public static void ConfirmSequencesSaved(List <string> pdbIdList, List <string> saveFilenameList, ProgressActionSet progressActionSet)
{
if (pdbIdList == null)
{
throw new ArgumentNullException(nameof(pdbIdList));
}
// Confirm the total number of sequences saved is equal to original number loaded
if (saveFilenameList == null || saveFilenameList.Count == 0)
{
ProgressActionSet.Report("Warning: no files were saved", progressActionSet);
return;
}
List <ISequence> confirmSequencesList = SequenceFileHandler.LoadSequenceFileList(saveFilenameList, StaticValues.MolNameProteinAcceptedValues);
List <string> confirmPdbIdList = FilterProteins.SequenceListToPdbIdList(confirmSequencesList);
if (pdbIdList.Count == confirmPdbIdList.Count)
{
ProgressActionSet.Report("All sequences sorted into categories", progressActionSet);
}
else
{
var missingPdbIdList = new List <string>(pdbIdList);
foreach (string pdbId in confirmPdbIdList)
{
missingPdbIdList.Remove(pdbId);
}
ProgressActionSet.Report("Some sequences are unaccounted for: " + string.Join(", ", missingPdbIdList), progressActionSet);
}
}
public static string AddSequenceAndProteinCountToFilename(List <ISequence> sequenceList, string saveFilename)
{
string path = Path.GetDirectoryName(saveFilename);
if (!string.IsNullOrEmpty(path) && (path[path.Length - 1] != '\\' && path[path.Length - 1] != '/'))
{
path = path + "/";
}
string file = Path.GetFileNameWithoutExtension(saveFilename);
string fileExt = Path.GetExtension(saveFilename);
if (!string.IsNullOrEmpty(fileExt) && fileExt[0] != '.')
{
fileExt = "." + fileExt;
}
var pdbIdList = FilterProteins.SequenceListToPdbIdList(sequenceList);
var totalPdbIds = pdbIdList.Count;
var totalSequences = sequenceList.Count;
string sequenceProteinStr = " [" + totalPdbIds + " proteins - " + totalSequences + " sequences]";
if (!saveFilename.Contains(sequenceProteinStr))
{
saveFilename = path + file + sequenceProteinStr + fileExt;
}
return(saveFilename);
}
/// <summary>
/// This method removes sequences not having the required number of chains.
/// </summary>
/// <returns></returns>
public static List <ISequence> RemoveSequencesWithIncorrectNumberOfChains(CancellationToken cancellationToken, List <ISequence> sequenceList, int numberOfChainsRequired = 2, ProgressActionSet progressActionSet = null)
{
if (sequenceList == null || sequenceList.Count == 0)
{
throw new ArgumentOutOfRangeException(nameof(sequenceList));
}
if (progressActionSet == null)
{
throw new ArgumentNullException(nameof(progressActionSet));
}
var pdbIdListNotDistinct = FilterProteins.SequenceListToPdbIdList(sequenceList, false);
ProgressActionSet.StartAction(pdbIdListNotDistinct.Count, progressActionSet);
var workDivision = new WorkDivision <List <string> >(pdbIdListNotDistinct.Count);
for (var threadIndex = 0; threadIndex < workDivision.ThreadCount; threadIndex++)
{
var localThreadIndex = threadIndex;
Task <List <string> > task = Task.Run(() =>
{
var taskResult = pdbIdListNotDistinct.Where((a, pdbIdIndex) =>
{
if (pdbIdIndex < workDivision.ThreadFirstIndex[localThreadIndex] || pdbIdIndex > workDivision.ThreadLastIndex[localThreadIndex])
{
return(false);
}
workDivision.IncrementItemsCompleted(1);
ProgressActionSet.ProgressAction(1, progressActionSet);
ProgressActionSet.EstimatedTimeRemainingAction(workDivision.StartTicks, workDivision.ItemsCompleted, workDivision.ItemsToProcess, progressActionSet);
return(pdbIdListNotDistinct.Count(b => a == b) != numberOfChainsRequired);
}).ToList();
return(taskResult);
}, cancellationToken);
workDivision.TaskList.Add(task);
}
workDivision.WaitAllTasks();
var sequencesWithIncorrectNumberOfChains = new List <string>();
foreach (var task in workDivision.TaskList.Where(t => t != null && t.Result != null && t.IsCompleted && !t.IsCanceled && !t.IsFaulted))
{
sequencesWithIncorrectNumberOfChains.AddRange(task.Result);
}
var result = RemoveSequences(cancellationToken, sequenceList, sequencesWithIncorrectNumberOfChains);
ProgressActionSet.FinishAction(true, progressActionSet);
return(result);
}
public static void FilterProteinInterfaceLengths(
CancellationToken cancellationToken,
decimal maxAtomInterationDistance,
