/usr/share/perl5/Bio/Graphics/DrawTransmembrane.pm is in libbio-graphics-perl 2.37-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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use strict;
use warnings;
use GD;
use base 'Bio::Root::Root';
my %DRAWOPTIONS = (
## general parameters
'topology' => { 'private' => 'topology_array',
'default' => []},
'topology_string' => { 'private' => 'topology_string',
'default' => 0},
'n_terminal' => { 'private' => 'n_term',
'default' => 'out', },
'title' => { 'private' => 'title',
'default' => ''},
'inside_label' => { 'private' => 'in',
'default' => "Cytoplasmic"},
'outside_label' => { 'private' => 'out',
'default' => "Extracellular"},
'membrane_label' => { 'private' => 'membrane',
'default' => "Plasma Membrane"},
## dimensions
'helix_height' => { 'private' => 'helix_height',
'default' => 130},
'helix_width' => { 'private' => 'helix_width',
'default' => 50},
'loop_width' => { 'private' => 'loop_width',
'default' => 20},
'vertical_padding' => { 'private' => 'vertical_padding',
'default' => 140},
'horizontal_padding' => { 'private' => 'horizontal_padding',
'default' => 150},
'membrane_offset' => { 'private' => 'offset',
'default' => 6},
## loop lengths and limits
'short_loop_height' => { 'private' => 'short_loop',
'default' => 90},
'medium_loop_height' => { 'private' => 'medium_loop',
'default' => 120},
'long_loop_height' => { 'private' => 'long_loop',
'default' => 150},
'short_loop_limit' => { 'private' => 'short_loop_limit',
'default' => 15},
'long_loop_limit' => { 'private' => 'long_loop_limit',
'default' => 30},
'n_terminal_height' => { 'private' => 'n_terminal_height',
'default' => 150},
'c_terminal_height' => { 'private' => 'c_terminal_height',
'default' => 80},
'loop_heights' => { 'private' => 'loop_heights',
'default' => {}},
'n_terminal_offset' => { 'private' => 'n_term_offset',
'default' => 0},
'c_terminal_offset' => { 'private' => 'c_term_offset',
'default' => 0},
## colour scheme & display options
'show_labels' => { 'private' => 'labels',
'default' => 'on'},
'bold_helices' => { 'private' => 'bold_helices',
'default' => 1},
'bold_labels' => { 'private' => 'bold_labels',
'default' => 0},
'colour_scheme' => { 'private' => 'scheme',
'default' => 'yellow'},
'draw_cytosol' => { 'private' => 'draw_cytosol',
'default' => 0},
'draw_bilayer' => { 'private' => 'draw_bilayer',
'default' => 1},
'draw_loops' => { 'private' => 'draw_loops',
'default' => 1},
'draw_terminai' => { 'private' => 'draw_terminai',
'default' => 1},
'draw_helices' => { 'private' => 'draw_helices',
'default' => 1},
## labeling options
'labels' => { 'private' => 'loop_labels',
'default' => []},
'text_offset' => { 'private' => 'text_offset',
'default' => 0},
'helix_label' => { 'private' => 'helix_label',
'default' => 'S'},
'n_term_label' => { 'private' => 'n_term_label',
'default' => 'N-Terminal'},
'c_term_label' => { 'private' => 'c_term_label',
'default' => 'C-Terminal'},
'dontsort' => { 'private' => 'dontsort',
'default' => 0},
'ttf_font' => { 'private' => 'ttf_font',
'default' => 0},
'ttf_font_size' => { 'private' => 'ttf_font_size',
'default' => 8},
);
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my %opt = @args;
%opt = map {my $k = $_;
$k =~ s{^-}{};
$k => $opt{$_}} keys %opt;
# need to shore up private variables, check for req'd parameters
for my $param (sort keys %DRAWOPTIONS) {
my ($priv, $def) = ($DRAWOPTIONS{$param}->{'private'},$DRAWOPTIONS{$param}->{'default'});
$self->{$priv} = (exists $opt{$param}) ? $opt{$param} : $def;
}
$self->{'loop_count'} = 1;
return $self;
}
sub png {
my $self = shift;
my @numeric = ('helix_height','helix_width','loop_width','vertical_padding','horizontal_padding','short_length','medium_loop_length','long_loop_length','short_loop_limit','long_loop_limit','n_terminal_height','membrane_offset','text_offset','n_term_offset','c_term_offset');
foreach (@numeric){
die "\nParameter $_ must be numeric.\n\n" if exists $self->{$_} && $self->{$_} =~ /-{?}\D+/;
}
foreach (keys %{$self->{'loop_labels'}}){
die "\nLabel position $_ must be numeric.\n\n" if $_ =~ /\D+/;
}
foreach (keys %{$self->{'loop_heights'}}){
die "\nLoop number $_ must be numeric.\n\n" if $_ =~ /\D+/;
}
foreach (values %{$self->{'loop_heights'}}){
die "\nLoop height $_ must be numeric.\n\n" if $_ =~ /\D+/;
}
## n-terminal defaults to outside in it's not in,inside,out,outside
$self->{'n_term'} = 'out' if (($self->{'n_term'} ne 'in')&&($self->{'n_term'} ne 'inside')&&($self->{'n_term'} ne 'out')||$self->{'n_term'} eq 'outside');
$self->{'n_term'} = 'in' if $self->{'n_term'} eq 'inside';
if ($self->{'topology_string'}){
$self->{'topology_string'} =~ s/\D\.//g;
$self->{'topology_string'} =~ s/;/,/g;
@{$self->{'topology_array'}} = split(/,/,$self->{'topology_string'});
