public Aa(IAa other, bool nTerminus, bool cTerminus)
{
_atoms = new ArraySource <IAtom>(this, other);
ResidueNumber = other.ResidueNumber;
IsNTerminus = nTerminus;
IsCTerminus = cTerminus;
AtomDefinition[] definitions = AaTable.GetAtomDefinitions(ResidueNumber, IsNTerminus, IsCTerminus);
Matrix unidentifiedAtomTransform = Matrix.Identity;
//if (TransformSetting == TransformSettings.Transform)
{
Vector3[] vLocal = new Vector3[] { definitions[N_].Xyz, definitions[CA_].Xyz, definitions[C_].Xyz };
Vector3[] vOther = new Vector3[] { other[N_].Xyz, other[CA_].Xyz, other[C_].Xyz };
unidentifiedAtomTransform = VectorMath.GetRmsdAlignmentMatrix(vLocal, false, vOther, false);
}
// Create atoms at final positions
for (int i = 0; i < definitions.Length; i++)
{
Vector3 position = Vector3.Transform(definitions[i].Xyz, unidentifiedAtomTransform);
Atom atom = new Atom(definitions[i], position);
Add(atom);
}
this[N_].Xyz = other[N_].Xyz;
this[CA_].Xyz = other[CA_].Xyz;
this[C_].Xyz = other[C_].Xyz;
this[O_].Xyz = other[O_].Xyz;
for (int i = Aa.SidechainStart_; i < other.Count; i++)
{
IAtom otherAtom = other[i];
IAtom thisAtom = this[otherAtom.Name];
if (thisAtom != null)
{
thisAtom.Xyz = otherAtom.Xyz;
}
}
// Remove parent context - this will result in atoms NOT BEING IN THE ORIGINAL LOCATION
this.Parent = null;
}
public Aa(char letter, bool nTerminus, bool cTerminus)
: this(AaTable.GetResidueTypeIndex(letter), nTerminus, cTerminus)
{
}
public Aa(string residueName, bool nTerminus, bool cTerminus)
: this(AaTable.GetResidueTypeIndex(residueName), nTerminus, cTerminus)
{
}