private ResultPtmSite GetResultPtmSitesModel(Guid resId, PostTranslationModificationsSiteDto ptmSite) //ResultPtmSites
{
var ptmSites = new ResultPtmSite
{
ResultId = resId.ToString(),
AminoAcid = ptmSite.AminoAcid.Aggregate("", (current, t) => current + t),
Index = ptmSite.Index,
ModName = ptmSite.ModName,
ModWeight = ptmSite.ModWeight,
Score = ptmSite.Score,
Site = ptmSite.Site //#MIGHTGETERROR //Converted it char(char(7000)) to avoiding string (nvarchar(MAX))
//Aik sa zyada modification sites of modifications ho skti hain...?
};
return(ptmSites);
}
public static void BlindPTM(List <double> experimentalSpectrum, double molW, List <ProteinDto> candidateProteinsList,
double pepTol, double userHopThreshold, string pepUnit)
{
var stopwatch = new Stopwatch();
// Data Preperation and Loading GPU Module
stopwatch.Start();
var peaks = new List <double>();
var aminoAcidList = new List <string>();
var modificationList = new List <string>();
var startList = new List <double>();
var endList = new List <double>();
foreach (var peak in experimentalSpectrum)
{
peaks.Add(peak + 1.00727647);
peaks.Add(molW - (peak + 1.00727647));
//peaks.Add(peak);
//peaks.Add(molW - (peak));
}
peaks.Sort();
GPGPU gpu = CudafyHost.GetDevice(CudafyModes.Target);
CudafyModule km = CudafyModule.TryDeserialize();
if (km == null || !km.TryVerifyChecksums())
{
km = CudafyTranslator.Cudafy();
km.Serialize();
}
gpu.LoadModule(km);
stopwatch.Stop();
Console.WriteLine("Data Preperation: " + stopwatch.Elapsed);
// GPU Module
stopwatch.Restart();
var lengthSquared = peaks.Count * peaks.Count;
var peaksArray = peaks.ToArray();
var lengthOfPeakList = new int[1];
lengthOfPeakList[0] = peaks.Count;
var outputArray = new char[peaks.Count, peaks.Count, 37];
var errorArray = new double[peaks.Count, peaks.Count, 37];
var modMassList = ModificationMass;
char[,,] outputArrayDevice = gpu.Allocate(outputArray);
double[,,] errorArrayDevice = gpu.Allocate(errorArray);
double[] peaksDevice = gpu.Allocate <double>(peaksArray.Length);
int[] lengthOfPeakListDevice = gpu.Allocate <int>(lengthOfPeakList.Length);
double[] ptmMassListDevice = gpu.Allocate <double>(modMassList.Length);
gpu.CopyToDevice(peaksArray, peaksDevice);
gpu.CopyToDevice(lengthOfPeakList, lengthOfPeakListDevice);
gpu.CopyToDevice(ModificationMass, ptmMassListDevice);
int block = (int)Math.Ceiling((double)lengthSquared * 37 / N);
gpu.Launch(block, N).PtmExtractor(peaksDevice, lengthOfPeakListDevice, ptmMassListDevice, outputArrayDevice,
errorArrayDevice);
gpu.CopyFromDevice(outputArrayDevice, outputArray);
gpu.CopyFromDevice(errorArrayDevice, errorArray);
gpu.FreeAll();
for (var i = 0; i < peaks.Count; i++)
{
for (var j = 0; j < peaks.Count; j++)
{
for (var k = 0; k < 37; k++)
{
if (outputArray[i, j, k] == '\0')
{
continue;
}
aminoAcidList.Add(ModificationAminoAcids[outputArray[i, j, k]].ToString());
modificationList.Add(ModificationName[outputArray[i, j, k]]);
startList.Add(peaks[i]);
endList.Add(peaks[j]);
}
}
}
stopwatch.Stop();
Console.WriteLine("GPU Generation: " + stopwatch.Elapsed);
// PTM Shortlisting
stopwatch.Restart();
foreach (var protein in candidateProteinsList)
{
var sequence = protein.Sequence.ToCharArray();
var hopI = 0;
var thrI = 0;
