Class: Bioroebe::CalculateMeltingTemperature

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/calculate/calculate_melting_temperature.rb

Overview

Bioroebe::CalculateMeltingTemperature

Constant Summary collapse

NAMESPACE =
#

NAMESPACE

#
inspect
DEFAULT_SEQUENCE =
#

DEFAULT_SEQUENCE

#
'CGACGTTGTAAAACGACGGCCAGT'
GAS_CONSTANT_R =
#

GAS_CONSTANT_R

#
1.987
DO_TRUNCATE_IF_INPUT_STRING_IS_TOO_LONG =
#

DO_TRUNCATE_IF_INPUT_STRING_IS_TOO_LONG

#
true

Constants inherited from CommandlineApplication

Bioroebe::CommandlineApplication::OLD_VERBOSE_VALUE

Constants included from ColoursForBase

Bioroebe::ColoursForBase::ARRAY_HTML_COLOURS_IN_USE

Class Method Summary collapse

Instance Method Summary collapse

Methods inherited from CommandlineApplication

#all_aminoacids?, #append_what_into, #at_home?, #be_silent, #be_verbose?, #cat, #ccliner, #change_directory, #cliner, #codon_table_dataset?, #codon_to_aminoacid, #codons_for?, #colourize_this_dna_sequence, #complement, #cp, #disable_warnings, #download_dir?, #editor?, #enable_warnings, #ensure_that_the_base_directories_exist, #esystem, #extract, #is_this_a_start_codon?, #is_this_a_stop_codon?, #leading_five_prime, #load_bioroebe_yaml_file, #log_directory?, #one_letter_to_long_name, #one_to_three, #only_numbers?, #open_in_browser, #opne, #opnn, #pad_with_double_quotes, #pad_with_single_quotes, #partner_nucleotide, #remove_numbers, #remove_trailing_ansii_escape_code, #return_all_possible_start_codons, #return_array_of_one_letter_aminoacids, #return_cheerful_person, #return_chunked_display, #return_ubiquitin_sequence, #set_be_verbose, #start_codon?, #stop_codons?, #strict_filter_away_invalid_aminoacids, #taxonomy_download_directory?, #three_to_one, #to_rna, #trailing_three_prime, #use_opn?, #verbose_truth, #was_or_were, #without_extname, #write_what_into

Methods included from CommandlineArguments

#commandline_arguments?, #commandline_arguments_that_are_files?, #e, #first?, #first_non_hyphen_argument?, #remove_hyphens_from_the_commandline_arguments, #return_commandline_arguments_as_string, #return_commandline_arguments_that_are_not_files, #return_entries_without_two_leading_hyphens, #select_commandline_arguments, #select_entries_starting_with_two_hyphens, #set_commandline_arguments

Methods included from ColoursForBase

#colourize_this_aminoacid_sequence_for_the_commandline, #colourize_this_nucleotide_sequence, #disable_colours, #ecomment, #efancy, #egold, #enable_colours, #eorange, #eparse, #erev, #red, #remove_trailing_escape_part, #return_colour_for_nucleotides, #rev, #sdir, #set_use_colours, #sfancy, #sfile, #simp, #swarn, #use_colours?, #use_colours_within_the_bioroebe_namespace?

Methods inherited from Base

#append_what_into, #can_base_pair?, #convert_global_env, #delete_file, #directory_to_the_codon_tables?, #file_readlines, #infer_the_namespace, #is_on_roebe?, #is_palindrome?, #main_encoding?, #mkdir, #move_file, #mv, #namespace?, #no_file_exists_at, #no_newlines, #project_yaml_directory?, #rds, #register_sigint, #return_pwd, #return_the_first_line_of_this_file, #word_wrap, #write_what_into

Constructor Details

#initialize(i = nil, run_already = true) ⇒ CalculateMeltingTemperature

#

initialize

#

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# File 'lib/bioroebe/calculate/calculate_melting_temperature.rb', line 57

def initialize(
    i           = nil,
    run_already = true
  )
  reset
  set_sequence(i)
  run if run_already
end

Class Method Details

.show_formulas ⇒ Object

#

CalculateMeltingTemperature.show_formulas

The Wallace Method:

http://www.sigmaaldrich.com/technical-documents/articles/biology/oligos-melting-temp.html#equations
http://openwetware.org/wiki/Primer_Tm_estimation_methods

This method will simply show the Wallace-Formula.

