Class: Bioroebe::GUI::UniversalWidgets::ParsePdbFile

Inherits:
UniversalWidgets::Base
  • Object
show all
Includes:
CommandlineArguments, Bioroebe::GUI
Defined in:
lib/bioroebe/gui/universal_widgets/parse_pdb_file/parse_pdb_file.rb

Overview

Bioroebe::GUI::UniversalWidgets::ParsePdbFile

Constant Summary collapse

TITLE =
#

TITLE

Specify which title to use for this widget.

#
' Parse a .pdb file '
WIDTH =
#

WIDTH

#
'75% or 1200px minimum'
HEIGHT =
#

HEIGHT

#
'55% or 500px minimum'
FONT_LARGE =
#

FONT_LARGE

#
'Calibri 32'
MONOSPACED_FONT =
#

MONOSPACED_FONT

When this font is changed, don’t forget to also change the font at SMALLER_FONT.

#
:hack_22
USE_THIS_FONT = 
MONOSPACED_FONT
USE_THIS_MONOFONT = 
MONOSPACED_FONT
SMALLER_FONT =
#

SMALLER_FONT

#
:hack_16
USE_THIS_SLIGHTLY_SMALLER_FONT =
#

USE_THIS_SLIGHTLY_SMALLER_FONT

#
:hack_16
USE_THIS_HEADER =
#

USE_THIS_HEADER

#
['one-letter abbreviation', 'n times']
GENERATE_N_AMINOACIDS_BY_DEFAULT =
#

GENERATE_N_AMINOACIDS_BY_DEFAULT

#
15
COLOUR_FOR_NON_MATCHES =
#

COLOUR_FOR_NON_MATCHES

This is the colour that will be used for non-matching nucleotides.

#
:magenta

Constants included from Bioroebe::GUI

ARRAY_ALL_GTK_WIDGETS, FONT_SIZE, OLD_VERBOSE_VALUE, Bioroebe::GUI::USE_THIS_FONT_FAMILY_FOR_GUI_APPLICATIONS

Constants included from ColoursForBase

ColoursForBase::ARRAY_HTML_COLOURS_IN_USE

Class Method Summary collapse

Instance Method Summary collapse

Methods included from Bioroebe::GUI

#disable_warnings, #enable_warnings, #log_dir?

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?

Constructor Details

#initialize(commandline_arguments = nil, run_already = true) ⇒ ParsePdbFile

#

initialize

#


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# File 'lib/bioroebe/gui/universal_widgets/parse_pdb_file/parse_pdb_file.rb', line 95

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

Class Method Details

.[](i = ARGV) ⇒ Object

#

Bioroebe::GUI::UniversalWidgets::ParsePdbFile[]

#


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# File 'lib/bioroebe/gui/universal_widgets/parse_pdb_file/parse_pdb_file.rb', line 436

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

.run(i = ARGV) ⇒ Object

#

Bioroebe::GUI::Gtk::ParsePdbFile.run

#


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# File 'lib/bioroebe/gui/universal_widgets/parse_pdb_file/parse_pdb_file.rb', line 443

def self.run(
    i = ARGV
  )
  r = ::Gtk.runner_factory(
    ::Bioroebe::GUI::Gtk::ParsePdbFile.new(i)
  )
  r.background_colour(:white)
  return r
end

Instance Method Details

#a_new_file_has_been_loaded(i = @file_name.text?) ⇒ Object

#

a_new_file_has_been_loaded

Use this method to indicate that a new file has been loaded.

