wheel/wheel.pl

   1 #! /usr/bin/perl -w
   2 # wheel.pl: Draw alpha helical wheel with hydrophobic moment using
   3 # wif (modifiable to woct) scale.
   4 # Copyright (C) 2001 Don Armstrong and Raphael Zidovetzki
   5
   6 # This program is free software; you can redistribute it and/or modify
   7 # it under the terms of the GNU General Public License as published by
   8 # the Free Software Foundation; either version 2 of the License, or
   9 # (at your option) any later version.
  10
  11 # This program is distributed in the hope that it will be useful,
  12 # but WITHOUT ANY WARRANTY; without even the implied warranty of
  13 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  14 # GNU General Public License for more details.
  15
  16 # You should have received a copy of the GNU General Public License
  17 # along with this program; if not, write to the Free Software
  18 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
  19
  20
  21
  22
  23 my $VERSION=q$Id: wheel.pl,v 1.2 2004-10-19 01:16:18 don Exp $;
  24
  25 # Intial Released Version 0.10
  26 # p01: Fixing displayed angle
  27 # p02: Added arrowhead, fixed lack of return in xy2deg(), added no color option
  28 # p03: Added round function, fixed rounding in angles, changed hm to line, added hm_up option
  29 # p04: Removed bounding box
  30 # p05: Changing user interface to allow simultaneous viewing of options and wheel
  31 # p06: Released to public under GPL
  32
  33 use CGI::Carp qw(fatalsToBrowser);
  34 use strict;
  35 use CGI;
  36
  37 use Math::Trig;
  38 use GD;
  39 use GD::Text::Align;
  40 use POSIX;
  41
  42
  43 sub round($) {
  44   my ($a) = @_;
  45   return (floor $a+0.5);
  46 }
  47
  48 sub min($$){
  49   my ($a,$b)=@_;
  50   if ($a>$b) {
  51     return $b;
  52   }
  53   return $a;
  54 }
  55
  56 sub max($$){
  57   my ($a,$b)=@_;
  58   if ($a<$b) {
  59     return $b;
  60   }
  61   return $a;
  62 }
  63
  64 my $q = new CGI;
  65
  66 sub xy2deg($$) {
  67   my ($x,$y) = @_;
  68   my $angle = rad2deg(atan($x/$y));
  69   if ($y<0) {
  70     $angle+=180;
  71   }
  72   elsif ($angle<0) {
  73     $angle+=360;
  74   }
  75   return $angle;
  76 }
  77
  78 sub calculate_hydrophobic_moment($$){
  79   my ($sequence,$param)=@_;
  80   my $phe=$param->{phe};
  81   my $theta=$param->{theta};
  82   my ($x,$y)=(0,0);
  83   foreach my $amino_acid (split(//,$sequence)) {
  84     $x+=-$param->{aa}->{$amino_acid}->{wif} * sin($phe);
  85     $y+=+$param->{aa}->{$amino_acid}->{wif} * cos($phe);
  86     $phe+=$theta;
  87   }
  88   return ($x,$y);
  89 }
  90
  91
  92 sub draw_wheel($$$){
  93   my ($im,$aasequence,$param)=@_;
  94   my $phe=$param->{phe};
  95   my $aanumber=0;
  96   my $point1;
  97   my @points;
  98   foreach my $aminoacid (split(//,$aasequence)) {
  99     push @points, calculate_geometry($param,$phe);
 100     $phe += $param->{theta};
 101     $aanumber++;
 102     last if ($aanumber>18);
 103   }
 104   for ($aanumber=0;$aanumber<19;$aanumber++) {
 105     my $point = pop @points;
 106     last if (!defined $point);
 107     if ($aanumber>0) {
 108       draw_connection($im,$aanumber,$point1,$point);
 109     }
 110     $point1 = $point;
 111   }
 112   $phe = $param->{phe};
 113   $aanumber = 0;
 114   foreach my $aminoacid (split(//,$aasequence)) {
 115     $point1=calculate_geometry($param,$phe);
 116     draw_aa($im,$aminoacid,
 117             $param->{centerx}+($point1->{bx}-$param->{centerx})*
 118             ($param->{d}+2.2*$param->{r}*POSIX::floor($aanumber/18))/
 119             $param->{d},$param->{centery}+($point1->{by}-$param->{centery})*
 120             ($param->{d}+2.2*$param->{r}*POSIX::floor($aanumber/18))/
 121             $param->{d},$phe,$param,$aanumber);
 122     $phe+=$param->{theta};
 123     $aanumber++;
 124   }
 125   my ($hydro_x,$hydro_y) = calculate_hydrophobic_moment($aasequence,$param);
 126   draw_hydrophobic_moment($im,$hydro_x,$hydro_y,$param);
 127 }
 128
 129 sub draw_hydrophobic_moment($$$$){
 130   my ($im,$x,$y,$param)=@_;
 131   my $norm=($x*$x+$y*$y)**(0.5);
 132   my $angle = xy2deg($x,-$y);
