]> git.donarmstrong.com Git - wheel.git/commitdiff
* move wheel to the right directory
authorDon Armstrong <don@donarmstrong.com>
Wed, 14 Jul 2010 05:24:10 +0000 (05:24 +0000)
committerDon Armstrong <don@donarmstrong.com>
Tue, 30 Dec 2014 02:36:08 +0000 (18:36 -0800)
wheel/wheel.pl [deleted file]

diff --git a/wheel/wheel.pl b/wheel/wheel.pl
deleted file mode 100755 (executable)
index 3facfe9..0000000
+++ /dev/null
@@ -1,644 +0,0 @@
-#! /usr/bin/perl -w
-# wheel.pl: Draw alpha helical wheel with hydrophobic moment using
-# wif (modifiable to woct) scale.
-# Copyright (C) 2001 Don Armstrong and Raphael Zidovetzki
-
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 2 of the License, or
-# (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
-
-
-
-
-my $VERSION=q$Id: wheel.pl,v 1.4 2009-10-20 21:23:36 don Exp $;
-
-# Intial Released Version 0.10
-# p01: Fixing displayed angle
-# p02: Added arrowhead, fixed lack of return in xy2deg(), added no color option
-# p03: Added round function, fixed rounding in angles, changed hm to line, added hm_up option
-# p04: Removed bounding box
-# p05: Changing user interface to allow simultaneous viewing of options and wheel
-# p06: Released to public under GPL
-
-use CGI::Carp qw(fatalsToBrowser);
-use strict;
-use CGI;
-
-use Math::Trig;
-use GD;
-use GD::Text::Align;
-use POSIX;
-
-use HTML::Entities qw(encode_entities);
-
-
-sub round($) {
-  my ($a) = @_;
-  return (floor $a+0.5);
-}
-
-sub min($$){
-  my ($a,$b)=@_;
-  if ($a>$b) {
-    return $b;
-  }
-  return $a;
-}
-
-sub max($$){
-  my ($a,$b)=@_;
-  if ($a<$b) {
-    return $b;
-  }
-  return $a;
-}
-
-my $q = new CGI;
-
-sub xy2deg($$) {
-  my ($x,$y) = @_;
-  my $angle = rad2deg(atan($x/$y));
-  if ($y<0) {
-    $angle+=180;
-  }
-  elsif ($angle<0) {
-    $angle+=360;
-  }
-  return $angle;
-}
-
-sub calculate_hydrophobic_moment($$){
-  my ($sequence,$param)=@_;
-  my $phe=$param->{phe};
-  my $theta=$param->{theta};
-  my ($x,$y)=(0,0);
-  foreach my $amino_acid (split(//,$sequence)) {
-    $x+=-$param->{aa}->{$amino_acid}->{wif} * sin($phe);
-    $y+=+$param->{aa}->{$amino_acid}->{wif} * cos($phe);
-    $phe+=$theta;
-  }
-  return ($x,$y);
-}
-
-
-sub draw_wheel($$$){
-  my ($im,$aasequence,$param)=@_;
-  my $phe=$param->{phe};
-  my $aanumber=0;
-  my $point1;
-  my @points;
-  foreach my $aminoacid (split(//,$aasequence)) {
-    push @points, calculate_geometry($param,$phe);
-    $phe += $param->{theta};
-    $aanumber++;
-    last if ($aanumber>18);
-  }
-  for ($aanumber=0;$aanumber<19;$aanumber++) {
-    my $point = pop @points;
-    last if (!defined $point);
-    if ($aanumber>0) {
-      draw_connection($im,$aanumber,$point1,$point);
-    }
-    $point1 = $point;
-  }
-  $phe = $param->{phe};
-  $aanumber = 0;
-  foreach my $aminoacid (split(//,$aasequence)) {
-    $point1=calculate_geometry($param,$phe);
-    draw_aa($im,$aminoacid,
-           $param->{centerx}+($point1->{bx}-$param->{centerx})*
-           ($param->{d}+2.2*$param->{r}*POSIX::floor($aanumber/18))/
-           $param->{d},$param->{centery}+($point1->{by}-$param->{centery})*
-           ($param->{d}+2.2*$param->{r}*POSIX::floor($aanumber/18))/
-           $param->{d},$phe,$param,$aanumber);
-    $phe+=$param->{theta};
-    $aanumber++;
-  }
-  my ($hydro_x,$hydro_y) = calculate_hydrophobic_moment($aasequence,$param);
-  draw_hydrophobic_moment($im,$hydro_x,$hydro_y,$param);
-}
-
-sub draw_hydrophobic_moment($$$$){
-  my ($im,$x,$y,$param)=@_;
-  my $norm=($x*$x+$y*$y)**(0.5);
-  my $angle = xy2deg($x,-$y);
-  if ($norm !=0 and $param->{hmscale}!=0) {
-    $x=$x/$norm*$param->{hmscale};
-    $y=$y/$norm*$param->{hmscale};
-  }
-
-  # Draw Moment Line (Box, really)
-  my $poly = GD::Polygon->new;
-  print STDERR "$angle\n";
-  $poly->addPt($param->{centerx}-round(($param->{hmscale}/50)*sin(deg2rad($angle+90))),
