structure information for a simulation


Simulations provide structure information, including atom information
and connectivity. It is generally easier to get and set this
information using the higher level <m atom>.Atom interface accessed
through the <m atomSel>.AtomSel class.

The following functions are provided:
  currentSimulation() 
    return the current Simulation

  makeCurrent(sim)
    make the specified Simulation current.

  numSimulations()
    return the current number of Simulations.
 

The following methods for the Simulation class are available

  currentSimulation() - static method returning the current active Simulation

  name() - Simulation name

  numAtoms() - number of atoms in Simulation
  numBonds() - number of bonds in Simulation

  atomByID(index)     - return an <m atom>.Atom object by its index
  bondPairByID(index) - return a pair of atom indices for bond indexed by index

  select(sel) - low level selector returns list of atom indices 
                given string sel. Use <m atomSel>.AtomSel object instead.

  kineticEnergy() - calculate kinetic energy associated with the current
                    masses, velocities.

  atomString(index) - a 19 character string unique identifier of an atom, 
                      given an atom index.

  deleteAtoms(string) - delete the atoms corresponding selected by select().
                        If this method is called after potential terms are
                        created (associated with this simulation) then an
                        exception will be raised.

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

  atomPosArr       - a CDSVector of all atom positions
  atomVelArr       - a CDSVector of all atom velocities
  atomMassArr      - a CDSVector of all atom masses

 The quantities below may be retrieved using the member function form
 quantity(index), while they are set using the form setQuantity(index,value), 
 where index is an atom index.

  atomPos
  atomVel
  atomMass
  atomFric
  atomCharge
  segmentName
  residueName
  residueNum
  atomName
  fullName