S^2 Order parameter potential

  allows refinement against the S2 order parameter, usually obtained
from relaxation experiments. This potential term should be used with
<m ensembleSimulation>.EnsembleSimulation calculations.

constructor:   
	OrderPot(instanceName,
	         restraints,
	         simulation)
  
  instanceName is a user-specified identifier. restraints is an optional 
  XPLOR-style restraints table- see below for details. simulation is an 
  optional <m simulation>.Simulation specification. 

methods:
  addRestraints(restraintList) - add the specified restraints- see
                                 below for details on the format. Note
                                 that this is a string and not a filename.

  calcEnergy()                 - calc energy, returns the value of energy.
  calcEnergyAndDerivs(derivs)  - calc energy, derivs, returns the energy value.


  rms()           - return the rms of calcedS2 - effS2
  numRestraints() - return the number of restraints defined for this term.
  violations()    - return number of violations
  
  info()                    - current info about the state of this instance
  showViolations()          - return a string listing violated restraints.

  restraints() - return a list of restraints. See the description of the
		 Restraint class below.
  simulation() - return the associated simulation.


 The following parameters can be set [defaults in square brackets]

  verbose   - if true, sporadically spit out info [False]
  scale	    - scale factor (force constant) [1]
  threshold - threshold in violation calculation [0]
  potType   - type of potential: "harmonic" or "square" ["harmonic"]
  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 above quantities may be retrieved using the member function form
 quantity(), while they are set using the form setQuantity(value).

assignment table:
  entries in the restraint list have the following form

      assign ( sel m  ) ( sel n  )  obsS2 error1 [error2] [! optional comment]

  the m and n selections specify the bonded atoms involved in the
  interaction. the observed value of S2 is given by
  the obsS2 argument, and the error bounds are given by error1 and
  error2.  If error2 is absent, it defaults to error1.


 The calculated order parameter is given by the equation

   calcedS2 = sum_ij w_i w_j ( 3/2 cos(dot(u_i,u_j)^2 - 1/2 )

 where w_i is the weight of ensemble member i (usually 1/Ne), and 
 u_i is the unitvector in the direction q_ni - q_mi.


 The energy function is defined as

       scale * rscale * (calcedS2 - effS2)^2

 where for potType=harmonic, effS2 = obsS2, and rscale = 1/error1^2
(if error1!=0). For potType=square, rscale=1, and 

       effS2 = calcedS2, if 
		    obsS2-error1 < calcedS2 < obsS2+error2
                = calcedS2+error1, if calcedS2 < obsS2-error1
                = calcedS2-error2, if calcedS2 > obsS2+error2

  

  Restraint class

methods:
  energy() - energy due to this restraint
    
  calcd()  - calculated value of S2.
  obs()    - observed value of S2.
  diff()   - return S2-effS2

  plusErr(), minusErr() - bounds for the square well potential

  aSel() - atomSel for atom A
  bSel() - atomSel for atom B

  comment() - return the optional comment string