bioroebe 0.12.24 → 0.13.31

data/lib/bioroebe/constants/files_and_directories.rb

@@ -1,606 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/constants/files_and_directories.rb'
-# Bioroebe.load_and_return_the_restriction_enzymes
-# Bioroebe.blosum_directory?
-# =========================================================================== #
-module Bioroebe
-
-  require 'bioroebe/project/project.rb'
-  require 'bioroebe/requires/require_yaml.rb'
-
-  # ========================================================================= #
-  # === FILE_HYDROPATHY_TABLE
-  # ========================================================================= #
-  FILE_HYDROPATHY_TABLE =
-    "#{BIOROEBE_YAML_AMINOACIDS_DIRECTORY}hydropathy_table.yml"
-
-  # ========================================================================= #
-  # === FILE_NUCLEAR_LOCALIZATION_SEQUENCES
-  # ========================================================================= #
-  FILE_NUCLEAR_LOCALIZATION_SEQUENCES =
-    "#{project_yaml_directory?}nuclear_localization_sequences.yml"
-
-  # ========================================================================= #
-  # === FILE_DEFAULT_COLOURS_FOR_THE_AMINOACIDS
-  # ========================================================================= #
-  FILE_DEFAULT_COLOURS_FOR_THE_AMINOACIDS =
-    "#{project_yaml_directory?}configuration/default_colours_for_the_aminoacids.yml"
-
-  # ========================================================================= #
-  # === FILE_BROWSER
-  # ========================================================================= #
-  FILE_BROWSER =
-    "#{project_yaml_directory?}configuration/browser.yml"
-
-  # ========================================================================= #
-  # === FILE_AMINOACIDS_MOLECULAR_FORMULA
-  # ========================================================================= #
-  FILE_AMINOACIDS_MOLECULAR_FORMULA =
-    "#{BIOROEBE_YAML_AMINOACIDS_DIRECTORY}amino_acids_molecular_formula.yml"
-
-  # ========================================================================= #
-  # === FILE_AMINOACIDS_THREE_TO_ONE
-  # ========================================================================= #
-  FILE_AMINOACIDS_THREE_TO_ONE = 
-    "#{BIOROEBE_YAML_AMINOACIDS_DIRECTORY}amino_acids_three_to_one.yml"
-
-  # ========================================================================= #
-  # === FILE_WEIGHT_OF_COMMON_PROTEINS
-  # ========================================================================= #
-  FILE_WEIGHT_OF_COMMON_PROTEINS = 
-    "#{BIOROEBE_YAML_AMINOACIDS_DIRECTORY}weight_of_common_proteins.yml"
-
-  # ========================================================================= #
-  # === FILE_AMINO_ACIDS_LONG_NAME_TO_ONE_LETTER
-  # ========================================================================= #
-  FILE_AMINO_ACIDS_LONG_NAME_TO_ONE_LETTER =
-    "#{BIOROEBE_YAML_AMINOACIDS_DIRECTORY}amino_acids_long_name_to_one_letter.yml"
-
-  # ========================================================================= #
-  # === FILE_AMINO_ACIDS_MOLECULAR_FORMULA
-  # ========================================================================= #
-  FILE_AMINO_ACIDS_MOLECULAR_FORMULA =
-    "#{BIOROEBE_YAML_AMINOACIDS_DIRECTORY}amino_acids_molecular_formula.yml"
-
-  # ========================================================================= #
-  # === FILE_AMINO_ACIDS_MASS_TABLE
-  #
-  #   bl $BIOROEBE_YAML/aminoacids/amino_acids_monoisotopic_mass_table.yml
-  #
-  # ========================================================================= #
-  FILE_AMINO_ACIDS_MASS_TABLE =
-    "#{BIOROEBE_YAML_AMINOACIDS_DIRECTORY}amino_acids_monoisotopic_mass_table.yml"
-
-  # ========================================================================= #
-  # === FILE_AMINO_ACIDS
-  # ========================================================================= #
-  FILE_AMINO_ACIDS =
-    "#{BIOROEBE_YAML_AMINOACIDS_DIRECTORY}amino_acids.yml"
-
-  # ========================================================================= #
-  # === Bioroebe.file_amino_acids
-  # ========================================================================= #
-  def self.file_amino_acids
-    FILE_AMINO_ACIDS
-  end
-
-  # ========================================================================= #
-  # === FILE_AMINO_ACIDS_ABBREVIATIONS
-  # ========================================================================= #
-  FILE_AMINO_ACIDS_ABBREVIATIONS =
-    "#{BIOROEBE_YAML_AMINOACIDS_DIRECTORY}amino_acids_abbreviations.yml"
-