decimal minimumProteinInterfaceDensity,
string[] sequenceListFileArray,
string[] pdbFileDirectoryLocationArray,
string filterProteinInterfacesLengthOutputFilename,
bool filterProteinInterfaceCountsWithoutLengths,
bool filterProteinInterfaceCountsWithLengths,
FileExistsHandler.FileExistsOptions fileExistsOptions,
ProgressActionSet progressActionSet)
{
if (sequenceListFileArray == null)
{
throw new ArgumentNullException(nameof(sequenceListFileArray));
}
if (pdbFileDirectoryLocationArray == null)
{
throw new ArgumentNullException(nameof(pdbFileDirectoryLocationArray));
}
if (filterProteinInterfacesLengthOutputFilename == null)
{
throw new ArgumentNullException(nameof(filterProteinInterfacesLengthOutputFilename));
}
if (!filterProteinInterfaceCountsWithoutLengths && !filterProteinInterfaceCountsWithLengths)
{
ProgressActionSet.Report("Cancelled: No filter options selected.", progressActionSet);
return;
}
// Check all sequence files are found
var missingSequenceFiles = sequenceListFileArray.Where(sequenceFile => !string.IsNullOrWhiteSpace(sequenceFile) && !File.Exists(sequenceFile)).ToList();
if (missingSequenceFiles.Count > 0)
{
foreach (string missingSequenceFile in missingSequenceFiles)
{
//throw new FileNotFoundException(sequenceFile);
ProgressActionSet.Report("Warning: Sequence file missing: " + missingSequenceFile, progressActionSet);
}
ProgressActionSet.Report("Cancelled: missing sequence files.", progressActionSet);
return;
}
// Check all pdb folders are found
var missingDirectoryList = pdbFileDirectoryLocationArray.Where(pdbDirectory => !string.IsNullOrWhiteSpace(pdbDirectory) && !Directory.Exists(pdbDirectory)).ToList();
if (missingDirectoryList.Count > 0)
{
foreach (string pdbDirectory in missingDirectoryList)
{
//throw new DirectoryNotFoundException(pdbDirectory);
ProgressActionSet.Report("Warning: Structure file directory missing: " + pdbDirectory, progressActionSet);
}
ProgressActionSet.Report("Cancelled: missing structure file directory.", progressActionSet);
return;
}
const string proteinInterfacesTemplateText = "%proteinInterfaces%";
if (string.IsNullOrWhiteSpace(filterProteinInterfacesLengthOutputFilename) || !filterProteinInterfacesLengthOutputFilename.Contains(proteinInterfacesTemplateText))
{
throw new ArgumentOutOfRangeException(nameof(filterProteinInterfacesLengthOutputFilename));
}
// Load fasta sequence files
List <ISequence> sequenceList = SequenceFileHandler.LoadSequenceFileList(sequenceListFileArray, StaticValues.MolNameProteinAcceptedValues);
// Get a list of the PDB Unique IDs with unique chain IDs which are wanted, ignoring others which may be present e.g. dna
var pdbIdChainIdList = ProteinDataBankFileOperations.PdbIdChainIdList(sequenceList);
// Get list of PDB Unique IDs
List <string> pdbIdList = FilterProteins.SequenceListToPdbIdList(sequenceList);
// Check PDB Unique IDs were successfully loaded
if (pdbIdList == null || pdbIdList.Count == 0)
{
//throw new Exception("PDB ID List is empty or could not be loaded.");
ProgressActionSet.Report("Error: Sequence list could not be loaded", progressActionSet);
return;
}
// 3: Get a list of PDB files found in user specified directory
string[] pdbFilesArray = ProteinDataBankFileOperations.RemoveNonWhiteListedPdbIdFromPdbFilesArray(pdbIdList, ProteinDataBankFileOperations.GetPdbFilesArray(pdbFileDirectoryLocationArray));
// Check all PDB files are found
List <string> missingPdbFilesList = ProteinDataBankFileOperations.CheckForMissingPdbFiles(pdbFilesArray, pdbIdList);
if (missingPdbFilesList != null && missingPdbFilesList.Count > 0)
{
ProgressActionSet.Report("Missing PDB Files: " + string.Join(", ", missingPdbFilesList), progressActionSet);
}
ProgressActionSet.StartAction(pdbFilesArray.Length, progressActionSet);
int progressIncrement = 0;
var proteinInterfacesCountResultWithLengths = new Dictionary <string, List <string> >();
var startTicks = DateTime.Now.Ticks;
// 4: Loop through each pdb file
for (int pdbFileNumber = 0; pdbFileNumber < pdbFilesArray.Length + 1; pdbFileNumber++) // +1 is for progress update
{
if (progressIncrement > 0)
{