}
## check to make sure we have pairs of helix boundaries and that data is numeric otherwise quit
if (scalar @{$self->{'topology_array'}} % 2){
die "\nUneven number of helix boundaries.\n\n";
}
foreach (@{$self->{'topology_array'}}){
if ($_ =~ /\D/){
die "\nTopology data is not numeric. $_\n\n";
}
}
## check to make sure the TTF font exists, otherwise use gdSmallFont
if ($self->{'ttf_font'}){
unless (-e $self->{'ttf_font'}){
print "\nCan't find font ".$self->{'ttf_font'}.".\n";
$self->{'ttf_font'} = 0;
}
}
my @sorted_topology = sort {$a <=> $b} @{$self->{'topology_array'}};
## Don't automatically sort the topology array
@sorted_topology = @{$self->{'topology_array'}} if $self->{'dontsort'};
$self->{'helix_count'} = scalar @{$self->{'topology_array'}} / 2;
unless ($self->{'helix_count'}){
die "\nNo topology data found.\n\n";
}
## put helix start/stop points in $self->{'helix_span'} and loop lengths in $self->{'loop_length'}
foreach (0..($self->{'helix_count'} - 1)){
my $count = $_ * 2;
$self->{'helix_span'}{$_ + 1}{'start'} = $sorted_topology[$count];
$self->{'helix_span'}{$_ + 1}{'stop'} = $sorted_topology[$count + 1];
$self->{'loop_length'}{$_ + 1} = scalar ($sorted_topology[$count + 2] - $sorted_topology[$count + 1]) unless ($_ + 1 == $self->{'helix_count'});
}
$self->{'width'} = ($self->{'horizontal_padding'} * 2) + ($self->{'helix_width'} * $self->{'helix_count'}) + ($self->{'loop_width'} * ($self->{'helix_count'} - 1));
$self->{'height'} = $self->{'helix_height'} + ($self->{'vertical_padding'} * 2);
## create a new image
$self->{'im'} = new GD::Image($self->{'width'},$self->{'height'});
$self->{'black'} = $self->{'im'}->colorAllocate(0,0,0);
$self->{'white'} = $self->{'im'}->colorAllocate(255,255,255);
$self->{'im'}->fill(0,0,$self->{'white'});
## write title
if ($self->{'ttf_font'}){
$self->{'im'}->stringFT($self->{'black'},$self->{'ttf_font'},$self->{'ttf_font_size'},0,4,12,$self->{'title'},{linespacing=>0.6,charmap => 'Unicode',}) if $self->{'title'};
}else{
$self->{'im'}->string(gdSmallFont,4,3,$self->{'title'},$self->{'black'}) if $self->{'title'};
}
$self->draw_cytosol if $self->{'draw_cytosol'};
$self->draw_bilayer if $self->{'draw_bilayer'};
$self->draw_loops if $self->{'draw_loops'};
$self->draw_terminai if $self->{'draw_terminai'};
$self->draw_helices if $self->{'draw_helices'};
## use GD to convert to png
return $self->{'im'}->GD::Image::png;
}
sub add_tmhmm_feat {
my $self = shift;
my $feat = shift;
#print Dumper $feat;
## add a helix from a tmhmm feature
if ($feat->{'_primary_tag'} eq 'transmembrane'){
push @{$self->{'topology_array'}},$feat->{'_location'}{'_start'};
push @{$self->{'topology_array'}},$feat->{'_location'}{'_end'};
}
## i've made a few changes to TmHmm.pm to include the inside/outside loops.
## this bit looks for the topology of the 1st residue so we can now position the n-terminal
if ($feat->{'_location'}{'_start'} == 1){
if ($feat->{'_primary_tag'} =~ /(\w+)_loop/){
$self->{'n_term'} = $1;
}
}
return $self;
}
sub draw_cytosol {
my $self = shift;
my $cytosol_offset = 5;
my $light_grey = $self->{'im'}->colorAllocate(164,164,164);
## draw cytosol
$self->{'im'}->filledRectangle(($self->{'horizontal_padding'} / 3) ,($self->{'vertical_padding'} + $self->{'helix_height'} - $cytosol_offset),($self->{'width'} - ($self->{'horizontal_padding'} / 3)),($self->{'vertical_padding'} + ($self->{'helix_height'} * 2 ) + $cytosol_offset),$light_grey);
return $self;
}
sub draw_bilayer {
my $self = shift;
my $dark_grey = $self->{'im'}->colorAllocate(40,40,40);
my $dark_grey1 = $self->{'im'}->colorAllocate(50,50,50);
my $dark_grey2 = $self->{'im'}->colorAllocate(60,60,60);
my $dark_grey3 = $self->{'im'}->colorAllocate(70,70,70);
## label either side of membrane
if ($self->{'ttf_font'}){
$self->{'im'}->stringFT($self->{'black'},$self->{'ttf_font'},$self->{'ttf_font_size'},0,($self->{'horizontal_padding'} / 3) + 2,($self->{'vertical_padding'} + $self->{'offset'} - 3),$self->{'out'},{linespacing=>0.6,charmap => 'Unicode',}) if $self->{'labels'};
$self->{'im'}->stringFT($self->{'black'},$self->{'ttf_font'},$self->{'ttf_font_size'},0,($self->{'horizontal_padding'} / 3) + 2,($self->{'vertical_padding'} + $self->{'helix_height'} - $self->{'offset'} + 12),$self->{'in'},{linespacing=>0.6,charmap => 'Unicode',}) if $self->{'labels'};
}else{
$self->{'im'}->string(gdSmallFont,($self->{'horizontal_padding'} / 3) + 2,($self->{'vertical_padding'} + $self->{'offset'} - 14),$self->{'out'},$self->{'black'}) if $self->{'labels'};
$self->{'im'}->string(gdSmallFont,($self->{'horizontal_padding'} / 3) + 2,($self->{'vertical_padding'} + $self->{'helix_height'} - $self->{'offset'} + 1),$self->{'in'},$self->{'black'}) if $self->{'labels'};
}
