chemistry_paradise 1.3.1

data/lib/chemistry_paradise/split_molecule_names.rb

@@ -0,0 +1,228 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === ChemistryParadise::SplitMoleculeNames
+#
+# Input to this class here can be something like 'C12H11O11'. See the
+# bottom of this file to find out what can be done.
+#
+# Do not input the charge of the molecule in question.
+# =========================================================================== #
+# require 'chemistry_paradise/split_molecule_names.rb'
+# =========================================================================== #
+require 'chemistry_paradise/base/base.rb'
+
+module ChemistryParadise
+
+class SplitMoleculeNames < ::ChemistryParadise::Base
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      i = 'C12H11O11'
+    )
+    reset
+    set_input(i)
+    split # This is the actual run method.
+  end
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  def reset
+    super()
+    # ======================================================================= #
+    # === @result
+    # ======================================================================= #
+    @result = []
+    # ======================================================================= #
+    # === @total
+    # ======================================================================= #
+    @total  = Hash.new(0) # Hash that keeps track of n elements each. Default value will be 0.
+  end
+
+  # ========================================================================= #
+  # === result?
+  # ========================================================================= #
+  def result?
+    @result
+  end; alias result result? # === result
+
+  # ========================================================================= #
+  # === is_number?
+  #
+  # This returns true if the input is a number, else false. For this it
+  # uses the .to_i method trick, which returns 0 for non-numbers.
+  # ========================================================================= #
+  def is_number?(i)
+    result = (i.to_i.to_s == i)
+    return result
+  end
+
+  # ========================================================================= #
+  # === split
+  #
+  # This method will return an array with all the elements.
+  # ========================================================================= #
+  def split(
+      i = @input
+    )
+    array = []
+    _ = ''.dup
+    i = i.first if i.is_a? Array
+    if i
+      chars = i.chars
+      chars.each_with_index {|token, index|
+        if is_number? token # We found a number here. We simply append it then.
+          _ << token # return the old data
+        elsif token.downcase == token
+          _ << token
+        else # Not a number, must be a character.
+          unless _.empty?
+            array << _
+            _ = ''.dup
+          end
+          _ = token
+        end
+        array << _ if (index + 1) == i.size
+      }
+      @result = array
+      determine_total
+      return array
+    end
+  end
+
+  # ========================================================================= #
+  # === ignore_numbers
+  #
+  # This will ignore numbers in a guaranteed manner.
+  # ========================================================================= #
+  def ignore_numbers(i)
+    return i.gsub(/\d+/,'')
+  end
+
+  # ========================================================================= #
+  # === return_n_elements
+  #
+  # Must return an Integer.
+  # ========================================================================= #
+  def return_n_elements(i)
+    result = 0
+    if i =~ /\d+/ # Ok has at least one number.
+      i = i[/(\d+)/][0]
+    else
+      i = 1
+    end
+    result = i.to_i
+    return result
+  end
+
+  # ========================================================================= #
+  # === determine_total
+  #
+  # If the input is @result then it was already properly pre-sorted for us.
+  # ========================================================================= #