ProgressActionSet.ProgressAction(progressIncrement, progressActionSet);
progressIncrement = 0;
if (pdbFileNumber >= pdbFilesArray.Length)
{
break;
}
}
ProgressActionSet.EstimatedTimeRemainingAction(startTicks, pdbFileNumber, pdbFilesArray.Length, progressActionSet);
progressIncrement++;
// get unique id of pdb file
string pdbFilename = pdbFilesArray[pdbFileNumber];
string proteinId = ProteinDataBankFileOperations.PdbIdFromPdbFilename(pdbFilename);
// check pdb unique id was in the loaded sequence list
if (!pdbIdList.Contains(proteinId))
{
continue;
}
// perform clustering to detect interaction proteinInterfaces
ClusterProteinDataBankFileResult clusterPdbFileResult = Clustering.ClusterProteinDataBankFile(cancellationToken, maxAtomInterationDistance, minimumProteinInterfaceDensity, pdbFilename, pdbIdChainIdList, ClusteringMethodOptions.ClusterWithResidueSequenceIndex, -1, -1, null);
if (clusterPdbFileResult == null)
{
continue;
}
int[] proteinInterfacesCount = new int[clusterPdbFileResult.ClusteringFullResultListContainer.ChainList.Count];
for (int chainIndex = 0; chainIndex < clusterPdbFileResult.ClusteringFullResultListContainer.ChainList.Count; chainIndex++)
{
int totalProteinInterfaces = clusterPdbFileResult.ProteinInterfaceAnalysisResultData.ProteinInterfacesSequenceAndPositionDataList.Count(proteinInterface => proteinInterface.FullProteinInterfaceId.ChainId == chainIndex);
proteinInterfacesCount[chainIndex] = totalProteinInterfaces;
}
var proteinInterfacesCountStr = string.Join(" ", proteinInterfacesCount.OrderBy(x => x));
List <ProteinInterfaceSequenceAndPositionData> proteinInterfaces = clusterPdbFileResult.ProteinInterfaceAnalysisResultData.ProteinInterfacesSequenceAndPositionDataList;
int[] proteinInterfacesLength = new int[proteinInterfaces.Count];
for (int index = 0; index < proteinInterfaces.Count; index++)
{
ProteinInterfaceSequenceAndPositionData proteinInterface = proteinInterfaces[index];
proteinInterfacesLength[index] = proteinInterface.ProteinInterfaceLength;
}
var proteinInterfacesLengthStr = string.Join(" ", proteinInterfacesLength.Distinct().OrderBy(x => x));
if (proteinInterfacesLength.Length == 0)
{
proteinInterfacesLengthStr = 0.ToString();
}
var chainsCountStr = clusterPdbFileResult.ClusteringFullResultListContainer.ChainList.Count;
if (filterProteinInterfaceCountsWithoutLengths)
{
var combinedKeyAll = "chains [" + chainsCountStr + "] proteinInterfaces [" + proteinInterfacesCountStr + "]";
if (!proteinInterfacesCountResultWithLengths.ContainsKey(combinedKeyAll))
{
proteinInterfacesCountResultWithLengths.Add(combinedKeyAll, new List <string>());
}
proteinInterfacesCountResultWithLengths[combinedKeyAll].Add(proteinId);
}
if (filterProteinInterfaceCountsWithLengths)
{
var combinedKeyWithLengths = "chains [" + chainsCountStr + "] proteinInterfaces [" + proteinInterfacesCountStr + "] lengths [" + proteinInterfacesLengthStr + "]";
if (!proteinInterfacesCountResultWithLengths.ContainsKey(combinedKeyWithLengths))
{
proteinInterfacesCountResultWithLengths.Add(combinedKeyWithLengths, new List <string>());
}
proteinInterfacesCountResultWithLengths[combinedKeyWithLengths].Add(proteinId);
}
}
var confirmSaveList = new List <string>();
foreach (var kvp in proteinInterfacesCountResultWithLengths)
{
var seq2 = new List <ISequence>(sequenceList);
seq2 = FilterProteins.RemoveSequences(cancellationToken, seq2, kvp.Value, FilterProteins.RemoveSequencesOptions.RemoveSequencesNotInList);
var saveFilename = filterProteinInterfacesLengthOutputFilename;
saveFilename = saveFilename.Replace(proteinInterfacesTemplateText, kvp.Key);
var actualSavedFilename = SequenceFileHandler.SaveSequencesAsFasta(seq2, saveFilename, true, fileExistsOptions, progressActionSet);
if (!string.IsNullOrWhiteSpace(actualSavedFilename))
{
confirmSaveList.Add(actualSavedFilename);
}
}
// Confirm the total number of sequences saved is equal to original number loaded
ConfirmSequencesSaved(pdbIdList, confirmSaveList, progressActionSet);
ProgressActionSet.FinishAction(true, progressActionSet);
}
/// <summary>
/// This method iterates through the provided FASTA files creating separate calculated outputs for each of them.