 133   if ($norm !=0 and $param->{hmscale}!=0) {
 134     $x=$x/$norm*$param->{hmscale};
 135     $y=$y/$norm*$param->{hmscale};
 136   }
 137
 138   # Draw Moment Line (Box, really)
 139   my $poly = GD::Polygon->new;
 140   print STDERR "$angle\n";
 141   $poly->addPt($param->{centerx}-round(($param->{hmscale}/50)*sin(deg2rad($angle+90))),
 142                $param->{centery}+round(($param->{hmscale}/50)*cos(deg2rad($angle+90))));
 143   $poly->addPt($param->{centerx}+round($x*0.85-($param->{hmscale}/50)*sin(deg2rad($angle+90))),
 144                $param->{centery}+round($y*0.85+($param->{hmscale}/50)*cos(deg2rad($angle+90))));
 145   $poly->addPt($param->{centerx}+round($x*0.85-($param->{hmscale}/50)*sin(deg2rad($angle-90))),
 146                $param->{centery}+round($y*0.85+($param->{hmscale}/50)*cos(deg2rad($angle-90))));
 147   $poly->addPt($param->{centerx}-round(($param->{hmscale}/50)*sin(deg2rad($angle-90))),
 148                $param->{centery}+round(($param->{hmscale}/50)*cos(deg2rad($angle-90))));
 149   $im->filledPolygon($poly,$param->{black});
 150
 151   # Draw Arowhead
 152   undef $poly;
 153   $poly = GD::Polygon->new;
 154   $poly->addPt($param->{centerx}+$x,$param->{centery}+$y);
 155   $poly->addPt($param->{centerx}+$x-round(($param->{hmscale}/5)*sin(deg2rad($angle+20))),
 156                $param->{centery}+$y+round(($param->{hmscale}/5)*cos(deg2rad($angle+20))));
 157   $poly->addPt($param->{centerx}+$x-round(($param->{hmscale}/5)*sin(deg2rad($angle-20))),
 158                $param->{centery}+$y+round(($param->{hmscale}/5)*cos(deg2rad($angle-20))));
 159   $im->filledPolygon($poly,$param->{black});
 160   my $text= GD::Text::Align->new($im,
 161                                  valign => 'center',
 162                                  halign => 'center',
 163                                  color=> $param->{black},
 164                                 );
 165   $text->set_font('/usr/share/fonts/truetype/Florsn01.ttf',$param->{fontsize2});
 166   if ($param->{disp_hm_angle}) {
 167     $text->set_text(POSIX::floor($norm*100+.5)/100 . '@' . POSIX::floor(($angle*10+0.5))/10);
 168   }
 169   else {
 170     $text->set_text(POSIX::floor($norm*100+.5)/100);
 171   }
 172   my $offset=-10-$param->{fontsize2}/2;
 173   if ($y<0) {
 174     $offset=-$offset;
 175   }
 176   $text->draw($param->{centerx},$param->{centery}+$offset);
 177 }
 178
 179 sub draw_connection($$$$) {
 180   my ($im,$aanumber,$point1,$point2) =  @_;
 181   my $color=$im->colorAllocate(240*((18-$aanumber)/18),
 182                                240*((18-$aanumber)/18),
 183                                240*((18-$aanumber)/18)
 184                               );
 185   my $poly = GD::Polygon->new;
 186   $poly->addPt($point1->{ex},$point1->{ey});
 187   $poly->addPt($point2->{ex},$point2->{ey});
 188   $poly->addPt($point2->{cx},$point2->{cy});
 189   $poly->addPt($point1->{cx},$point1->{cy});
 190   $im->filledPolygon($poly,$color);
 191   return;
 192 }
 193
 194 sub calculate_geometry($$){
 195   my ($param,$phe)=@_;
 196   return {bx=>($param->{d})*sin($phe)+$param->{centerx},
 197           cx=>($param->{d}-($param->{w}/2)/sin((pi-$param->{theta})/2))*sin($phe)+$param->{centerx},
 198           dx=>($param->{centerx}),
 199           ex=>($param->{d}+($param->{w}/2)/sin((pi-$param->{theta})/2))*sin($phe)+$param->{centerx},
 200           by=>-($param->{d})*cos($phe)+$param->{centery},
 201           cy=>-($param->{d}-($param->{w}/2)/sin((pi-$param->{theta})/2))*cos($phe)+$param->{centery},
 202           dy=>($param->{centery}),
 203           ey=>-($param->{d}+($param->{w}/2)/sin((pi-$param->{theta})/2))*cos($phe)+$param->{centery},
 204          };
 205 }
 206
 207
 208 sub draw_n_gon($$$$){
 209   my ($x,$y,$r,$n)=@_;
 210   my $ngon=GD::Polygon->new;
 211   for (my $v = 0;$v<$n;$v++) {
 212     $ngon->addPt($x+$r*sin((2*pi/$n)*$v),$y-$r*cos((2*pi/$n)*$v));
 213   }
 214   return($ngon);
 215 }
 216
 217 sub draw_aa($$$$$$$){
 218   my ($im,$aasymbol,$bx,$by,$phe,$param,$aanumber)=@_;
 219   my $r=$param->{r};
 220
 221   my $ax=$bx;
 222   my $ay=$by;
