Class: Bioroebe::GUI::Gtk::ParsePdbFile

Inherits:
Gtk::Frame
  • Object
show all
Includes:
Gtk::BaseModule
Defined in:
lib/bioroebe/gui/gtk3/parse_pdb_file/parse_pdb_file.rb

Overview

Bioroebe::GUI::Gtk::ParsePdbFile

Constant Summary collapse

NAMESPACE =
#

NAMESPACE

#
inspect
TITLE =
#

TITLE

#
' Parse a .pdb file '
WIDTH =
#

WIDTH

#
1200
HEIGHT =
#

HEIGHT

#
500
USE_THIS_FONT =
#

USE_THIS_FONT

#
:dejavu_condensed_22

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

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

#

initialize

#

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# File 'lib/bioroebe/gui/gtk3/parse_pdb_file/parse_pdb_file.rb', line 54

def initialize(
    commandline_arguments = ARGV,
    run_already           = true
  )
  super(" #{TITLE} ")
  make_bold
  reset
  set_commandline_arguments(
    commandline_arguments
  )
  run if run_already
end

Class Method Details

.run(i = ARGV) ⇒ Object

#

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

#

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# File 'lib/bioroebe/gui/gtk3/parse_pdb_file/parse_pdb_file.rb', line 327

def self.run(
    i = ARGV
  )
  require 'gtk_paradise/run'
  _ = ::Bioroebe::GUI::Gtk::ParsePdbFile.new(i)
  r = ::Gtk.run
  r << _
  r.automatic_size_then_automatic_title
  r.middle_then_run
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/gtk3/parse_pdb_file/parse_pdb_file.rb', line 266

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/gtk3/parse_pdb_file/parse_pdb_file.rb', line 205

def add_how_many_alpha_helices_can_be_found_in_this_protein
  _ = gtk_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/gtk3/parse_pdb_file/parse_pdb_file.rb', line 306

def add_information_about_how_many_atom_entries_are_part_of_that_pdb_file
  _ = gtk_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/gtk3/parse_pdb_file/parse_pdb_file.rb', line 189

def add_the_aminoacid_sequence
  _ = gtk_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/gtk3/parse_pdb_file/parse_pdb_file.rb', line 173

def add_the_maximum_difference_between_the_atoms
  _ = gtk_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/gtk3/parse_pdb_file/parse_pdb_file.rb', line 92

def border_size?
  25
end

#connect_skeleton ⇒ Object

#

connect_skeleton (connect tag)

#

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# File 'lib/bioroebe/gui/gtk3/parse_pdb_file/parse_pdb_file.rb', line 120

def connect_skeleton
  abort_on_exception
  @outer_vbox = gtk_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 = gtk_hbox
  hbox.minimal(text('File name: '))
  @file_name = text_bold(File.absolute_path(_))
  hbox.minimal(@file_name)
  hbox.minimal(return_widget_containing_a_file_open_button, 9)
  @outer_vbox.minimal(hbox, 8)
  @outer_vbox.minimal(gtk_horizontal_spacer, 2)
  hbox = gtk_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.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
  add(@outer_vbox)
  set_border_width(5)
end

#create_skeleton ⇒ Object

#

create_skeleton (create tag)

#

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# File 'lib/bioroebe/gui/gtk3/parse_pdb_file/parse_pdb_file.rb', line 113

def create_skeleton
  create_the_scrolled_window_containing_the_aminoacid_sequence
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/gtk3/parse_pdb_file/parse_pdb_file.rb', line 99

def create_the_scrolled_window_containing_the_aminoacid_sequence
  @text_buffer = gtk_text_buffer
  @text_view = gtk_text_view(@text_buffer)
  @scrolled_window = gtk_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

#padding? ⇒ Boolean

#

padding?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/gui/gtk3/parse_pdb_file/parse_pdb_file.rb', line 85

def padding?
  12
end

#reset ⇒ Object

#

reset (reset tag)

#

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# File 'lib/bioroebe/gui/gtk3/parse_pdb_file/parse_pdb_file.rb', line 70

def reset
  reset_the_internal_variables
  # ======================================================================= #
  # === @configuration
  # ======================================================================= #
  @configuration = [true, __dir__, NAMESPACE]
  title_width_height_font(TITLE, WIDTH, HEIGHT, USE_THIS_FONT)
  use_gtk_paradise_project_css_file
  append_project_CSS_file 
  infer_the_size_automatically
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/gtk3/parse_pdb_file/parse_pdb_file.rb', line 281

def return_widget_containing_a_file_open_button
  button_open_file = gtk_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/gtk3/parse_pdb_file/parse_pdb_file.rb', line 320

def run
  create_skeleton_then_connect_skeleton
end

#update_label_taxid ⇒ Object

#

update_label_taxid

#

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# File 'lib/bioroebe/gui/gtk3/parse_pdb_file/parse_pdb_file.rb', line 249

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/gtk3/parse_pdb_file/parse_pdb_file.rb', line 218

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/gtk3/parse_pdb_file/parse_pdb_file.rb', line 229

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/gtk3/parse_pdb_file/parse_pdb_file.rb', line 240

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