-              $param->{centery}+round(($param->{hmscale}/50)*cos(deg2rad($angle+90))));
-  $poly->addPt($param->{centerx}+round($x*0.85-($param->{hmscale}/50)*sin(deg2rad($angle+90))),
-              $param->{centery}+round($y*0.85+($param->{hmscale}/50)*cos(deg2rad($angle+90))));
-  $poly->addPt($param->{centerx}+round($x*0.85-($param->{hmscale}/50)*sin(deg2rad($angle-90))),
-              $param->{centery}+round($y*0.85+($param->{hmscale}/50)*cos(deg2rad($angle-90))));
-  $poly->addPt($param->{centerx}-round(($param->{hmscale}/50)*sin(deg2rad($angle-90))),
-              $param->{centery}+round(($param->{hmscale}/50)*cos(deg2rad($angle-90))));
-  $im->filledPolygon($poly,$param->{black});
-
-  # Draw Arowhead
-  undef $poly;
-  $poly = GD::Polygon->new;
-  $poly->addPt($param->{centerx}+$x,$param->{centery}+$y);
-  $poly->addPt($param->{centerx}+$x-round(($param->{hmscale}/5)*sin(deg2rad($angle+20))),
-              $param->{centery}+$y+round(($param->{hmscale}/5)*cos(deg2rad($angle+20))));
-  $poly->addPt($param->{centerx}+$x-round(($param->{hmscale}/5)*sin(deg2rad($angle-20))),
-              $param->{centery}+$y+round(($param->{hmscale}/5)*cos(deg2rad($angle-20))));
-  $im->filledPolygon($poly,$param->{black});
-  my $text= GD::Text::Align->new($im,
-                                valign => 'center',
-                                halign => 'center',
-                                color=> $param->{black},
-                               );
-  $text->set_font('/usr/share/fonts/truetype/Florsn01.ttf',$param->{fontsize2});
-  if ($param->{disp_hm_angle}) {
-    $text->set_text(POSIX::floor($norm*100+.5)/100 . '@' . POSIX::floor(($angle*10+0.5))/10);
-  }
-  else {
-    $text->set_text(POSIX::floor($norm*100+.5)/100);
-  }
-  my $offset=-10-$param->{fontsize2}/2;
-  if ($y<0) {
-    $offset=-$offset;
-  }
-  $text->draw($param->{centerx},$param->{centery}+$offset);
-}
-
-sub draw_connection($$$$) {
-  my ($im,$aanumber,$point1,$point2) =  @_;
-  my $color=$im->colorAllocate(240*((18-$aanumber)/18),
-                              240*((18-$aanumber)/18),
-                              240*((18-$aanumber)/18)
-                             );
-  my $poly = GD::Polygon->new;
-  $poly->addPt($point1->{ex},$point1->{ey});
-  $poly->addPt($point2->{ex},$point2->{ey});
-  $poly->addPt($point2->{cx},$point2->{cy});
-  $poly->addPt($point1->{cx},$point1->{cy});
-  $im->filledPolygon($poly,$color);
-  return;
-}
-
-sub calculate_geometry($$){
-  my ($param,$phe)=@_;
-  return {bx=>($param->{d})*sin($phe)+$param->{centerx},
-         cx=>($param->{d}-($param->{w}/2)/sin((pi-$param->{theta})/2))*sin($phe)+$param->{centerx},
-         dx=>($param->{centerx}),
-         ex=>($param->{d}+($param->{w}/2)/sin((pi-$param->{theta})/2))*sin($phe)+$param->{centerx},
-         by=>-($param->{d})*cos($phe)+$param->{centery},
-         cy=>-($param->{d}-($param->{w}/2)/sin((pi-$param->{theta})/2))*cos($phe)+$param->{centery},
-         dy=>($param->{centery}),
-         ey=>-($param->{d}+($param->{w}/2)/sin((pi-$param->{theta})/2))*cos($phe)+$param->{centery},
-        };
-}
-
-
-sub draw_n_gon($$$$){
-  my ($x,$y,$r,$n)=@_;
-  my $ngon=GD::Polygon->new;
-  for (my $v = 0;$v<$n;$v++) {
-    $ngon->addPt($x+$r*sin((2*pi/$n)*$v),$y-$r*cos((2*pi/$n)*$v));
-  }
-  return($ngon);
-}
-
-sub draw_aa($$$$$$$){
-  my ($im,$aasymbol,$bx,$by,$phe,$param,$aanumber)=@_;
-  my $r=$param->{r};
-
-  my $ax=$bx;
-  my $ay=$by;
-  $_ = $param->{aa}->{$aasymbol}->{shape};
-  if (defined && /square/) {
-    $im->filledRectangle($ax-$r,$ay-$r,$ax+$r,$ay+$r,$param->{aa}->{$aasymbol}->{bcolor});
-    $im->rectangle($ax-$r,$ay-$r,$ax+$r,$ay+$r,$param->{aa}->{$aasymbol}->{fcolor});
-  }
-  elsif (defined && /triangle/) {
-    $im->filledPolygon(draw_n_gon($ax,$ay,1.25*$r,3),
-                      $param->{aa}->{$aasymbol}->{bcolor});
