Class: Bioroebe::UsefulFormulas
- Inherits:
-
CommandlineApplication
- Object
- Base
- CommandlineApplication
- Bioroebe::UsefulFormulas
- Defined in:
- lib/bioroebe/misc/useful_formulas.rb
Overview
Bioroebe::UsefulFormulas
Constant Summary
Constants inherited from CommandlineApplication
CommandlineApplication::OLD_VERBOSE_VALUE
Constants included from ColoursForBase
ColoursForBase::ARRAY_HTML_COLOURS_IN_USE
Constants inherited from Base
Class Method Summary collapse
-
.[](i = ARGV) ⇒ Object
# === Bioroebe::UsefulFormulas[] ========================================================================= #.
Instance Method Summary collapse
-
#col1(i) ⇒ Object
# === col1 ========================================================================= #.
-
#initialize(i = nil, run_already = true) ⇒ UsefulFormulas
constructor
# === initialize ========================================================================= #.
-
#quantification_of_proteins ⇒ Object
# === quantification_of_proteins ========================================================================= #.
-
#reset ⇒ Object
# === reset (reset tag) ========================================================================= #.
-
#run ⇒ Object
# === run (run tag) ========================================================================= #.
-
#working_with_dna ⇒ Object
# === working_with_dna ========================================================================= #.
-
#working_with_rna ⇒ Object
# === working_with_rna ========================================================================= #.
-
#working_with_temperatures_and_pressure ⇒ Object
# === working_with_temperatures_and_pressure.
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, #opnerev, #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, #runmode?, #set_be_verbose, #set_runmode, #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 BaseModule
#absolute_path, #default_file_read, #file_readlines
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_will_we_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?, #is_on_roebe?, #is_palindrome?, #main_encoding?, #mkdir, #move_file, #mv, #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
Methods included from InternalHashModule
#internal_hash?, #reset_the_internal_hash
Methods included from InferTheNamespaceModule
#infer_the_namespace, #namespace?
Constructor Details
#initialize(i = nil, run_already = true) ⇒ UsefulFormulas
#
initialize
#
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# File 'lib/bioroebe/misc/useful_formulas.rb', line 26 def initialize( i = nil, run_already = true ) reset run if run_already end |
Class Method Details
.[](i = ARGV) ⇒ Object
#
Bioroebe::UsefulFormulas[]
#
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# File 'lib/bioroebe/misc/useful_formulas.rb', line 121 def self.[](i = ARGV) new end |
Instance Method Details
#col1(i) ⇒ Object
#
col1
#
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# File 'lib/bioroebe/misc/useful_formulas.rb', line 103 def col1(i) e mediumvioletred(i) end |
#quantification_of_proteins ⇒ Object
#
quantification_of_proteins
#
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# File 'lib/bioroebe/misc/useful_formulas.rb', line 74 def quantification_of_proteins col1 'Quantification of Proteins' e e ' Molar conversions for Proteins' e ' Protein/DNA conversions (1 kb of DNA encodes '\ '333 amino acids = 3.7 x 10 4 Da)' e end |
#reset ⇒ Object
#
reset (reset tag)
#
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# File 'lib/bioroebe/misc/useful_formulas.rb', line 37 def reset super() end |
#run ⇒ Object
#
run (run tag)
#
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# File 'lib/bioroebe/misc/useful_formulas.rb', line 110 def run working_with_dna working_with_rna working_with_temperatures_and_pressure quantification_of_proteins # e # And a happy trailing newline. No longer needed as of Nov 2023. end |
#working_with_dna ⇒ Object
#
working_with_dna
#
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# File 'lib/bioroebe/misc/useful_formulas.rb', line 44 def working_with_dna col1 'Working with DNA' e e ' Calculation of molecular weight in Dalton' e e ' MW of dsDNA = [number of basepairs] x [660 Da]' e ' MW of ssDNA = [number of bases] x [330 Da]' e e " Calculation of pmol of 5' (or 3') ends" e ' Conversion of µg to pmol' e ' Conversion of Pmol to µg' e end |
#working_with_rna ⇒ Object
#
working_with_rna
#
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# File 'lib/bioroebe/misc/useful_formulas.rb', line 61 def working_with_rna col1 'Working with RNA' e e ' Calculation of molecular weight in Dalton' e " Calculation of pmol of 5' (or 3') ends" e ' Conversion of µg to pmol' e ' Conversion of Pmol to µg' e end |
#working_with_temperatures_and_pressure ⇒ Object
#
working_with_temperatures_and_pressure
Do note that Celsius may also be called Centigrade, to some extent.
See: www.thoughtco.com/celsius-vs-centigrade-3976012
#
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# File 'lib/bioroebe/misc/useful_formulas.rb', line 90 def working_with_temperatures_and_pressure col1 'Working with Temperatures and Pressure' e e ' Conversions between Celsius and Fahrenheit' e ' F° = 32 + (C° x 0.555)' e ' C° = 0.555 x (F°-32)' e ' From millibars (mbar) to different units' e end |