaceId.ChainId, interaction.Atom1.FullProteinInterfaceId.ProteinInterfaceId, interaction.Atom1.Atom); result[index] = true; } } return(result); }
/// <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); }