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#!/usr/bin/perl # Coded by Guy Ashkenazi, guy@fh.huji.ac.il # Based on the work of Peter Ertl, peter.ertl@pharma.novartis.com use strict; use lib '/home/httpd/lib/perl'; use GD; use LONCAPA::loncgi(); if (! &LONCAPA::loncgi::check_cookie_and_load_env()) { print < Bad Cookie Your cookie information is incorrect. END exit; } sub unescape { my $str=shift; $str =~ s/%([a-fA-F0-9][a-fA-F0-9])/pack("C",hex($1))/eg; return $str; } # read the width and the JME string from the cgi query my $id=$ENV{'QUERY_STRING'}; my @JMEstring = split(/ /,&unescape($ENV{'cgi.'.$id.'.JME'})); my $width = $ENV{'cgi.'.$id.'.WIDTH'}; if (!$width) { $width = 200; } # parse JME string my $natoms= shift @JMEstring; my $nbonds= shift @JMEstring; my (@name,@x,@y); for (my $i = 0; $i < $natoms; $i++) { @name[$i] = shift @JMEstring; @x[$i] = shift @JMEstring; @y[$i] = shift @JMEstring; } my (@atomA,@atomB,@bondType); for (my $i = 0; $i < $nbonds; $i++) { @atomA[$i] = (shift @JMEstring)-1; @atomB[$i] = (shift @JMEstring)-1; @bondType[$i] = shift @JMEstring; } # Find border and move lower left corner to (1.5,1.0) my $xmin = my $xmax = @x[0]; my $ymin = my $ymax = $y[0]; my $maxName = 0; for (my $i = 1; $i < $natoms; $i++) { $xmax = @x[$i] if (@x[$i] > $xmax); $xmin = @x[$i] if (@x[$i] < $xmin); $ymax = @y[$i] if (@y[$i] > $ymax); $ymin = @y[$i] if (@y[$i] < $ymin); @name[$i] =~ /(\@{1,2})?(\w+)([\+|\-])?(\d)?/; $maxName = length $2 if (length $2 > $maxName); } $maxName = ($maxName-3 < 0) ? 0 : $maxName-3; my $scale = $width / ($xmax-$xmin+3+$maxName); my $height = $scale * ($ymax-$ymin+2); for (my $i = 0; $i < $natoms; $i++) { @x[$i] += (1.5+$maxName/2-$xmin); @x[$i] *= $scale; @y[$i] += (1.0-$ymin); @y[$i] *= $scale; } # Count bonds my @bonds = map {0} 0..$natoms-1; my @adjacent = map {0} 0..$natoms-1; my @bondsx = map {0} 0..$natoms-1; my @bondsy = map {0} 0..$natoms-1; for (my $i = 0; $i < $nbonds; $i++) { @bonds[@atomA[$i]] += (@bondType[$i]>0) ? @bondType[$i] : 1; @bonds[@atomB[$i]] += (@bondType[$i]>0) ? @bondType[$i] : 1; @adjacent[@atomA[$i]]++; @adjacent[@atomB[$i]]++; @bondsx[@atomA[$i]] += @x[@atomB[$i]] - @x[@atomA[$i]]; @bondsy[@atomA[$i]] += @y[@atomB[$i]] - @y[@atomA[$i]]; @bondsx[@atomB[$i]] += @x[@atomA[$i]] - @x[@atomB[$i]]; @bondsy[@atomB[$i]] += @y[@atomA[$i]] - @y[@atomB[$i]]; } # Create a new PostScript object my $im = new GD::Image($width,$height); my $white = $im->colorAllocate(255,255,255); my $black = $im->colorAllocate(0,0,0); my $gray = $im->colorAllocate(200,200,200); #$gdAntiAliased = $im->colorAllocate(1,1,1); $im->setAntiAliased($black); # Draw bonds my $doubleWidth = 0.10*$scale; my $tripleWidth = 0.15*$scale; for (my $i = 0; $i < $nbonds; $i++) { my $xa = @x[@atomA[$i]]; my $ya = @y[@atomA[$i]]; my $xb = @x[@atomB[$i]]; my $yb = @y[@atomB[$i]]; my ($sina,$cosa,$dx,$dy); if (@bondType[$i] != 1) { $dx = $xb-$xa; $dy = $yb-$ya; my $dd = sqrt($dx*$dx + $dy*$dy); $sina=$dy/$dd; $cosa=$dx/$dd; } if (@bondType[$i] == -2) { for (my $t = 0; $t <= 1; $t += 0.1) { my $xab = $xa + $t*$dx; my $yab = $ya + $t*$dy; my $xperp = $tripleWidth*$sina*$t; my $yperp = $tripleWidth*$cosa*$t; $im->line($xab+$xperp,$height-($yab-$yperp), $xab-$xperp,$height-($yab+$yperp), gdAntiAliased); } } elsif (@bondType[$i] == -1) { my $xperp = $tripleWidth*$sina; my $yperp = $tripleWidth*$cosa; my $poly = new GD::Polygon; $poly->addPt($xa,$height-$ya); $poly->addPt($xb+$xperp,$height-($yb-$yperp)); $poly->addPt($xb-$xperp,$height-($yb+$yperp)); $im->filledPolygon($poly,$black); } elsif (@bondType[$i] == 1) { $im->line($xa,$height-$ya,$xb,$height-$yb,gdAntiAliased); } elsif (@bondType[$i] == 2 && ((@adjacent[@atomA[$i]] == 1 && @adjacent[@atomB[$i]] > 2)|| (@adjacent[@atomB[$i]] == 1 && @adjacent[@atomA[$i]] > 2))) { # centered bond my $xperp = $doubleWidth*$sina; my $yperp = $doubleWidth*$cosa; $im->line($xa+$xperp,$height-($ya-$yperp), $xb+$xperp,$height-($yb-$yperp), gdAntiAliased); $im->line($xa-$xperp,$height-($ya+$yperp), $xb-$xperp,$height-($yb+$yperp), gdAntiAliased); } elsif (@bondType[$i] == 2) { my $xperp = 2*$doubleWidth*$sina; my $yperp = 2*$doubleWidth*$cosa; $im->line($xa,$height-$ya,$xb,$height-$yb,gdAntiAliased); $im->line($xa+0.1*$dx-$xperp,$height-($ya+0.1*$dy+$yperp), $xb-0.1*$dx-$xperp,$height-($yb-0.1*$dy+$yperp), gdAntiAliased); } elsif (@bondType[$i] == 3) { my $xperp = $tripleWidth*$sina; my $yperp = $tripleWidth*$cosa; $im->line($xa,$height-$ya,$xb,$height-$yb,gdAntiAliased); $im->line($xa+$xperp,$height-($ya-$yperp), $xb+$xperp,$height-($yb-$yperp), gdAntiAliased); $im->line($xa-$xperp,$height-($ya+$yperp), $xb-$xperp,$height-($yb+$yperp), gdAntiAliased); } } # Write labels my %valence = ("C",4,"N",3,"P",3,"O",2,"S",2); my $font = '/usr/share/fonts/default/Type1/n021003l.pfb'; my $pointsize = 20; my @bounds = GD::Image->stringTTF($black,$font,100,0,0,0,"H"); my $ptsize = 100*0.662*$pointsize*(2.54/72)*$scale/(@bounds[3]-@bounds[5]); for (my $i = 0; $i < $natoms; $i++) { my ($formula,$sign,$charge) = (@name[$i] =~ /(\w+)([\+|\-])?(\d)?/); $sign = "–" if ($sign eq "-"); # replace by n-dash if ($formula ne "C" || $sign ne ""|| @adjacent[$i] < 2 || (@adjacent[$i] == 2 && @bonds[$i] == 4)) { # don't show C, unless charged, terminal, or linear my $nH = 0; if (exists $valence{$formula}) { $nH = $valence{$formula} - @bonds[$i]; $nH += (($charge eq "")? 1 : $charge) if ($sign eq "+"); $nH -= (($charge eq "")? 1 : $charge) if ($sign eq "-"); } $formula .= "H" if ($nH > 0); $formula .= $nH if ($nH > 1); my @formula = $formula=~ /[A-Z][a-z]?\d*/g; my $PI = 3.1415; my $bondAngle; if (abs(@bondsy[$i]) < 0.01 && abs(@bondsx[$i]) < 0.01) { $bondAngle = -$PI; } else { $bondAngle = atan2(@bondsy[$i],@bondsx[$i]); } my $direction; if (@adjacent[$i] < 2) { $direction = (@bondsx[$i] < 0.01) ? "r" : "l"; } else { if ($bondAngle >= -$PI/4 && $bondAngle <= $PI/4) { $direction = "l"; } elsif ($bondAngle > $PI/4 && $bondAngle < 3*$PI/4) { $direction = "d"; } elsif ($bondAngle < -$PI/4 && $bondAngle > -3*$PI/4) { $direction = "u"; } else { $direction = "r"; } } if ($direction eq "r") { # direction = right @formula[0] =~ /([A-Z][a-z]?)