#


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# File 'lib/bioroebe/gui/universal_widgets/parse_pdb_file/parse_pdb_file.rb', line 230

def a_new_file_has_been_loaded(
    i = @file_name.text?
  )
  @dataset = ::Bioroebe::ParsePdbFile.new(i) { :be_silent }
  update_the_scrolled_window_with_the_current_aminoacid_sequence
  update_the_label_protein_contans_n_alpha_helices
  update_the_aminoacid_sequence_is_label
  update_label_taxid
end

#add_how_many_alpha_helices_can_be_found_in_this_protein ⇒ Object

#

add_how_many_alpha_helices_can_be_found_in_this_protein

#


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# File 'lib/bioroebe/gui/universal_widgets/parse_pdb_file/parse_pdb_file.rb', line 270

def add_how_many_alpha_helices_can_be_found_in_this_protein
  _ = create_hbox
  @label_protein_contans_n_alpha_helices = left_aligned_text('This protein contains <b>'+
       @dataset.n_alpha_helices?.to_s+
       '</b> alpha-helices.')
  @label_protein_contans_n_alpha_helices.make_selectable
  _ << @label_protein_contans_n_alpha_helices
  @outer_vbox.minimal(_, 2)
end

#add_information_about_how_many_atom_entries_are_part_of_that_pdb_file ⇒ Object

#

add_information_about_how_many_atom_entries_are_part_of_that_pdb_file

#


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# File 'lib/bioroebe/gui/universal_widgets/parse_pdb_file/parse_pdb_file.rb', line 168

def add_information_about_how_many_atom_entries_are_part_of_that_pdb_file
  _ = create_hbox
  text = left_aligned_text(
    "\n<b>#{@dataset.n_atom_entries?.to_s}"\
    "</b> ATOM entries were found being part of this file."
  )
  text.make_selectable
  _ << text
  @outer_vbox.add(_)
end

#add_the_aminoacid_sequence ⇒ Object

#

add_the_aminoacid_sequence

#


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# File 'lib/bioroebe/gui/universal_widgets/parse_pdb_file/parse_pdb_file.rb', line 399

def add_the_aminoacid_sequence
  _ = create_vbox
  @text_for_the_aminoacid_sequence = left_aligned_text(
    'The aminoacid sequence (<b>'+@dataset.n_aminoacids?.to_s+
    '</b> aminoacids) is:'
  )
  @text_for_the_aminoacid_sequence.make_selectable
  _.minimal(@text_for_the_aminoacid_sequence, 10)
  update_the_scrolled_window_with_the_current_aminoacid_sequence
  _.minimal(@scrolled_window, 15)
  @outer_vbox.add(_)
end

#add_the_maximum_difference_between_the_atoms ⇒ Object

#

add_the_maximum_difference_between_the_atoms

#


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# File 'lib/bioroebe/gui/universal_widgets/parse_pdb_file/parse_pdb_file.rb', line 383

def add_the_maximum_difference_between_the_atoms
  _ = create_hbox
  if @dataset
    text = left_aligned_text(
             'The maximum difference between the atoms is <b>'+
             @dataset.max_distance?.to_s.to_f.round(3).to_s+'</b>.'
           )
    text.make_selectable
    _ << text
  end
  @outer_vbox.add(_)
end

#border_size? ⇒ Boolean

#

border_size?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/parse_pdb_file/parse_pdb_file.rb', line 136

def border_size?
  25
end

#connect_the_skeleton ⇒ Object

#

connect_the_skeleton (connect tag, skeleton tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/parse_pdb_file/parse_pdb_file.rb', line 304

def connect_the_skeleton
  abort_on_exception
  
  @outer_vbox = create_vbox
  @outer_vbox.set_border_width(18)
  _ = first_argument?.to_s
  if _.start_with? '--'
    _ = '' # In this case ignore it.
  end
  if File.exist? _
  else
    ::Bioroebe.no_file_exists_at(_)
  end
  @dataset = ::Bioroebe::ParsePdbFile.new(_) { :be_silent }
  hbox = create_hbox
  hbox.minimal(
    text('File name: ')
  )
  @file_name = bold_text(File.absolute_path(_))