-  # ========================================================================= #
-  # === Bioroebe.file_amino_acids_abbreviations
-  # ========================================================================= #
-  def self.file_amino_acids_abbreviations
-    FILE_AMINO_ACIDS_ABBREVIATIONS
-  end
-
-  # ========================================================================= #
-  # === AMINO_ACIDS_ABBREVIATIONS
-  # ========================================================================= #
-  if File.exist? FILE_AMINO_ACIDS_ABBREVIATIONS
-    begin
-      # $BIOROEBE/amino_acids_abbreviations.yml
-      AMINO_ACIDS_ABBREVIATIONS = YAML.load_file(FILE_AMINO_ACIDS_ABBREVIATIONS)
-    rescue Psych::SyntaxError => error
-      pp error
-      AMINO_ACIDS_ABBREVIATIONS = {}
-    end
-  end
-
-  # ========================================================================= #
-  # === DIRECTORY_CODON_TABLES_FREQUENCIES
-  #
-  # This constant may point to a directory such as:
-  #
-  #   /home/Programs/Ruby/2.7.0/lib/ruby/site_ruby/2.7.0/bioroebe/codon_tables/frequencies/
-  #
-  # ========================================================================= #
-  DIRECTORY_CODON_TABLES_FREQUENCIES =
-    "#{CODON_TABLES_DIRECTORY}frequencies/"
-
-  # ========================================================================= #
-  # === Bioroebe.directory_frequencies?
-  #
-  # Preferentially use this method past the year 2022 - it is a tiny bit
-  # more flexible than the above constant.
-  # ========================================================================= #
-  def self.directory_frequencies?(
-      codon_tables_directory = CODON_TABLES_DIRECTORY
-    )
-    "#{codon_tables_directory}frequencies/"
-  end
-
-  # ========================================================================= #
-  # === FILE_NUCLEOTIDES
-  # ========================================================================= #
-  FILE_NUCLEOTIDES =
-    "#{project_yaml_directory?}nucleotides/nucleotides.yml"
-
-  # ========================================================================= #
-  # === NUCLEOTIDES
-  # ========================================================================= #
-  if File.exist? FILE_NUCLEOTIDES
-    NUCLEOTIDES = YAML.load_file(FILE_NUCLEOTIDES)
-  else
-    NUCLEOTIDES = nil
-  end
-
-  require 'bioroebe/toplevel_methods/log_directory.rb'
-  # ========================================================================= #
-  # === Bioroebe.file_statistics?
-  #
-  # This file can normally be found here:
-  #
-  #   $BIOROEBE/yaml/statistics.yml
-  #
-  # ========================================================================= #
-  def self.file_statistics?
-    "#{Bioroebe.log_dir?}statistics.yml"
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.fasta_dir?
-  # ========================================================================= #
-  def self.fasta_dir?
-    "#{Bioroebe.log_dir?}fasta/"
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.file_fastq_quality_schemes
-  #
-  # This constant will point to a location such as this one here:
-  #
-  #   /Programs/Ruby/2.6.4/lib/ruby/site_ruby/2.6.0/bioroebe/yaml/fastq_quality_schemes.yml
-  #
-  # ========================================================================= #
-  def self.file_fastq_quality_schemes
-    "#{project_yaml_directory?}fasta_and_fastq/fastq_quality_schemes.yml"
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.file_talens
-  # ========================================================================= #
-  def self.file_talens
-    "#{project_yaml_directory?}talens.yml"
-  end
-
-  # ========================================================================= #
-  # === FILE_GFP_SEQUENCE
-  # ========================================================================= #
-  FILE_GFP_SEQUENCE = 
-    "#{project_yaml_directory?}sequences/"\
-    "JX472995_Green_fluorescent_protein_from_Aequorea_victoria.fasta"
-
-  # ========================================================================= #
-  # === FILE_RESTRICTION_ENZYMES
-  #
-  # bl $BIOROEBE/yaml/restriction/enzymes/restriction_enzymes.yml
-  # ========================================================================= #
-  FILE_RESTRICTION_ENZYMES =
-    "#{project_yaml_directory?}restriction_enzymes/restriction_enzymes.yml"
-
-  # ========================================================================= #
-  # === FILE_COLOURIZE_FASTA_SEQUENCES
-  #
-  # This constants points to the .yml file that will hold information
-  # in how to colourize the FASTA sequences.
