princelab/msplinter

# Add rules to these two variables as needed
#Rule_names << :rule_names
#Rearrangements << :any_rule_names_that_are_just_rearrangements
require_relative "../fragmentable"

module Rubabel
  class Molecule
    module Fragmentable
      ::Rule_names << def phosphate_attack_on_ester_carbon(only_uniqs = true)
        # Create a fragmentation block method
        fragment_sets = []
        fragment = lambda do |leaving_oxygen, attacked_carbon, anionic_oxygen|
          # Duplication and mapping identity to new atoms
          nmol = self.dup
          leaving_group_oxygen = nmol.atom(leaving_oxygen.id)
          product_carbon_to_link = nmol.atom(attacked_carbon.id)
          attacking_oxygen = nmol.atom(anionic_oxygen.id)
          #1
          nmol.delete_bond(leaving_group_oxygen, product_carbon_to_link)
          #2
          attacking_oxygen.charge=0
          #3
          leaving_group_oxygen.charge=-1
          #4
          nmol.add_bond!(product_carbon_to_link, attacking_oxygen)
          nmol.split
        end

        # Call the block on any search strings which make sense in the context of the code
        self.matches("[CX3](=[OX1])[OX2]CCCO-P(=[OX1])[O-]", only_uniqs).each do |arr|
          fragment_sets << fragment.call(arr[2], arr[3], arr.last)
        end
        self.matches("[CX3](=[OX1])[OX2]CCO-P(=[OX1])[O-]" , only_uniqs).each do |arr|
          fragment_sets << fragment.call(arr[2], arr[3], arr.last)
        end
        fragment_sets
      end
      ::Rearrangements << ::Rule_names.last
    end # Fragmentable
  end # Molecule
end #Rubabel