## draw membrane with graded fill
$self->{'im'}->filledRectangle(($self->{'horizontal_padding'} / 3),($self->{'vertical_padding'} + $self->{'offset'}),($self->{'width'} - $self->{'horizontal_padding'} / 3),($self->{'vertical_padding'} + $self->{'helix_height'} - $self->{'offset'}),$dark_grey);
$self->{'im'}->filledRectangle(($self->{'horizontal_padding'} / 3) + 1,($self->{'vertical_padding'} + $self->{'offset'}) + 1,($self->{'width'} - $self->{'horizontal_padding'} / 3) - 1,($self->{'vertical_padding'} + $self->{'helix_height'} - $self->{'offset'}) - 1,$dark_grey1);
$self->{'im'}->filledRectangle(($self->{'horizontal_padding'} / 3) + 2,($self->{'vertical_padding'} + $self->{'offset'}) + 2,($self->{'width'} - $self->{'horizontal_padding'} / 3) - 2,($self->{'vertical_padding'} + $self->{'helix_height'} - $self->{'offset'}) - 2,$dark_grey2);
$self->{'im'}->filledRectangle(($self->{'horizontal_padding'} / 3) + 3,($self->{'vertical_padding'} + $self->{'offset'}) + 3,($self->{'width'} - $self->{'horizontal_padding'} / 3) - 3,($self->{'vertical_padding'} + $self->{'helix_height'} - $self->{'offset'}) - 3,$dark_grey3);
## label membrane
if ($self->{'ttf_font'}){
$self->{'im'}->stringFT($self->{'white'},$self->{'ttf_font'},$self->{'ttf_font_size'},0,($self->{'horizontal_padding'} + ($self->{'helix_count'} * $self->{'helix_width'}) + (($self->{'helix_count'} - 1) * $self->{'loop_width'}) + 4) + 1,($self->{'vertical_padding'} + $self->{'helix_height'} - $self->{'offset'} - 3),$self->{'membrane'},{linespacing=>0.6,charmap => 'Unicode',}) if $self->{'labels'};
}else{
$self->{'im'}->string(gdSmallFont,($self->{'horizontal_padding'} + ($self->{'helix_count'} * $self->{'helix_width'}) + (($self->{'helix_count'} - 1) * $self->{'loop_width'}) + 4) + 1,($self->{'vertical_padding'} + $self->{'helix_height'} - $self->{'offset'} - 14),$self->{'membrane'},$self->{'white'}) if $self->{'labels'};
}
return $self;
}
sub draw_helices {
my $self = shift;
my $x = $self->{'horizontal_padding'};
my $y = $self->{'vertical_padding'};
my ($colour,$colour1,$colour2,$colour3,$colour4,$colour5,$colour6);
if($self->{'scheme'} eq 'blue'){
$colour = $self->{'im'}->colorAllocate(90,160,255);
$colour1 = $self->{'im'}->colorAllocate(80,150,255);
$colour2 = $self->{'im'}->colorAllocate(70,140,255);
$colour3 = $self->{'im'}->colorAllocate(60,130,255);
$colour4 = $self->{'im'}->colorAllocate(50,120,255);
$colour5 = $self->{'im'}->colorAllocate(40,110,255);
$colour6 = $self->{'im'}->colorAllocate(30,100,255);
}elsif($self->{'scheme'} eq 'pink'){
$colour = $self->{'im'}->colorAllocate(255,1,255);
$colour1 = $self->{'im'}->colorAllocate(240,1,255);
$colour2 = $self->{'im'}->colorAllocate(230,1,255);
$colour3 = $self->{'im'}->colorAllocate(220,1,255);
$colour4 = $self->{'im'}->colorAllocate(200,1,255);
$colour5 = $self->{'im'}->colorAllocate(180,1,255);
$colour6 = $self->{'im'}->colorAllocate(160,1,255);
}elsif($self->{'scheme'} eq 'green'){
$colour = $self->{'im'}->colorAllocate(5,240,0);
$colour1 = $self->{'im'}->colorAllocate(5,230,0);
$colour2 = $self->{'im'}->colorAllocate(5,220,0);
$colour3 = $self->{'im'}->colorAllocate(5,205,0);
$colour4 = $self->{'im'}->colorAllocate(5,195,0);
$colour5 = $self->{'im'}->colorAllocate(5,185,0);
$colour6 = $self->{'im'}->colorAllocate(5,155,0);
}elsif($self->{'scheme'} eq 'red'){
$colour = $self->{'im'}->colorAllocate(240,0,0);
$colour1 = $self->{'im'}->colorAllocate(230,0,0);
$colour2 = $self->{'im'}->colorAllocate(220,0,0);
$colour3 = $self->{'im'}->colorAllocate(205,0,0);
$colour4 = $self->{'im'}->colorAllocate(190,0,0);
$colour5 = $self->{'im'}->colorAllocate(170,0,0);
$colour6 = $self->{'im'}->colorAllocate(150,0,0);
}elsif($self->{'scheme'} eq 'white'){
$colour = $self->{'white'};
$colour1 = $self->{'white'};
$colour2 = $self->{'white'};
$colour3 = $self->{'white'};
$colour4 = $self->{'white'};
$colour5 = $self->{'black'};
$colour6 = $self->{'black'};
}else{
## default is yellow
$colour = $self->{'im'}->colorAllocate(255,235,55);
$colour1 = $self->{'im'}->colorAllocate(255,230,50);
$colour2 = $self->{'im'}->colorAllocate(255,220,40);
$colour3 = $self->{'im'}->colorAllocate(255,210,30);
$colour4 = $self->{'im'}->colorAllocate(255,200,20);
$colour5 = $self->{'im'}->colorAllocate(255,190,10);
$colour6 = $self->{'im'}->colorAllocate(255,180,0);
}
for (1..$self->{'helix_count'}){
## draw helix, with graduated fill
$self->{'im'}->filledRectangle($x,$y,($x + $self->{'helix_width'})-1,($y + $self->{'helix_height'})-1,$colour6);
$self->{'im'}->filledRectangle($x+1,$y+1,($x + $self->{'helix_width'})-1,($y + $self->{'helix_height'})-1,$colour5);
$self->{'im'}->filledRectangle($x+2,$y+2,($x + $self->{'helix_width'})-2,($y + $self->{'helix_height'})-2,$colour4);
