Bio::Graphics::DrawTransmembrane - draw a cartoon of an Alpha-helical transmembrane protein.

- NAME
- SYNOPSIS
- DESCRIPTION
- AUTHOR

# NAME

Bio::Graphics::DrawTransmembrane - draw a cartoon of an Alpha-helical transmembrane protein.

# SYNOPSIS

      use Bio::Graphics::DrawTransmembrane;
      my @topology = (20,45,59,70,86,109,145,168,194,220);

      ## Simple use - -topology is the only option that is required

      my $im = Bio::Graphics::DrawTransmembrane->new(
          -title => 'This is a cartoon displaying transmembrane helices.',
          -topology => \@topology);

      ## More advanced use
      my %labels = (5 => '5 - Sulphation Site',
                    21 => '1st Helix',
                    47 => '40 - Mutation',
                    60 => 'Voltage Sensor',
                    72 => '72 - Mutation 2',
                    73 => '73 - Mutation 3',
                    138 => '138 - Glycosylation Site',
                    170 => '170 - Phosphorylation Site',
                    200 => 'Last Helix');

      my $im = Bio::Graphics::DrawTransmembrane->new(-n_terminal=> 'out',
                                      -topology => \@topology,
                                      -bold_helices=> 1,
                                      -labels=> \%labels,
                                      -text_offset=> -15,
                                      -outside_label=>'Lumen',
                                      -inside_label=>'Cytoplasm',
                                      -membrane_label=>'Membrane',
                                      -vertical_padding=> 155);

      ## Parse Tmhmm data
      use Bio::Tools::Tmhmm;
      my $im = Bio::Graphics::DrawTransmembrane->new(
          -title=>'Let\'s parse some Tmhmm output...',
          -bold_helices=> 1);
      open(FILE, 'tmhmm.out');
      my $parser = new Bio::Tools::Tmhmm(-fh => \*FILE );
      while(my $tmhmm_feat = $parser->next_result ) {
            ## Load features into DrawTransmembrane object
            $im->add_tmhmm_feat($tmhmm_feat);
      }
      close FILE;

      ## Now write the image to a .png file
      open(OUTPUT, ">output.png");
      binmode OUTPUT;
      print OUTPUT $im->png;
      close OUTPUT;

# DESCRIPTION

A module to draw a cartoon of an alpha-helical transmembrane protein. It uses GD and allows the image to be written to a .png file.

The options are a set of tag/value pairs as follows:

      Option              Value                                         Default
      ------              -----                                         -------

      -topology           Array containing transmembrane helix          none
                          boundaries. This is the only option that
                          is required

      -topology_string    Alternative to -topology, provide a string    none
                          containing the topology data in the form
                          A.11,31;B.41,59;C.86,107;D.145,166

      -n_terminal         Location of the N-terminal of the sequence,   out
                          either 'in' or 'out'

      -title              Title to add to the image                     none

      -inside_label       Label for the inside of the membrane          Cytoplasmic

      -outside_label      Label for the outside of the membrane         Extracellular

      -membrane_label     Label for the membrane                        Plasma Membrane

      -colour_scheme      Colour scheme to use. Current choices are     blue
                          blue, yellow, red, green, pink or white.

      -labels             Label loops and helices using data from a     none
                          hash, e.g.

                          %labels = (138 => 'Glycosylation Site',
                                     190 => 'Binding Site');

                          The hash key must be numeric, ranges are
                          not allowed.

      -bold_helices       Draws black boxes round helices               1

      -bold_labels        Draws black boxes round labels                0

      -text_offset        Shift the text labeling the loops. Use a      0
                          negative value to shift it left, a positive
                          value to shift it right

      -helix_height       Transmembrane helix height                    130

      -helix_width        Transmembrane helix width                     50

      -loop_width         Loop width                                    20

      -vertical_padding   Vertical padding                              140

      -horizontal_padding Horizontal Padding                            150

      -membrane_offset    Offest between helix end and membrane         6

      -short_loop_height  Height of short loops                         90

      -medium_loop_height Height of medium loops                        120

      -long_loop_height   Height of long loops                          150

      -short_loop_limit   Length in residues below which a loop is      15
                          classed as short

      -long_loop_limit    Length in residues above which a loop is      30
                          classed as long

      -loop_heights       Explicitly set heights of each loop, e.g.

                          %loop_heights = (1 => 45,
                                           2 => 220,
                                           3 => 50,
                                           4 => 220,
                                           9 => 70);

                          The key corresponds to the loop number. Both
                          key and value must be numeric. If you use
                          -loop_height and there is a defined height
                          for the current loop then other height values
                          will be overridden

      -n_terminal_height  Height of N-terminal                          150

      -c_terminal_height  Height of C-terminal                          80

      -n_terminal_offset  Shift the N-terminal left by this amount      0

      -c_terminal_offset  Shift the C-terminal right by this amount     0

      -helix_label        Change the 'S' label on each helix. Only 1    S
                          character is allowed

      -show_labels        Display text labels                           on

      -draw_cytosol       Show the cytosol                              false

      -draw_bilayer       Show the membrane                             true

      -draw_loops         Show the loops                                true

      -draw_terminai      Show the terminai                             true

      -draw_helices       Show the helices                              true

      -dontsort           Don't automatically sort the topology array   0

      -ttf_font           Path to TTF font, e.g.                        none
                          /usr/share/fonts/msttcorefonts/arial.ttf

      -ttf_font_size      Default size for TTF font. Use 7-9 with       8
                          Arial for best results

Height, width, padding and other numerical values can gernerally be left alone. They are useful if your labels consists of a lot of text as this may lead to them overlapping. In this case try increasing the loop_width or helix_width options. -text_offset is also very useful for avoiding overlapping.

# AUTHOR

Tim Nugent <timnugent@gmail.com>

Bio::Graphics::DrawTransmembrane - draw a cartoon of an Alpha-helical transmembrane protein.