-    $im->polygon(draw_n_gon($ax,$ay,1.25*$r,3),
-                $param->{aa}->{$aasymbol}->{fcolor});
-  }
-  elsif (defined && /hexagon/) {
-    $im->filledPolygon(draw_n_gon($ax,$ay,1.18*$r,6),
-                    $param->{aa}->{$aasymbol}->{bcolor});
-    $im->polygon(draw_n_gon($ax,$ay,1.18*$r,6),
-                $param->{aa}->{$aasymbol}->{fcolor});
-  }
-  elsif (defined && /diamond/) {
-    $im->filledPolygon(draw_n_gon($ax,$ay,1.25*$r,4),
-                     $param->{aa}->{$aasymbol}->{bcolor});
-    $im->polygon(draw_n_gon($ax,$ay,1.25*$r,4),
-                $param->{aa}->{$aasymbol}->{fcolor});
-  }
-  elsif (defined && /pentagon/) {
-    $im->filledPolygon(draw_n_gon($ax,$ay,1.2*$r,5),
-                     $param->{aa}->{$aasymbol}->{bcolor});
-    $im->polygon(draw_n_gon($ax,$ay,1.2*$r,5),
-                $param->{aa}->{$aasymbol}->{fcolor});
-  }
-  elsif (defined && /octagon/){
-    $im->filledPolygon(draw_n_gon($ax,$ay,1.1*$r,8),
-                     $param->{aa}->{$aasymbol}->{bcolor});
-    $im->polygon(draw_n_gon($ax,$ay,1.1*$r,8),
-                $param->{aa}->{$aasymbol}->{fcolor});
-  }
-  else {  #cicle
-    $im->filledPolygon(draw_n_gon($ax,$ay,$r*0.99,360),
-                     $param->{aa}->{$aasymbol}->{bcolor});
-    $im->arc($ax,$ay,2*$r,2*$r,0,360,$param->{aa}->{$aasymbol}->{fcolor});
-  }
-  $im->fill($ax,$ay,$param->{aa}->{$aasymbol}->{bcolor});
-  my $text= GD::Text::Align->new($im,
-                                valign => 'center',
-                                halign => 'center',
-                                color=> $param->{black},
-                               );
-  $text->set_font('/usr/share/fonts/truetype/Florsn01.ttf',$param->{fontsize});
-  my $label_text=$aasymbol  . abs($aanumber+$param->{indexaa});
-  $text->set_text($label_text);
-  $text->draw($ax,$ay,0);
-}
-
-
-if (defined $q->param('draw') and $q->param('draw')=~/yes/) {
-  my $param={
-            indexaa=>1,
-             d=>320,
-             centerx=>500,
-             centery=>500,
-            xsize=>1000,
-            ysize=>1000,
-             w=>14,
-             theta=>(100/180)*pi,
-             phe=>(0/180)*pi,
-            r=>40,
-             fontsize=>20,
-            fontsize2=>20,
-            hmscale=>50,
-            wifcolor=>1,
-            maxwif=>0.5802,
-            minwif=>-1.8502,
-            hmdisp=>'',
-           };
-  # Merge in query params
-  # DGwoct[woct] and DGwif[wif] are octanol and interface hydrophobicity values
-  # as seen on http://blanco.biomol.uci.edu/Whole_residue_HFscales.txt
-  # and used in MPEx.
-  # Wimley and White
-  # Nature Struc. Biol 3:842 (1996) [wif values]
-  # Wimley, Creamer and White
-  # Biochemistry 34:5108 (1996) [woct values]
-
-  $param->{aa} = {G=>{name=>'Glycine',
-                     abbr=>'gly',
-                     woct=>1.15,
-                     wif=>0.01,
-                    },
-                 A=>{name=>'Alanine',
-                     abbr=>'ala',
-                     woct=>0.50,
-                     wif=>0.17,
-                    },
-                 V=>{name=>'Valine',
-                     abbr=>'val',
-                     woct=>-0.46,
-                     wif=>0.07,
-                    },
-                 L=>{name=>'Leucine',
-                     abbr=>'leu',
-                     woct=>-1.25,
-                     wif=>-0.56,
-                     shape=>'diamond',
-                    },
-                 I=>{name=>'Isoleucine',
-                     abbr=>'ile',
-                     woct=>-1.12,
-                     wif=>-0.31,
-                     shape=>'diamond',
-                    },
-                 M=>{name=>'Methionine',
-                     abbr=>'met',
-                     woct=>-0.67,
-                     wif=>-0.23,
-                     shape=>'diamond',