 223   $_ = $param->{aa}->{$aasymbol}->{shape};
 224   if (defined && /square/) {
 225     $im->filledRectangle($ax-$r,$ay-$r,$ax+$r,$ay+$r,$param->{aa}->{$aasymbol}->{bcolor});
 226     $im->rectangle($ax-$r,$ay-$r,$ax+$r,$ay+$r,$param->{aa}->{$aasymbol}->{fcolor});
 227   }
 228   elsif (defined && /triangle/) {
 229     $im->filledPolygon(draw_n_gon($ax,$ay,1.25*$r,3),
 230                        $param->{aa}->{$aasymbol}->{bcolor});
 231     $im->polygon(draw_n_gon($ax,$ay,1.25*$r,3),
 232                  $param->{aa}->{$aasymbol}->{fcolor});
 233   }
 234   elsif (defined && /hexagon/) {
 235     $im->filledPolygon(draw_n_gon($ax,$ay,1.18*$r,6),
 236                      $param->{aa}->{$aasymbol}->{bcolor});
 237     $im->polygon(draw_n_gon($ax,$ay,1.18*$r,6),
 238                  $param->{aa}->{$aasymbol}->{fcolor});
 239   }
 240   elsif (defined && /diamond/) {
 241     $im->filledPolygon(draw_n_gon($ax,$ay,1.25*$r,4),
 242                       $param->{aa}->{$aasymbol}->{bcolor});
 243     $im->polygon(draw_n_gon($ax,$ay,1.25*$r,4),
 244                  $param->{aa}->{$aasymbol}->{fcolor});
 245   }
 246   elsif (defined && /pentagon/) {
 247     $im->filledPolygon(draw_n_gon($ax,$ay,1.2*$r,5),
 248                       $param->{aa}->{$aasymbol}->{bcolor});
 249     $im->polygon(draw_n_gon($ax,$ay,1.2*$r,5),
 250                  $param->{aa}->{$aasymbol}->{fcolor});
 251   }
 252   elsif (defined && /octagon/){
 253     $im->filledPolygon(draw_n_gon($ax,$ay,1.1*$r,8),
 254                       $param->{aa}->{$aasymbol}->{bcolor});
 255     $im->polygon(draw_n_gon($ax,$ay,1.1*$r,8),
 256                  $param->{aa}->{$aasymbol}->{fcolor});
 257   }
 258   else {  #cicle
 259     $im->filledPolygon(draw_n_gon($ax,$ay,$r*0.99,360),
 260                       $param->{aa}->{$aasymbol}->{bcolor});
 261     $im->arc($ax,$ay,2*$r,2*$r,0,360,$param->{aa}->{$aasymbol}->{fcolor});
 262   }
 263   $im->fill($ax,$ay,$param->{aa}->{$aasymbol}->{bcolor});
 264   my $text= GD::Text::Align->new($im,
 265                                  valign => 'center',
 266                                  halign => 'center',
 267                                  color=> $param->{black},
 268                                 );
 269   $text->set_font('/usr/share/fonts/truetype/Florsn01.ttf',$param->{fontsize});
 270   my $label_text=$aasymbol  . abs($aanumber+$param->{indexaa});
 271   $text->set_text($label_text);
 272   $text->draw($ax,$ay,0);
 273 }
 274
 275
 276 if (defined $q->param('draw') and $q->param('draw')=~/yes/) {
 277   my $param={
 278              indexaa=>1,
 279              d=>320,
 280              centerx=>500,
 281              centery=>500,
 282              xsize=>1000,
 283              ysize=>1000,
 284              w=>14,
 285              theta=>(100/180)*pi,
 286              phe=>(0/180)*pi,
 287              r=>40,
 288              fontsize=>20,
 289              fontsize2=>20,
 290              hmscale=>50,
 291              wifcolor=>1,
 292              maxwif=>0.5802,
 293              minwif=>-1.8502,
 294              hmdisp=>'',
 295             };
 296   # Merge in query params
 297   # DGwoct[woct] and DGwif[wif] are octanol and interface hydrophobicity values
 298   # as seen on http://blanco.biomol.uci.edu/Whole_residue_HFscales.txt
 299   # and used in MPEx.
 300   # Wimley and White
 301   # Nature Struc. Biol 3:842 (1996) [wif values]
 302   # Wimley, Creamer and White
 303   # Biochemistry 34:5108 (1996) [woct values]
 304
 305   $param->{aa} = {G=>{name=>'Glycine',
 306                       abbr=>'gly',
 307                       woct=>1.15,
 308                       wif=>0.01,
 309                      },
 310                   A=>{name=>'Alanine',
 311                       abbr=>'ala',
 312                       woct=>0.50,
 313                       wif=>0.17,
 314                      },
 315                   V=>{name=>'Valine',
 316                       abbr=>'val',
 317                       woct=>-0.46,
 318                       wif=>0.07,
 319                      },
 320                   L=>{name=>'Leucine',
 321                       abbr=>'leu',
