Class: Bioroebe::ReportSecondaryStructuresFromThisPdbFile

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/pdb/report_secondary_structures_from_this_pdb_file.rb

Overview

Bioroebe::ReportSecondaryStructuresFromThisPdbFile

Constant Summary

Constants inherited from CommandlineApplication

CommandlineApplication::OLD_VERBOSE_VALUE

Constants included from ColoursForBase

ColoursForBase::ARRAY_HTML_COLOURS_IN_USE

Constants inherited from Base

Base::NAMESPACE

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(commandline_arguments = nil, run_already = true) ⇒ ReportSecondaryStructuresFromThisPdbFile

#

initialize

#

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# File 'lib/bioroebe/pdb/report_secondary_structures_from_this_pdb_file.rb', line 25

def initialize(
    commandline_arguments = nil,
    run_already           = true
  )
  reset
  set_commandline_arguments(
    commandline_arguments
  )
  run if run_already
end

Class Method Details

.[](i = '') ⇒ Object

#

Bioroebe::ReportSecondaryStructuresFromThisPdbFile[]

#

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# File 'lib/bioroebe/pdb/report_secondary_structures_from_this_pdb_file.rb', line 216

def self.[](i = '')
  new(i)
end

Instance Method Details

#colourize_this_aminoacid(i) ⇒ Object

#

colourize_this_aminoacid

#

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# File 'lib/bioroebe/pdb/report_secondary_structures_from_this_pdb_file.rb', line 191

def colourize_this_aminoacid(i)
  skyblue(i)
end

#colourize_this_aminoacid_three_to_one(i) ⇒ Object

#

colourize_this_aminoacid_three_to_one

#

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# File 'lib/bioroebe/pdb/report_secondary_structures_from_this_pdb_file.rb', line 198

def colourize_this_aminoacid_three_to_one(i)
  colourize_this_aminoacid(
    three_to_one(i)
  )
end

#left_pad_this_index(index) ⇒ Object

#

left_pad_this_index

#

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# File 'lib/bioroebe/pdb/report_secondary_structures_from_this_pdb_file.rb', line 70

def left_pad_this_index(index)
  (index.to_s+')'.ljust(3)).rjust(5)
end

#report_alpha_helices ⇒ Object

#

report_alpha_helices

An entry may look like this:

HELIX    1  1A GLN A   18  SER A   30  1      13
 0       1   2  3  4    5   6  7    8  9      10
#

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# File 'lib/bioroebe/pdb/report_secondary_structures_from_this_pdb_file.rb', line 83

def report_alpha_helices
  @alpha_helices.each_with_index {|line, index| index += 1
    splitted = line.split(' ')
    this_chain         = splitted[4]
    starting_aminoacid = splitted[3]
    last_aminoacid     = splitted[6]
    start_position     = splitted[5].to_i
    end_position       = splitted[8].to_i
    padded_index = left_pad_this_index(index)
    e steelblue(
        padded_index
      )+
      royalblue('Alpha-helix:  ')+
      'Starting aminoacid: '+
      colourize_this_aminoacid(starting_aminoacid)+
      ','+
      lightgreen(start_position.to_s.rjust(3))+
      ' ('+
      colourize_this_aminoacid_three_to_one(last_aminoacid)+
      ')'+
      ' Last aminoacid: '+colourize_this_aminoacid(last_aminoacid)+
      ' Length: '+
      mediumpurple(
        (end_position - (start_position-1)).to_s.rjust(2)
      )+
      ' (chain: '+this_chain+')'
  }
end

#report_beta_sheets ⇒ Object

#

report_beta_sheets

A line may look like this:

SHEET    1   A 9 ILE A   7  ASN A  11  0                          \n
 0       1   2 3  4  5   6   7  8  9   10
#

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# File 'lib/bioroebe/pdb/report_secondary_structures_from_this_pdb_file.rb', line 121

def report_beta_sheets
  keep_track_of_this_chain = ''
  last_end_position = 0
  @beta_sheets.each_with_index {|line, index|
    splitted = line.split(' ')
    this_chain         = splitted[2]
    starting_aminoacid = splitted[4]
    last_aminoacid     = splitted[7]
    start_position     = splitted[6].to_i
    end_position       = splitted[9].to_i
    keep_track_of_this_chain = this_chain
    if keep_track_of_this_chain.empty?
      keep_track_of_this_chain = this_chain
    end
    index += 1
    if this_chain == keep_track_of_this_chain
      if (last_end_position < end_position)
        # In this case we may display that position.
        padded_index = left_pad_this_index(index)
        last_end_position = end_position
        e steelblue(
            padded_index
          )+
          royalblue('Beta-sheet:   ')+
          'Starting aminoacid: '+
          colourize_this_aminoacid(starting_aminoacid)+
          ','+lightgreen(start_position.to_s.rjust(3))+
          ' ('+colourize_this_aminoacid_three_to_one(starting_aminoacid)+
          ')'+
          ' Last aminoacid: '+colourize_this_aminoacid(last_aminoacid)+
          ','+lightgreen(end_position.to_s.rjust(3))+
          ' ('+
          colourize_this_aminoacid_three_to_one(last_aminoacid)+
          ')'+
          ' Length: '+
          mediumpurple(
            (end_position - (start_position-1)).to_s.rjust(2)
          )+
          ' (chain: '+this_chain+')'
      else
        # In that case we may not as it is an illogical
        # result.
        index -= 1
      end
    else
      e steelblue(
            padded_index
        )+
        royalblue('Beta-sheet:   ')+
        'Starting aminoacid: '+
        colourize_this_aminoacid(starting_aminoacid)+
        ','+lightgreen(start_position.to_s.rjust(3))+
        ' ('+
        colourize_this_aminoacid_three_to_one(starting_aminoacid)+
        ')'+
        ' Last aminoacid: '+colourize_this_aminoacid(last_aminoacid)+
        ','+lightgreen(end_position.to_s.rjust(3))+
        ' ('+
        colourize_this_aminoacid_three_to_one(starting_aminoacid)+
        ')'+
        ' Length: '+
        (end_position - (start_position-1)).to_s+
        ' (chain: '+this_chain+')'
    end
  }
end

#reset ⇒ Object

#

reset (reset tag)

#

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# File 'lib/bioroebe/pdb/report_secondary_structures_from_this_pdb_file.rb', line 39

def reset
  super()
  # ======================================================================= #
  # === @alpha_helices
  # ======================================================================= #
  @alpha_helices = nil
  # ======================================================================= #
  # === @beta_sheets
  # ======================================================================= #
  @beta_sheets   = nil
end

#run ⇒ Object

#

run (run tag)

#

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# File 'lib/bioroebe/pdb/report_secondary_structures_from_this_pdb_file.rb', line 207

def run
  commandline_arguments?.each {|this_pdb_file|
    work_on_this_pdb_file(this_pdb_file)
  }
end

#work_on_this_pdb_file(i) ⇒ Object

#

work_on_this_pdb_file

#

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# File 'lib/bioroebe/pdb/report_secondary_structures_from_this_pdb_file.rb', line 54

def work_on_this_pdb_file(i)
  if File.exist? i
    dataset = File.readlines(i)
    @alpha_helices = dataset.select {|entry| entry.start_with?('HELIX  ') }
    @beta_sheets   = dataset.select {|entry| entry.start_with?('SHEET  ') }
    report_alpha_helices
    cliner {{ colour: 'steelblue' }}
    report_beta_sheets
  else
    no_file_exists_at(i)
  end    
end