+  def determine_total(i = @result)
+    i.each {|entry|
+      this_real_key = ignore_numbers(entry)
+      if @total.has_key? this_real_key
+        @total[this_real_key] = @total[this_real_key]+return_n_elements(entry)
+      else # Else we must make a new key; the Laufindex kann aber 1-n sein.
+        @total[this_real_key] = return_n_elements(entry)
+      end
+    }
+  end
+
+  # ========================================================================= #
+  # === total?
+  # ========================================================================= #
+  def total?
+    @total # This must always be a Hash.
+  end
+
+  # ========================================================================= #
+  # === set_input
+  # ========================================================================= #
+  def set_input(i)
+    if i
+      i = i.join(' ').strip if i.is_a? Array
+      i = i.dup if i.frozen?
+      if i.include?(' ') and (i =~ /^\d+/) # starts with a number.
+        # Input is e. g. "5 H2O"
+        splitted = i.split(' ')
+        n_times = splitted.first.to_i
+        new_result = ''.dup
+        splitted.last.chars.each {|this_char|
+          if this_char =~ /\d+/
+            this_char = this_char.to_i * n_times
+          end
+          new_result << this_char.to_s
+        }
+        unless new_result[-1, 1] =~ /\d+/
+          new_result << n_times.to_s
+        end
+        i = new_result
+      end
+      i.tr!('₁', '1') if i.include? '₁'
+      i.tr!('₂', '2') if i.include? '₂'
+      i.tr!('₃', '3') if i.include? '₃'
+      i.tr!('₄', '4') if i.include? '₄'
+      i.tr!('₅', '5') if i.include? '₅'
+      i.tr!('₆', '6') if i.include? '₆'
+      i.tr!('₇', '7') if i.include? '₇'
+      i.tr!('₈', '8') if i.include? '₈'
+      i.tr!('₉', '9') if i.include? '₉'
+      i = convert_parens(i) if i.include? ')'
+      if i.include? ' '
+        i.strip!
+        if i.include? '+' # Ok, input here can be like: '2 Fe + 3 Cl2'
+          i.gsub!(/(\d)+ /,'\1')
+          i.gsub!(/ \+ /,'')
+        end
+        # ===================================================================== #
+        # But it can also include internal ' ', which we will remove next.
+        # ===================================================================== #
+        i.delete!(' ')
+      end
+    end
+    @input = i
+  end
+
+end
+
+# =========================================================================== #
+# === ChemistryParadise.split_this_molecular_formula_into_a_hash
+# =========================================================================== #
+def self.split_this_molecular_formula_into_a_hash(i)
+  i = i.first if i.is_a? Array
+  SplitMoleculeNames.new(i).result
+end
+
+end
+
+if __FILE__ == $PROGRAM_NAME
+  include ChemistryParadise
+  alias e puts
+  puts 'Testing whether this class can properly Split Compound Names:'
+  if ARGV.empty?
+    pp SplitMoleculeNames.new.result
+    e
+    _ = 'P2O5';      e 'Input is: '+_; print '  '; pp SplitMoleculeNames.new(_).result
+    _ = 'C6H14N4O2'; e 'Input is: '+_; print '  '; pp SplitMoleculeNames.new(_).result
+    _ = 'Al2(SO4)3'; e 'Input is: '+_; print '  '; pp SplitMoleculeNames.new(_).result
+    _ = 'Fe(OH)3';   e 'Input is: '+_; print '  '; pp SplitMoleculeNames.new(_).result
+    _ = 'H2SO4';     e 'Input is: '+_; print '  '; pp SplitMoleculeNames.new(_).result
+    _ = '(NH₄)₂SO₄'; e 'Input is: '+_; print '  '; pp SplitMoleculeNames.new(_).result
+    _ = 'Fe2(SO4)3'; e 'Input is: '+_; print '  '; pp SplitMoleculeNames.new(_).result
+    _ = 'P2O5';      e 'Input is: '+_; print '  '; pp SplitMoleculeNames.new(_).result
+    _ = '5 H2O';     e 'Input is: '+_; print '  '; pp SplitMoleculeNames.new(_).result
+    e
+    pp SplitMoleculeNames.new('Fe2(SO4)3').total?
+    p 'Will test this input next: 2 Fe + 3 Cl2'
+    pp SplitMoleculeNames.new('2 Fe + 3 Cl2').result
+  else
+    SplitMoleculeNames.new(ARGV).result
+  end
+end # $CHEMISTRY/split_molecule_names.rb

