public static List <AminoAcidDistributionSpreadsheetRecord> PatternDistributionSpreadsheetRecords(List <VectorProteinInterfaceWhole> vectorProteinInterfaceWholeList, List <string> pdbIdList, List <ISequence> seqList, int vectorType)
{
if (vectorProteinInterfaceWholeList == null)
{
throw new ArgumentNullException(nameof(vectorProteinInterfaceWholeList));
}
if (pdbIdList == null)
{
throw new ArgumentNullException(nameof(pdbIdList));
}
if (seqList == null)
{
throw new ArgumentNullException(nameof(seqList));
}
var result = new List <AminoAcidDistributionSpreadsheetRecord>();
// patterns
var patternProteinDictionary = new Dictionary <string, AminoAcidChainComposition>();
var patternProteinInterfaceDictionary = new Dictionary <string, AminoAcidChainComposition>();
var patternProteinInterfaceInteractionDictionary = new Dictionary <string, AminoAcidChainComposition>();
var patternProteinInterfaceNonInteractionDictionary = new Dictionary <string, AminoAcidChainComposition>();
foreach (var vectorProteinInterfaceWhole in vectorProteinInterfaceWholeList)
{
var interactionBools = vectorProteinInterfaceWhole.InteractionBools();
string pattern;
if (vectorType >= 0 && vectorType <= 3)
{
pattern = vectorProteinInterfaceWhole.VectorString(vectorType);
}
else if (vectorType == 4)
{
pattern = vectorProteinInterfaceWhole.SecondaryStructure;
}
else if (vectorType == 5)
{
pattern = "ProteinInterface Length " + vectorProteinInterfaceWhole.ProteinInterfaceLength;
}
else
{
throw new ArgumentOutOfRangeException(nameof(vectorType));
}
if (!patternProteinDictionary.ContainsKey(pattern))
{
patternProteinDictionary.Add(pattern, new AminoAcidChainComposition());
}
if (!patternProteinInterfaceDictionary.ContainsKey(pattern))
{
patternProteinInterfaceDictionary.Add(pattern, new AminoAcidChainComposition());
}
if (!patternProteinInterfaceInteractionDictionary.ContainsKey(pattern))
{
patternProteinInterfaceInteractionDictionary.Add(pattern, new AminoAcidChainComposition());
}
if (!patternProteinInterfaceNonInteractionDictionary.ContainsKey(pattern))
{
patternProteinInterfaceNonInteractionDictionary.Add(pattern, new AminoAcidChainComposition());
}
var aminoAcids1L = vectorProteinInterfaceWhole.ProteinInterfaceAminoAcids1L();
for (int index = 0; index < aminoAcids1L.Length; index++)
{
var c = aminoAcids1L[index];
patternProteinInterfaceDictionary[pattern].IncrementAminoAcidCount(c);
if (interactionBools[index])
{
patternProteinInterfaceInteractionDictionary[pattern].IncrementAminoAcidCount(c);
}
else
{
patternProteinInterfaceNonInteractionDictionary[pattern].IncrementAminoAcidCount(c);
}
}
patternProteinDictionary[pattern].NumberSamples++;
patternProteinInterfaceDictionary[pattern].NumberSamples++;
patternProteinInterfaceInteractionDictionary[pattern].NumberSamples++;
patternProteinInterfaceNonInteractionDictionary[pattern].NumberSamples++;
var bsSeqList = seqList.Where(a => SequenceIdSplit.SequenceIdToPdbIdAndChainId(a.ID).PdbId == vectorProteinInterfaceWhole.FullProteinInterfaceId.ProteinId && SequenceIdSplit.SequenceIdToPdbIdAndChainId(a.ID).ChainId == SpreadsheetFileHandler.AlphabetLetterRollOver(vectorProteinInterfaceWhole.FullProteinInterfaceId.ChainId)).ToList();
foreach (var chain in bsSeqList)
{
var seq = chain.ConvertToString();
foreach (var c in seq)
{
patternProteinDictionary[pattern].IncrementAminoAcidCount(c);
}
}
}
foreach (var kvp in patternProteinDictionary)
{
var recordAllComposition = new AminoAcidDistributionSpreadsheetRecord();
var recordProteinInterfaceComposition = new AminoAcidDistributionSpreadsheetRecord();
var recordProteinInterfaceInteractionComposition = new AminoAcidDistributionSpreadsheetRecord();
var recordProteinInterfaceNonInteractionComposition = new AminoAcidDistributionSpreadsheetRecord();
result.Add(recordAllComposition);
result.Add(recordProteinInterfaceComposition);
result.Add(recordProteinInterfaceInteractionComposition);
result.Add(recordProteinInterfaceNonInteractionComposition);
recordAllComposition.Pattern = kvp.Key;
recordProteinInterfaceComposition.Pattern = kvp.Key;
recordProteinInterfaceInteractionComposition.Pattern = kvp.Key;