The shorthand notation is:

Tm = 2°C(A+T) + 4°C(G+C)

Note that this is also known as the “GCx4+ATx2” rule. It works for DNA oligomers not longer than 13 nucleotides. This rule also does not take into account the order of nucleotides in the sequence, so it really is not the ideal solution.

#

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# File 'lib/bioroebe/calculate/calculate_melting_temperature.rb', line 370

def self.show_formulas
  Colours.e
    '  Tm = 2°C(A+T) + 4°C(G+C) # <-- The Wallace-Formula, proposed in 1979'
end

.wallace_method(at, gc) ⇒ Object

#

CalculateMeltingTemperature.wallace_method

The argument “at” means the sum of a and t, and “gc” means the sum of g and c.

So for instance, the string TGCTCA has 3 AT, and 3 GC, so the method will yield to us:

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#

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# File 'lib/bioroebe/calculate/calculate_melting_temperature.rb', line 387

def self.wallace_method(at, gc)
  result = 4 * (gc) + 2 * (at)
  result
end

Instance Method Details

#calculate_tm(ct = 0.5, na = 50, formamide_concentration = 0) ⇒ Object

#

calculate_tm

Calculate the melting temperature.

Note that there are several different ways how the melting temperature (Tm) of an oligo-nucleotide can be calculated.

All of these methods will yield slightly different results.

All of these calculations are also theoretical calculations based on certain assumptions.

The Optimum Tm values should still be determined empirically.

Now, let's explain the arguments to this method:

* ct: concentration of oligo nucleotide(mM) (default 0.5)
* na: concentration of Na⁺ (mM) (default 50)
* formamide_concentration: concentration of Formamide (mol/L) (default 0)
* This method will return a Float.
#

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# File 'lib/bioroebe/calculate/calculate_melting_temperature.rb', line 162

def calculate_tm(
    ct = 0.5,
    na =  50,
    formamide_concentration = 0
  )
  # ======================================================================= #
  # === How much formamide we threw into this
  # ======================================================================= #
  formamide_concentration = formamide_concentration.to_f # concentration of Formamide (mol/L)
  ct = ct / 1000000.0 # concentration of oligo (mol/L)
  na = na /    1000.0 # concentration of Na+ (mol/L)
  len = sequence?.length # .prec_f # base length
  # ======================================================================= #
  # === Thermodynamic parameters
  # 
  #   delta_enthalpy ... delta enthalpy
  #   delta_entropy  ... delta entropy
  #
  # ======================================================================= #

