public static void SetChiAngleRadians(IAa residue, int chiIndex, float radians)
{
RotamerDefinition rotamerDefinition = definitions_[residue.ResidueNumber]; 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);
List <string> torsionBackboneNames = rotamerDefinition.GetBackboneAtomNames(chiIndex);
List <string> dependentNames = rotamerDefinition.GetDependentAtomNames(chiIndex);
Debug.Assert(dependentNames.Contains(torsionBackboneNames[3]), "The last atom that defines a torsion should move when that torsion is changed. Fix JSON 'dependents' for residue '" + residue.Name + "' atom '" + torsionBackboneNames[3] + "'");
string name1 = torsionBackboneNames[0];
string name2 = torsionBackboneNames[1];
string name3 = torsionBackboneNames[2];
string name4 = torsionBackboneNames[3];
double currentTorsionRadians = VectorMath.GetDihedralAngleRadians(residue[name1].Xyz, residue[name2].Xyz, residue[name3].Xyz, residue[name4].Xyz);
double deltaDegrees = radians - currentTorsionRadians;
Vector3 coord2 = residue[name2].Xyz;
Vector3 coord3 = residue[name3].Xyz;
Vector3 axis = Vector3.Normalize(coord3 - coord2);
Quaternion rotation = Quaternion.CreateFromAxisAngle(axis, radians);
foreach (string dependentName in dependentNames)
{
IAtom atom = residue[dependentName];
atom.Xyz -= coord3;
atom.Xyz = Vector3.Transform(atom.Xyz, rotation);
atom.Xyz += coord3;
}
}
public static void ParseJsonDefinitions()
{
string json = File.ReadAllText(Database.Paths.Rotamer.JsonRotamerDefinitions);
JArray jArray = JArray.Parse(json);
RotamerDefinition[] definitions = new RotamerDefinition[jArray.Count];
for (int definitionIndex = 0; definitionIndex < jArray.Count; definitionIndex++)
{
RotamerDefinition definition = JsonConvert.DeserializeObject <RotamerDefinition>((jArray.ElementAt(definitionIndex).ToString()));
definitions[definitionIndex] = definition;
}
definitions_ = definitions;
}
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;
}
}
}
}
