private static PdbModel ConstructModel(
IList <string> modelLines,
IList <string> annotationLines,
PdbReaderOptions options)
{
var chainIds = ExtractChainIds(modelLines);
var chains = new List <Peptide>();
foreach (var chainId in chainIds)
{
try
{
var chain = ExtractChain(modelLines, annotationLines, chainId, options);
if (!chain.AminoAcids.Any())
{
continue;
}
chains.Add(chain);
}
catch (ChemistryException chemException)
{
// TODO: Log
}
catch
{
chains.ForEach(chain => chain.Dispose());
throw;
}
}
return(new PdbModel(chains.ToArray()));
}
private static Peptide ExtractChain(
IList <string> modelLines,
IList <string> annotationLines,
char chainId,
PdbReaderOptions options)
{
var aminoAcidSequence = ExtractSequence(modelLines, chainId);
if (!aminoAcidSequence.Any())
{
return(new Peptide(new MoleculeReference(new Molecule()), new List <AminoAcidReference>()));
}
var peptide = PeptideBuilder.PeptideFromSequence(aminoAcidSequence, new PeptideBuilderOptions {
BuildMolecule = options.BuildMolecule
});
peptide.ChainId = chainId;
var annotations = ExtractAnnotations(annotationLines, chainId, peptide);
peptide.Annotations.AddRange(annotations);
if (options.BuildMolecule)
{
ReadAtomPositions(modelLines, chainId, peptide);
}
return(peptide);
}
public static PdbReaderResult ReadFile(string filename, PdbReaderOptions options = null)
{
if (options == null)
{
options = new PdbReaderOptions();
}
var lines = File.ReadAllLines(filename);
var models = ExtractModels(lines, options);
return(new PdbReaderResult(models));
}
private static PdbModel[] ExtractModels(
string[] lines,
PdbReaderOptions options)
{
var annotationLines = GetAnnotationLines(lines);
var models = new List <PdbModel>();
var modelLines = new List <string>();
var modelStarted = false;
try
{
foreach (var line in lines)
{
if (!modelStarted && ReadLineCode(line).InSet("MODEL", "ATOM"))
{
modelStarted = true;
}
if (!modelStarted)
{
continue;
}
modelLines.Add(line);
if (ReadLineCode(line) == "ENDMDL")
{
models.Add(ConstructModel(modelLines, annotationLines, options));
modelStarted = false;
modelLines.Clear();
if (options.MaximumModelCount.HasValue && models.Count >= options.MaximumModelCount.Value)
{
break;
}
}
}
if (modelStarted)
{
models.Add(ConstructModel(modelLines, annotationLines, options));
}
}
catch
{
models.ForEach(model => model.Dispose());
throw;
}
return(models.ToArray());
}