/// </summary>
/// <param name="fastaFiles">The FASTA files to process.</param>
/// <param name="pdbFilesFolders">The locations where PDB files may be found.</param>
/// <param name="spreadsheetSaveFilenameTemplate">A template filename to save the outputs.</param>
/// <param name="saveTsv"></param>
/// <param name="saveXl"></param>
/// <param name="cancellationToken"></param>
/// <param name="progressActionSet"></param>
/// <param name="fileExistsOptions"></param>
public static void MakeHomodimerStatisticsSpreadsheetsAndOutputFiles(decimal maxAtomInterationDistance, string[] fastaFiles, string[] pdbFilesFolders, string spreadsheetSaveFilenameTemplate, bool saveTsv, bool saveXl, CancellationToken cancellationToken, ProgressActionSet progressActionSet = null, FileExistsHandler.FileExistsOptions fileExistsOptions = FileExistsHandler.FileExistsOptions.AppendNumberToFilename)
{
if (fastaFiles == null || fastaFiles.Length == 0)
{
throw new ArgumentOutOfRangeException(nameof(fastaFiles));
}
if (pdbFilesFolders == null || pdbFilesFolders.Length == 0)
{
throw new ArgumentOutOfRangeException(nameof(pdbFilesFolders));
}
if (!saveTsv && !saveXl)
{
throw new ArgumentOutOfRangeException(nameof(saveTsv));
}
for (int fastaFileNumber = 0; fastaFileNumber < fastaFiles.Length; fastaFileNumber++)
{
string fastaFilename = fastaFiles[fastaFileNumber];
if (string.IsNullOrWhiteSpace(fastaFilename))
{
continue;
}
ProgressActionSet.Report("Attempting to open file: " + fastaFilename, progressActionSet);
List <ISequence> sequences = SequenceFileHandler.LoadSequenceFile(fastaFilename, StaticValues.MolNameProteinAcceptedValues);
var pdbIdChainIdList = ProteinDataBankFileOperations.PdbIdChainIdList(sequences);
if ((sequences == null) || (sequences.Count == 0))
{
ProgressActionSet.Report("Error could not load file: " + fastaFilename, progressActionSet);
continue;
}
ProgressActionSet.Report("Loaded " + sequences.Count + " sequences from file: " + fastaFilename, progressActionSet);
List <string> pdbIdList = FilterProteins.SequenceListToPdbIdList(sequences);
string appendFilename = FileAndPathMethods.FullPathToFilename(fastaFilename);
ProgressActionSet.Report("Creating spreadsheets...", progressActionSet);
Stopwatch stopwatch = Stopwatch.StartNew();
var spreadsheetList = MakeHomodimerStatisticsSpreadsheetsList(cancellationToken, maxAtomInterationDistance, pdbFilesFolders, pdbIdList, pdbIdChainIdList, progressActionSet);
stopwatch.Stop();
ProgressActionSet.Report("Finished calculating spreadsheet data [Elapsed: " + stopwatch.Elapsed.ToString(@"dd\:hh\:mm\:ss") + "]", progressActionSet);
if (cancellationToken.IsCancellationRequested)
{
//UserProteinInterfaceOperations.ProgressBarReset(progressBar, 0, 100, 0);
////UserProteinInterfaceOperations.LabelEstimatedTimeRemainingUpdate(estimatedTimeRemaining, 0, 1, 1);
ProgressActionSet.StartAction(100, progressActionSet);
ProgressActionSet.ProgressAction(100, progressActionSet);
ProgressActionSet.FinishAction(false, progressActionSet);
ProgressActionSet.Report("Cancelled.", progressActionSet);
break;
}
for (int spreadsheetIndex = 0; spreadsheetIndex < spreadsheetList.Count; spreadsheetIndex++)
{
var spreadsheet = spreadsheetList[spreadsheetIndex];
if (cancellationToken.IsCancellationRequested)
{
break;
}
// Remove the first row (which has the name for use in a worksheet title, not currently used)
var sheetName = spreadsheet[0][0].CellData;
var spreadsheetName = spreadsheet[1][0].CellData;
spreadsheet.RemoveAt(0);
// "c:/dResults/Results - %date% %time% - %fasta_filename% - %spreadsheet_name%.tsv"
string saveFilename = spreadsheetSaveFilenameTemplate;
saveFilename = saveFilename.Replace("%spreadsheet_name%", spreadsheetName);
