public Atom(AtomDefinition definition)
{
_definition = definition;
_xyz.X = definition.X;
_xyz.Y = definition.Y;
_xyz.Z = definition.Z;
}
static void Initialize()
{
#if DEBUG
if (IsInitialized)
{
return;
}
IsInitialized = true;
#endif
string json = File.ReadAllText(Database.Paths.Json.ResiduesPath);
JArray residues = JArray.Parse(json);
aaDefinitions_ = new AaDefinition[residues.Count, 2, 2];
atomDefinitions_ = new AtomDefinition[residues.Count, 2, 2][];
residueClassNumberToLetter_ = new char[residues.Count];
AaCount = residues.Count;
// index 1
for (int residueIndex = 0; residueIndex < residues.Count; residueIndex++)
{ // keep array calling convention reference: AtomQuickDefinition[] allPossibleResidueAtoms = JsonConvert.DeserializeObject<AtomQuickDefinition[]>((residues.ElementAt(i)["atoms"].ToString()));
AaDefinition residue = JsonConvert.DeserializeObject <AaDefinition>((residues.ElementAt(residueIndex).ToString()));
if (!residueCharToIndex_.ContainsKey(residue.Letter))
{
residueCharToIndex_[residue.Letter] = residueIndex;
}
residueClassNumberToLetter_[residueIndex] = residue.Letter;
// index 2
for (int nTerminus = 0; nTerminus <= 1; nTerminus++)
{
//index 3
Terminus nTerminusCase = nTerminus == 0 ? Terminus.NotNTerminus : Terminus.NTerminus;
for (int cTerminus = 0; cTerminus <= 1; cTerminus++)
{
// TODO: create json files for each residue class (centroid, heavy-atom, etc). will require minor changes like jagged arrays.
Terminus cTerminusCase = cTerminus == 0 ? Terminus.NotCTerminus : Terminus.CTerminus;
AtomDefinition[] subsetAtoms = residue.Atoms.Where(definition => definition.TerminusCase == Terminus.Always || definition.TerminusCase == nTerminusCase || definition.TerminusCase == cTerminusCase).ToArray();
atomDefinitions_[residueIndex, nTerminus, cTerminus] = subsetAtoms;
aaDefinitions_[residueIndex, nTerminus, cTerminus] = new AaDefinition(residue.Name, residue.Letter, subsetAtoms);
for (int i = 0; subsetAtoms != null && i < subsetAtoms.Length; i++)
{
AtomDefinition atom = subsetAtoms[i];
switch (atom.Name)
{
case "N": Debug.Assert(i == AaDefinition.IndexN); break;
case "CA": Debug.Assert(i == AaDefinition.IndexCA); break;
case "C": Debug.Assert(i == AaDefinition.IndexC); break;
case "O": Debug.Assert(i == AaDefinition.IndexO); break;
//case "H": Debug.Assert(i == ResidueQuickDefinition.IndexH); break;
}
}
}
}
residueNameToIndex_[residue.Name] = residueIndex;
}
}
public Atom(Atom other)
{
_xyz = other._xyz;
_definition = other._definition;
}
public Atom(AtomDefinition definition, Vector3 xyz)
{
_definition = definition;
Xyz = xyz;
}