$self->{'im'}->filledRectangle($x+3,$y+3,($x + $self->{'helix_width'})-3,($y + $self->{'helix_height'})-3,$colour3);
$self->{'im'}->filledRectangle($x+4,$y+4,($x + $self->{'helix_width'})-4,($y + $self->{'helix_height'})-4,$colour2);
$self->{'im'}->filledRectangle($x+5,$y+5,($x + $self->{'helix_width'})-5,($y + $self->{'helix_height'})-5,$colour1);
$self->{'im'}->filledRectangle($x+6,$y+6,($x + $self->{'helix_width'})-6,($y + $self->{'helix_height'})-6,$colour);
## draw a white box around it
if ($self->{'bold_helices'}){
$self->{'im'}->rectangle($x,$y,($x + $self->{'helix_width'}),($y + $self->{'helix_height'}),$self->{'black'});
$self->{'im'}->rectangle($x - 1,$y - 1,($x + $self->{'helix_width'} + 1),($y + $self->{'helix_height'} + 1),$self->{'white'});
}else{
$self->{'im'}->rectangle($x,$y,($x + $self->{'helix_width'}),($y + $self->{'helix_height'}),$self->{'white'});
}
## this is the text on each helix
my $text = substr($self->{'helix_label'},0,1).$_;
## draw a white box in the centre and label the helix
my $x_offset = 5;
$x_offset = 8 if $_ >= 10;
my $white_box = 12;
$white_box = 17 if $_ >= 10;
$self->{'im'}->filledRectangle(($x + ($self->{'helix_width'} / 2) - $x_offset) - 5,($y + ($self->{'helix_height'} / 2) - 7) - 3,$white_box + ($x + ($self->{'helix_width'} / 2) - $x_offset) + 3,12 + ($y + ($self->{'helix_height'} / 2) - 4),$colour1) if $self->{'labels'};
$self->{'im'}->filledRectangle(($x + ($self->{'helix_width'} / 2) - $x_offset) - 4,($y + ($self->{'helix_height'} / 2) - 7) - 2,$white_box + ($x + ($self->{'helix_width'} / 2) - $x_offset) + 2,12 + ($y + ($self->{'helix_height'} / 2) - 5),$colour2) if $self->{'labels'};
$self->{'im'}->filledRectangle(($x + ($self->{'helix_width'} / 2) - $x_offset) - 3,($y + ($self->{'helix_height'} / 2) - 7) - 1,$white_box + ($x + ($self->{'helix_width'} / 2) - $x_offset) + 1,12 + ($y + ($self->{'helix_height'} / 2) - 6),$colour3) if $self->{'labels'};
$self->{'im'}->filledRectangle(($x + ($self->{'helix_width'} / 2) - $x_offset) - 2,($y + ($self->{'helix_height'} / 2) - 7),$white_box + ($x + ($self->{'helix_width'} / 2) - $x_offset),12 + ($y + ($self->{'helix_height'} / 2) - 7),$self->{'white'}) if $self->{'labels'};
if ($self->{'ttf_font'}){
$self->{'im'}->stringFT($self->{'black'},$self->{'ttf_font'},$self->{'ttf_font_size'},0,($x + ($self->{'helix_width'} / 2) - $x_offset - 1),($y + ($self->{'helix_height'} / 2) + 4),$text,{linespacing=>0.6,charmap => 'Unicode',}) if $self->{'labels'};
}else{
$self->{'im'}->string(gdSmallFont,($x + ($self->{'helix_width'} / 2) - $x_offset),($y + ($self->{'helix_height'} / 2) - 7),$text,$self->{'black'}) if $self->{'labels'};
}
## label start and end positions of helices
$self->{'x'} = $x;
$self->{'y'} = $y;
if ($self->{'labels'}){
if (($self->{'n_term'} eq 'out')&&($_ % 2)){
$self->label_helix_o_i();
}elsif($self->{'n_term'} eq 'out'){
$self->label_helix_i_o();
}elsif(($self->{'n_term'} eq 'in')&&($_ % 2)){
$self->label_helix_i_o();
}else{
$self->label_helix_o_i();
}
}
$x = $self->{'horizontal_padding'} + ($_ * ($self->{'helix_width'} + $self->{'loop_width'}));
}
if ($self->{'labels'}){
$x = $self->{'horizontal_padding'};
$y = $self->{'vertical_padding'};
for (1..$self->{'helix_count'}){
my $y_mod = 0;
foreach my $l (sort {$b <=> $a} keys %{$self->{'loop_labels'}}){
if (($l >= $self->{'helix_span'}{$_}{'start'})&&($l <= $self->{'helix_span'}{$_}{'stop'})){
my $label_length = 0;
if ($self->{'ttf_font'}){
## Might need to fiddle with this
my $size_dif = $self->{'ttf_font_size'} - 8;
$label_length = 6 + (6 * (length $self->{'loop_labels'}{$l}) + (8 * $size_dif));
}else{
$label_length = 9 + (6 * length $self->{'loop_labels'}{$l});
}
if ($_ % 2){
if ($self->{'bold_labels'}){
$self->{'im'}->filledRectangle(($x + ($self->{'helix_width'} / 2)) + 5,($y + ($self->{'helix_height'} / 2) - 30) + $y_mod,$label_length + ($x + ($self->{'helix_width'} / 2)) + 2,12 + ($y + ($self->{'helix_height'} / 2) - 24) + $y_mod,$self->{'black'});
my $b = new GD::Polygon;
$b->addPt(($x + ($self->{'helix_width'} / 2)) + 4,($y + ($self->{'helix_height'} / 2) - 30) + $y_mod,$label_length + ($x + ($self->{'helix_width'} / 2)));
$b->addPt(($x + ($self->{'helix_width'} / 2)) - 5,($y + ($self->{'helix_height'} / 2) - 21) + $y_mod,$label_length + ($x + ($self->{'helix_width'} / 2)));
$b->addPt(($x + ($self->{'helix_width'} / 2)) + 4,($y + ($self->{'helix_height'} / 2) - 12) + $y_mod,$label_length + ($x + ($self->{'helix_width'} / 2)));
$self->{'im'}->filledPolygon($b,$self->{'black'});
}
## add darker box
$self->{'im'}->filledRectangle(($x + ($self->{'helix_width'} / 2)) + 6,($y + ($self->{'helix_height'} / 2) - 29) + $y_mod,$label_length + ($x + ($self->{'helix_width'} / 2)) + 1,12 + ($y + ($self->{'helix_height'} / 2) - 25) + $y_mod,$colour6);