var shortlistedAminoAcid = new List <string>();
var shortlistedModification = new List <string>();
var shortlistedEnd = new List <double>();
var shortlistedStart = new List <double>();
var shortlistedIndex = new List <int>();
while (true)
{
try
{
if (startList.Count > 0)
{
if (shortlistedStart.Count > 0)
{
if (shortlistedEnd[shortlistedEnd.Count - 1] > startList[hopI])
{
hopI = hopI + 1;
if (hopI == startList.Count)
{
break;
}
continue;
}
}
var diff = startList[hopI] - protein.InsilicoDetails.InsilicoMassLeft[thrI];
if (diff <= userHopThreshold && diff >= -userHopThreshold)
{
if (aminoAcidList[hopI] == sequence[thrI + 2].ToString())
{
var temproray = modificationList[hopI].Split('_');
var modMass = AminoAcids.ModificationTable(temproray[0]);
//var modMass = AminoAcids.ModTable(modificationList[hopI]);
diff =
Math.Abs(endList[hopI] -
(protein.InsilicoDetails.InsilicoMassLeft[thrI + 1
] +
modMass));
if (string.Compare(pepUnit, "ppm", StringComparison.Ordinal) == 0)
{
diff = (diff / molW) * 1000000;
}
else if (string.Compare(pepUnit, "%", StringComparison.Ordinal) == 0)
{
diff = (diff / molW) * 100;
}
if (diff < pepTol)
{
for (var i = thrI + 1;
i < protein.InsilicoDetails.InsilicoMassLeft.Count;
i++)
{
protein.InsilicoDetails.InsilicoMassLeft[i] =
protein.InsilicoDetails.InsilicoMassLeft[i] +
modMass;
}
protein.Mw = protein.Mw + modMass;
shortlistedAminoAcid.Add(aminoAcidList[hopI]);
shortlistedModification.Add(modificationList[hopI]);
shortlistedEnd.Add(endList[hopI]);
shortlistedStart.Add(startList[hopI]);
shortlistedIndex.Add(thrI);
}
}
}
else if (diff > userHopThreshold)
{
thrI = thrI + 1;
if (thrI == protein.InsilicoDetails.InsilicoMassLeft.Count - 1)
{
break;
}
continue;
}
else if (diff < -userHopThreshold)
{
hopI = hopI + 1;
if (hopI == startList.Count)
{
break;
}
continue;
}
hopI = hopI + 1;
if (hopI == startList.Count)
{
break;
}
}
}
catch (Exception exception)
{
Debug.WriteLine(exception.Message);
}
}
for (var hopIndex = 0; hopIndex < shortlistedStart.Count; hopIndex++)
{
var site = new PostTranslationModificationsSiteDto
{
Index = shortlistedIndex[hopIndex],
ModName = shortlistedModification[hopIndex],
ModWeight = AminoAcids.ModificationTable(shortlistedModification[hopIndex]),
Site = Convert.ToChar(shortlistedAminoAcid[hopIndex])
};
protein.PtmParticulars.Add(site);
}
var massError = Math.Abs(molW - protein.Mw);
protein.MwScore = Math.Abs(massError) < 0 ? 1 : Math.Pow(massError, 0.5);
}
stopwatch.Stop();
Console.WriteLine("Shortlisting :" + stopwatch.Elapsed);
}
public static void BlindPTM(List <double> experimentalSpectrum, double molW, List <ProteinDto> candidateProteinsList, double pepTol, double userHopThreshold, string pepUnit)
{
var stopwatch = new Stopwatch();
// Data Preperation
stopwatch.Start();
var peaks = new List <double>();
foreach (var peak in experimentalSpectrum)
{
peaks.Add(peak + 1.00727647);
peaks.Add(molW - (peak + 1.00727647));
//peaks.Add(peak);
//peaks.Add(molW - (peak));
}
peaks.Sort();
stopwatch.Stop();
Console.WriteLine("Data Preperation: " + stopwatch.Elapsed);
// PTM Extraction
stopwatch.Restart();
var aminoAcidList = new List <string>();
var modificationList = new List <string>();
var startList = new List <double>();