saveFilename = saveFilename.Replace("%fasta_filename%", appendFilename);
saveFilename = saveFilename.Replace("%date%", DateTime.Now.ToString("yyyy-MM-dd"));
saveFilename = saveFilename.Replace("%time%", DateTime.Now.ToString("HH.mm.ss"));
saveFilename = saveFilename.Replace("%batch_number%", ""); //string.Empty + (fastaFileNumber + 1));
saveFilename = saveFilename.Replace("%batch_letter%", ""); //SpreadsheetFileHandler.AlphabetLetterRollOver(spreadsheetIndex));
sheetName = sheetName.Replace("%spreadsheet_name%", spreadsheetName);
sheetName = sheetName.Replace("%fasta_filename%", appendFilename);
sheetName = sheetName.Replace("%date%", DateTime.Now.ToString("yyyy-MM-dd"));
sheetName = sheetName.Replace("%time%", DateTime.Now.ToString("HH.mm.ss"));
sheetName = sheetName.Replace("%batch_number%", ""); //string.Empty + (fastaFileNumber + 1));
sheetName = sheetName.Replace("%batch_letter%", ""); //SpreadsheetFileHandler.AlphabetLetterRollOver(spreadsheetIndex));
//var tsvFilename = new FileInfo(FileAndPathMethods.RemoveFileExtension(saveFilename) + ".tsv");
var xlFilename = new FileInfo(FileAndPathMethods.RemoveFileExtension(saveFilename) + ".xlsx");
var savedFiles = SpreadsheetFileHandler.SaveSpreadsheet(xlFilename.FullName, new[] { sheetName }, spreadsheet, null, saveTsv, saveXl, fileExistsOptions);
ProgressActionSet.ReportFilesSaved(savedFiles, progressActionSet);
}
}
ProgressActionSet.Report("Finished processing files.", progressActionSet);
}
/// <summary>
/// Filters the given FASTA files and PDB files with the given options and saves the results to disk. Data needs to be
/// cleaned for two reasons, firstly to not pollute or distort the results, and secondly to save unnecessary processing
/// operations.
/// </summary>
/// <param name="cancellationToken"></param>
/// <param name="pdbFilesFolders"></param>
/// <param name="fastaFiles"></param>
/// <param name="proteinOperationOptionFlags"></param>
/// <param name="saveFastaFilenameTemplate"></param>
/// <param name="consoleTextBox"></param>
/// <param name="progressBar"></param>
/// <param name="estimatedTimeRemaining"></param>
public static void CleanProteins(CancellationToken cancellationToken, decimal maxAtomInterationDistance, string[] pdbFilesFolders, string[] fastaFiles, ProteinOperation proteinOperationOptionFlags, string saveFastaFilenameTemplate, ProgressActionSet progressActionSet, FileExistsHandler.FileExistsOptions fileExistsOptions = FileExistsHandler.FileExistsOptions.AppendNumberToFilename)
{
if (pdbFilesFolders == null || pdbFilesFolders.Length == 0)
{
if (proteinOperationOptionFlags.HasFlag(ProteinOperation.RemoveMultipleModelsInStructure) || proteinOperationOptionFlags.HasFlag(ProteinOperation.RemoveNonInteractingProteinsInStructure) || proteinOperationOptionFlags.HasFlag(ProteinOperation.RemoveNonSymmetricalInStructure) || proteinOperationOptionFlags.HasFlag(ProteinOperation.RemoveWrongNumberOfChainsInStructure))
{
throw new ArgumentOutOfRangeException(nameof(pdbFilesFolders));
}
}
if (fastaFiles == null || fastaFiles.Length == 0)
{
throw new ArgumentOutOfRangeException(nameof(fastaFiles));
}
if (string.IsNullOrWhiteSpace(saveFastaFilenameTemplate))
{
throw new ArgumentOutOfRangeException(nameof(saveFastaFilenameTemplate));
}
string[] pdbFilesArray = ProteinDataBankFileOperations.GetPdbFilesArray(pdbFilesFolders);
//List<string> pdbIdList = null;
int beforeCount = 0;
int afterCount = 0;
string saveFilename = saveFastaFilenameTemplate;
var currentProteinOperation = ProteinOperation.LoadFile;
int[] numberSequencesLoaded;
var sequences = new List <ISequence> [3];
//UserProteinInterfaceOperations.TextBoxClear(consoleTextBox);
ProgressActionSet.Report("Filtering proteins.", progressActionSet);
// Load fasta/sequence files.
