/// <summary>
/// Calculates the Root-Mean-Squared Deviation(RMSD) between the two proteins using alpha carbons.
/// The RMSD is the square root of the mean of the distance between a set of points.
/// The set of points it examines comprise the alpha carbon backbone of the proteins. This exludes the side atoms.
/// It calls Nearest(int) to populate the list that it uses to determine RMSD and sums the squared of the returned distance.
/// It divides that by the number of alpha carbons to get the mean, which is the then rooted to get the RMSD.
/// Also marks the atom pair with the greatest distance.
/// </summary>
/// <returns>The RMSD between the two proteins' alpha carbon backbone.</returns>
private double RMSD()
{
RMSDDictClear();
int count = 0;
double SumDist = 0;
for(int i = 0; i < Protein1.Count; i++)
{
if (Protein1.Atoms[i].CA)
{
double dist = Nearest(i);
SumDist += dist*dist;
count++;
}
}
m_maxDistPair = m_CAPair.Max();
return Math.Sqrt(SumDist/ count);
}
/// <summary>
/// Clears the list associated with finding RMSD. Resets the value of the ResNumPair with the greatest distance.
/// </summary>
private void RMSDDictClear()
{
m_CAPair.Clear();
m_maxDistPair = new ResNumPair();
}