 322                       woct=>-1.25,
 323                       wif=>-0.56,
 324                       shape=>'diamond',
 325                      },
 326                   I=>{name=>'Isoleucine',
 327                       abbr=>'ile',
 328                       woct=>-1.12,
 329                       wif=>-0.31,
 330                       shape=>'diamond',
 331                      },
 332                   M=>{name=>'Methionine',
 333                       abbr=>'met',
 334                       woct=>-0.67,
 335                       wif=>-0.23,
 336                       shape=>'diamond',
 337                      },
 338                   P=>{name=>'Proline',
 339                       abbr=>'pro',
 340                       woct=>0.14,
 341                       wif=>0.45,
 342                      },
 343                   F=>{name=>'Phenylalanine',
 344                       abbr=>'phe',
 345                       woct=>-1.71,
 346                       wif=>-1.13,
 347                       shape=>'diamond',
 348                      },
 349                   W=>{name=>'Tryptophan',
 350                       abbr=>'trp',
 351                       woct=>-2.09,
 352                       wif=>-1.85,
 353                       shape=>'diamond',
 354                      },
 355                   S=>{name=>'Serine',
 356                       abbr=>'ser',
 357                       woct=>0.46,
 358                       wif=>0.13,
 359                      },
 360                   T=>{name=>'Threonine',
 361                       abbr=>'thr',
 362                       woct=>0.25,
 363                       wif=>0.14,
 364                      },
 365                   N=>{name=>'Asparagine',
 366                       abbr=>'asn',
 367                       woct=>0.85,
 368                       wif=>0.42,
 369                      },
 370                   Q=>{name=>'Glutamine',
 371                       abbr=>'gln',
 372                       woct=>0.77,
 373                       wif=>0.58,
 374                      },
 375                   Y=>{name=>'Tyrosine',
 376                       abbr=>'tyr',
 377                       woct=>-0.71,
 378                       wif=>-0.94,
 379                       shape=>'diamond',
 380                      },
 381                   C=>{name=>'Cysteine',
 382                       abbr=>'cys',
 383                       woct=>-0.02,
 384                       wif=>-0.24,
 385                       shape=>'diamond',
 386                      },
 387                   K=>{name=>'Lysine',
 388                       abbr=>'lys',
 389                       woct=>2.80,
 390                       wif=>0.99,
 391                       shape=>'pentagon',
 392                       fill=>[187,187,255],
 393                       border=>[187,187,255],
 394                      },
 395                   R=>{name=>'Arginine',
 396                       abbr=>'arg',
 397                       woct=>1.81,
 398                       wif=>0.81,
 399                       shape=>'pentagon',
 400                       fill=>[187,187,255],
 401                       border=>[187,187,255],
 402                      },
 403                   H=>{name=>'Histidine',
 404                       abbr=>'his',
 405                       woct=>2.33,
 406                       wif=>0.96,
 407                       shape=>'pentagon',
 408                       fill=>[187,187,255],
 409                       border=>[187,187,255],
 410                      },
 411                   D=>{name=>'Aspartic Acid',
 412                       abbr=>'asp',
 413                       woct=>3.64,
 414                       wif=>1.23,
 415                       shape=>'triangle',
 416                       fill=>[187,187,255],
 417                       border=>[187,187,255],
 418                      },
 419                   E=>{name=>'Glutamic Acid',
 420                       abbr=>'glu',
 421                       woct=>3.63,
 422                       wif=>2.02,
 423                       shape=>'triangle',
 424                       fill=>[187,187,255],
