Atom Object

constructor:

  Atom(simulation,index)

    references the specified atom in the given simulation. Note that the
index is 0-offset, unlike XPLOR's id specifier (which is 1-offest).

The following methods return the constructor arguments:

  simulation()
  index()

The following accessor methods are defined:

  string()      - a unique descriptive string
  segmentName() 
  residueName() - residue name (e.g. 'ALA')
  atomName()    - atom name (e.g. 'HN')
  chemType()    - chemical type used for type-based parameters
  residueNum()  - residue number (note that this is an integer)
  pos()         - a <m vec3>.Vec3 describing Cartesian position
  vel()         - a Vec3 describing Cartesian velocoty
  mass()        - atomic mass
  fric()        - friction used for bath-coupling by dynamics engines
  charge()      - atomic partial charge.

The above functions get the named quantities. These quantities may be
set using functions named setQuantity(arg), where Quantiy is the
appropriate name and arg is the desired new value.

Additionally, there is the following function:
 isValid() - specifying whether the atom pos has been set.