Created alpharmsd collective variable. Input for this variable is done

in terms of the residues for the chains for which one wishes to calculate the distances
from the alpha helical secondary structure.  For these reasons I had to adjust the PDB
parser so that it reads in atom symbol, resdiue and chainID data.  I then I have an
ActionSetup class (MolInfo) that can read and store the data on the various chains inside the
pdb file.  I have that you can calculate the distances from the secondary structure using either
DRMSD (like plumed 1.0) or using Davide's RMSD class.  This required a very small change to Davide's
RMSD class.