Class: Bioroebe::HelixWheel

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/pdb_and_protein_structure/helical_wheel.rb

Overview

Bioroebe::HelixWheel

Constant Summary collapse

GS_HEADER_START =
#

GS_HEADER_START

#
<<EOF;
%!PS-Adobe-
%%BoundingBox: (atend)
%1 0 0 setrgbcolor
%newpath
%37.5 161 moveto 557.5 161 lineto 557.5 681 lineto 37.5 681 lineto
%closepath stroke
297.5 421. translate 2 setlinewidth 1 setlinecap
/Helvetica findfont 20 scalefont setfont 0 0 moveto
EO
HELVETICA_FONT = 
'Helvetica'
HELVETICA_FONT_BOLD = 
'Helvetica-Bold'
FONT =
#

FONT

Define fonts to associate with each amino acid

#
{}

Constants inherited from CommandlineApplication

CommandlineApplication::OLD_VERBOSE_VALUE

Constants included from ColoursForBase

ColoursForBase::ARRAY_HTML_COLOURS_IN_USE

Constants inherited from Base

Base::NAMESPACE

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, #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(run_already = true) ⇒ HelixWheel

#

initialize

#


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# File 'lib/bioroebe/pdb_and_protein_structure/helical_wheel.rb', line 76

def initialize(
    run_already = true
  )
  reset
  run if run_already
end

Instance Method Details

#_(i) ⇒ Object

#

_

#


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# File 'lib/bioroebe/pdb_and_protein_structure/helical_wheel.rb', line 97

def _(i)
  @_ << i
end

#build_string ⇒ Object

#

build_string

#


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# File 'lib/bioroebe/pdb_and_protein_structure/helical_wheel.rb', line 104

def build_string
  _ GS_HEADER_START
  fetch_input
end

#cos(i) ⇒ Object

#

cos

#


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# File 'lib/bioroebe/pdb_and_protein_structure/helical_wheel.rb', line 112

def cos(i)
  Math.cos(i)
end

#fetch_input ⇒ Object

#

fetch_input

#


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# File 'lib/bioroebe/pdb_and_protein_structure/helical_wheel.rb', line 126

def fetch_input
  @input = $stdin.gets.chomp.strip # Read line of input
  # @input =~ s/\s//g # remove terminal carriage return and blanks
  use_this_regex = /^(\d+)/
  if ( @input =~ use_this_regex ) # if input begins with integer
    resno = $1 # extract it as initial residue number
  else
    resno = 1  # if not, set initial residue number = 1
  end
  radius =  50 # initialize values for radius,
  x      =   0
  y      = -50
  theta  = -90 # x, y and angle theta
  # print light gray spiral arc as succession of
  # line segments, 10 per residue
  npoints = 10 * (@input.size - 1)
  _ '0.8 0.8 0.8 setrgbcolor'+N # set colour to light gray
  _ 'newpath'+N                 # draw spiral arc
  _ sprintf('%8.3f %8.3f moveto'+N,x,y)
  (1 .. npoints).each {|d|             # 10 points per residue
    theta  += 10
    radius += 0.6          # increase radius and theta
    x = radius * cos(theta * 0.01747737)   # calculate new value of x
    y = radius * sin(theta * 0.01747737)   # and y
    printf("%8.3f %8.3f lineto"+N,x,y)
  }
  _ 'stroke'+N
  # ======================================================================= #
  # print residues and residue numbers
  # ======================================================================= #
  radius =  50 # reinitialize values for radius,
  x      =   0
  y      = -50
  theta  = -90 # x, y and angle theta
  _ '0 setgray'+N  # set colour to black
  @input.split('').each {|line|       # loop over characters from input line
    _ "/FONT{@input} findfont"        # set font appropriate
    _ ' 20 scalefont setfont'+N       # for this amino acid
    _ sprintf('%8.3f %8.3f moveto'+N,x,y)  # move to current point
    _ " (resno@input) stringwidth"    # adjust position to center residue
    _ ' pop -0.5 mul -7 rmoveto'+N    #    identification on point on spiral
    _ " (resno@input) show"+N         # print residue number and id
    _ "% theta resno@input"+N
    theta += 100
    radius += 6           #  set new values of angle, radius
    x = radius * cos(theta * 0.01747737) #  compute new values of x
    y = radius * sin(theta * 0.01747737) #     and y
    resno += 1                           #  increase residue number
  }
  _ 'showpage'+N             # postscript signals to
  _ "%%BoundingBox:"         # print
  xl = 297.5 - 1.05 * radius #   x
  xr = 297.5 + 1.05 * radius # and
  yb = 421.  - 1.05 * radius #   y
  yt = 421.  + 1.05 * radius # limits
  _ sprintf('%8.3f %8.3f %8.3f %8.3f'+N,xl,xr,yb,yt)
  _ 'showpage'+N
  _ '%%EOF'+N              #  and wind up
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/pdb_and_protein_structure/helical_wheel.rb', line 86

def reset
  super()
  # ======================================================================= #
  # === @_
  # ======================================================================= #
  @_ = ''.dup
end

#run ⇒ Object

#

run

#


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# File 'lib/bioroebe/pdb_and_protein_structure/helical_wheel.rb', line 196

def run
  build_string
  show_result
end

#show_result ⇒ Object

#

show_result

#


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# File 'lib/bioroebe/pdb_and_protein_structure/helical_wheel.rb', line 189

def show_result
  e @_
end

#sin(i) ⇒ Object

#

sin

#


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# File 'lib/bioroebe/pdb_and_protein_structure/helical_wheel.rb', line 119

def sin(i)
  Math.sin(i)
end