sequences[0] = SequenceFileHandler.LoadSequenceFileList(fastaFiles, StaticValues.MolNameProteinAcceptedValues, out numberSequencesLoaded, true);
var pdbIdChainIdList = ProteinDataBankFileOperations.PdbIdChainIdList(sequences[0]);
for (int numberSequencesLoadedIndex = 0; numberSequencesLoadedIndex < numberSequencesLoaded.Length; numberSequencesLoadedIndex++)
{
if (numberSequencesLoaded[numberSequencesLoadedIndex] > 0)
{
ProgressActionSet.Report("Loaded " + numberSequencesLoaded[numberSequencesLoadedIndex] / 2 + " proteins from file: " + fastaFiles[numberSequencesLoadedIndex], progressActionSet);
}
else
{
ProgressActionSet.Report("Error could not load file: " + fastaFiles[numberSequencesLoadedIndex], progressActionSet);
}
}
if (numberSequencesLoaded.Count(a => a > 0) == 0)
{
return;
}
// Replace placeholder variable names.
saveFilename = saveFilename.Replace("%date%", DateTime.Now.ToString("yyyy-MM-dd"));
saveFilename = saveFilename.Replace("%time%", DateTime.Now.ToString("HH.mm.ss"));
// Save initial loaded sequences.
if (File.Exists(saveFilename))
{
if (fileExistsOptions == FileExistsHandler.FileExistsOptions.AppendNumberToFilename)
{
saveFilename = FileExistsHandler.FindNextFreeOutputFilename(saveFilename);
}
else if (fileExistsOptions == FileExistsHandler.FileExistsOptions.OverwriteFile)
{
}
else if (fileExistsOptions == FileExistsHandler.FileExistsOptions.SkipFile)
{
return;
}
}
// Removes any entries not having a protein alphabet.
while (currentProteinOperation != ProteinOperation.Finished)
{
if (cancellationToken.IsCancellationRequested)
{
break;
}
currentProteinOperation = (ProteinOperation)((int)currentProteinOperation * 2);
sequences[1] = null;
sequences[2] = null;
var sequencesDescriptions = new string[3];
if (currentProteinOperation == ProteinOperation.Finished)
{
break;
}
if (currentProteinOperation == ProteinOperation.RemoveNonProteinAlphabetInSequence && !proteinOperationOptionFlags.HasFlag(ProteinOperation.RemoveNonProteinAlphabetInSequence))
{
continue;
}
if (currentProteinOperation == ProteinOperation.RemoveWrongNumberOfChainsInSequence && !proteinOperationOptionFlags.HasFlag(ProteinOperation.RemoveWrongNumberOfChainsInSequence))
{
continue;
}
if (currentProteinOperation == ProteinOperation.RemoveExactDuplicatesInSequence && !proteinOperationOptionFlags.HasFlag(ProteinOperation.RemoveExactDuplicatesInSequence))
{
continue;
}
if (currentProteinOperation == ProteinOperation.RemoveNonHomodimersInSequence && !proteinOperationOptionFlags.HasFlag(ProteinOperation.RemoveNonHomodimersInSequence))
{
continue;
}
if (currentProteinOperation == ProteinOperation.RemoveWrongNumberOfChainsInStructure && !proteinOperationOptionFlags.HasFlag(ProteinOperation.RemoveWrongNumberOfChainsInStructure))
{
continue;
}
if (currentProteinOperation == ProteinOperation.RemoveMultipleModelsInStructure && !proteinOperationOptionFlags.HasFlag(ProteinOperation.RemoveMultipleModelsInStructure))
{
continue;
}
if (currentProteinOperation == ProteinOperation.RemoveNonInteractingProteinsInStructure && !proteinOperationOptionFlags.HasFlag(ProteinOperation.RemoveNonInteractingProteinsInStructure))
{
continue;
}
if (currentProteinOperation == ProteinOperation.RemoveNonSymmetricalInStructure && !proteinOperationOptionFlags.HasFlag(ProteinOperation.RemoveNonSymmetricalInStructure))
{
continue;
}
// Count sequences before operation.
beforeCount = sequences[0].Count / 2;
// Update user about what is happening.
ProgressActionSet.Report("", progressActionSet);
ProgressActionSet.Report("Removing " + ProteinOperationString(currentProteinOperation) + " entries [from " + beforeCount + " proteins]", progressActionSet);
// Start stopwatch to count duration of operation.