-  # ========================================================================= #
-  FILE_COLOURIZE_FASTA_SEQUENCES =
-    "#{project_yaml_directory?}configuration/colourize_fasta_sequences.yml"
-
-  # ========================================================================= #
-  # === FILE_BLOSUM45
-  # ========================================================================= #
-  FILE_BLOSUM45 = "#{BLOSUM_DIRECTORY}/blosum45.yml"
-
-  # ========================================================================= #
-  # === FILE_BLOSUM50
-  # ========================================================================= #
-  FILE_BLOSUM50 = "#{BLOSUM_DIRECTORY}/blosum50.yml"
-
-  # ========================================================================= #
-  # === FILE_BLOSUM62
-  # ========================================================================= #
-  FILE_BLOSUM62 = "#{BLOSUM_DIRECTORY}/blosum62.yml"
-
-  # ========================================================================= #
-  # === FILE_BLOSUM80
-  # ========================================================================= #
-  FILE_BLOSUM80 = "#{BLOSUM_DIRECTORY}/blosum80.yml"
-
-  # ========================================================================= #
-  # === FILE_BLOSUM90
-  # ========================================================================= #
-  FILE_BLOSUM90 = "#{BLOSUM_DIRECTORY}/blosum90.yml"
-
-  # ========================================================================= #
-  # === BLOSUM_MATRIX
-  # ========================================================================= #
-  FILE_BLOSUM_MATRIX = "#{BLOSUM_DIRECTORY}blosum_matrix.yml"
-
-  # ========================================================================= #
-  # === Bioroebe.blosum_matrix
-  # ========================================================================= #
-  def self.blosum_matrix(i = FILE_BLOSUM_MATRIX)
-    YAML.load_file(i)
-  end
-
-  # ========================================================================= #
-  # === HYDROPATHY_TABLE
-  # ========================================================================= #
-  if File.exist? FILE_HYDROPATHY_TABLE
-    HYDROPATHY_TABLE =
-      YAML.load_file(
-        FILE_HYDROPATHY_TABLE
-      )
-  end
-
-  # ========================================================================= #
-  # === FILE_CHROMOSOME_NUMBERS
-  # ========================================================================= #
-  FILE_CHROMOSOME_NUMBERS =
-    "#{project_yaml_directory?}chromosomes/chromosome_numbers.yml"
-
-  # ========================================================================= #
-  # === FILE_AMINO_ACIDS_FREQUENCY
-  # ========================================================================= #
-  FILE_AMINO_ACIDS_FREQUENCY =
-    "#{BIOROEBE_YAML_AMINOACIDS_DIRECTORY}amino_acids_frequency.yml"
-
-  # ========================================================================= #
-  # === Bioroebe.file_amino_acids_frequency
-  # ========================================================================= #
-  def self.file_amino_acids_frequency
-    "#{BIOROEBE_YAML_AMINOACIDS_DIRECTORY}amino_acids_frequency.yml"
-  end
-
-  # ========================================================================= #
-  # === FILE_AMINO_ACIDS_RESTE_YAML
-  # ========================================================================= #
-  FILE_AMINO_ACIDS_RESTE_YAML =
-    "#{BIOROEBE_YAML_AMINOACIDS_DIRECTORY}amino_acids_reste.yml"
-
-  # ========================================================================= #
-  # === FILE_AMINO_ACIDS_THREE_TO_ONE
-  #
-  # We'll keep the keys downcased.
-  #
-  #   bl $RUBY_SRC/bioroebe/lib/bioroebe/yaml/aminoacids/amino_acids_three_to_one.yml
-  #
-  # ========================================================================= #
-  FILE_AMINO_ACIDS_THREE_TO_ONE =
-    "#{BIOROEBE_YAML_AMINOACIDS_DIRECTORY}amino_acids_three_to_one.yml"
-
-  # ========================================================================= #
-  # === FILE_AMINO_ACIDS_AVERAGE_MASS_TABLE
-  #
-  # This will point to the file amino_acids_average_mass_table.yml.