 425                       border=>[187,187,255],
 426                      },
 427                  };
 428   foreach my $param_key ($q->param) {
 429     my $param_value=$q->param($param_key);
 430     if ($param_value=~/^(\-{0,1}\d*\.{0,1}\d+)$/) {
 431       $param->{$param_key}=$q->param($param_key);
 432       if ($param_key=~/^(phe|theta|hmdisp)$/) {
 433         $param->{$param_key}=$param->{$param_key}/180*pi;
 434       }
 435     }
 436   }
 437   if ($q->param('disp_hm_angle') =~ /on/) {
 438     $param->{'disp_hm_angle'}=1;
 439   }
 440   else {
 441     $param->{'disp_hm_angle'}=0;
 442   }
 443   if ($q->param('reverse_helix') =~ /on/) {
 444     $param->{'reverse_helix'}=1;
 445   }
 446   else {
 447     $param->{'reverse_helix'}=0;
 448   }
 449   if ($q->param('wo_color') =~ /on/) {
 450     $param->{'wifcolor'}=0;
 451   }
 452   else {
 453     $param->{'wifcolor'}=1;
 454   }
 455   my $im = new GD::Image($param->{xsize},$param->{ysize});
 456   $param->{white} = $im->colorAllocate(255,255,255);
 457   $param->{black} = $im->colorAllocate(0,0,0);
 458   $param->{red} = $im->colorAllocate(255,0,0);
 459   $param->{blue} = $im->colorAllocate(0,0,255);
 460   foreach my $aminoacid (keys %{$param->{aa}}) {
 461     if ($param->{wifcolor} && $param->{aa}->{$aminoacid}->{wif}<=$param->{maxwif} && !(defined $param->{aa}->{$aminoacid}->{charged} && $param->{aa}->{$aminoacid}->{charged})) {
 462       $param->{aa}->{$aminoacid}->{fcolor} =
 463         $im->colorAllocate(min(($param->{aa}->{$aminoacid}->{wif}-$param->{minwif})/
 464                                (0-$param->{minwif})*255,255),
 465                            255-max(($param->{aa}->{$aminoacid}->{wif})/
 466                                    ($param->{maxwif}),0)*255,0);
 467     }
 468     elsif ($param->{wifcolor} && defined $param->{aa}->{$aminoacid}->{border}) {
 469       $param->{aa}->{$aminoacid}->{fcolor} = $im->colorAllocate($param->{aa}->{$aminoacid}->{border}[0],
 470                                                       $param->{aa}->{$aminoacid}->{border}[1],
 471                                                       $param->{aa}->{$aminoacid}->{border}[2]);
 472     }
 473     else {
 474       $param->{aa}->{$aminoacid}->{fcolor} = $param->{black};
 475     }
 476     if ($param->{wifcolor} && $param->{aa}->{$aminoacid}->{wif}<=$param->{maxwif} && !(defined $param->{aa}->{$aminoacid}->{charged} && $param->{aa}->{$aminoacid}->{charged})) {
 477       $param->{aa}->{$aminoacid}->{bcolor} =
 478         $im->colorAllocate(min(($param->{aa}->{$aminoacid}->{wif}-$param->{minwif})/
 479                                (0-$param->{minwif})*255,255),
 480                            255-max(($param->{aa}->{$aminoacid}->{wif})/
 481                                    ($param->{maxwif}),0)*255,0);
 482     }
 483     elsif ($param->{wifcolor} && defined $param->{aa}->{$aminoacid}->{fill}) {
 484       $param->{aa}->{$aminoacid}->{bcolor} = $im->colorAllocate($param->{aa}->{$aminoacid}->{fill}[0],
 485                                                       $param->{aa}->{$aminoacid}->{fill}[1],
 486                                                       $param->{aa}->{$aminoacid}->{fill}[2]);
 487     }
 488     else {
 489       $param->{aa}->{$aminoacid}->{bcolor} = $param->{white};
 490     }
 491   }
 492 # Draw Bounding Box
 493 #  $im->rectangle(0,0,$param->{xsize}-1,$param->{ysize}-1,$param->{black});
 494   my $aasequence = $q->param('sequence');
 495   $aasequence =~ s/[^AC-IK-NP-TV-WY]//gs;
 496   if ($param->{reverse_helix}) {
 497     my $aaseq=$aasequence;
 498     $param->{indexaa}*=-1;
 499     my $numberofaa=0;
 500     $aasequence='';
 501     foreach my $aa(split(//,$aaseq)) {
 502       $aasequence = $aa . $aasequence;
 503       $numberofaa++;
 504     }
 505     $param->{indexaa}-=$numberofaa-1;
 506     $param->{theta}*=-1;
 507   }
 508   print STDERR "hmdisp: $param->{hmdisp}\n";
 509   if ($param->{'hmdisp'} =~ /^(\-{0,1}\d*\.{0,1}\d+)$/) {
 510     my ($x,$y) = calculate_hydrophobic_moment($aasequence,$param);
 511     $param->{phe} = - deg2rad(xy2deg($x,-$y)) + $param->{'hmdisp'};