data/lib/chemistry_paradise/toplevel_methods/atomgewichte.rb

@@ -0,0 +1,31 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'chemistry_paradise/toplevel_methods/atomgewichte.rb'
+# =========================================================================== #
+require 'chemistry_paradise/constants/file_constants.rb'
+
+module ChemistryParadise
+
+  # ========================================================================= #
+  # === ChemistryParadise.file_atomgewichte
+  # ========================================================================= #
+  def self.file_atomgewichte
+    Constants::FILE_ATOMGEWICHTE
+  end
+
+  # ========================================================================= #
+  # === ChemistryParadise.atomgewichte?
+  # ========================================================================= #
+  def self.atomgewichte?
+    require 'yaml'
+    YAML.load_file(Constants::FILE_ATOMGEWICHTE)
+  end
+
+end
+
+if __FILE__ == $PROGRAM_NAME
+  puts ChemistryParadise.file_atomgewichte
+  pp ChemistryParadise.atomgewichte?
+end

data/lib/chemistry_paradise/toplevel_methods/convert_parens.rb

@@ -0,0 +1,64 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'chemistry_paradise/toplevel_methods/convert_parens.rb'
+# =========================================================================== #
+module ChemistryParadise
+
+  # ========================================================================= #
+  # === ChemistryParadise.convert_parens
+  #
+  # This method will properly convert the () parens that can be found
+  # in a chemical formula.
+  #
+  # For instance:
+  #
+  #    Al2(SO4)3
+  #
+  # Is effectively the same such as:
+  #
+  #    Al2SO4SO4SO4
+  #
+  # ========================================================================= #
+  def self.convert_parens(i)
+    if i.is_a? Array
+      i.each {|entry| convert_parens(entry) }
+    else
+      i = i.dup if i.frozen?
+      i.tr!('₁', '1') if i.include? '₁'
+      i.tr!('₂', '2') if i.include? '₂'
+      i.tr!('₃', '3') if i.include? '₃'
+      i.tr!('₄', '4') if i.include? '₄'
+      i.tr!('₅', '5') if i.include? '₅'
+      i.tr!('₆', '6') if i.include? '₆'
+      i.tr!('₇', '7') if i.include? '₇'
+      i.tr!('₈', '8') if i.include? '₈'
+      i.tr!('₉', '9') if i.include? '₉'
+      if i.include? '('
+        n_parens = i.count('(')
+        if n_parens > 1 # Ok, this may be a really complex formula, like:
+                        #   Fe(OH)3 + H2SO4 -> Fe2(SO4)3 + H2O
+          splitted = i.split(' ')
+          splitted = splitted.map {|entry| convert_parens(entry) } # For now we remove some things. 
+          return splitted.join(' ')
+        else
+          regex = /\((.+)\)(\d)([A-Za-z]{0,3}\d{0,3})/ # See: https://rubular.com/r/clShxRBIpzEtlF
+          i =~ regex
+          i = i[0, i.index('(')]
+          i << $1 * $2.to_i # Which group * n repetition
+          i << $3.dup if $3
+        end
+      end
+      return i
+    end
+  end
+
+end
+
+if __FILE__ == $PROGRAM_NAME
+  alias e puts
+  e ChemistryParadise.convert_parens('Al2(SO4)3')
+  e ChemistryParadise.convert_parens('(NH4)2SO4')
+  e ChemistryParadise.convert_parens('(NH₄)₂SO₄')
+end

data/lib/chemistry_paradise/toplevel_methods/display_where_the_molmasses_are_kept.rb

@@ -0,0 +1,24 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'chemistry_paradise/toplevel_methods/display_where_the_molmasses_are_kept.rb'
+# =========================================================================== #
+require 'chemistry_paradise/toplevel_methods/e.rb'
+require 'chemistry_paradise/requires/common_external_requires.rb'
+require 'chemistry_paradise/constants/file_constants.rb'
+
+module ChemistryParadise
+
+  # ========================================================================= #
+  # === ChemistryParadise.display_where_the_molmasses_are_kept
+  # ========================================================================= #
+  def self.display_where_the_molmasses_are_kept
+    Colours.e(Constants::FILE_ATOMGEWICHTE)
+  end
+
+end
+
+if __FILE__ == $PROGRAM_NAME
+  ChemistryParadise.display_where_the_molmasses_are_kept  
+end

data/lib/chemistry_paradise/toplevel_methods/e.rb

@@ -0,0 +1,16 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'chemistry_paradise/toplevel_methods/e.rb'
+# =========================================================================== #
+module ChemistryParadise
+
+  # ========================================================================= #
+  # === ChemistryParadise.e
+  # ========================================================================= #
+  def self.e(i = '')
+    puts i
+  end
+
+end

data/lib/chemistry_paradise/toplevel_methods/kelvin.rb

@@ -0,0 +1,34 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'chemistry_paradise/toplevel_methods/kelvin.rb'
+# =========================================================================== #
+module ChemistryParadise
+
+  # ========================================================================= #
+  # === ChemistryParadise.kelvin
+  #
+  # This method will output how many Kelvin n Celsius are.
+  #
+  # The temperature T in Kelvin (K) is equal to the temperature T in
+  # degrees Celsius (°C) plus 273.1.
+  #
+  # The formula thus is:
+  #
+  #   T(K) = T(°C) + 273.15
+  #
+  # ========================================================================= #
+  def self.kelvin(n_celsius)
+    if n_celsius.is_a? Array
+      n_celsius = n_celsius.first
+    end
+    n_kelvin = n_celsius.to_f + 273.15
+    return n_kelvin
+  end; self.instance_eval { alias celsius_to_kelvin kelvin } # === ChemistryParadise.celsius_to_kelvin
+
+end
+
+if __FILE__ == $PROGRAM_NAME
+  puts ChemistryParadise.kelvin(ARGV)
+end # kelvin 37

