#pragma warning disable CA1810 // Initialize reference type static fields inline
static AminoAcids()
#pragma warning restore CA1810 // Initialize reference type static fields inline
{
// Create set of AtomContainers
proteinogenics = new AminoAcid[20];
#region Create proteinogenics
{
IChemFile list = new ChemFile();
using (var reader = new CMLReader(ResourceLoader.GetAsStream("NCDK.Templates.Data.list_aminoacids.cml")))
{
try
{
list = (IChemFile)reader.Read(list);
var containersList = ChemFileManipulator.GetAllAtomContainers(list);
int counter = 0;
foreach (var ac in containersList)
{
Debug.WriteLine($"Adding AA: {ac}");
// convert into an AminoAcid
var aminoAcid = new AminoAcid();
foreach (var next in ac.GetProperties().Keys)
{
Debug.WriteLine("Prop: " + next.ToString());
if (next is DictRef dictRef)
{
// Debug.WriteLine("DictRef type: " + dictRef.Type}");
if (string.Equals(dictRef.Type, "pdb:residueName", StringComparison.Ordinal))
{
aminoAcid.SetProperty(ResidueNameKey, ac.GetProperty <string>(next).ToUpperInvariant());
aminoAcid.MonomerName = ac.GetProperty <string>(next);
}
else if (string.Equals(dictRef.Type, "pdb:oneLetterCode", StringComparison.Ordinal))
{
aminoAcid.SetProperty(ResidueNameShortKey, ac.GetProperty <string>(next));
}
else if (string.Equals(dictRef.Type, "pdb:id", StringComparison.Ordinal))
{
aminoAcid.SetProperty(IdKey, ac.GetProperty <string>(next));
Debug.WriteLine($"Set AA ID to: {ac.GetProperty<string>(next)}");
}
else
{
Trace.TraceError("Cannot deal with dictRef!");
}
}
}
foreach (var atom in ac.Atoms)
{
string dictRef = atom.GetProperty <string>("org.openscience.cdk.dict");
switch (dictRef)
{
case "pdb:nTerminus":
aminoAcid.AddNTerminus(atom);
break;
case "pdb:cTerminus":
aminoAcid.AddCTerminus(atom);
break;
default:
aminoAcid.Atoms.Add(atom);
break;
}
}
foreach (var bond in ac.Bonds)
{
aminoAcid.Bonds.Add(bond);
}
AminoAcidManipulator.RemoveAcidicOxygen(aminoAcid);
aminoAcid.SetProperty(NoAtomsKey, "" + aminoAcid.Atoms.Count);
aminoAcid.SetProperty(NoBoundsKey, "" + aminoAcid.Bonds.Count);
if (counter < proteinogenics.Length)
{
proteinogenics[counter] = aminoAcid;
}
else
{
Trace.TraceError("Could not store AminoAcid! Array too short!");
}
counter++;
}
}
catch (Exception exception)
{
if (exception is CDKException | exception is IOException)
{
Trace.TraceError($"Failed reading file: {exception.Message}");
Debug.WriteLine(exception);
}
else
{
throw;
}
}
}
}
#endregion
int count = proteinogenics.Length;
singleLetterCodeMap = new Dictionary <string, IAminoAcid>(count);
threeLetterCodeMap = new Dictionary <string, IAminoAcid>(count);
singleLetterToThreeLetter = new Dictionary <string, string>(count);
threeLetterToSingleLetter = new Dictionary <string, string>(count);
foreach (IAminoAcid aa in proteinogenics)
{
var single = aa.GetProperty <string>(ResidueNameShortKey);
var three = aa.GetProperty <string>(ResidueNameKey);
singleLetterCodeMap[single] = aa;
threeLetterCodeMap[three] = aa;
singleLetterToThreeLetter[single] = three;
threeLetterToSingleLetter[three] = single;
}
}