 512     print STDERR $param->{phe};
 513   }
 514   draw_wheel($im,$aasequence,$param);
 515   print $q->header(-type=>'image/png');
 516   print $im->png;
 517
 518 }
 519
 520 else {
 521   print $q->header();
 522   print $q->start_html('Helical Wheel Projections');
 523   if (defined $q->param('submit') and $q->param('submit')=~/Submit/) {
 524     print $q->h1('Wheel:'.$q->param('sequence'));
 525     print $q->img({-src=>$q->self_url.'&draw=yes'});
 526   }
 527   print $q->h1('Helical Wheel Projections'),
 528     $q->start_form(-method=>'GET'),
 529       $q->table($q->Tr([
 530                         $q->td({-bgcolor=>'#ddddff'},['Sequence:',
 531                                                       $q->textarea(-name=>'sequence',
 532                                                                    -rows=>5,
 533                                                                    -columns=>50)
 534                                                      ]),
 535                         $q->td({-bgcolor=>'#bbbbff'},['Initial AA Number:',
 536                                                       $q->textfield(-name=>'indexaa',
 537                                                                     -size=>5,
 538                                                                     -maxlength=>5
 539                                                                    )
 540                                                      ]),
 541                         $q->td({-bgcolor=>'#ddddff'},['Initial AA Rotation:',
 542                                                       $q->textfield(-name=>'phe',
 543                                                                     -size=>6,
 544                                                                     -maxlength=>6)
 545                                                      ]),
 546                         $q->td({-bgcolor=>'#ddddff'},['Per AA Rotation:',
 547                                                       $q->textfield(-name=>'theta',
 548                                                                     -size=>6,
 549                                                                     -maxlength=>6)
 550                                                      ]),
 551                           $q->td({-bgcolor=>'#bbbbff'},['Xsize:',
 552                                                         $q->textfield(-name=>'xsize',
 553                                                                       -size=>5,
 554                                                                       -maxlength=>5)
 555                                                        ]),
 556                           $q->td({-bgcolor=>'#ddddff'},['Ysize:',
 557                                                         $q->textfield(-name=>'ysize',
 558                                                                       -size=>5,
 559                                                                       -maxlength=>5)
 560                                                        ]),
 561                           $q->td({-bgcolor=>'#bbbbff'},['CenterX:',
 562                                                         $q->textfield(-name=>'centerx',
 563                                                                       -size=>5,
 564                                                                       -maxlength=>5)
 565                                                        ]),
 566                           $q->td({-bgcolor=>'#ddddff'},['CenterY:',
 567                                                         $q->textfield(-name=>'centery',
 568                                                                       -size=>5,
 569                                                                       -maxlength=>5)
 570                                                        ]),
 571                           $q->td({-bgcolor=>'#bbbbff'},['Connection Width:',
 572                                                         $q->textfield(-name=>'w',
 573                                                                       -size=>5,