-                    },
-                 P=>{name=>'Proline',
-                     abbr=>'pro',
-                     woct=>0.14,
-                     wif=>0.45,
-                    },
-                 F=>{name=>'Phenylalanine',
-                     abbr=>'phe',
-                     woct=>-1.71,
-                     wif=>-1.13,
-                     shape=>'diamond',
-                    },
-                 W=>{name=>'Tryptophan',
-                     abbr=>'trp',
-                     woct=>-2.09,
-                     wif=>-1.85,
-                     shape=>'diamond',
-                    },
-                 S=>{name=>'Serine',
-                     abbr=>'ser',
-                     woct=>0.46,
-                     wif=>0.13,
-                    },
-                 T=>{name=>'Threonine',
-                     abbr=>'thr',
-                     woct=>0.25,
-                     wif=>0.14,
-                    },
-                 N=>{name=>'Asparagine',
-                     abbr=>'asn',
-                     woct=>0.85,
-                     wif=>0.42,
-                    },
-                 Q=>{name=>'Glutamine',
-                     abbr=>'gln',
-                     woct=>0.77,
-                     wif=>0.58,
-                    },
-                 Y=>{name=>'Tyrosine',
-                     abbr=>'tyr',
-                     woct=>-0.71,
-                     wif=>-0.94,
-                     shape=>'diamond',
-                    },
-                 C=>{name=>'Cysteine',
-                     abbr=>'cys',
-                     woct=>-0.02,
-                     wif=>-0.24,
-                     shape=>'diamond',
-                    },
-                 K=>{name=>'Lysine',
-                     abbr=>'lys',
-                     woct=>2.80,
-                     wif=>0.99,
-                     shape=>'pentagon',
-                     fill=>[187,187,255],
-                     border=>[187,187,255],
-                    },
-                 R=>{name=>'Arginine',
-                     abbr=>'arg',
-                     woct=>1.81,
-                     wif=>0.81,
-                     shape=>'pentagon',
-                     fill=>[187,187,255],
-                     border=>[187,187,255],
-                    },
-                 H=>{name=>'Histidine',
-                     abbr=>'his',
-                     woct=>2.33,
-                     wif=>0.96,
-                     shape=>'pentagon',
-                     fill=>[187,187,255],
-                     border=>[187,187,255],
-                    },
-                 D=>{name=>'Aspartic Acid',
-                     abbr=>'asp',
-                     woct=>3.64,
-                     wif=>1.23,
-                     shape=>'triangle',
-                     fill=>[187,187,255],
-                     border=>[187,187,255],
-                    },
-                 E=>{name=>'Glutamic Acid',
-                     abbr=>'glu',
-                     woct=>3.63,
-                     wif=>2.02,
-                     shape=>'triangle',
-                     fill=>[187,187,255],
-                     border=>[187,187,255],
-                    },
-                };
-  foreach my $param_key ($q->param) {
-    my $param_value=$q->param($param_key);
-    if ($param_value=~/^(\-{0,1}\d*\.{0,1}\d+)$/) {
-      $param->{$param_key}=$q->param($param_key);
-      if ($param_key=~/^(phe|theta|hmdisp)$/) {
-       $param->{$param_key}=$param->{$param_key}/180*pi;
-      }
-    }
-  }
-  if ($q->param('disp_hm_angle') =~ /on/) {
-    $param->{'disp_hm_angle'}=1;
-  }
-  else {
-    $param->{'disp_hm_angle'}=0;
-  }
-  if ($q->param('reverse_helix') =~ /on/) {
-    $param->{'reverse_helix'}=1;
-  }
-  else {
-    $param->{'reverse_helix'}=0;
-  }
-  if ($q->param('wo_color') =~ /on/) {
-    $param->{'wifcolor'}=0;