-  # ========================================================================= #
-  FILE_AMINO_ACIDS_AVERAGE_MASS_TABLE =
-    "#{BIOROEBE_YAML_AMINOACIDS_DIRECTORY}amino_acids_average_mass_table.yml"
-
-  # ========================================================================= #
-  # === FILE_NUCLEOTIDES_WEIGHT
-  #
-  # The path to the file that holds the weight of the nucleotides.
-  # ========================================================================= #
-  FILE_NUCLEOTIDES_WEIGHT =
-    "#{project_yaml_directory?}nucleotides/nucleotides_weight.yml"
-
-  # ========================================================================= #
-  # === Bioroebe.load_and_return_the_restriction_enzymes
-  #
-  # This method will load, and then return the restriction enzymes that
-  # are bundled within the bioroebe-project.
-  # ========================================================================= #
-  def self.load_and_return_the_restriction_enzymes
-    YAML.load_file(FILE_RESTRICTION_ENZYMES)
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.file_restriction_enzymes
-  # ========================================================================= #
-  def self.file_restriction_enzymes
-    FILE_RESTRICTION_ENZYMES
-  end
-
-  # ========================================================================= #
-  # === file_restriction_enzymes
-  # ========================================================================= #
-  def file_restriction_enzymes
-    ::Bioroebe.file_restriction_enzymes
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.blosum_directory?
-  # ========================================================================= #
-  def self.blosum_directory?
-    "#{project_yaml_directory?}blosum/"
-  end
-
-  # ========================================================================= #
-  # === AMINO_ACIDS_MOLECULAR_FORMULA
-  # ========================================================================= #
-  if File.exist? FILE_AMINO_ACIDS_MOLECULAR_FORMULA
-    AMINO_ACIDS_MOLECULAR_FORMULA = YAML.load_file(
-      FILE_AMINO_ACIDS_MOLECULAR_FORMULA
-    )
-  end
-
-  # ========================================================================= #
-  # === AMINO_ACIDS_RESTE
-  # ========================================================================= #
-  if File.exist? FILE_AMINO_ACIDS_RESTE_YAML
-    hash = {}
-    begin
-      _ = YAML.load_file(FILE_AMINO_ACIDS_RESTE_YAML)
-      # ======================================================================= #
-      # As of August 2015, we will keep the keys downcased.
-      # ======================================================================= #
-      _.each_pair {|key, value|
-        key = key.dup if key.frozen?
-        key.downcase!
-        hash[key] = value
-      }
-      AMINO_ACIDS_RESTE = hash
-    rescue Psych::SyntaxError
-      AMINO_ACIDS_RESTE = {}
-    end
-  else
-    AMINO_ACIDS_RESTE = {}
-  end
-
-  # ========================================================================= #
-  # === AMINO_ACIDS_LONG_NAME_TO_ONE_LETTER
-  #
-  # Load up the dataset stored in the file
-  # amino_acids_long_name_to_one_letter.yml.
-  # ========================================================================= #
-  _ = FILE_AMINO_ACIDS_LONG_NAME_TO_ONE_LETTER
-  if File.exist? _
-    AMINO_ACIDS_LONG_NAME_TO_ONE_LETTER = YAML.load_file(_)
-  else
-    puts "No file exists at #{_}."
-  end
-
-  # ========================================================================= #
-  # === AMINO_ACIDS_MASS_TABLE
-  # ========================================================================= #
-  if File.exist? FILE_AMINO_ACIDS_MASS_TABLE # bl $BIOROEBE/yaml/amino_acids_mass_table.yml
-    AMINO_ACIDS_MASS_TABLE = YAML.load_file(FILE_AMINO_ACIDS_MASS_TABLE)
-  else # Else hardcode the AminoAcid table here. This may no longer be necessary, though.