recordProteinInterfaceNonInteractionComposition.Pattern = kvp.Key;
var vectorTypeStr = VectorProteinInterfaceWhole.VectorStringDescription(vectorType);
recordAllComposition.Type = vectorTypeStr;
recordProteinInterfaceComposition.Type = vectorTypeStr;
recordProteinInterfaceInteractionComposition.Type = vectorTypeStr;
recordProteinInterfaceNonInteractionComposition.Type = vectorTypeStr;
recordAllComposition.Metric = "Protein";
recordProteinInterfaceComposition.Metric = "ProteinInterface";
recordProteinInterfaceInteractionComposition.Metric = "ProteinInterface interactions";
recordProteinInterfaceNonInteractionComposition.Metric = "ProteinInterface non interactions";
// number of samples
recordAllComposition.NumberOfSamples = kvp.Value.NumberSamples;
recordProteinInterfaceComposition.NumberOfSamples = patternProteinInterfaceDictionary[kvp.Key].NumberSamples;
recordProteinInterfaceInteractionComposition.NumberOfSamples = patternProteinInterfaceInteractionDictionary[kvp.Key].NumberSamples;
recordProteinInterfaceNonInteractionComposition.NumberOfSamples = patternProteinInterfaceNonInteractionDictionary[kvp.Key].NumberSamples;
// number of amino acids
recordAllComposition.TotalAminoAcids = kvp.Value.AminoAcidGroupsCount[(int)AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.AminoAcids].Sum();
recordProteinInterfaceComposition.TotalAminoAcids = patternProteinInterfaceDictionary[kvp.Key].AminoAcidGroupsCount[(int)AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.AminoAcids].Sum();
recordProteinInterfaceInteractionComposition.TotalAminoAcids = patternProteinInterfaceInteractionDictionary[kvp.Key].AminoAcidGroupsCount[(int)AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.AminoAcids].Sum();
recordProteinInterfaceNonInteractionComposition.TotalAminoAcids = patternProteinInterfaceNonInteractionDictionary[kvp.Key].AminoAcidGroupsCount[(int)AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.AminoAcids].Sum();
var allPercentage = AminoAcidChainComposition.ConvertToPercentage(kvp.Value);
var proteinInterfacePercentage = AminoAcidChainComposition.ConvertToPercentage(patternProteinInterfaceDictionary[kvp.Key]);
var proteinInterfaceInteractionPercentage = AminoAcidChainComposition.ConvertToPercentage(patternProteinInterfaceInteractionDictionary[kvp.Key]);
var proteinInterfaceNonInteractionPercentage = AminoAcidChainComposition.ConvertToPercentage(patternProteinInterfaceNonInteractionDictionary[kvp.Key]);
foreach (AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups enumAminoAcidGroups in Enum.GetValues(typeof(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups)))
{
var groupItemsTotal = AminoAcidGroups.AminoAcidGroups.GetTotalSubgroups(enumAminoAcidGroups);
for (var groupItemIndex = 0; groupItemIndex < groupItemsTotal; groupItemIndex++)
{
recordAllComposition.Distribution[(int)enumAminoAcidGroups][groupItemIndex] = allPercentage.AminoAcidGroupsCount[(int)enumAminoAcidGroups][groupItemIndex];
recordProteinInterfaceComposition.Distribution[(int)enumAminoAcidGroups][groupItemIndex] = proteinInterfacePercentage.AminoAcidGroupsCount[(int)enumAminoAcidGroups][groupItemIndex];
recordProteinInterfaceInteractionComposition.Distribution[(int)enumAminoAcidGroups][groupItemIndex] = proteinInterfaceInteractionPercentage.AminoAcidGroupsCount[(int)enumAminoAcidGroups][groupItemIndex];
recordProteinInterfaceNonInteractionComposition.Distribution[(int)enumAminoAcidGroups][groupItemIndex] = proteinInterfaceNonInteractionPercentage.AminoAcidGroupsCount[(int)enumAminoAcidGroups][groupItemIndex];
}
}
}
return(result);
}
/// <summary>
/// This method returns a dictionary entry for each protein id (pdb id), with a list of interaction vectors
/// </summary>
/// <returns></returns>
public static List <VectorProteinInterfaceWhole> LoadProteinInterfaceVectorFromFiles(
CancellationToken cancellationToken,
decimal maxAtomInterationDistance,
decimal minimumProteinInterfaceDensity,
string[] sequenceListFileArray,
string[] pdbFileDirectoryLocationArray,
ProgressActionSet progressActionSet)
{
if (sequenceListFileArray == null)