-  }
-  else {
-    $param->{'wifcolor'}=1;
-  }
-  my $im = new GD::Image($param->{xsize},$param->{ysize});
-  $param->{white} = $im->colorAllocate(255,255,255);
-  $param->{black} = $im->colorAllocate(0,0,0);
-  $param->{red} = $im->colorAllocate(255,0,0);
-  $param->{blue} = $im->colorAllocate(0,0,255);
-  foreach my $aminoacid (keys %{$param->{aa}}) {
-    if ($param->{wifcolor} && $param->{aa}->{$aminoacid}->{wif}<=$param->{maxwif} && !(defined $param->{aa}->{$aminoacid}->{charged} && $param->{aa}->{$aminoacid}->{charged})) {
-      $param->{aa}->{$aminoacid}->{fcolor} =
-       $im->colorAllocate(min(($param->{aa}->{$aminoacid}->{wif}-$param->{minwif})/
-                              (0-$param->{minwif})*255,255),
-                          255-max(($param->{aa}->{$aminoacid}->{wif})/
-                                  ($param->{maxwif}),0)*255,0);
-    }
-    elsif ($param->{wifcolor} && defined $param->{aa}->{$aminoacid}->{border}) {
-      $param->{aa}->{$aminoacid}->{fcolor} = $im->colorAllocate($param->{aa}->{$aminoacid}->{border}[0],
-                                                     $param->{aa}->{$aminoacid}->{border}[1],
-                                                     $param->{aa}->{$aminoacid}->{border}[2]);
-    }
-    else {
-      $param->{aa}->{$aminoacid}->{fcolor} = $param->{black};
-    }
-    if ($param->{wifcolor} && $param->{aa}->{$aminoacid}->{wif}<=$param->{maxwif} && !(defined $param->{aa}->{$aminoacid}->{charged} && $param->{aa}->{$aminoacid}->{charged})) {
-      $param->{aa}->{$aminoacid}->{bcolor} =
-       $im->colorAllocate(min(($param->{aa}->{$aminoacid}->{wif}-$param->{minwif})/
-                              (0-$param->{minwif})*255,255),
-                          255-max(($param->{aa}->{$aminoacid}->{wif})/
-                                  ($param->{maxwif}),0)*255,0);
-    }
-    elsif ($param->{wifcolor} && defined $param->{aa}->{$aminoacid}->{fill}) {
-      $param->{aa}->{$aminoacid}->{bcolor} = $im->colorAllocate($param->{aa}->{$aminoacid}->{fill}[0],
-                                                     $param->{aa}->{$aminoacid}->{fill}[1],
-                                                     $param->{aa}->{$aminoacid}->{fill}[2]);
-    }
-    else {
-      $param->{aa}->{$aminoacid}->{bcolor} = $param->{white};
-    }
-  }
-# Draw Bounding Box
-#  $im->rectangle(0,0,$param->{xsize}-1,$param->{ysize}-1,$param->{black});
-  my $aasequence = $q->param('sequence');
-  $aasequence =~ s/[^AC-IK-NP-TV-WY]//gs;
-  if ($param->{reverse_helix}) {
-    my $aaseq=$aasequence;
-    $param->{indexaa}*=-1;
-    my $numberofaa=0;
-    $aasequence='';
-    foreach my $aa(split(//,$aaseq)) {
-      $aasequence = $aa . $aasequence;
-      $numberofaa++;
-    }
-    $param->{indexaa}-=$numberofaa-1;
-    $param->{theta}*=-1;
-  }
-  print STDERR "hmdisp: $param->{hmdisp}\n";
-  if ($param->{'hmdisp'} =~ /^(\-{0,1}\d*\.{0,1}\d+)$/) {
-    my ($x,$y) = calculate_hydrophobic_moment($aasequence,$param);
-    $param->{phe} = - deg2rad(xy2deg($x,-$y)) + $param->{'hmdisp'};
-    print STDERR $param->{phe};
-  }
-  draw_wheel($im,$aasequence,$param);
-  print $q->header(-type=>'image/png');
-  print $im->png;
-
-}
-
-else {
-  print $q->header();
-  print $q->start_html('Helical Wheel Projections');
-  if (defined $q->param('submit') and $q->param('submit')=~/Submit/) {
-    print $q->h1('Wheel:'.encode_entities($q->param('sequence')));
-    print $q->img({-src=>$q->self_url.'&draw=yes'});
-
-    print <<OUT
-<table width="400"><tr><td>By default the output presents the
-hydrophilic residues as circles, hydrophobic residues as diamonds,
-potentially negatively charged as triangles, and potentially
-positively charged as pentagons. Hydrophobicity is color coded as
-well: the most hydrophobic residue is green, and the amount of green
