public static ProteinStructure GetInstance(string pdbFilename)
{
List <Dictionary <int, Residue> > residues = new List <Dictionary <int, Residue> >();
string line;
int currentModel = -1;
bool onlyOneModel = false;
using (TextReader reader = Bio.Util.FileUtils.OpenTextStripComments(pdbFilename))
{
while ((line = reader.ReadLine()) != null)
{
if (line.StartsWith("MODEL"))
{
Helper.CheckCondition(!onlyOneModel, "Thought we wouldn't see any of these for this particular file.");
currentModel = int.Parse(line.Substring(10, 4).Trim());
residues.Add(new Dictionary <int, Residue>());
}
if (line.StartsWith("ATOM"))
{
if (currentModel < 0)
{
currentModel = 1;
residues.Add(new Dictionary <int, Residue>());
onlyOneModel = true;
}
Atom atom = Atom.GetInstance(line);
if (!residues[currentModel - 1].ContainsKey(atom.Position))
{
residues[currentModel - 1].Add(atom.Position, Residue.GetInstance(atom.Position, atom.ResidueName));
}
residues[currentModel - 1][atom.Position].AddAtom(atom);
}
}
}
return(new ProteinStructure(residues));
}