data/lib/chemistry_paradise/toplevel_methods/language.rb

@@ -0,0 +1,50 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# This class can help set a different language for the project. By default,
+# the german language is used, but you can call the module-method below,
+# called ChemistryParadise.use_english, to enable english instead.
+# =========================================================================== #
+# require 'chemistry_paradise/toplevel_methods/language.rb'
+# =========================================================================== #
+module ChemistryParadise
+
+  # ========================================================================= #
+  # === @use_this_language
+  # ========================================================================= #
+  @use_this_language = :german
+
+  # ========================================================================= #
+  # === ChemistryParadise.set_use_this_language
+  # ========================================================================= #
+  def self.set_use_this_language(i = :german)
+    @use_this_language = i
+  end
+
+  # ========================================================================= #
+  # === ChemistryParadise.use_which_language?
+  # ========================================================================= #
+  def self.use_which_language?
+    @use_this_language
+  end
+
+  # ========================================================================= #
+  # === ChemistryParadise.do_use_english
+  #
+  # Use this method if you want to use the english language.
+  # ========================================================================= #
+  def self.do_use_english
+    set_use_this_language(:english)
+  end; self.instance_eval { alias use_english do_use_english } # === ChemistryParadise.use_english
+
+  # ========================================================================= #
+  # === ChemistryParadise.do_use_german
+  #
+  # Use this method if you want to use the german language.
+  # ========================================================================= #
+  def self.do_use_german
+    set_use_this_language(:german)
+  end; self.instance_eval { alias use_german do_use_german } # === ChemistryParadise.use_german
+
+end

data/lib/chemistry_paradise/toplevel_methods/misc.rb

@@ -0,0 +1,147 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'chemistry_paradise/toplevel_methods/misc.rb'
+# =========================================================================== #
+module ChemistryParadise
+
+  # ========================================================================= #
+  # === ChemistryParadise.sanitize
+  #
+  # Usage example:
+  #
+  #   ChemistryParadise.sanitize('C6H13N3O3') # => "C₆H₁₃N₃O₃"
+  #
+  # ========================================================================= #
+  def self.sanitize(i)
+    if i.is_a? Array
+      i = i.first
+    end
+    i = i.dup
+    i.gsub!(/1/, '₁')
+    i.gsub!(/2/, '₂')
+    i.gsub!(/3/, '₃')
+    i.gsub!(/4/, '₄')
+    i.gsub!(/5/, '₅')
+    i.gsub!(/6/, '₆')
+    i.gsub!(/7/, '₇')
+    i.gsub!(/8/, '₈')
+    i.gsub!(/9/, '₉')
+    i.gsub!(/0/, '₀')
+    return i
+  end
+
+  # ========================================================================= #
+  # === ChemistryParadise.calculate_atomic_mass_based_on_isotope_percentage
+  #
+  # This method accepts as many arguments as the user wants to.
+  #
+  # It has to follow a specific format. The first entry must be
+  # the "Häufigkeit" and the second entry must be the corresponding
+  # atomic mass ("relative_atommasse").
+  #
+  # Usage example:
+  #
+  #   ChemistryParadise.calculate_atomic_mass_based_on_isotope_percentage(78.99, 23.985, 10.00, 24.985, 11.01, 25.983)
+  #
+  # ========================================================================= #
+  def self.calculate_atomic_mass_based_on_isotope_percentage(*array)
+    round_to_n_positions = 3
+    result = 0
+    array.map! {|entry| entry.to_s.tr(',','.').to_f }
+    entries = array.each_slice(2)
+    entries.each {|häufigkeit, relative_atommasse|
+      if häufigkeit > 0
+        häufigkeit = häufigkeit / 100.0
+      end
+      zwischenergebnis = relative_atommasse * häufigkeit
+      result += zwischenergebnis
+    }
+    return result.round(round_to_n_positions)
+  end; self.instance_eval { alias berechne_atommasse calculate_atomic_mass_based_on_isotope_percentage } # === ChemistryParadise.berechne_atommasse
+
+  # ========================================================================= #
+  # === ChemistryParadise.torr_to_bar
+  #
+  # This method can be used to convert n Torr into n bar.
+  #
+  # The first argument is "n Torr".
+  #
+  # The result will be in "n bar".
+  # ========================================================================= #
+  def self.torr_to_bar(i = 720)
+    if i.is_a? Array
+      i = i.first
+    end
+    result = i.to_f * (1.013 / 760)
+    rounded_result = result.round(3)
+    beautified_result = '%.3f' % rounded_result 
+    return beautified_result
+  end
+ 
+  # ========================================================================= #
+  # === ChemistryParadise.log
+  #  
+  # Calculate the log of something.
+  # ========================================================================= #
+  def self.log(of)
+    return Math.log10(of)
+  end
+
+  require 'chemistry_paradise/constants/file_constants.rb'
+  require 'chemistry_paradise/split_molecule_names.rb'
+  # ========================================================================= #
+  # === ChemistryParadise.logempirische_formel
+  #
+  # This variant is german.
+  #
+  # We will assume 100 g as input.
+  # ========================================================================= #
+  def self.empirische_formel(
+      i                            = 'KClO4', # 'H2O'
+      round_to_n_decimal_positions = 2
+    )
+    i = i.to_s.strip.dup
+    require 'yaml'
+    dataset = YAML.load_file(Constants::FILE_ATOMGEWICHTE)
+    # ======================================================================= #
+    # So, 100 g H2O here.
+    # ======================================================================= #
+    array = SplitMoleculeNames.new(i).result
+    hash = {} # Store the mol here.
+    result = {}
+    # ======================================================================= #
+    # array may look like this: ["H2", "O"]
+    # ======================================================================= #
+    array.each {|entry|
+      n_times = 1
+      if entry =~ /\d+/ # At the least one number.
+        n_times = entry.scan(/\d+/).flatten.first.to_i
+        # =================================================================== #
+        # Now remove the number.
+        # =================================================================== #
+        entry.gsub!(/\d+/,'')
+      end
+      key = dataset[entry]
+      molmass = key * n_times
+      hash[entry] = molmass
+    }
+    total_mass = hash.values.sum
+    hash.each_pair {|key, value|
+      new_value = (100.0 / total_mass) * value
+      if round_to_n_decimal_positions
+        new_value = new_value.round(round_to_n_decimal_positions)
+      end
+      result[key] = new_value
+    }
+    return result
+  end
+
+end
+
+if __FILE__ == $PROGRAM_NAME
+  alias e puts
+  pp ChemistryParadise.empirische_formel
+  e ChemistryParadise.torr_to_bar(720).to_s+' bar'
+end

