public static AminoAcidDistributionSpreadsheetRecord UniProtKb()
{
// UniProtKB/TrEMBL composition
var record = new AminoAcidDistributionSpreadsheetRecord
{
Pattern = "UniProtKB/TrEMBL",
Type = "UniProtKB/TrEMBL",
Metric = "UniProtKB/TrEMBL",
TotalAminoAcids = UniProtProteinDatabaseComposition.TotalAminoAcidsInDatabase,
NumberOfSamples = UniProtProteinDatabaseComposition.TotalSamplesInDatabase,
};
var uniprotComposition = UniProtProteinDatabaseComposition.AminoAcidCompositionAsChain();
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++)
{
record.Distribution[(int)enumAminoAcidGroups][groupItemIndex] = uniprotComposition.AminoAcidGroupsCount[(int)enumAminoAcidGroups][groupItemIndex];
}
}
return(record);
}
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);
}
public static List <AminoAcidDistributionSpreadsheetRecord> OverallDistributionRecords(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>();
// over all composition
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);
var allComposition = new AminoAcidChainComposition();
var proteinInterfaceComposition = new AminoAcidChainComposition();
var proteinInterfaceInteractionComposition = new AminoAcidChainComposition();
var proteinInterfaceNonInteractionComposition = new AminoAcidChainComposition();
foreach (var chain in seqList)
{
var seq = chain.ConvertToString();
foreach (var c in seq)
{
allComposition.IncrementAminoAcidCount(c);
}
}
foreach (var vectorProteinInterfaceWhole in vectorProteinInterfaceWholeList)
{
var aminoAcids1L = vectorProteinInterfaceWhole.ProteinInterfaceAminoAcids1L();
var interactionBools = vectorProteinInterfaceWhole.InteractionBools();
for (int index = 0; index < aminoAcids1L.Length; index++)
{
var c = aminoAcids1L[index];
proteinInterfaceComposition.IncrementAminoAcidCount(c);
if (interactionBools[index])
{
proteinInterfaceInteractionComposition.IncrementAminoAcidCount(c);
}
else
{
proteinInterfaceNonInteractionComposition.IncrementAminoAcidCount(c);
}
}
}
recordAllComposition.Pattern = "*";
recordProteinInterfaceComposition.Pattern = "*";
recordProteinInterfaceInteractionComposition.Pattern = "*";
recordProteinInterfaceNonInteractionComposition.Pattern = "*";
recordAllComposition.Type = "*";
recordProteinInterfaceComposition.Type = "*";
recordProteinInterfaceInteractionComposition.Type = "*";
recordProteinInterfaceNonInteractionComposition.Type = "*";
recordAllComposition.Metric = "Proteins";
recordProteinInterfaceComposition.Metric = "ProteinInterfaces";
recordProteinInterfaceInteractionComposition.Metric = "ProteinInterface interactions";
recordProteinInterfaceNonInteractionComposition.Metric = "ProteinInterface non interactions";
// number of samples
recordAllComposition.NumberOfSamples = seqList.Count;
recordProteinInterfaceComposition.NumberOfSamples = vectorProteinInterfaceWholeList.Count;
recordProteinInterfaceInteractionComposition.NumberOfSamples = vectorProteinInterfaceWholeList.Count;
recordProteinInterfaceNonInteractionComposition.NumberOfSamples = vectorProteinInterfaceWholeList.Count;
// number of amino acids
recordAllComposition.TotalAminoAcids = allComposition.AminoAcidGroupsCount[(int)AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.AminoAcids].Sum();
recordProteinInterfaceComposition.TotalAminoAcids = proteinInterfaceComposition.AminoAcidGroupsCount[(int)AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.AminoAcids].Sum();
recordProteinInterfaceInteractionComposition.TotalAminoAcids = proteinInterfaceInteractionComposition.AminoAcidGroupsCount[(int)AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.AminoAcids].Sum();
recordProteinInterfaceNonInteractionComposition.TotalAminoAcids = proteinInterfaceNonInteractionComposition.AminoAcidGroupsCount[(int)AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.AminoAcids].Sum();
// convert composition to percentage
var allCompositionPercentage = AminoAcidChainComposition.ConvertToPercentage(allComposition);
var proteinInterfaceCompositionPercentage = AminoAcidChainComposition.ConvertToPercentage(proteinInterfaceComposition);
var proteinInterfaceInteractionCompositionPercentage = AminoAcidChainComposition.ConvertToPercentage(proteinInterfaceInteractionComposition);
var proteinInterfaceNonInteractionCompositionPercentage = AminoAcidChainComposition.ConvertToPercentage(proteinInterfaceNonInteractionComposition);
// output composition to result spreadsheet matrix
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] = allCompositionPercentage.AminoAcidGroupsCount[(int)enumAminoAcidGroups][groupItemIndex];
recordProteinInterfaceComposition.Distribution[(int)enumAminoAcidGroups][groupItemIndex] = proteinInterfaceCompositionPercentage.AminoAcidGroupsCount[(int)enumAminoAcidGroups][groupItemIndex];
recordProteinInterfaceInteractionComposition.Distribution[(int)enumAminoAcidGroups][groupItemIndex] = proteinInterfaceInteractionCompositionPercentage.AminoAcidGroupsCount[(int)enumAminoAcidGroups][groupItemIndex];
recordProteinInterfaceNonInteractionComposition.Distribution[(int)enumAminoAcidGroups][groupItemIndex] = proteinInterfaceNonInteractionCompositionPercentage.AminoAcidGroupsCount[(int)enumAminoAcidGroups][groupItemIndex];
}
}
return(result);
}