## add white box
$self->{'im'}->filledRectangle(($x + ($self->{'helix_width'} / 2)) + 7,($y + ($self->{'helix_height'} / 2) - 28) + $y_mod,$label_length + ($x + ($self->{'helix_width'} / 2)),12 + ($y + ($self->{'helix_height'} / 2) - 26) + $y_mod,$self->{'white'});
## draw darker arrowhead
my $poly = new GD::Polygon;
$poly->addPt(($x + ($self->{'helix_width'} / 2)) + 5,($y + ($self->{'helix_height'} / 2) - 29) + $y_mod,$label_length + ($x + ($self->{'helix_width'} / 2)));
$poly->addPt(($x + ($self->{'helix_width'} / 2)) - 3,($y + ($self->{'helix_height'} / 2) - 21) + $y_mod,$label_length + ($x + ($self->{'helix_width'} / 2)));
$poly->addPt(($x + ($self->{'helix_width'} / 2)) + 5,($y + ($self->{'helix_height'} / 2) - 13) + $y_mod,$label_length + ($x + ($self->{'helix_width'} / 2)));
$self->{'im'}->filledPolygon($poly,$colour6);
## draw white arrowhead
my $poly2 = new GD::Polygon;
$poly2->addPt(($x + ($self->{'helix_width'} / 2)) + 6,($y + ($self->{'helix_height'} / 2) - 28) + $y_mod,$label_length + ($x + ($self->{'helix_width'} / 2)));
$poly2->addPt(($x + ($self->{'helix_width'} / 2)) - 1,($y + ($self->{'helix_height'} / 2) - 21) + $y_mod,$label_length + ($x + ($self->{'helix_width'} / 2)));
$poly2->addPt(($x + ($self->{'helix_width'} / 2)) + 6,($y + ($self->{'helix_height'} / 2) - 14) + $y_mod,$label_length + ($x + ($self->{'helix_width'} / 2)));
$self->{'im'}->filledPolygon($poly2,$self->{'white'});
## add label
if ($self->{'ttf_font'}){
$self->{'im'}->stringFT($self->{'black'},$self->{'ttf_font'},$self->{'ttf_font_size'},0,($x + ($self->{'helix_width'} / 2)) + 10,($y + ($self->{'helix_height'} / 2) - 16) + $y_mod,$self->{'loop_labels'}{$l},{linespacing=>0.6,charmap => 'Unicode',});
}else{
$self->{'im'}->string(gdSmallFont,($x + ($self->{'helix_width'} / 2)) + 9,($y + ($self->{'helix_height'} / 2) - 27) + $y_mod,$self->{'loop_labels'}{$l},$self->{'black'});
}
$y_mod = $y_mod - 19;
}else{
if ($self->{'bold_labels'}){
$self->{'im'}->filledRectangle(($x + ($self->{'helix_width'} / 2)) + 5,($y + ($self->{'helix_height'} / 2) + 9) + $y_mod,$label_length + ($x + ($self->{'helix_width'} / 2)) + 2,13 + ($y + ($self->{'helix_height'} / 2) + 15) + $y_mod,$self->{'black'});
my $b = new GD::Polygon;
$b->addPt(($x + ($self->{'helix_width'} / 2)) + 4,($y + ($self->{'helix_height'} / 2) + 10) + $y_mod,$label_length + ($x + ($self->{'helix_width'} / 2)));
$b->addPt(($x + ($self->{'helix_width'} / 2)) - 5,($y + ($self->{'helix_height'} / 2) + 19) + $y_mod,$label_length + ($x + ($self->{'helix_width'} / 2)));
$b->addPt(($x + ($self->{'helix_width'} / 2)) + 4,($y + ($self->{'helix_height'} / 2) + 28) + $y_mod,$label_length + ($x + ($self->{'helix_width'} / 2)));
$self->{'im'}->filledPolygon($b,$self->{'black'});
}
## add darker box
$self->{'im'}->filledRectangle(($x + ($self->{'helix_width'} / 2)) + 6,($y + ($self->{'helix_height'} / 2) + 11) + $y_mod,$label_length + ($x + ($self->{'helix_width'} / 2)) + 1,12 + ($y + ($self->{'helix_height'} / 2) + 15) + $y_mod,$colour6);
## add white box
$self->{'im'}->filledRectangle(($x + ($self->{'helix_width'} / 2)) + 7,($y + ($self->{'helix_height'} / 2) + 12) + $y_mod,$label_length + ($x + ($self->{'helix_width'} / 2)),12 + ($y + ($self->{'helix_height'} / 2) + 14) + $y_mod,$self->{'white'});
## draw darker arrowhead
my $poly = new GD::Polygon;
$poly->addPt(($x + ($self->{'helix_width'} / 2)) + 5,($y + ($self->{'helix_height'} / 2) + 11) + $y_mod,$label_length + ($x + ($self->{'helix_width'} / 2)));
$poly->addPt(($x + ($self->{'helix_width'} / 2)) - 3,($y + ($self->{'helix_height'} / 2) + 19) + $y_mod,$label_length + ($x + ($self->{'helix_width'} / 2)));
$poly->addPt(($x + ($self->{'helix_width'} / 2)) + 5,($y + ($self->{'helix_height'} / 2) + 27) + $y_mod,$label_length + ($x + ($self->{'helix_width'} / 2)));
$self->{'im'}->filledPolygon($poly,$colour6);
## draw white arrowhead
my $poly2 = new GD::Polygon;
$poly2->addPt(($x + ($self->{'helix_width'} / 2)) + 6,($y + ($self->{'helix_height'} / 2) + 12) + $y_mod,$label_length + ($x + ($self->{'helix_width'} / 2)));
$poly2->addPt(($x + ($self->{'helix_width'} / 2)) - 1,($y + ($self->{'helix_height'} / 2) + 19) + $y_mod,$label_length + ($x + ($self->{'helix_width'} / 2)));
$poly2->addPt(($x + ($self->{'helix_width'} / 2)) + 6,($y + ($self->{'helix_height'} / 2) + 26) + $y_mod,$label_length + ($x + ($self->{'helix_width'} / 2)));
$self->{'im'}->filledPolygon($poly2,$self->{'white'});
## add label
if ($self->{'ttf_font'}){
$self->{'im'}->stringFT($self->{'black'},$self->{'ttf_font'},$self->{'ttf_font_size'},0,($x + ($self->{'helix_width'} / 2)) + 10,($y + ($self->{'helix_height'} / 2) + 24) + $y_mod,$self->{'loop_labels'}{$l},{linespacing=>0.6,charmap => 'Unicode',});
}else{