-    AMINO_ACIDS_MASS_TABLE = {
-      'A' =>  71.03711, 'C' => 103.00919, 'D' => 115.02694,
-      'E' => 129.04259, 'F' => 147.06841, 'G' =>  57.02146,
-      'H' => 137.05891, 'I' => 113.08406, 'K' => 128.09496,
-      'L' => 113.08406, 'M' => 131.04049, 'N' => 114.04293,
-      'P' =>  97.05276, 'Q' => 128.05858, 'R' => 156.10111,
-      'S' =>  87.03203, 'T' => 101.04768, 'V' =>  99.06841,
-      'W' => 186.07931, 'Y' => 163.06333
-    }
-  end; AMINO_ACIDS_AVERAGE_MONOISOTOPIC_TABLE = AMINO_ACIDS_MASS_TABLE # An alias.
-
-
-  # ========================================================================= #
-  # Next determine some important constants.
-  # ========================================================================= #
-  if File.exist? FILE_AMINO_ACIDS
-    # ======================================================================= #
-    # === Bioroebe::AMINO_ACIDS
-    #
-    # Currently listing 21 AminoAcids from amino_acids.yml
-    #
-    #   bl $BIOROEBE/yaml/aminoacids/amino_acids.yml
-    #
-    # ======================================================================= #
-    AMINO_ACIDS = YAML.load_file(
-      FILE_AMINO_ACIDS
-    )
-    # ======================================================================= #
-    # === ::Bioroebe::AMINO_ACIDS_ENGLISH
-    # ======================================================================= #
-    FILE_AMINO_ACIDS_ENGLISH = YAML.load_file("#{BIOROEBE_YAML_AMINOACIDS_DIRECTORY}amino_acids_english.yml")
-      AMINO_ACIDS_ENGLISH = FILE_AMINO_ACIDS_ENGLISH # === AMINO_ACIDS_ENGLISH
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.aminoacids?
-  #
-  # Note that this will return a Hash that looks like this:
-  #
-  #   {"A"=>{"ala"=>"alanine", "d
-  #
-  # ========================================================================= #
-  def self.aminoacids?
-    AMINO_ACIDS
-  end
-
-  # ========================================================================= #
-  # === AMINO_ACIDS_AVERAGE_MASS_TABLE
-  #
-  # And here is the average mass table.
-  # ========================================================================= #
-  if File.exist? FILE_AMINO_ACIDS_AVERAGE_MASS_TABLE # bl $BIOROEBE/yaml/aminoacids/amino_acids_average_mass_table.yml
-    AMINO_ACIDS_AVERAGE_MASS_TABLE = YAML.load_file(FILE_AMINO_ACIDS_AVERAGE_MASS_TABLE)
-  else # Else simply hardcode the AminoAcid table here.
-    AMINO_ACIDS_AVERAGE_MASS_TABLE = {
-      'A' =>  71.0788,
-      'C' => 103.1388,
-      'D' => 115.0886,
-      'E' => 129.1155,
-      'F' => 147.1766,
-      'G' =>  57.0519,
-      'H' => 137.1411,
-      'I' => 113.1594,
-      'K' => 128.1741,
-      'L' => 113.1594,
-      'M' => 131.1926,
-      'N' => 114.1038,
-      'P' =>  97.1167,
-      'Q' => 128.1307,
-      'R' => 156.1875,
-      'S' =>  87.0782,
-      'T' => 101.1051,
-      'V' =>  99.1326,
-      'W' => 186.2132,
-      'Y' => 163.1760
-    }
-  end
-
-  # ========================================================================= #
-  # === AMINO_ACIDS_THREE_TO_ONE
-  #
-  # An "alias" to this constant exists, named AA_THREE_TO_ONE.
-  #
-  #   bl $BIOROEBE/yaml/aminoacids/amino_acids_three_to_one.yml
-  #
-  # ========================================================================= #
-  if File.exist? FILE_AMINO_ACIDS_THREE_TO_ONE
-    hash = {}
-    YAML.load_file(
-      FILE_AMINO_ACIDS_THREE_TO_ONE
-    ).each {|key, value|
-      hash[key.to_s.downcase] = value
-    }
-    AMINO_ACIDS_THREE_TO_ONE = hash
-             # AA_THREE_TO_ONE = AMINO_ACIDS_THREE_TO_ONE # Legacy pointer. Is mildly deprecated.
-             # ^^^ Disabled as of 25.03.2020. Use the longer variant instead. 
-  end
-
-  # ========================================================================= #
-  # === NUCLEAR_LOCALIZATION_SEQUENCES
-  #
-  # We must be careful and check whether it exists or not.
