File asms_2002_scheme1.rb has 490 lines of code (exceeds 250 allowed). Consider refactoring.

Open

require_relative "../fragmentable"

module Rubabel
  class Molecule
    module Fragmentable

File asms_2002_scheme2.rb has 421 lines of code (exceeds 250 allowed). Consider refactoring.

Open

require_relative "../fragmentable"

#        self.write( 'root.svg', :add_atom_index => true)
module Rubabel
  class Molecule

File asms_2002_scheme3-5.rb has 412 lines of code (exceeds 250 allowed). Consider refactoring.

Open

require_relative "../fragmentable"

#        self.write( 'root.svg', :add_atom_index => true)
module Rubabel
  class Molecule

Method fragment has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

Open

      def fragment(rules: @@rules- @@rearrangements, errors: :ignore, uniq: false, rearrange: true, fragment_adduct_state: DEFAULT_OPTIONS[:fragment_adduct_state], add_rule_names: false)
        only_uniqs = true # Option is currently ignored.
        # opts = DEFAULT_OPTIONS.merge(opts)
        rules.each do |rule| 
          raise ArgumentError, "bad rule: #{rule}\nThe allowed rules are #{@@rules.entries.join(", ")}" unless @@rules.include?(rule)

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Method fragment has 46 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      def fragment(rules: @@rules- @@rearrangements, errors: :ignore, uniq: false, rearrange: true, fragment_adduct_state: DEFAULT_OPTIONS[:fragment_adduct_state], add_rule_names: false)
        only_uniqs = true # Option is currently ignored.
        # opts = DEFAULT_OPTIONS.merge(opts)
        rules.each do |rule| 
          raise ArgumentError, "bad rule: #{rule}\nThe allowed rules are #{@@rules.entries.join(", ")}" unless @@rules.include?(rule)

Method jasms_2002_scheme1_b_d1_water_loss has 35 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      ::Rearrangements << def jasms_2002_scheme1_b_d1_water_loss(only_uniqs: true, fragment_adduct_state: :as_published)
        fragment_sets = []
        fragment = lambda do |lo, lc, lh|
          #duplications and mapping
          nmol = self.dup

Method jasms_2002_scheme1_c_e2aprime_formaldehyde_loss has 34 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      ::Rule_names << def jasms_2002_scheme1_c_e2aprime_formaldehyde_loss(only_uniqs: true, fragment_adduct_state: :as_published)
        fragment_sets = []
        fragment = lambda do |*arr|
          #duplications and mapping
          (nmol,(carbon1, carbon2, oxygen, carbon3)) = self.dup_molecule(arr)

Method jasms_2002_scheme1_c_e1aprime has 34 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      ::Rule_names << def jasms_2002_scheme1_c_e1aprime(only_uniqs: true, fragment_adduct_state: :as_published)
        fragment_sets = []
        fragment = lambda do |co, c1, c3, lo, n|
          #duplications and mapping
          nmol = self.dup

Method jasms_2002_scheme1_c_e1bprime has 32 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      ::Rule_names << def jasms_2002_scheme1_c_e1bprime(only_uniqs: true, fragment_adduct_state: :as_published)
        fragment_sets = []
        fragment = lambda do |n, c2, lo|
          #duplications and mapping
          nmol = self.dup

Method jasms_2002_scheme1_c_e1b_to_d1bprime has 32 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      ::Rule_names << def jasms_2002_scheme1_c_e1b_to_d1bprime(only_uniqs: true, fragment_adduct_state: :as_published)
        fragment_sets = []
        fragment = lambda do |co, c, n|
          #duplications and mapping
          nmol = self.dup

Method jasms_2002_scheme1_c_e1 has 32 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      ::Rule_names << def jasms_2002_scheme1_c_e1(only_uniqs: true, fragment_adduct_state: :as_published)
        fragment_sets = []
        fragment = lambda do |n, cc, o, tbvc|
          #duplications and mapping
          nmol = self.dup

Method jasms_2002_scheme1_a_c1 has 31 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      ::Rule_names << def jasms_2002_scheme1_a_c1(only_uniqs: true, fragment_adduct_state: :as_published)
        # Create a fragmentation block method
        fragment_sets = []
        fragment = lambda do |tbcc, o, lc|
          # Duplication and mapping identity to new atoms

Method jasms_2002_2_e2_b_formaldehyde_loss has 31 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      ::Rule_names << def jasms_2002_2_e2_b_formaldehyde_loss(only_uniqs: true, fragment_adduct_state: :as_published)
        fragment_sets = []
        fragment = lambda do |*arr|
          # duplicate
          (nmol, (nitrogen, c1, c2, ester_oxygen, c3)) = self.dup_molecule(arr)

Method jasms_2002_5_e5_formaldehyde_loss has 31 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      ::Rule_names << def jasms_2002_5_e5_formaldehyde_loss(only_uniqs: true, fragment_adduct_state: :as_published)
        fragment_sets = []
        fragment = lambda do |*arr|
          # duplicate
          (nmol, (nitrogen, ring_carbon, lost_carbon, lost_oxygen, ring_carbon2)) = self.dup_molecule(arr)

Method jasms_2002_scheme1_b_d1 has 31 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      ::Rule_names << def jasms_2002_scheme1_b_d1(only_uniqs: true, fragment_adduct_state: :as_published)
        fragment_sets = []
        fragment = lambda do |n, tcc, o|
          #duplications and mapping
          nmol = self.dup

Method jasms_2002_2_f2_b_methoxy_loss has 31 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      ::Rearrangements << def jasms_2002_2_f2_b_methoxy_loss(only_uniqs: true, fragment_adduct_state: :as_published)
        fragment_sets = []
        fragment = lambda do |*arr|
          # duplicate
          (nmol, (c1, lost_carbon, oxygen, c2)) = self.dup_molecule(arr)

Method jasms_2002_2_e1 has 31 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      ::Rule_names << def jasms_2002_2_e1(only_uniqs: true, fragment_adduct_state: :as_published)
        fragment_sets = []
        fragment = lambda do |*arr|
          # duplicate
          (nmol, (nitrogen, carbonyl_carbon, carbonyl_oxygen, alcohol_carbon, alcohol_oxygen)) = self.dup_molecule(arr)

Method jasms_2002_scheme1_b_d1_formaldehyde_loss has 31 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      ::Rearrangements << def jasms_2002_scheme1_b_d1_formaldehyde_loss(only_uniqs: true, fragment_adduct_state: :as_published)
        fragment_sets = []
        fragment = lambda do |tco, leavingc, leftc|
          #duplications and mapping
          nmol = self.dup

Method jasms_2002_scheme1_c_e1_aprimeprime_formaldehyde_loss has 31 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      ::Rearrangements << def jasms_2002_scheme1_c_e1_aprimeprime_formaldehyde_loss(only_uniqs: true, fragment_adduct_state: :as_published)
        fragment_sets = []
        fragment = lambda do |*arr|
          #duplications and mapping
          (nmol,(cyclized_oxygen, freed_carbon, carbon_linked_to_nitrogen, carbon_linker, nitrogen)) = self.dup_molecule(arr)

Method jasms_2002_4_g2a_formaldehyde_loss has 30 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      ::Rule_names << def jasms_2002_4_g2a_formaldehyde_loss(only_uniqs: true, fragment_adduct_state: :as_published)
        fragment_sets = []
        fragment = lambda do |*arr|
          # duplicate
          (nmol, (ring_carbon, ring_oxygen, c3, link_carbon)) = self.dup_molecule(arr)