Stopwatch stopwatch = Stopwatch.StartNew();
// Perform specified operation.
switch (currentProteinOperation)
{
case ProteinOperation.RemoveNonProteinAlphabetInSequence:
{
sequencesDescriptions[0] = "01 - Removed non-protein sequences (sequence filter)";
sequences[0] = FilterProteins.RemoveNonProteinAlphabetSequences(cancellationToken, sequences[0], progressActionSet);
break;
}
case ProteinOperation.RemoveWrongNumberOfChainsInSequence:
{
sequencesDescriptions[0] = "02 - Removed non-dimers (sequence filter)";
sequences[0] = FilterProteins.RemoveSequencesWithIncorrectNumberOfChains(cancellationToken, sequences[0], 2, progressActionSet);
break;
}
case ProteinOperation.RemoveExactDuplicatesInSequence:
{
sequencesDescriptions[0] = "03 - Removed exact duplicates (sequence filter)";
sequences[0] = FilterProteins.RemoveDuplicates(cancellationToken, sequences[0], progressActionSet);
break;
}
case ProteinOperation.RemoveNonHomodimersInSequence:
{
// homodimers - all types - unfiltered for interactions or symmetry
var result = FilterProteins.SplitDimerTypes(cancellationToken, sequences[0], 30, 90, progressActionSet);
sequencesDescriptions[0] = "04 - Homodimers only (sequence filter)";
sequences[0] = result.HomoDimerPdbIdList;
sequencesDescriptions[1] = "04 - Heterodimers only (sequence filter)";
sequences[1] = result.HeteroDimerPdbIdList;
sequencesDescriptions[2] = "04 - Homology dimers only (sequence filter)";
sequences[2] = result.HomologyDimerPdbIdList;
break;
}
case ProteinOperation.RemoveMultipleModelsInStructure:
{
sequencesDescriptions[0] = "05 - Removed multiple models (structure filter)";
List <string> pdbIdList = FilterProteins.SequenceListToPdbIdList(sequences[0]);
pdbIdList = FilterProteins.RemoveMultipleStructureModels(cancellationToken, pdbFilesFolders, pdbIdList, progressActionSet);
sequences[0] = FilterProteins.RemoveSequences(cancellationToken, sequences[0], pdbIdList, FilterProteins.RemoveSequencesOptions.RemoveSequencesInList);
break;
}
case ProteinOperation.RemoveWrongNumberOfChainsInStructure:
{
sequencesDescriptions[0] = "06 - Removed non-dimers (structure filter)";
List <string> pdbIdList = FilterProteins.SequenceListToPdbIdList(sequences[0]);
//var pdbIdChainIdList = ProteinDataBankFileOperations.PdbIdChainIdList(sequences[0]);
pdbIdList = FilterProteins.RemoveStructuresWithIncorrectNumberOfChains(cancellationToken, pdbFilesFolders, pdbIdList, pdbIdChainIdList, 2, progressActionSet);
sequences[0] = FilterProteins.RemoveSequences(cancellationToken, sequences[0], pdbIdList, FilterProteins.RemoveSequencesOptions.RemoveSequencesInList);
break;
}
case ProteinOperation.RemoveNonInteractingProteinsInStructure:
{
// Make copy of sequences as we will split the list into two parts - with and without interactions.
sequences[1] = new List <ISequence>(sequences[0]);
// Get pdb id list from sequences, to check for pdb file, load, perform processing.
List <string> pdbIdList = FilterProteins.SequenceListToPdbIdList(sequences[0]);
// Makes a list of sequences with interactions.
pdbIdList = FilterProteins.RemoveSequencesWithoutInteractions(cancellationToken, maxAtomInterationDistance, pdbFilesFolders, pdbIdList, pdbIdChainIdList, progressActionSet);
// Remove any protein not in the list, keep the ones in the list.
sequencesDescriptions[0] = "08 - dimers - with interactions - unfiltered for symmetry";
sequences[0] = FilterProteins.RemoveSequences(cancellationToken, sequences[0], pdbIdList, FilterProteins.RemoveSequencesOptions.RemoveSequencesNotInList);
sequencesDescriptions[1] = "07 - dimers - no observed interactions";
sequences[1] = FilterProteins.RemoveSequences(cancellationToken, sequences[1], pdbIdList, FilterProteins.RemoveSequencesOptions.RemoveSequencesInList);
break;
}
case ProteinOperation.RemoveNonSymmetricalInStructure:
{
// Make copy of sequences as we will split the list into two parts - with and without symmetry.
