#   In this example, we define two types of molecules: "H" and "P",
#   both containing two atoms, named "CA" and "R".
#
#                @R 
#                 | 
#                @CA
#
#   Eventually, we will connect multiple "H" and "P" molecules
#   together to form a polymer, as shown below:
#
#                @R           @R       
#                 |           |        
#               _@CA_       _@CA_      
#   ...  -.@CA-'     `-@CA-'     `  ... 
#           |          |               
#          @R          @R              
#
#   Suppose that the "H" and "P" molecules both use the same 
#   type of backbone atom ("CA"), but have their own custom "R" 
#   sidechain atoms with different properties:
#   The "R" atoms belonging to "H" molecules are attracted to each other.
#   The "R" atoms in "P" molecules are not.
#
# (Note: There is no reason the "H" and "P" molecules in this example need 
#        to contain the same number of atoms, or the same atom names.
#        The point of this example is to illustrate how to share atom types
#        and also the difference between local and global atom types.)
# 
# By default, all counter variables are local.  This means that whenever
# an atom type (or other counter variable) appears inside a molecule 
# definition using the normal syntax "@atom:R", that atom type is a local 
# property of the the "H" or "P" molecule in which it appears.
# Any properties assigned to the "R" atoms in either molecule are unique
# to that molecule.
#
# However in order to share "CA" atom types, we will override this behavior
# using the "@atom:../CA" syntax instead of "@atom:CA".  This will define 
# the "CA" atom in the outer (global) environment, and any properties 
# (mass, radius, etc...) assigned to the "@atom:../CA" atom apply to 
# "CA" atoms in both the the "H" and "P" molecules (and everywhere else).
#
#    This might not be a desirable.  "CA" is a popular name for carbon 
# atoms in different types of molecules.  We don't want to prevent other 
# molecules from using this atom name.  So we enclose the "CA" atom,
# (along with the definitions of the "H" and "P" molecules) within a 
# namespace/environment object ("2bead").  This makes the definition 
# of "H" and "P" more portable.  Later on we can combine "H" and "P" 
# molecules with other molecules without worrying whether they contain 
# "CA" atoms with different properties.
#
# Note: In this example "2bead" is NOT a molecule.  (Because it contains no
#       "write("Data Atoms")" section of its own.)  "2bead" is simply the 
#       name of an environment in which other molecules "H" and "P" are defined.




2bead {

  write_once("In Init") {
    units           real
    atom_style      full
  }

  # Define H (the "hydrophobic" residue)
  H {
    # atom-id  mol-id   atom-type  charge  x     y        z
    write("Data Atoms") {
      $atom:CA $mol:... @atom:../CA 0.0  0.000  1.0000   0.0000000
      $atom:R  $mol:... @atom:R     0.0  0.000  4.4000   0.0000000
    }

    # Old Data Bonds style
    # write("Data Bonds") {
    #   $bond:CR  @bond:../sidechain  $atom:CA $atom:R
    # }

    # New Data Bond List style
    write("Data Bond List") {
      $bond:CR $atom:CA $atom:R
    }
  }


  # Define P (the "polar" residue)
  P {
    # atom-id  mol-id   atom-type  charge  x     y        z
    write("Data Atoms") {
      $atom:CA $mol:... @atom:../CA 0.0  0.000  1.0000   0.0000000
      $atom:R  $mol:... @atom:R     0.0  0.000  4.4000   0.0000000
    }

    # Old Data Bonds style
    # write("Data Bonds") {
    #   $bond:CR  @bond:../sidechain  $atom:CA $atom:R
    # }

    # New Data Bond List style
    write("Data Bond List") {
      $bond:CR $atom:CA $atom:R
    }
  }


  # (Note: Again, atom types, bond-types, (dihedral-types, any variable, etc) 
  #        can be shared.  The ".." in "@atom:../CA" tells moltemplate that 
  #        atom type CA is defined in the parent's environment. (We are 
  #        sharing the CA atom type between both the H and P residues.
  #        The same is true of the ".." in "@bond:../sidechain".
  #        
  #
  #  Note: The "..." in "$mol:..." tells moltemplate that this molecule may
  #        be a part of a larger molecule, and (if so) to use the larger
  #        molecule's id number as it's own.



  # There are 3 atom types: the R sidechain (belonging to the H and P residues)
  #                         and the CA sidechain atom (shared by both residues)

  write_once("Data Masses") {
    @atom:CA   13.0
    @atom:H/R  50.0
    @atom:P/R  50.0
  }

} # 2bead