-is decreasing proportionally to the hydrophobicity, with zero
-hydrophobicity coded as yellow. Hydrophilic residues are coded red
-with pure red being the most hydrophilic (uncharged) residue, and the
-amount of red decreasing proportionally to the hydrophilicity. The
-potentially charged residues are light blue. (The color will not apply
-if you turn off color.)</td></tr></table>
-OUT
-
-  }
-  print $q->h1('Helical Wheel Projections'),
-    $q->start_form(-method=>'GET'),
-      $q->table($q->Tr([
-                       $q->td({-bgcolor=>'#ddddff'},['Sequence:',
-                                                     $q->textarea(-name=>'sequence',
-                                                                  -rows=>5,
-                                                                  -columns=>50)
-                                                    ]),
-                       $q->td({-bgcolor=>'#bbbbff'},['Initial AA Number:',
-                                                     $q->textfield(-name=>'indexaa',
-                                                                   -size=>5,
-                                                                   -maxlength=>5
-                                                                  )
-                                                    ]),
-                       $q->td({-bgcolor=>'#ddddff'},['Initial AA Rotation:',
-                                                     $q->textfield(-name=>'phe',
-                                                                   -size=>6,
-                                                                   -maxlength=>6)
-                                                    ]),
-                       $q->td({-bgcolor=>'#ddddff'},['Per AA Rotation:',
-                                                     $q->textfield(-name=>'theta',
-                                                                   -size=>6,
-                                                                   -maxlength=>6)
-                                                    ]),
-                         $q->td({-bgcolor=>'#bbbbff'},['Xsize:',
-                                                       $q->textfield(-name=>'xsize',
-                                                                     -size=>5,
-                                                                     -maxlength=>5)
-                                                      ]),
-                         $q->td({-bgcolor=>'#ddddff'},['Ysize:',
-                                                        $q->textfield(-name=>'ysize',
-                                                                      -size=>5,
-                                                                      -maxlength=>5)
-                                                       ]),
-                         $q->td({-bgcolor=>'#bbbbff'},['CenterX:',
-                                                        $q->textfield(-name=>'centerx',
-                                                                      -size=>5,
-                                                                      -maxlength=>5)
-                                                       ]),
-                          $q->td({-bgcolor=>'#ddddff'},['CenterY:',
-                                                        $q->textfield(-name=>'centery',
-                                                                      -size=>5,
-                                                                      -maxlength=>5)
-                                                       ]),
-                         $q->td({-bgcolor=>'#bbbbff'},['Connection Width:',
-                                                        $q->textfield(-name=>'w',
-                                                                      -size=>5,
