original_docstring: Create a new Atom and add it to the Topology.
  
          Parameters
          ----------
          name : string
              The name of the atom to add
          element : Element
              The element of the atom to add
          residue : Residue
              The Residue to add it to
          id : string=None
              An optional identifier for the atom.  If this is omitted, an id is
              generated based on the atom index.
  
          Returns
          -------
          Atom
               the newly created Atom
          
docstring: Create a new Atom and add it to the Topology.
  Parameters
  
  name : string
  The name of the atom to add
  element : Element
  The element of the atom to add
  residue : Residue
  The Residue to add it to
  id : string=None
  An optional identifier for the atom.  If this is omitted, an id is
  generated based on the atom index.
  
  Returns
  
  Atom
  the newly created Atom
docstring_tokens: Create a new Atom and add it to the Topology . Parameters name : string The name of the atom to add element : Element The element of the atom to add residue : Residue The Residue to add it to id : string = None An optional identifier for the atom . If this is omitted an id is generated based on the atom index . Returns Atom the newly created Atom
code: def addAtom(self, name, element, residue, id=None):
          """Create a new Atom and add it to the Topology.
  
          Parameters
          ----------
          name : string
              The name of the atom to add
          element : Element
              The element of the atom to add
          residue : Residue
              The Residue to add it to
          id : string=None
              An optional identifier for the atom.  If this is omitted, an id is
              generated based on the atom index.
  
          Returns
          -------
          Atom
               the newly created Atom
          """
          if len(residue._atoms) > 0 and self._numAtoms != residue._atoms[-1].index+1:
              raise ValueError('All atoms within a residue must be contiguous')
          if id is None:
              id = str(self._numAtoms+1)
          atom = Atom(name, element, self._numAtoms, residue, id)
          self._numAtoms += 1
          residue._atoms.append(atom)
          return atom
code_tokens: def addAtom ( self , name , element , residue , id = None ) : if len ( residue . _atoms ) > 0 and self . _numAtoms != residue . _atoms [ - 1 ] . index + 1 : raise ValueError ( 'All atoms within a residue must be contiguous' ) if id is None : id = str ( self . _numAtoms + 1 ) atom = Atom ( name , element , self . _numAtoms , residue , id ) self . _numAtoms += 1 residue . _atoms . append ( atom ) return atom
short_docstring: Create a new Atom and add it to the Topology.
short_docstring_tokens: Create a new Atom and add it to the Topology .
comment: """Create a new Atom and add it to the Topology.
  
          Parameters
          ----------
          name : string
              The name of the atom to add
          element : Element
              The element of the atom to add
          residue : Residue
              The Residue to add it to
          id : string=None
              An optional identifier for the atom.  If this is omitted, an id is
              generated based on the atom index.
  
          Returns
          -------
          Atom
               the newly created Atom
          """