public static SymbolReader Create(PdbReaderOptions options, Metadata metadata, byte[] pdbData)
{
var pdbContext = new PdbReaderContext(metadata.PEImage, options);
if (!pdbContext.HasDebugInfo)
{
return(null);
}
return(CreateCore(pdbContext, metadata, ByteArrayDataReaderFactory.Create(pdbData, filename: null)));
}
public static SymbolReader Create(PdbReaderOptions options, Metadata metadata, string pdbFileName)
{
var pdbContext = new PdbReaderContext(metadata.PEImage, options);
if (!pdbContext.HasDebugInfo)
{
return(null);
}
return(CreateCore(pdbContext, metadata, DataReaderFactoryUtils.TryCreateDataReaderFactory(pdbFileName)));
}
public static SymbolReader TryCreateEmbeddedPdbReader(PdbReaderOptions options, Metadata metadata)
{
var pdbContext = new PdbReaderContext(metadata.PEImage, options);
if (!pdbContext.HasDebugInfo)
{
return(null);
}
return(TryCreateEmbeddedPortablePdbReader(pdbContext, metadata));
}
static ISymUnmanagedReader CreateSymUnmanagedReader(PdbReaderOptions options)
{
bool useDiaSymReader = (options & PdbReaderOptions.NoDiaSymReader) == 0;
bool useOldDiaSymReader = (options & PdbReaderOptions.NoOldDiaSymReader) == 0;
if (useDiaSymReader && canTry_Microsoft_DiaSymReader_Native)
{
try {
var guid = CLSID_CorSymReader_SxS;
object symReaderObj;
var machine = ProcessorArchUtils.GetProcessCpuArchitecture();
switch (machine)
{
case Machine.AMD64:
CreateSymReader_x64(ref guid, out symReaderObj);
break;
case Machine.I386:
CreateSymReader_x86(ref guid, out symReaderObj);
break;
case Machine.ARMNT:
CreateSymReader_arm(ref guid, out symReaderObj);
break;
case Machine.ARM64:
CreateSymReader_arm64(ref guid, out symReaderObj);
break;
default:
Debug.Fail($"Microsoft.DiaSymReader.Native doesn't support this CPU arch: {machine}");
symReaderObj = null;
break;
}
if (symReaderObj is ISymUnmanagedReader symReader)
{
return(symReader);
}
}
catch (DllNotFoundException) {
Debug.WriteLine("Microsoft.DiaSymReader.Native not found, using diasymreader.dll instead");
}
catch {
}
canTry_Microsoft_DiaSymReader_Native = false;
}
if (useOldDiaSymReader)
{
return((ISymUnmanagedReader)Activator.CreateInstance(CorSymReader_Type ??= Type.GetTypeFromCLSID(CLSID_CorSymReader_SxS)));
}
return(null);
}
public static SymbolReader CreateFromAssemblyFile(PdbReaderOptions options, Metadata metadata, string assemblyFileName)
{
var pdbContext = new PdbReaderContext(metadata.PEImage, options);
if (!pdbContext.HasDebugInfo)
{
return(null);
}
if (!pdbContext.TryGetCodeViewData(out var guid, out uint age, out var pdbWindowsFilename))
{
return(null);
}
string pdbFilename;
int index = pdbWindowsFilename.LastIndexOfAny(windowsPathSepChars);
if (index >= 0)
{
pdbFilename = pdbWindowsFilename.Substring(index + 1);
}
else
{
pdbFilename = pdbWindowsFilename;
}
string fileToCheck;
try {
fileToCheck = assemblyFileName == string.Empty ? pdbFilename : Path.Combine(Path.GetDirectoryName(assemblyFileName), pdbFilename);
if (!File.Exists(fileToCheck))
{
var ext = Path.GetExtension(pdbFilename);
if (string.IsNullOrEmpty(ext))
{
ext = "pdb";
}
fileToCheck = Path.ChangeExtension(assemblyFileName, ext);
}
}
catch (ArgumentException) {
return(null); // Invalid filename
}
return(Create(options, metadata, fileToCheck));
}
public PdbReaderContext(IPEImage peImage, PdbReaderOptions options)
{
this.peImage = peImage;
Options = options;
codeViewDebugDir = TryGetDebugDirectoryEntry(peImage, ImageDebugType.CodeView);
}
public static SymbolReader Create(PdbReaderOptions options, Metadata metadata, DataReaderFactory pdbStream)
{
var pdbContext = new PdbReaderContext(metadata.PEImage, options);
return(CreateCore(pdbContext, metadata, pdbStream));
}
public void ExtractAndAnnotateHelixSequences()
{
var directory = @"G:\Projects\HumanGenome\Protein-PDBs\HumanProteins\SingleChain\FullyPositioned\ByProtein";
var outputFilePath = @"G:\Projects\HumanGenome\Protein-PDBs\HumanProteins\humanFullyPositionedSingleChainUniqueProteinHelixMarked.txt";
var pdbLookupFiles = Directory.EnumerateFiles(directory, "*.csv");
var pdbReaderOptions = new PdbReaderOptions {
MaximumModelCount = 1, BuildMolecule = false
};
var outputLock = new object();
File.Delete(outputFilePath);
Parallel.ForEach(pdbLookupFiles, pdbLookupFile =>
{
var pdbFilePaths = File.ReadAllLines(pdbLookupFile);
var proteinOutput = new List <string>();
var maxProteinAminoAcidCount = 0;
foreach (var pdbFilePath in pdbFilePaths)
{
try
{
var pdbResult = PdbReader.ReadFile(pdbFilePath, pdbReaderOptions);
if (!pdbResult.Models.Any())
{
return;
}
var firstModel = pdbResult.Models.First();
if (!firstModel.Chains.Any())
{
return;
}
var hasHelixAnnotations = firstModel.Chains
.SelectMany(chain => chain.Annotations)
.Any(annotation => annotation.Type == PeptideSecondaryStructure.AlphaHelix);
if (!hasHelixAnnotations)
{
return;
}
var aminoAcidCount = firstModel.Chains.Sum(chain => chain.AminoAcids.Count);
if (aminoAcidCount <= maxProteinAminoAcidCount)
{
return;
}
proteinOutput.Clear();
proteinOutput.Add("#" + Path.GetFileNameWithoutExtension(pdbFilePath));
foreach (var chain in pdbResult.Models.First().Chains)
{
var helixAnnotations = chain.Annotations.Where(annot => annot.Type == PeptideSecondaryStructure.AlphaHelix).ToList();
var fullSequence = AlphaHelixAnnotationTool.GetFullSequence(chain, helixAnnotations);
//var helixSequence = AlphaHelixAnnotationTool.GetHelixSequences(helixAnnotations);
proteinOutput.Add(fullSequence);
}
maxProteinAminoAcidCount = aminoAcidCount;
}
catch (Exception e)
{
var errorMessage = $"Exception: {e.Message}(Path: {pdbFilePath})";
Console.WriteLine(errorMessage);
File.AppendAllLines(@"C:\Temp\errors.txt", new [] { errorMessage });
}
}
lock (outputLock)
{
File.AppendAllLines(outputFilePath, proteinOutput);
}
});
}