-                                                                      -maxlength=>5)
-                                                       ]),
-                          $q->td({-bgcolor=>'#ddddff'},['Symbol Size:',
-                                                        $q->textfield(-name=>'r',
-                                                                      -size=>5,
-                                                                      -maxlength=>5)
-                                                       ]),
-                         $q->td({-bgcolor=>'#bbbbff'},['Font Size:',
-                                                        $q->textfield(-name=>'fontsize',
-                                                                      -size=>5,
-                                                                      -maxlength=>5)
-                                                       ]),
-                          $q->td({-bgcolor=>'#ddddff'},['Graph Radius:',
-                                                        $q->textfield(-name=>'d',
-                                                                      -size=>5,
-                                                                      -maxlength=>5)
-                                                       ]),
-                         $q->td({-bgcolor=>'#bbbbff'},['HM Font Size:',
-                                                        $q->textfield(-name=>'fontsize2',
-                                                                      -size=>5,
-                                                                      -maxlength=>5)
-                                                       ]),
-                          $q->td({-bgcolor=>'#ddddff'},['HM Scale:',
-                                                        $q->textfield(-name=>'hmscale',
-                                                                      -size=>5,
-                                                                      -maxlength=>5)
-                                                       ]),
-                         $q->td({-bgcolor=>'#bbbbff'},['Display HM Angle:',
-                                                       $q->checkbox(-name=>'disp_hm_angle',
-                                                                   -checked=>'checked',
-                                                                   -label=>'')
-                                                       ]),
-                         $q->td({-bgcolor=>'#ddddff'},['Reverse Helix:',
-                                                     $q->checkbox(-name=>'reverse_helix',
-                                                                 -label=>'')
-                                                     ]),
-                         $q->td({-bgcolor=>'#bbbbff'},['No Color:',
-                                                     $q->checkbox(-name=>'wo_color',
-                                                                 -label=>'')
-                                                     ]),
-                         $q->td({-bgcolor=>'#ddddff'},['Hydrophobic Moment Displacement:',
-                                                     $q->textfield(-name=>'hmdisp',
-                                                                  -size=>5,
-                                                                  -maxlength=>5)
-                                                     ]),
-                         $q->td({-bgcolor=>'#bbbbff',-colspan=>2},
-                                [$q->center($q->submit(-name=>'submit',-value=>'Submit'))
-                                ]),
-                        ])
-                ),
-         $q->endform,
-           $q->hr,$q->i("Created by ".$q->a({-href=>"mailto:don\@donarmstrong.com"},'Don Armstrong')." and Raphael Zidovetzki. Version: ".$q->b($VERSION));
-}
-