# Define the "CH2" and "CH3" objects:

import "ch2group.lt"
import "ch3group.lt"



Hexadecane inherits Alkanes {

  # Create an array of 16 "CH2" objects

  monomers = new CH2.move(0,0.4431163,0) [16].rot(180,1,0,0).move(1.2533223,0,0)

  # "monomers" is a 1-dimensional array containing 16 copies of the CH2 molecule
  # Each copy is rotated 180 degrees and shifted along the x axix.
  # (For an explanation, read sections 7.1-7.3 of the moltemplate manual.)
  # Notes:
  #   1.2533223 = DeltaXc   = how far each CH2 group is shifted along the axis
  #   0.4431163 = DeltaYc/2 = lateral displacement of carbons along axis

  # ---- Now, modify the ends: ---
  # Delete the CH2 groups at the beginning and end, and replace them with CH3.
  # (Note: Alternately, instead of deleting the CH2 groups at each end, you 
  #        could modify them by adding an extra hydrogen atom to those carbons.)

  delete monomers[0]
  delete monomers[15]
  monomer_begin = new CH3
  monomer_end   = new CH3

  # Move the CH3 groups to the correct location at either end of the chain:

  monomer_begin.move(0,0.4431163,0)
  monomer_end.move(0,0.4431163,0).rot(180,0,0,1).move(18.7998345,0,0)

  # Note: 18.7998345 = (16-1) * DeltaXc


  # Now add a list of bonds connecting the carbon atoms together:

  write('Data Bonds') {
    $bond:b1 @bond:CC  $atom:monomer_begin/C $atom:monomers[1]/C
    $bond:b2 @bond:CC  $atom:monomers[1]/C $atom:monomers[2]/C
    $bond:b3 @bond:CC  $atom:monomers[2]/C $atom:monomers[3]/C
    $bond:b4 @bond:CC  $atom:monomers[3]/C $atom:monomers[4]/C
    $bond:b5 @bond:CC  $atom:monomers[4]/C $atom:monomers[5]/C
    $bond:b6 @bond:CC  $atom:monomers[5]/C $atom:monomers[6]/C
    $bond:b7 @bond:CC  $atom:monomers[6]/C $atom:monomers[7]/C
    $bond:b8 @bond:CC  $atom:monomers[7]/C $atom:monomers[8]/C
    $bond:b9  @bond:CC  $atom:monomers[8]/C  $atom:monomers[9]/C
    $bond:b10 @bond:CC  $atom:monomers[9]/C  $atom:monomers[10]/C
    $bond:b11 @bond:CC  $atom:monomers[10]/C  $atom:monomers[11]/C
    $bond:b12 @bond:CC  $atom:monomers[11]/C  $atom:monomers[12]/C
    $bond:b13 @bond:CC  $atom:monomers[12]/C  $atom:monomers[13]/C
    $bond:b14 @bond:CC  $atom:monomers[13]/C  $atom:monomers[14]/C
    $bond:b15 @bond:CC  $atom:monomers[14]/C $atom:monomer_end/C
  }

  create_var { $mol }  # Define a molecule ID number for this polymer

  # This causes monomer[0], monomer[1], ... to share the same molecule-ID.
  # (because in the ch2group.lt file, the "..." in "$mol:..." looks for
  #  a counter of type "$mol" in a parent molecule or earlier ancestor.)

} # Hexadecane










######### (scratchwork calculations for the atomic coordinates) #########
# Lcc = 1.5350 # length of the C-C bond (Sp3)
# Lch = 1.0930 # length of the C-H bond
# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle)
# DeltaXc = Lcc*sin(theta/2)  # = 1.2533222517240594
# DeltaYc = Lcc*cos(theta/2)  # = 0.8862326632060754
#                             # 0.5*DeltaYc = 0.4431163316030377
# DeltaZh = Lch*sin(theta/2)  # = 0.8924307629540046
# DeltaYh = Lch*cos(theta/2)  # = 0.6310438442242609