  @file_name.make_selectable
  hbox.minimal(@file_name)
  hbox.minimal(return_widget_containing_a_file_open_button, 9)
  @outer_vbox.minimal(hbox, 8)
  @outer_vbox.minimal(horizontal_spacer, 2)
  hbox = create_hbox
  @label_the_name_of_the_organism = text(
    'The name of the organism (Entry: '+
    '<span weight="bold" color="steelblue">ORGANISM_SCIENTIFIC</span>'+
    +') is'
  )
  @label_the_name_of_the_organism.make_selectable
  @label_the_name_of_the_organism.do_markify
  hbox.minimal(@label_the_name_of_the_organism, 5)
  @outer_vbox.add(hbox)
  if @dataset
    taxid = @dataset.taxid_of_the_species?.to_s
    @label_taxid = text(
      '<span weight="bold" color="indigo">'+@dataset.name_of_the_species?.to_s+
      '</span>'+
      ' (Taxid: ➡️ '+
      '<span weight="bold"><a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id='+taxid+'">'+
      taxid+'</a></span>; '+@dataset.organism_common?.to_s+')'
    )
    @label_taxid.make_selectable
    @label_taxid.do_markify
    @outer_vbox.add(hbox(@label_taxid))
  end
  add_information_about_how_many_atom_entries_are_part_of_that_pdb_file
  add_the_aminoacid_sequence
  add_how_many_alpha_helices_can_be_found_in_this_protein
  add_the_maximum_difference_between_the_atoms

  window = runner_widget(nil, width?, height?, title?)
  window << @outer_vbox

  ::UniversalWidgets.set_main_window(window)
  upon_delete_event_quit_the_application
  window.use_this_font = font?
  window.show_all
  window.set_size_request(width?, height?)
  window.set_default_size(width?, height?)
  window.set_padding(padding?)
  window.set_border_size(border_size?)
  jump_into_the_first_entry
  window.top_left
  run_main
end

#create_the_scrolled_window_containing_the_aminoacid_sequence ⇒ Object

#

create_the_scrolled_window_containing_the_aminoacid_sequence

#


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# File 'lib/bioroebe/gui/universal_widgets/parse_pdb_file/parse_pdb_file.rb', line 415

def create_the_scrolled_window_containing_the_aminoacid_sequence
  @text_buffer = create_text_buffer
  @text_view = create_text_view(@text_buffer)
  @scrolled_window = create_scrolled_window(@text_view) { :left_right }
  @scrolled_window.clear_background
  @scrolled_window.css_class('royalblue')
  @scrolled_window.bblack1
  @scrolled_window.width_height(400, 50)
  @scrolled_window.set_name('differently_coloured_selection')
end

#create_the_skeleton ⇒ Object

#

create_the_skeleton (create tag, skeleton tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/parse_pdb_file/parse_pdb_file.rb', line 283

def create_the_skeleton
  create_the_scrolled_window_containing_the_aminoacid_sequence
end

#handle_CSS_rules ⇒ Object Also known as: handle_CSS

#

handle_CSS_rules (CSS tag, css tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/parse_pdb_file/parse_pdb_file.rb', line 157

def handle_CSS_rules
  use_gtk_paradise_project_css_file
  append_project_css_file
  add_these_custom_CSS_rules '
'
  apply_the_CSS_rules
end

#jump_into_the_first_entry ⇒ Object

#

jump_into_the_first_entry

#


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# File 'lib/bioroebe/gui/universal_widgets/parse_pdb_file/parse_pdb_file.rb', line 376

def jump_into_the_first_entry
  entry1?.do_focus
end

#main_font? ⇒ Boolean

#

main_font?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/parse_pdb_file/parse_pdb_file.rb', line 143

def main_font?
  USE_THIS_FONT
end

#padding? ⇒ Boolean

#

padding?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/parse_pdb_file/parse_pdb_file.rb', line 129

def padding?
  12
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/parse_pdb_file/parse_pdb_file.rb', line 110

def reset
  super() if respond_to?(:super)
  reset_the_internal_variables
  reset_the_base_module # This must come after reset_the_internal_variables().
  infer_the_namespace
  # ======================================================================= #
  # === @configuration
  # ======================================================================= #
  @configuration = [true, __dir__, namespace?]
  # ======================================================================= #
  # === Set the title, width, height and the font in use.
  # ======================================================================= #
  title_width_height_font(TITLE, WIDTH, HEIGHT, USE_THIS_FONT)
  handle_CSS if use_gtk3?
end

#return_widget_containing_a_file_open_button ⇒ Object

#

return_widget_containing_a_file_open_button (open tag)

This is the widget with the “open file” functionality.

