public static void ParseJsonInstanceSets()
{
string json = File.ReadAllText(Database.Paths.Rotamer.JsonRotamerInstances);
JArray jArray = JArray.Parse(json);
RotamerInstanceSet[] sets = new RotamerInstanceSet[jArray.Count];
for (int definitionIndex = 0; definitionIndex < jArray.Count; definitionIndex++)
{
RotamerInstanceSet set = JsonConvert.DeserializeObject <RotamerInstanceSet>((jArray.ElementAt(definitionIndex).ToString()));
sets[definitionIndex] = set;
}
sets_ = sets;
}
public static void CacheInstanceCoordinates()
{
coordinates_ = new Vector3[AaTable.AaCount][][];
for (int residueTypeIndex = 0; residueTypeIndex < AaTable.AaCount; residueTypeIndex++)
{
IAa residue = new Aa(residueTypeIndex, true, true);
RotamerInstanceSet rotamerSet = sets_.First(match => match.ResidueNames.Contains(residue.Name)); Debug.Assert(rotamerSet != null, "Residue type " + residue.Name + " was not found in rotamer_dynameomics.json");
int rotamerCount = rotamerSet.Torsions.GetLength(0);
coordinates_[residueTypeIndex] = new Vector3[rotamerCount][];
if (rotamerCount == 0)
{
continue;
}
// Record the OXT index. This is shitty [TODO - rethink], but all required atoms (N,CA,C and sidechain) come first in the ResidueQuick atom list,
// and atoms that may not exist (OXT, H, H1,H2,H3) are last in the list. This allows for caching of coordinates for just the sidechain (as necessary when
// dealing with rotamers) using a continuous list of indices in the range [0, index(OXT) - 1].
int oxtIndex = 0;
while (residue[oxtIndex].Name != "OXT")
{
oxtIndex++;
}
// Iterate rotamers belonging to this residue type
for (int rotamerIndex = 0; rotamerIndex < rotamerSet.Torsions.GetLength(0); rotamerIndex++)
{
// Create a scratch residue to work with, to prevent floating point error buildup
IAa tmp = new Aa(residue);
// Apply torsions at each chi index
for (int chiIndex = 1; chiIndex <= rotamerSet.ChiCount; chiIndex++)
{
RotamerDefinition rotamerDefinition = definitions_[residueTypeIndex]; Debug.Assert(rotamerDefinition.ResidueName == residue.Name, "JSON for rotamer definitions and residue definitions is out of sync, rotamer definition=" + rotamerDefinition.ResidueName + ", residue definition=" + residue.Name);
float torsion = rotamerSet.GetTorsionDegrees(rotamerIndex, chiIndex);
SetChiAngleDegrees(tmp, chiIndex, torsion);
//SetChiAngleDegrees(tmp, torsion, rotamerDefinition.GetBackboneAtomNames(chiIndex), rotamerDefinition.GetDependentAtomNames(chiIndex));
}
// Cache the final coordinates
coordinates_[residueTypeIndex][rotamerIndex] = new Vector3[oxtIndex];
for (int atomIndex = 0; atomIndex < oxtIndex; atomIndex++)
{
coordinates_[residueTypeIndex][rotamerIndex][atomIndex] = tmp[atomIndex].Xyz;
}
}
}
}