  # ======================================================================= #
  # === Delta Enthalpy
  #
  # Different combinations of nucleotides have a different enthalpy.
  # ======================================================================= #
  delta_enthalpy = {
    'AA' =>  -9.1, 'TT' =>  -9.1, 'AT' =>  -8.6, 'TA' =>  -6.0,
    'CA' =>  -5.8, 'TG' =>  -5.8, 'GT' =>  -6.5, 'AC' =>  -6.5,
    'CT' =>  -7.8, 'AG' =>  -7.8, 'GA' =>  -5.6, 'TC' =>  -5.6,
    'CG' => -11.9, 'GC' => -11.1, 'GG' => -11.0, 'CC' => -11.0
  }
  # ======================================================================= #
  # === Delta entropy
  # ======================================================================= #
  delta_entropy = {
    'AA' => -24.0, 'TT' => -24.0, 'AT' => -23.9, 'TA' => -16.9,
    'CA' => -12.9, 'TG' => -12.9, 'GT' => -17.3, 'AC' => -17.3,
    'CT' => -20.8, 'AG' => -20.8, 'GA' => -13.5, 'TC' => -13.5,
    'CG' => -27.8, 'GC' => -26.7, 'GG' => -26.6, 'CC' => -26.6
  }
  tot_h = 0.0
  tot_s = 0.0
  # ======================================================================= #
  # Count up the total enthalpy and entropy.
  # ======================================================================= #
  (sequence?.size - 2).times {|counter|
    enthalpy = @sequence.slice(counter, 2)
    tot_h += delta_enthalpy[enthalpy]
    entropy = @sequence.slice(counter, 2)
    tot_s += delta_entropy[entropy]
  }
  # ======================================================================= #
  # Obtain the amount of AT and GC.
  # ======================================================================= #
  at = ::Bioroebe.count_AT(@sequence)
  gc = ::Bioroebe.count_GC(@sequence)
  report_total_length # Notify the user of the current total length.
  # ======================================================================= #
  # === Show AT and GC counts next, including percentage.
  # ======================================================================= #
  erev 'AT count is: '+simp(at.to_s)+rev+' nucleotides ('+
       sfancy(at * 100 / @sequence.size).to_s+rev+'%)'
  erev 'GC count is: '+simp(gc.to_s)+rev+' nucleotides ('+
       sfancy(gc * 100 / @sequence.size).to_s+rev+'%)'
  # ======================================================================= #
  # We have to calculate the tm first. We do this by also considering
  # the gas constant. 
  # ======================================================================= #
  tm = (
    (1000 * tot_h) / (-10.8+tot_s+GAS_CONSTANT_R * Math.log(ct/4))
  ) - 273.15 + 16.6 * Math.log10(na)
  # ======================================================================= #
  # === First the traditional GC% method.
  # ======================================================================= #
  if    tm > 80
    # ===================================================================== #
    # The traditional GC% method comes next.
    # ===================================================================== #
    tm = 81.5+16.6 * Math.log10(na) +
         41 * ((gc)/len)-500/len-0.62 * formamide_concentration
  elsif tm < 20
    # ===================================================================== #
    # === Wallace Method
    #
    # The Wallace method, also known as "2+4 rule of thumb".
    #
    # This very simple method assigns 2°C to each A-T pair and 4°C to
    # each G-C pair. The Tm then is the sum of these values for all
    # individual pairs in a DNA double strand.
    #
    # This takes into account that the G-C bond is stronger than the
    # A-T bond. Note that the 2+4 rule is valid only for a small
    # length-range, about 20-40 nt - rather 20, than towards 40,
    # though.
    #
    # The Wallace equation was developed for short DNA oligos of
    # 14-20 base pairs.
    #
    # See documentation at:
    #
    #   https://www.sigmaaldrich.com/technical-documents/articles/biology/oligos-melting-temp.html#equations
    #
    # It is very easy to compute, but is of course also very inaccurate.
    #
    # Whenever possible, it should be avoided.
    # ===================================================================== #
    tm = CalculateMeltingTemperature.wallace_method(at, gc)
  else
    # tm = tm
  end
  @result = tm
  return tm
end

#length? ⇒ Boolean

#

length?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/calculate/calculate_melting_temperature.rb', line 108

def length?
  @sequence.size
end

#report_molecular_weight ⇒ Object

#

report_molecular_weight

This method will report the molecular weight of the nucleotides at hand, in Dalton.