var endList = new List <double>();
for (var expI = 0; expI < peaks.Count; expI++)
{
for (var expJ = expI + 1; expJ < peaks.Count; expJ++)
{
var peakDiff = peaks[expJ] - peaks[expI];
var modification = AminoAcids.GetModifiedAminoAcid(peakDiff, userHopThreshold);
foreach (var mod in modification)
{
var temproray = mod.Split('_');
if (temproray.Length <= 1)
{
continue;
}
aminoAcidList.Add(temproray[1]);
modificationList.Add(temproray[0]);
startList.Add(peaks[expI]);
endList.Add(peaks[expJ]);
}
}
}
stopwatch.Stop();
Console.WriteLine("Generation: " + stopwatch.Elapsed);
// PTM Shortlisting
stopwatch.Restart();
foreach (var protein in candidateProteinsList)
{
var sequence = protein.Sequence;
var hopIndex = 0;
var thrI = 0;
var shortlistedAminoAcid = new List <string>();
var shortlistedModification = new List <string>();
var shortlistedEnd = new List <double>();
var shortlistedStart = new List <double>();
var shortlistedIndex = new List <int>();
while (true)
{
try
{
if (startList.Count > 0)
{
if (shortlistedStart.Count > 0)
{
if (shortlistedEnd[shortlistedEnd.Count - 1] > startList[hopIndex])
{
hopIndex = hopIndex + 1;
if (hopIndex == startList.Count)
{
break;
}
continue;
}
}
var diff = startList[hopIndex] - protein.InsilicoDetails.InsilicoMassLeft[thrI];
if (diff <= userHopThreshold && diff >= -userHopThreshold)
{
if (aminoAcidList[hopIndex] == sequence[thrI + 2].ToString())
{
var modMass = AminoAcids.ModificationTable(modificationList[hopIndex]);
diff =
Math.Abs(endList[hopIndex] -
(protein.InsilicoDetails.InsilicoMassLeft[thrI + 1
] +
modMass));
if (string.Compare(pepUnit, "ppm", StringComparison.Ordinal) == 0)
{
diff = (diff / molW) * 1000000;
}
else if (string.Compare(pepUnit, "%", StringComparison.Ordinal) == 0)
{
diff = (diff / molW) * 100;
}
if (diff < pepTol)
{
for (var i = thrI + 1;
i < protein.InsilicoDetails.InsilicoMassLeft.Count;
i++)
{
protein.InsilicoDetails.InsilicoMassLeft[i] =
protein.InsilicoDetails.InsilicoMassLeft[i] +
modMass;
}
protein.Mw = protein.Mw + modMass;
shortlistedAminoAcid.Add(aminoAcidList[hopIndex]);
shortlistedModification.Add(modificationList[hopIndex]);
shortlistedEnd.Add(endList[hopIndex]);
shortlistedStart.Add(startList[hopIndex]);
shortlistedIndex.Add(thrI);
}
}
}
else if (diff > userHopThreshold)
{
thrI = thrI + 1;
if (thrI == protein.InsilicoDetails.InsilicoMassLeft.Count - 1)
{
break;
}
continue;
}
else if (diff < -userHopThreshold)
{
hopIndex = hopIndex + 1;
if (hopIndex == startList.Count)
{
break;
}
continue;
}
hopIndex = hopIndex + 1;
if (hopIndex == startList.Count)
{
break;
}
}
}
catch (Exception exception)
{
Debug.WriteLine(exception.Message);
}
}
for (var hopIter = 0; hopIter < shortlistedStart.Count; hopIter++)
{
var site = new PostTranslationModificationsSiteDto
{
Index = shortlistedIndex[hopIter],
ModName = shortlistedModification[hopIter],
ModWeight = AminoAcids.ModificationTable(shortlistedModification[hopIter]),
Site = Convert.ToChar(shortlistedAminoAcid[hopIter])
};
protein.PtmParticulars.Add(site);
}
var massError = Math.Abs(molW - protein.Mw);
protein.MwScore = Math.Abs(massError) < 0 ? 1 : Math.Pow(massError, 0.5);
}
stopwatch.Stop();
Console.WriteLine("Shortlisting :" + stopwatch.Elapsed);
}
