potential terms restraining atomic positional RMSD.

restrains the position of selected atoms relative to those in other
members of an <m ensembleSimulation>.EnsembleSimulation. 

Constructor:

  It is suggested that this potential term be created using the helper 
  functions <m posRMSDPotTools>.create_BFactorPot() or
  <m ncsPot>.NCSPot().


  PosRMSDPot(instanceName,
	     restraints="",
	     simulation)  - creates a potential term with the given name. 
		         restraints is an optional string of restraints.
                         simulation should specify the appropriate 
                         EnsembleSimulation (default: currentSimulation)
  
Methods:



  calcEnergy()                    - calcs energy
  calcEnergyAndDerivs(DerivList)  - calcs energy and derivative info
    note that these routines also update all other potential-specific data.

  addRestraints(restraints) - add restraints in the given string.


  rms()                      - report rmsd value for this potential term.
  numRestraints()            - report number of restraints defined for this 
                               term.
  violations()               - report number of violations for this term.

  info()                     - return a string giving summary info for this
			     - term.

  showRestraints(violated)   - return a string listing restraints. If the 
			       boolean violated is True, only violated 
			       restraints are included, else all restraints are
			       listed.
  showViolations()           - return a string listing violated restraints.
  showPositions()            - return a string containing atom position info.

  restraints()               - return a list of restraints.

Read-Write accessors:
  scale         - scale factor for potential
  potType       - potential type: 'harmonic' or 'square' [default: harmonic]
  threshold     - tolerance for violation determination.
  centerSel     - selection specifying qc. If it is empty, distances are 
		  measured with respect to the origin.
  rmsdType      - string: either "bfactor" or "rap" [default: "bfactor"]
  showAllRestraints - boolean which changes the behavior of showViolations. If 
                      this parameter is set to True, the behavior of
		      showViolations is modified such that all restraints are
      	              printed. Violated restraints are indicated by an
                      asterisk in the first column. [0]

The restraint class terms have the follow members

  pot           - the owning potential term.
  calcd         - the most recent calculated value.
  obs           - the observed value. 
  diff          - for rmsdType='rap':
		      diff = calcd
                  for rmsdType='bfactor':
                      sqrt of V term.
                  see below.
  obsErr        - estimated error in obs 
		  (obsErrB   for rmsdType=='bfactor'
		   obsErrRAP for rmsdType=='rap'    )
  
  AtomSel sel   - <m atomSel>.AtomSel associated with the restraint.

  avePos        - list of average atomic positions in each ensemble member.
  rmsd2_contrib - list of rsmd2 contributions from each ensemble member.


The potential term is defined as

  E = scale() * V

   where 
     for rmsdType='rap':
        V = calcd
     for rmsdType='bfactor':
        V = Vsq(calcd-obs,obsErrB)
     
where,
  q_{i,j} is the position of atom j in ensemble member i
  qAve_j is the ensemble-averaged position of atom j
  calcd = const sum_i w_i * rmsd2_contrib[i]
   where 
     for rmsdType='rap':
        const = 1
     for rmsdType='bfactor':
        const = 8*pi^2
  

  rmsd2_contrib[i] = Vsq( | (q_ij-qc) - (qAve_j-qc) | , obsErrRAP)


and
  Vsq(x,tol) = x^2             if potType=='harmonic'
               (abs(x)-tol)^2  if potType=='square'