List <string> pdbIdList = FilterProteins.SequenceListToPdbIdList(sequences[0]);
sequences[1] = new List <ISequence>(sequences[0]);
sequences[2] = new List <ISequence>(sequences[0]);
Dictionary <string, decimal> symmetryPercentage = FilterProteins.CalculateStructureSymmetry(cancellationToken, maxAtomInterationDistance, pdbFilesFolders, pdbIdList, pdbIdChainIdList, progressActionSet);
var pdbSymmetrical = new List <string>();
var pdbPartSymmetrical = new List <string>();
var pdbNonSymmetrical = new List <string>();
foreach (var symmetryPercentageKeyValuePair in symmetryPercentage)
{
if (symmetryPercentageKeyValuePair.Value == 0.0m)
{
pdbNonSymmetrical.Add(symmetryPercentageKeyValuePair.Key);
}
else if (symmetryPercentageKeyValuePair.Value == 100.0m)
{
pdbSymmetrical.Add(symmetryPercentageKeyValuePair.Key);
}
else if (symmetryPercentageKeyValuePair.Value > 0.0m && symmetryPercentageKeyValuePair.Value < 100.0m)
{
pdbPartSymmetrical.Add(symmetryPercentageKeyValuePair.Key);
}
else
{
ProgressActionSet.Report("Error: Out of bounds symmetry value of " + symmetryPercentageKeyValuePair.Value + " was found in " + symmetryPercentageKeyValuePair.Key + ".", progressActionSet);
}
}
sequencesDescriptions[0] = "11 - dimers - with interactions - 100% symmetrical";
sequences[0] = FilterProteins.RemoveSequences(cancellationToken, sequences[0], pdbSymmetrical, FilterProteins.RemoveSequencesOptions.RemoveSequencesNotInList);
sequencesDescriptions[1] = "10 - dimers - with interactions - 1% to 99% symmetrical";
sequences[1] = FilterProteins.RemoveSequences(cancellationToken, sequences[1], pdbPartSymmetrical, FilterProteins.RemoveSequencesOptions.RemoveSequencesNotInList);
sequencesDescriptions[2] = "09 - dimers - with interactions - 0% symmetrical";
sequences[2] = FilterProteins.RemoveSequences(cancellationToken, sequences[2], pdbNonSymmetrical, FilterProteins.RemoveSequencesOptions.RemoveSequencesNotInList);
break;
}
}
// Stop stopwatch immediately after operation.
stopwatch.Stop();
// Count sequences after operation.
afterCount = sequences[0].Count / 2;
if (!cancellationToken.IsCancellationRequested)
{
for (int sequencesIndex = sequences.GetLowerBound(0); sequencesIndex <= sequences.GetUpperBound(0); sequencesIndex++)
{
if (sequences[sequencesIndex] != null)
{
// Find free filename to save the latest sequence results of operations.
string localSaveFilename = saveFilename;
localSaveFilename = localSaveFilename.Replace("%fasta_filename%", sequencesDescriptions[sequencesIndex]);
bool skipFile = false;
if (File.Exists(localSaveFilename))
{
if (fileExistsOptions == FileExistsHandler.FileExistsOptions.AppendNumberToFilename)
{
localSaveFilename = FileExistsHandler.FindNextFreeOutputFilename(localSaveFilename);
}
else if (fileExistsOptions == FileExistsHandler.FileExistsOptions.OverwriteFile)
{
}
else if (fileExistsOptions == FileExistsHandler.FileExistsOptions.SkipFile)
{
skipFile = true;
}
}
if (!skipFile)
{
// Save the sequence results to previous set filename.
string savedFile /*s*/ = SequenceFileHandler.SaveSequencesAsFasta(sequences[sequencesIndex], localSaveFilename);
// Inform user that file has been saved.
//foreach (char savedFile in savedFiles)
//{
ProgressActionSet.Report("Saved file: " + savedFile, progressActionSet);
//}
}
}
}
// Update the user about the results.
ProgressActionSet.Report("Removed " + (beforeCount - afterCount) + " proteins. [" + afterCount + " proteins remaining]. Elapsed: " + stopwatch.Elapsed.ToString(@"dd\:hh\:mm\:ss"), progressActionSet);
}
}
if (!cancellationToken.IsCancellationRequested)
{
ProgressActionSet.Report("Finished all selected filtering operations.", progressActionSet);
}
else
{
ProgressActionSet.Report("Cancelled.", progressActionSet);
//UserProteinInterfaceOperations.ProgressBarReset(progressBar, 0, 100, 0);
////UserProteinInterfaceOperations.LabelEstimatedTimeRemainingUpdate(estimatedTimeRemaining, 0, 1, 1);
ProgressActionSet.StartAction(100, progressActionSet);
ProgressActionSet.ProgressAction(100, progressActionSet);
ProgressActionSet.FinishAction(false, progressActionSet);
}
}