$self->{'im'}->string(gdSmallFont,($x + ($self->{'helix_width'} / 2)) + 9,($y + ($self->{'helix_height'} / 2) + 12) + $y_mod,$self->{'loop_labels'}{$l},$self->{'black'});
}
$y_mod = $y_mod + 19;
}
}
}
$x = $self->{'horizontal_padding'} + ($_ * ($self->{'helix_width'} + $self->{'loop_width'}));
}
}
return $self;
}
sub draw_terminai {
my $self = shift;
my $loop_number = ($self->{'helix_count'} - 1);
## width of terminal
$self->{'w'} = $self->{'helix_width'} + $self->{'loop_width'};
$self->{'cx'} = $self->{'horizontal_padding'} - ($self->{'loop_width'} / 2);
$self->{'cy'} = $self->{'vertical_padding'};
## draw N-terminal
if ($self->{'n_term'} eq 'out'){
$self->{'im'}->arc(($self->{'cx'} - $self->{'n_term_offset'}),$self->{'cy'},($self->{'w'} + (2 * $self->{'n_term_offset'})),$self->{'n_terminal_height'},270,360,$self->{'black'});
if ($self->{'ttf_font'}){
$self->{'im'}->stringFT($self->{'black'},$self->{'ttf_font'},$self->{'ttf_font_size'},0,($self->{'horizontal_padding'} - ($self->{'w'} / 2) - 33 - $self->{'n_term_offset'}),($self->{'cy'} - ($self->{'n_terminal_height'} / 2) + 5),$self->{'n_term_label'},{linespacing=>0.6,charmap => 'Unicode',}) if $self->{'labels'};
}else{
$self->{'im'}->string(gdSmallFont,($self->{'horizontal_padding'} - ($self->{'w'} / 2) - 40 - $self->{'n_term_offset'}),($self->{'cy'} - ($self->{'n_terminal_height'} / 2) - 6),$self->{'n_term_label'},$self->{'black'}) if $self->{'labels'};
}
## label n-terminal
my $y_mod = 0;
foreach (sort {$b <=> $a} keys %{$self->{'loop_labels'}}){
if ($_ <= $self->{'helix_span'}{1}{'start'}){
if ($self->{'ttf_font'}){
$self->{'im'}->stringFT($self->{'black'},$self->{'ttf_font'},$self->{'ttf_font_size'},0,($self->{'horizontal_padding'} - ($self->{'w'} / 2) - 33 - $self->{'n_term_offset'}),($self->{'cy'} - ($self->{'n_terminal_height'} / 2) - 6) - 4 + $y_mod,$self->{'loop_labels'}{$_},{linespacing=>0.6,charmap => 'Unicode',}) if $self->{'labels'};
}else{
$self->{'im'}->string(gdSmallFont,($self->{'horizontal_padding'} - ($self->{'w'} / 2) - 40 - $self->{'n_term_offset'}),($self->{'cy'} - ($self->{'n_terminal_height'} / 2) - 6) - 15 + $y_mod,$self->{'loop_labels'}{$_},$self->{'black'}) if $self->{'labels'};
}
$y_mod = $y_mod - 15;
}
}
}else{
$self->{'cy'} = $self->{'cy'} + $self->{'helix_height'};
$self->{'im'}->arc(($self->{'cx'} - $self->{'n_term_offset'}),$self->{'cy'},($self->{'w'} + (2 * $self->{'n_term_offset'})),$self->{'n_terminal_height'},0,90,$self->{'black'});
if ($self->{'ttf_font'}){
$self->{'im'}->stringFT($self->{'black'},$self->{'ttf_font'},$self->{'ttf_font_size'},0,($self->{'horizontal_padding'} - ($self->{'w'} / 2) - 33 - $self->{'n_term_offset'}),($self->{'cy'} + ($self->{'n_terminal_height'} / 2) + 5),$self->{'n_term_label'},{linespacing=>0.6,charmap => 'Unicode',}) if $self->{'labels'};
}else{
$self->{'im'}->string(gdSmallFont,($self->{'horizontal_padding'} - ($self->{'w'} / 2) - 40 - $self->{'n_term_offset'}),($self->{'cy'} + ($self->{'n_terminal_height'} / 2) - 6),$self->{'n_term_label'},$self->{'black'}) if $self->{'labels'};
}
## label n-terminal
my $y_mod = 0;
foreach (sort {$a <=> $b} keys %{$self->{'loop_labels'}}){
if ($_ <= $self->{'helix_span'}{1}{'start'}){
if ($self->{'ttf_font'}){
$self->{'im'}->stringFT($self->{'black'},$self->{'ttf_font'},$self->{'ttf_font_size'},0,($self->{'horizontal_padding'} - ($self->{'w'} / 2) - 33 - $self->{'n_term_offset'}),($self->{'cy'} + ($self->{'n_terminal_height'} / 2) - 6) + 26 + $y_mod,$self->{'loop_labels'}{$_},{linespacing=>0.6,charmap => 'Unicode',}) if $self->{'labels'};
}else{
$self->{'im'}->string(gdSmallFont,($self->{'horizontal_padding'} - ($self->{'w'} / 2) - 40 - $self->{'n_term_offset'}),($self->{'cy'} + ($self->{'n_terminal_height'} / 2) - 6) + 15 + $y_mod,$self->{'loop_labels'}{$_},$self->{'black'}) if $self->{'labels'};
}
$y_mod = $y_mod + 15;
}
}
}
$self->{'cx'} = ($self->{'helix_count'} * $self->{'helix_width'}) + (($self->{'helix_count'} - 1) * $self->{'loop_width'}) + $self->{'horizontal_padding'} + ($self->{'loop_width'} / 2);
## draw C-terminal
if (($self->{'n_term'} eq 'out')&&($loop_number % 2)){
$self->draw_ext_c_term;
}elsif($self->{'n_term'} eq 'out'){
$self->draw_int_c_term;
}elsif(($self->{'n_term'} eq 'in')&&($loop_number % 2)){
$self->draw_int_c_term;
}elsif($self->{'n_term'} eq 'in'){
$self->draw_ext_c_term;
}
return $self;
}
sub draw_loops {
my $self = shift;
$self->{'x'} = $self->{'horizontal_padding'} + ($self->{'helix_width'} / 2);
$self->{'h'} = $self->{'medium_loop'};
$self->{'w'} = $self->{'helix_width'} + $self->{'loop_width'};
for (1..($self->{'helix_count'} - 1)){
## Alter loop height according to its actual length
if ($self->{'loop_length'}{$_} < $self->{'short_loop_limit'}){
$self->{'h'} = $self->{'short_loop'};