-  # ========================================================================= #
-  _ = FILE_NUCLEAR_LOCALIZATION_SEQUENCES
-  if File.exist? _
-    begin
-      NUCLEAR_LOCALIZATION_SEQUENCES = YAML.load_file(_)
-      # ======================================================================= #
-      # === Bioroebe::ARRAY_NLS_SEQUENCES
-      #
-      # All NLS sequences should be registered here.
-      # ======================================================================= #
-      ARRAY_NLS_SEQUENCES = NUCLEAR_LOCALIZATION_SEQUENCES.values.map {|entry|
-        entry = entry[0, entry.index(' ')] if entry.include? ' '
-        entry.delete!('[') if entry.include? '['
-        entry.delete!(']') if entry.include? ']'
-        entry
-      }
-    rescue Psych::SyntaxError => error
-      pp error
-      ARRAY_NLS_SEQUENCES = []
-    end
-  else
-    NUCLEAR_LOCALIZATION_SEQUENCES = ''
-    ARRAY_NLS_SEQUENCES = []
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.random_aminoacid?
-  #
-  # This method will return a random aminoacid.
-  #
-  # A number can be passed to this method, which specifies how many
-  # random aminoacids are to be returned, e. g. 20 as argument refers
-  # to 20 aminoacids that will be generated here.
-  #
-  # Usage example:
-  #
-  #   Bioroebe.random_aminoacid? 20 # => "UAVHYQQESWUYAOVESEIY"
-  #
-  # ========================================================================= #
-  def self.random_aminoacid?(optional_return_n_aminoacids = 1)
-    case optional_return_n_aminoacids
-    when 1
-      AMINO_ACIDS.keys.sample # This should be a bit faster.
-    else
-      optional_return_n_aminoacids.to_i.times.map {
-        AMINO_ACIDS.keys.sample
-      }.join.strip
-    end
-  end; self.instance_eval { alias random_aminoacid        random_aminoacid? } # === Bioroebe.random_aminoacid
-       self.instance_eval { alias return_random_aminoacid random_aminoacid? } # === Bioroebe.return_random_aminoacid
-
-  # ========================================================================= #
-  # === Bioroebe.return_array_of_common_aminoacids
-  # ========================================================================= #
-  def self.return_array_of_common_aminoacids
-    AMINO_ACIDS.keys - ['O'] - ['U']
-  end
-
-  # ========================================================================= #
-  # === FILE_ALU_ELEMENTS
-  # ========================================================================= #
-  # FILE_ALU_ELEMENTS =
-  #   "#{project_yaml_directory?}alu_elements.yml"
-
-  # ========================================================================= #
-  # === Bioroebe.file_molecular_weight
-  # ========================================================================= #
-  def self.file_molecular_weight
-    "#{project_yaml_directory?}aminoacids/molecular_weight.yml"
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.file_amino_acids_long_name_to_one_letter
-  #
-  # This method will return a String such as:
-  #
-  #   "/home/Programs/Ruby/3.1.2/lib/ruby/site_ruby/3.1.0/bioroebe/yaml/aminoacids/amino_acids_long_name_to_one_letter.yml"
-  #
-  # ========================================================================= #
-  def self.file_amino_acids_long_name_to_one_letter
-    "#{project_yaml_directory?}aminoacids/amino_acids_long_name_to_one_letter.yml"
-  end
-
-end
-
-if __FILE__ == $PROGRAM_NAME
-  alias e puts
-  include Bioroebe
-  e FILE_FASTQ_QUALITY_SCHEMES
-  pp NUCLEOTIDES
-  e 'Restriction enzymes can be found here: '+
-    FILE_RESTRICTION_ENZYMES
-  e FILE_HYDROPATHY_TABLE
-  pp HYDROPATHY_TABLE
-  e '='*80
-  e FILE_AMINO_ACIDS_FREQUENCY
-  e FILE_NUCLEOTIDES_WEIGHT
-  e FILE_AMINOACIDS_MOLECULAR_FORMULA
-  e FILE_AMINOACIDS_THREE_TO_ONE
-  e '='*80
-  pp AMINO_ACIDS
-  e '='*80
-  pp AMINO_ACIDS_AVERAGE_MASS_TABLE
-  e '='*80
-  pp AMINO_ACIDS_THREE_TO_ONE
-  e '='*80
-end