#


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# File 'lib/bioroebe/gui/universal_widgets/parse_pdb_file/parse_pdb_file.rb', line 245

def return_widget_containing_a_file_open_button
  button_open_file = file_open_button
  button_open_file.bblack1
  button_open_file.on_click {
    create_a_new_file_chooser_dialog(
      button_open_file,
      'Open file'
    ) {{
      filter_for: '.pdb', # We only need .pdb files.
      additional_directories: Bioroebe.project_log_directory?+'pdb/'
    }}
    _ = ::Gtk.main_file?
    if _ and !_.empty?
      @file_name.set_text(
        _.to_s
      )
      a_new_file_has_been_loaded
    end
  }
  return button_open_file
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/parse_pdb_file/parse_pdb_file.rb', line 290

def run
  run_super
end

#scrolled_window? ⇒ Boolean Also known as: entry1?

#

scrolled_window?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/parse_pdb_file/parse_pdb_file.rb', line 429

def scrolled_window?
  @scrolled_window
end

#slightly_smaller_font? ⇒ Boolean

#

slightly_smaller_font?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/parse_pdb_file/parse_pdb_file.rb', line 150

def slightly_smaller_font?
  USE_THIS_SLIGHTLY_SMALLER_FONT
end

#smaller_font? ⇒ Boolean

#

smaller_font?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/parse_pdb_file/parse_pdb_file.rb', line 297

def smaller_font?
  SMALLER_FONT
end

#update_label_taxid ⇒ Object

#

update_label_taxid

#


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# File 'lib/bioroebe/gui/universal_widgets/parse_pdb_file/parse_pdb_file.rb', line 213

def update_label_taxid
  taxid = @dataset.taxid_of_the_species?.to_s
  @label_taxid.set_text(
    '<span weight="bold" color="indigo">'+@dataset.name_of_the_species?.to_s+
    '</span>'+
    ' (Taxid: ➡️ '+
    '<span weight="bold"><a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id='+taxid+'">'+
    taxid+'</a></span>; '+@dataset.organism_common?.to_s+')'
  )
  @label_taxid.do_markify
end

#update_the_aminoacid_sequence_is_label ⇒ Object

#

update_the_aminoacid_sequence_is_label

#


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# File 'lib/bioroebe/gui/universal_widgets/parse_pdb_file/parse_pdb_file.rb', line 182

def update_the_aminoacid_sequence_is_label
  @text_for_the_aminoacid_sequence.set_text(
    'The aminoacid sequence (<b>'+@dataset.n_aminoacids?.to_s+
    '</b> aminoacids) is:'
  )
  @text_for_the_aminoacid_sequence.do_markify
end

#update_the_label_protein_contans_n_alpha_helices ⇒ Object

#

update_the_label_protein_contans_n_alpha_helices

#


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# File 'lib/bioroebe/gui/universal_widgets/parse_pdb_file/parse_pdb_file.rb', line 193

def update_the_label_protein_contans_n_alpha_helices
  _ = 'This protein contains <b>'+
  @dataset.n_alpha_helices?.to_s+
  '</b> alpha-helices.'
  @label_protein_contans_n_alpha_helices.set_text(_)
  @label_protein_contans_n_alpha_helices.do_markify
end

#update_the_scrolled_window_with_the_current_aminoacid_sequence ⇒ Object

#

update_the_scrolled_window_with_the_current_aminoacid_sequence

#


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# File 'lib/bioroebe/gui/universal_widgets/parse_pdb_file/parse_pdb_file.rb', line 204

def update_the_scrolled_window_with_the_current_aminoacid_sequence
  @scrolled_window.set_text(
    @dataset.aminoacid_sequence?.to_s
  )
end