}elsif($self->{'loop_length'}{$_} > $self->{'long_loop_limit'}){
$self->{'h'} = $self->{'long_loop'};
}
$self->{'l_start'} = $self->{'helix_span'}{$_}{'stop'};
$self->{'l_stop'} = $self->{'helix_span'}{$_ + 1}{'start'};
if (($self->{'n_term'} eq 'out')&&($_ % 2)){
$self->draw_int_loop;
}elsif($self->{'n_term'} eq 'out'){
$self->draw_ext_loop;
}elsif(($self->{'n_term'} eq 'in')&&($_ % 2)){
$self->draw_ext_loop;
}elsif($self->{'n_term'} eq 'in'){
$self->draw_int_loop;
}
$self->{'x'} = $self->{'x'} + $self->{'helix_width'} + $self->{'loop_width'};
$self->{'x'} = $self->{'horizontal_padding'} if $_ == ($self->{'helix_count'} - 1);
}
return $self;
}
sub label_helix_o_i {
my $self = shift;
my $offset = 6;
$offset = 3 if $self->{'helix_span'}{$_}{'start'} < 100;
if ($self->{'ttf_font'}){
$self->{'im'}->stringFT($self->{'black'},$self->{'ttf_font'},$self->{'ttf_font_size'},0,($self->{'x'} + ($self->{'helix_width'} / 2) - $offset) - 1,$self->{'y'} + 13,$self->{'helix_span'}{$_}{'start'},{linespacing=>0.6,charmap => 'Unicode',});
}else{
$self->{'im'}->string(gdSmallFont,($self->{'x'} + ($self->{'helix_width'} / 2) - $offset) - 1,$self->{'y'} + 1,$self->{'helix_span'}{$_}{'start'},$self->{'black'});
}
$offset = 3 if $self->{'helix_span'}{$_}{'stop'} < 100;
$offset = 6 if $self->{'helix_span'}{$_}{'stop'} >= 100;
if ($self->{'ttf_font'}){
$self->{'im'}->stringFT($self->{'black'},$self->{'ttf_font'},$self->{'ttf_font_size'},0,($self->{'x'} + ($self->{'helix_width'} / 2) - $offset) - 1,($self->{'y'} + $self->{'helix_height'} - 3),$self->{'helix_span'}{$_}{'stop'},{linespacing=>0.6,charmap => 'Unicode',});
}else{
$self->{'im'}->string(gdSmallFont,($self->{'x'} + ($self->{'helix_width'} / 2) - $offset) - 1,($self->{'y'} + $self->{'helix_height'} - 14),$self->{'helix_span'}{$_}{'stop'},$self->{'black'});
}
return $self;
}
sub label_helix_i_o {
my $self = shift;
my $offset = 6;
$offset = 3 if $self->{'helix_span'}{$_}{'stop'} < 100;
if ($self->{'ttf_font'}){
$self->{'im'}->stringFT($self->{'black'},$self->{'ttf_font'},$self->{'ttf_font_size'},0,($self->{'x'} + ($self->{'helix_width'} / 2) - $offset) - 1,$self->{'y'} + 13,$self->{'helix_span'}{$_}{'stop'},{linespacing=>0.6,charmap => 'Unicode',});
}else{
$self->{'im'}->string(gdSmallFont,($self->{'x'} + ($self->{'helix_width'} / 2) - $offset) - 1,$self->{'y'} + 1,$self->{'helix_span'}{$_}{'stop'},$self->{'black'});
}
$offset = 3 if $self->{'helix_span'}{$_}{'start'} < 100;
if ($self->{'ttf_font'}){
$self->{'im'}->stringFT($self->{'black'},$self->{'ttf_font'},$self->{'ttf_font_size'},0,($self->{'x'} + ($self->{'helix_width'} / 2) - $offset) - 1,($self->{'y'} + $self->{'helix_height'} - 3),$self->{'helix_span'}{$_}{'start'},{linespacing=>0.6,charmap => 'Unicode',});
}else{
$self->{'im'}->string(gdSmallFont,($self->{'x'} + ($self->{'helix_width'} / 2) - $offset) - 1,($self->{'y'} + $self->{'helix_height'} - 14),$self->{'helix_span'}{$_}{'start'},$self->{'black'});
}
return $self;
}
sub draw_int_c_term {
my $self = shift;
## draw internal c-terminal
$self->{'im'}->arc(($self->{'cx'} + $self->{'c_term_offset'}),($self->{'vertical_padding'} + $self->{'helix_height'}),($self->{'w'} + (2 * $self->{'c_term_offset'})),$self->{'c_terminal_height'},90,180,$self->{'black'});
if ($self->{'ttf_font'}){
$self->{'im'}->stringFT($self->{'black'},$self->{'ttf_font'},$self->{'ttf_font_size'},0,($self->{'cx'} + 4 + $self->{'c_term_offset'}),(($self->{'vertical_padding'} + $self->{'helix_height'}) + ($self->{'c_terminal_height'} / 2) + 5),$self->{'c_term_label'},{linespacing=>0.6,charmap => 'Unicode',}) if $self->{'labels'};
}else{
$self->{'im'}->string(gdSmallFont,($self->{'cx'} + 3 + $self->{'c_term_offset'}),(($self->{'vertical_padding'} + $self->{'helix_height'}) + ($self->{'c_terminal_height'} / 2) - 6),$self->{'c_term_label'},$self->{'black'}) if $self->{'labels'};
}
## label terminal
if ($self->{'labels'}){
my $y_mod = 0;
foreach (sort {$a <=> $b} keys %{$self->{'loop_labels'}}){
if ($_ >= $self->{'helix_span'}{$self->{'helix_count'}}{'stop'}){
if ($self->{'ttf_font'}){
$self->{'im'}->stringFT($self->{'black'},$self->{'ttf_font'},$self->{'ttf_font_size'},0,($self->{'cx'} + 4 + $self->{'c_term_offset'}),(($self->{'vertical_padding'} + $self->{'helix_height'}) + ($self->{'c_terminal_height'} / 2) - 6) + 26 + $y_mod,$self->{'loop_labels'}{$_},{linespacing=>0.6,charmap => 'Unicode',}) if $self->{'labels'};
}else{
$self->{'im'}->string(gdSmallFont,($self->{'cx'} + 3 + $self->{'c_term_offset'}),(($self->{'vertical_padding'} + $self->{'helix_height'}) + ($self->{'c_terminal_height'} / 2) - 6) + 15 + $y_mod,$self->{'loop_labels'}{$_},$self->{'black'});
}
$y_mod = $y_mod + 15;
}
}
}
return $self;
}
sub draw_ext_c_term {
my $self = shift;
