Potential term restraining atomic positions relative to those in a
similar structure. This term is similar to the (nonstrict) NCS XPLOR
energy term, but there is no need that the equivalent pairs of atoms
have the same atom name, have the same residue name, or even be of the
same number.


Constructor:

  It is suggested that this potential term be created using the helper 
  function <m posSymmPotTools>.create_PosSymmPot().


  PosSymmPot(instanceName)  - creates a potential term with the given name. 
  
Methods:

  calcEnergy()                    - calcs energy
  calcEnergyAndDerivs(DerivList)  - calcs energy and derivative info
  
  
  addEquivAtomSelPair(atomSel1,
                      atomSel2)    - specify a pair of <m atomSel>.AtomSels, 
                                     the centroids of which will be restrained
                                     to have the same relative position.
  equivAtomSelPairs()              - return a list containing the current
                                     set of AtomSel pairs.
  removeEquivAtomSelPair(atomSel1,
                         atomSel2) - remove the specified pair.

  addEquivAtomPair(atomSel1,
                   atomSel2)       - specify a pair of <m atom>.Atoms,
				     whose positions will be restrained
                                     to have the same relative position.
  equivAtomPairs()                 - return a list containing the current
                                     set of Atom pairs.
  removeEquivAtomPair(atomSel1,
                      atomSel2)   - remove the specified pair.

  rms()                           - returns the best-fit RMSD between the two
                                    selection sets.
  violations()                    - returns 0 if upperBound > rms > lowerBound,
                                    1 otherwise.
  
  individualRMSDs()               - returns a list containg the distances
                                    between each equivalent pair after 
                                    best-fitting

  rotMat()                        - returns the rotation matrix which best-
                                    fits the two selection sets translated
                                    to the origin.

  centroid(whichOne)              - returns the centroid position of each
                                    selection set, specified by whichOne
			            (either 0 or 1).

  translatedCoords(whichOne)      - returns a sequence of <m vec3>.Vec3s
                                    which represent the positions of the 
                                    specified selection set (by whichOne - 
                                    either 0 or 1).



 Read-Write accessors:
  scale           - scale factor for the potential term.
  lowerBound      - see below. If lowerBound>0, equivalent pairs
                    will be forced apart [default: 0].
  upperBound      - see below. This specifies the rmsd amount the equivalent 
                    pairs are allowed to differ [default: 0].

 the above quantities may be retrieved using the member function form
 quantity(), while they are set using the form setQuantity(value).

The potential term is defined as

  E = scale() * dRMSD^2

with

          / rmsd - upperBound, if rmsd > upperBound
  dRMSD = | rmsd - lowerBound, if rmsd < lowerBound
          \ 0                , if rmsd < upperBound and rmsd > lowerBound

and

  rmsd^2 =  1/Ni sum_i |(q_1i-q_1c) - R(q_2i-q_2c)|^2

where q_1i and q_2i are the average position of the ith respective
equivalent pair, and the sum is over all pairs, and Ni is the number of
equivalent pairs. R is the rotation matrix which minimizes rmsd2.

q_1c and q_2c are the average positions of the equivalent pair
positions, e.g.

  q_1c = 1/N1 * sum_i q_1i.