data/lib/chemistry_paradise/toplevel_methods/periodic_table.rb

@@ -0,0 +1,16 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'chemistry_paradise/toplevel_methods/periodic_table.rb'
+# =========================================================================== #
+module ChemistryParadise
+
+  # ========================================================================= #
+  # === ChemistryParadise.periodic_table?
+  # ========================================================================= #
+  def self.periodic_table?
+    '/Users/x/DATA/SCIENCE/YAML/periodic_table.yml'
+  end
+
+end

data/lib/chemistry_paradise/toplevel_methods/remove_this_molecule_from.rb

@@ -0,0 +1,63 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'chemistry_paradise/toplevel_methods/remove_this_molecule_from.rb'
+# =========================================================================== #
+require 'chemistry_paradise/split_molecule_names.rb'
+
+module ChemistryParadise
+
+  # ========================================================================= #
+  # === ChemistryParadise.remove_this_molecule_from
+  #
+  # The first argument is the molecule that should be deducted from
+  # the formula.
+  # ========================================================================= #
+  def self.remove_this_molecule_from(
+      this_molecule = 'OH',
+      from          = 'C2H5NO2'
+    )
+    array_big_molecule  = ::ChemistryParadise.split_this_molecular_formula_into_a_hash(from)
+    array_this_molecule = ::ChemistryParadise.split_this_molecular_formula_into_a_hash(this_molecule)
+    # ======================================================================= #
+    # Next, iterate over the small molecule.
+    # ======================================================================= #
+    array_this_molecule.each {|this_compound|
+      unless this_compound =~ /\d+/
+        this_compound << '1' # Must be at the least one.
+      end
+      # ===================================================================== #
+      # Select the entry that is the correct one.
+      # ===================================================================== #
+      this_entry = array_big_molecule.find {|entry|
+        entry[0,1] == this_compound[0,1]
+      }
+      begin
+        n_times_in_the_big_molecule   = /(\d{1,3})/.match(this_entry)[1].to_i
+        n_times_in_the_small_molecule = /(\d{1,3})/.match(this_compound)[1].to_i
+        new_n_times = n_times_in_the_big_molecule - n_times_in_the_small_molecule
+        new_entry = this_compound[0,1]+new_n_times.to_s
+        # ===================================================================== #
+        # Now we have the new entry; we need to re-insert it into the big
+        # original Array.
+        # ===================================================================== #
+        proper_index = array_big_molecule.index {|entry|
+          entry[0,1] == this_compound[0,1]
+        }
+        array_big_molecule[proper_index] = new_entry
+      rescue NoMethodError => error
+        pp error
+      end
+    }
+    return array_big_molecule.join # Join it up again.
+  end
+
+end
+
+if __FILE__ == $PROGRAM_NAME
+  puts 'Deducting OH from C2H5NO2 next:'
+  puts ::ChemistryParadise.remove_this_molecule_from('OH', 'C2H5NO2')  
+  puts 'Deducting H2O from C2H5NO2 next:'
+  puts ::ChemistryParadise.remove_this_molecule_from('H2O', 'C2H5NO2')
+end