## draw external c-terminal
$self->{'im'}->arc(($self->{'cx'} + $self->{'c_term_offset'}),$self->{'vertical_padding'},($self->{'w'} + (2 * $self->{'c_term_offset'})),$self->{'c_terminal_height'},180,270,$self->{'black'});
if ($self->{'ttf_font'}){
$self->{'im'}->stringFT($self->{'black'},$self->{'ttf_font'},$self->{'ttf_font_size'},0,,($self->{'cx'} + 3 + $self->{'c_term_offset'}),($self->{'vertical_padding'} - ($self->{'c_terminal_height'} / 2) + 5),$self->{'c_term_label'},{linespacing=>0.6,charmap => 'Unicode',}) if $self->{'labels'};
}else{
$self->{'im'}->string(gdSmallFont,($self->{'cx'} + 3 + $self->{'c_term_offset'}),($self->{'vertical_padding'} - ($self->{'c_terminal_height'} / 2) - 6),$self->{'c_term_label'},$self->{'black'}) if $self->{'labels'};
}
## label terminal
if ($self->{'labels'}){
my $y_mod = 0;
foreach (sort {$b <=> $a} keys %{$self->{'loop_labels'}}){
if ($_ >= $self->{'helix_span'}{$self->{'helix_count'}}{'stop'}){
if ($self->{'ttf_font'}){
$self->{'im'}->stringFT($self->{'black'},$self->{'ttf_font'},$self->{'ttf_font_size'},0,($self->{'cx'} + 3 + $self->{'c_term_offset'}),($self->{'vertical_padding'} - ($self->{'c_terminal_height'} / 2) - 6) - 4 - $y_mod,$self->{'loop_labels'}{$_},{linespacing=>0.6,charmap => 'Unicode',}) if $self->{'labels'};
}else{
$self->{'im'}->string(gdSmallFont,($self->{'cx'} + 3 + $self->{'c_term_offset'}),($self->{'vertical_padding'} - ($self->{'c_terminal_height'} / 2) - 6) - 15 - $y_mod,$self->{'loop_labels'}{$_},$self->{'black'});
}
$y_mod = $y_mod + 15;
}
}
}
return $self;
}
sub draw_int_loop {
my $self = shift;
## draw internal loop
$self->{'cx'} = $self->{'x'} + ($self->{'helix_width'} / 2) + ($self->{'loop_width'} / 2);
## this sets the height to the value given by the loop_heights hash
foreach (sort {$a <=> $b} keys %{$self->{'loop_heights'}}){
$self->{'h'} = $self->{'loop_heights'}{$_} if $_ == $self->{'loop_count'};
}
$self->{'im'}->arc($self->{'cx'},($self->{'vertical_padding'} + $self->{'helix_height'}),$self->{'w'},$self->{'h'},0,180,$self->{'black'});
## label loop
if ($self->{'labels'}){
my $y_mod = 0;
foreach (sort {$a <=> $b} keys %{$self->{'loop_labels'}}){
if (($_ >= $self->{'l_start'})&&($_ <= $self->{'l_stop'})){
$self->{'im'}->line($self->{'cx'},($self->{'vertical_padding'} + $self->{'helix_height'} + ($self->{'h'} / 2)),$self->{'cx'},($self->{'vertical_padding'} + $self->{'helix_height'} + ($self->{'h'} / 2) + 5),$self->{'black'}) unless $y_mod;
if ($self->{'ttf_font'}){
$self->{'im'}->stringFT($self->{'black'},$self->{'ttf_font'},$self->{'ttf_font_size'},0,($self->{'cx'} + $self->{'text_offset'} - 3),($self->{'vertical_padding'} + $self->{'helix_height'} + ($self->{'h'} / 2) + 17) + $y_mod,$self->{'loop_labels'}{$_},{linespacing=>0.6,charmap => 'Unicode',}) if $self->{'labels'};
}else{
$self->{'im'}->string(gdSmallFont,($self->{'cx'} + $self->{'text_offset'}),($self->{'vertical_padding'} + $self->{'helix_height'} + ($self->{'h'} / 2) + 6) + $y_mod,$self->{'loop_labels'}{$_},$self->{'black'}) ;
}
$y_mod = $y_mod + 15;
}
}
}
$self->{'loop_count'}++;
return $self;
}
sub draw_ext_loop {
my $self = shift;
## draw external loop
$self->{'cx'} = $self->{'x'} + ($self->{'helix_width'} / 2) + ($self->{'loop_width'} / 2);
## this sets the height to the value given by the loop_heights hash
foreach (sort {$a <=> $b} keys %{$self->{'loop_heights'}}){
$self->{'h'} = $self->{'loop_heights'}{$_} if $_ == $self->{'loop_count'};
}
$self->{'im'}->arc($self->{'cx'},$self->{'vertical_padding'},$self->{'w'},$self->{'h'},180,360,$self->{'black'});
## label loop
if ($self->{'labels'}){
my $y_mod = 0;
foreach (sort {$b <=> $a} keys %{$self->{'loop_labels'}}){
if (($_ >= $self->{'l_start'})&&($_ <= $self->{'l_stop'})){
$self->{'im'}->line($self->{'cx'},($self->{'vertical_padding'} - ($self->{'h'} / 2)),$self->{'cx'},($self->{'vertical_padding'} - ($self->{'h'} / 2) - 5),$self->{'black'}) unless $y_mod;
if ($self->{'ttf_font'}){
$self->{'im'}->stringFT($self->{'black'},$self->{'ttf_font'},$self->{'ttf_font_size'},0,($self->{'cx'} + $self->{'text_offset'} - 3),($self->{'vertical_padding'} - ($self->{'h'} / 2) - 8) + $y_mod,$self->{'loop_labels'}{$_},{linespacing=>0.6,charmap => 'Unicode',}) if $self->{'labels'};
}else{
$self->{'im'}->string(gdSmallFont,($self->{'cx'} + $self->{'text_offset'}),($self->{'vertical_padding'} - ($self->{'h'} / 2) - 19) + $y_mod,$self->{'loop_labels'}{$_},$self->{'black'});
}
$y_mod = $y_mod - 15;
}
}
}
$self->{'loop_count'}++;
return $self;
}
1;
=head1 NAME
Bio::Graphics::DrawTransmembrane - draw a cartoon of an Alpha-helical transmembrane protein.
=head1 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;
=head1 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.
=head1 AUTHOR
Tim Nugent E<lt>timnugent@gmail.comE<gt>
=cut
|