{
throw new ArgumentNullException(nameof(sequenceListFileArray));
}
if (pdbFileDirectoryLocationArray == null)
{
throw new ArgumentNullException(nameof(pdbFileDirectoryLocationArray));
}
var vectorProteinInterfaceWholeList = new List <VectorProteinInterfaceWhole>();
// 1: Open list of sequences already cleaned to have only symmetrical homodimers (fasta file only contains 100% symmetrical homodimers with all other junk removed - but could have any number of proteinInterfaces per chain)
List <ISequence> sequenceList = SequenceFileHandler.LoadSequenceFileList(sequenceListFileArray, StaticValues.MolNameProteinAcceptedValues);
var pdbIdChainIdList = ProteinDataBankFileOperations.PdbIdChainIdList(sequenceList);
// 2: Get a list of the unique ids for the sequences
List <string> pdbIdList = FilterProteins.SequenceListToPdbIdList(sequenceList);
if (pdbIdList == null || pdbIdList.Count == 0)
{
throw new ArgumentOutOfRangeException(nameof(sequenceListFileArray), "Error loading PDB ID list");
}
// 3: Get a list of PDB files found in user specified directory
string[] pdbFilesArray = ProteinDataBankFileOperations.GetPdbFilesArray(pdbFileDirectoryLocationArray);
ProgressActionSet.StartAction(pdbFilesArray.Length, progressActionSet);
var startTicks = DateTime.Now.Ticks;
// 4: Loop through each pdb file
for (int pdbFileNumber = 0; pdbFileNumber < pdbFilesArray.Length; pdbFileNumber++) // +1 is for progress update
{
ProgressActionSet.ProgressAction(1, progressActionSet);
ProgressActionSet.EstimatedTimeRemainingAction(startTicks, pdbFileNumber + 1, pdbFilesArray.Length, progressActionSet);
// 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;
}
ClusterProteinDataBankFileResult clusterPdbFileResult = Clustering.ClusterProteinDataBankFile(cancellationToken, maxAtomInterationDistance, minimumProteinInterfaceDensity, pdbFilename, pdbIdChainIdList, ClusteringMethodOptions.ClusterWithResidueSequenceIndex, -1, -1, progressActionSet);
if (clusterPdbFileResult == null)
{
continue;
}
List <ProteinInterfaceSequenceAndPositionData> proteinInterfaceSequenceAndPositionDataList = clusterPdbFileResult.ProteinInterfaceAnalysisResultData.ProteinInterfacesSequenceAndPositionDataList;
proteinInterfaceSequenceAndPositionDataList = proteinInterfaceSequenceAndPositionDataList.OrderBy(a => a.FullProteinInterfaceId.ProteinId).ThenBy(a => a.FullProteinInterfaceId.ChainId).ThenBy(a => a.FullProteinInterfaceId.ProteinInterfaceId).ToList();
for (int proteinInterfaceSequenceAndPositionDataListIndex = 0; proteinInterfaceSequenceAndPositionDataListIndex < proteinInterfaceSequenceAndPositionDataList.Count; proteinInterfaceSequenceAndPositionDataListIndex++)
{
ProteinInterfaceSequenceAndPositionData proteinInterfaceSequenceAndPositionData = proteinInterfaceSequenceAndPositionDataList[proteinInterfaceSequenceAndPositionDataListIndex];
var seq = sequenceList.FirstOrDefault(a =>
{
var p = SequenceIdSplit.SequenceIdToPdbIdAndChainId(a.ID);
return(p.PdbId.ToUpperInvariant() == proteinInterfaceSequenceAndPositionData.FullProteinInterfaceId.ProteinId.ToUpperInvariant() && p.ChainId.ToUpperInvariant() == proteinInterfaceSequenceAndPositionData.ChainIdLetter.ToUpperInvariant());
});
var seqLen = seq != null ? seq.Count : -1;
var vectorProteinInterfaceWholeFwd = MakeVectorProteinInterfaceWhole(pdbFilename, proteinInterfaceSequenceAndPositionData, false, false);
vectorProteinInterfaceWholeFwd.FullSequenceLength = seqLen;
vectorProteinInterfaceWholeList.Add(vectorProteinInterfaceWholeFwd);
var vectorProteinInterfaceWholeRev = MakeVectorProteinInterfaceWhole(pdbFilename, proteinInterfaceSequenceAndPositionData, true, false);
vectorProteinInterfaceWholeRev.FullSequenceLength = seqLen;
vectorProteinInterfaceWholeList.Add(vectorProteinInterfaceWholeRev);
}
}
ProgressActionSet.FinishAction(true, progressActionSet);
vectorProteinInterfaceWholeList = vectorProteinInterfaceWholeList.OrderBy(a => a.FullProteinInterfaceId.ProteinId).ThenBy(a => a.FullProteinInterfaceId.ChainId).ThenBy(a => a.FullProteinInterfaceId.ProteinInterfaceId).ToList();
return(vectorProteinInterfaceWholeList);
}