#

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# File 'lib/bioroebe/calculate/calculate_melting_temperature.rb', line 312

def report_molecular_weight
  molecular_weight = 0
  hash = {}
  if File.exist? FILE_NUCLEOTIDES
    dataset = YAML.load_file(FILE_NUCLEOTIDES)
  end
  unless Object.const_defined? :ChemistryParadise
    begin
      require 'chemistry_paradise/utility_scripts/calculate_atomic_mass.rb'
    rescue LoadError; end
  end
  hash['A'] = ::ChemistryParadise.return_molmasse(dataset['Desoxyadenosin'])
  hash['T'] = ::ChemistryParadise.return_molmasse(dataset['Desoxythymidin'])
  hash['C'] = ::ChemistryParadise.return_molmasse(dataset['Desoxycytidin'])
  hash['G'] = ::ChemistryParadise.return_molmasse(dataset['Desoxyguanosin'])
  internal_PO2_group = 62.972
  index = 0 
  sequence?.split(//).each {|this_nucleotide|
    add_this = hash[this_nucleotide].to_f
    case index
    when 0
    else # Else add an internal PO2 group, its weight that is.
      add_this += internal_PO2_group
    end
    molecular_weight += add_this
    index += 1
  }
  erev "Molecular weight:        "\
       "#{sfancy(molecular_weight.to_s)}"\
       "#{rev}"
end

#report_result ⇒ Object Also known as: report

#

report_result

#

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# File 'lib/bioroebe/calculate/calculate_melting_temperature.rb', line 293

def report_result
  round_to_n_numbers = 5
  report_molecular_weight
  erev "The melting temperature of `#{simp(return_possibly_truncated_input)}"\
       "#{rev}` is #{sfancy(@result.round(round_to_n_numbers).to_s)}#{rev} °C."
  if @sequence.to_s.empty?
    erev 'Notification: it seems as if you did not pass any nucleotide '\
         'string to this.'
    erev 'You could try to "assign" a string or generate a random one '\
         'via "assign random".'
  end
end

#report_total_length ⇒ Object

#

report_total_length

#

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# File 'lib/bioroebe/calculate/calculate_melting_temperature.rb', line 100

def report_total_length
  e "#{rev}The total length of this nucleotide-sequence "\
    "is #{simp(length?.to_s)}."
end

#reset ⇒ Object

#

reset (reset tag)

#

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# File 'lib/bioroebe/calculate/calculate_melting_temperature.rb', line 69

def reset
  super()
  # ======================================================================= #
  # === @namespace
  # ======================================================================= #
  @namespace = NAMESPACE
end

#result? ⇒ Boolean Also known as: result

#

result?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/calculate/calculate_melting_temperature.rb', line 128

def result?
  @result
end

#return_possibly_truncated_input ⇒ Object

#

return_possibly_truncated_input

This method is needed to truncate too long input.

#

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# File 'lib/bioroebe/calculate/calculate_melting_temperature.rb', line 117

def return_possibly_truncated_input
  _ = @sequence.to_s
  if _.size > 60 # Bit more than 50 to account for the length of the message below.
    _ = _[0..49]+' [TRUNCATED PAST 50 CHARACTERS]'
  end if DO_TRUNCATE_IF_INPUT_STRING_IS_TOO_LONG
  return _
end

#run ⇒ Object

#

run (run tag)

#

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# File 'lib/bioroebe/calculate/calculate_melting_temperature.rb', line 347

def run
  calculate_tm
end

#sequence? ⇒ Boolean Also known as: input?

#

sequence?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/calculate/calculate_melting_temperature.rb', line 135

def sequence?
  @sequence
end

#set_sequence(i = DEFAULT_SEQUENCE) ⇒ Object

#

set_sequence

Set the main sequence, the input, to this method.

#

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# File 'lib/bioroebe/calculate/calculate_melting_temperature.rb', line 82

def set_sequence(i = DEFAULT_SEQUENCE)
  i = i.first if i.is_a? Array
  i = DEFAULT_SEQUENCE if i.nil?
  i = i.to_s
  case i.delete('-') # case tag
  # ======================================================================= #
  # === melting_temperature --help
  # ======================================================================= #
  when 'help'
    show_help; exit
  end
  i = i.upcase
  @sequence = i
end

#show_help ⇒ Object

#

show_help (help tag)

To show this help section, try:

cmt --help
#

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# File 'lib/bioroebe/calculate/calculate_melting_temperature.rb', line 284

def show_help
  e
  opnn; e 'Simply input the DNA sequence.'
  e
end