 574                                                                       -maxlength=>5)
 575                                                        ]),
 576                           $q->td({-bgcolor=>'#ddddff'},['Symbol Size:',
 577                                                         $q->textfield(-name=>'r',
 578                                                                       -size=>5,
 579                                                                       -maxlength=>5)
 580                                                        ]),
 581                           $q->td({-bgcolor=>'#bbbbff'},['Font Size:',
 582                                                         $q->textfield(-name=>'fontsize',
 583                                                                       -size=>5,
 584                                                                       -maxlength=>5)
 585                                                        ]),
 586                           $q->td({-bgcolor=>'#ddddff'},['Graph Radius:',
 587                                                         $q->textfield(-name=>'d',
 588                                                                       -size=>5,
 589                                                                       -maxlength=>5)
 590                                                        ]),
 591                           $q->td({-bgcolor=>'#bbbbff'},['HM Font Size:',
 592                                                         $q->textfield(-name=>'fontsize2',
 593                                                                       -size=>5,
 594                                                                       -maxlength=>5)
 595                                                        ]),
 596                           $q->td({-bgcolor=>'#ddddff'},['HM Scale:',
 597                                                         $q->textfield(-name=>'hmscale',
 598                                                                       -size=>5,
 599                                                                       -maxlength=>5)
 600                                                        ]),
 601                           $q->td({-bgcolor=>'#bbbbff'},['Display HM Angle:',
 602                                                         $q->checkbox(-name=>'disp_hm_angle',
 603                                                                     -checked=>'checked',
 604                                                                     -label=>'')
 605                                                        ]),
 606                           $q->td({-bgcolor=>'#ddddff'},['Reverse Helix:',
 607                                                       $q->checkbox(-name=>'reverse_helix',
 608                                                                   -label=>'')
 609                                                       ]),
 610                           $q->td({-bgcolor=>'#bbbbff'},['No Color:',
 611                                                       $q->checkbox(-name=>'wo_color',
 612                                                                   -label=>'')
 613                                                       ]),
 614                           $q->td({-bgcolor=>'#ddddff'},['Hydrophobic Moment Displacement:',
 615                                                       $q->textfield(-name=>'hmdisp',
 616                                                                    -size=>5,
 617                                                                    -maxlength=>5)
 618                                                       ]),
 619                           $q->td({-bgcolor=>'#bbbbff',-colspan=>2},
 620                                  [$q->center($q->submit(-name=>'submit',-value=>'Submit'))
 621                                  ]),
 622                          ])
 623                  ),
 624           $q->endform,
 625             $q->hr,$q->i("Created by ".$q->a({-href=>"mailto:don\@donarmstrong.com"},'Don Armstrong')." and Raphael Zidovetzki. Version: ".$q->b($VERSION));
 626 }
 627