(\d*)/; my $carrige = @x[$i]-stringWidth($1)/2; foreach (@formula) { $_ =~ /([A-Z][a-z]?)(\d*)/; $carrige = printElement ($1,$2,$carrige,@y[$i]); } printCharge ($sign,$charge,$carrige,@y[$i]) if ($sign ne ""); } elsif ($direction eq "l") { # direction = left, reverse hydrogens @formula[0] =~ /([A-Z][a-z]?)(\d*)/; my $carrige = @x[$i]+ stringWidth($1)/2+stringWidth($2)-stringWidth($formula); foreach (reverse @formula) { $_ =~ /([A-Z][a-z]?)(\d*)/; $carrige = printElement ($1,$2,$carrige,@y[$i]); } printCharge ($sign,$charge,$carrige,@y[$i]) if ($sign ne ""); } elsif ($direction eq "u") { # direction = up (shift @formula) =~ /([A-Z][a-z]?)(\d*)/; my $carrige = @x[$i]-stringWidth($1)/2; $carrige = printElement ($1,$2,$carrige,@y[$i]); my $y = (@formula > 0) ? @y[$i] + fm2cm(800) : @y[$i]; $carrige = (@formula > 0) ? @x[$i]-stringWidth($1)/2 : $carrige; foreach (@formula) { $_ =~ /([A-Z][a-z]?)(\d*)/; $carrige = printElement ($1,$2,$carrige,$y); } printCharge ($sign,$charge,$carrige,$y) if ($sign ne ""); } else { # direction = down (shift @formula) =~ /([A-Z][a-z]?)(\d*)/; my $carrige = @x[$i]-stringWidth($1)/2; $carrige = printElement ($1,$2,$carrige,@y[$i]); my $y = (@formula > 0) ? @y[$i] + fm2cm(-800) : @y[$i]; $carrige = (@formula > 0) ? @x[$i]-stringWidth($1)/2 : $carrige; foreach (@formula) { $_ =~ /([A-Z][a-z]?)(\d*)/; $carrige = printElement ($1,$2,$carrige,$y); } printCharge ($sign,$charge,$carrige,$y) if ($sign ne ""); } } } # make sure we are writing to a binary stream binmode STDOUT; # Convert the image to PNG and print it on standard output print "Content-type: image/png\n\n"; print $im->png; sub stringWidth { my ($string) = @_; my $width = 0; while ($string =~ /[A-Za-z]/g) { my @bounds = GD::Image->stringTTF($black,$font,$ptsize,0,0,0,$&); $width += @bounds[2]-@bounds[0]+2; } while ($string =~ /[\d+-]/g) { my @bounds = GD::Image->stringTTF($black,$font,0.6*$ptsize,0,0,0,$&); $width += @bounds[2]-@bounds[0]+2; } return $width; } sub fm2cm { #font metrics to cm my ($fm) = @_; return $scale*(2.54/72)*$pointsize*$fm/1000; } sub printElement { #element symbol + optional subscript my ($element,$subscript,$x,$y) = @_; my $yy = 662; my @bounds = GD::Image->stringTTF($black,$font,$ptsize,0, $x,$height-($y+fm2cm(-$yy/2)),$element); $im->filledRectangle( @bounds[6]-1,@bounds[7]-fm2cm(135), @bounds[2]+1,@bounds[3]+fm2cm(135),$white); $im->stringTTF($black,$font,$ptsize,0, $x,$height-($y+fm2cm(-$yy/2)),$element); $x = @bounds[2] + 1; if ($subscript ne "") { @bounds = GD::Image->stringTTF($black,$font,0.6*$ptsize,0, $x,$height-($y+fm2cm(-0.8*$yy)),$subscript); $im->filledRectangle( @bounds[6]-1,@bounds[7]-fm2cm(45), @bounds[2]+1,@bounds[3]+fm2cm(45),$white); $im->stringTTF($black,$font,0.6*$ptsize,0, $x,$height-($y+fm2cm(-0.8*$yy)),$subscript); } $x = @bounds[2] + 1; } sub printCharge { my ($sign,$charge,$x,$y) = @_; my $yy = 662; $charge = "" if ($charge == 1); $charge .= $sign; my @bounds = GD::Image->stringTTF($black,$font,0.6*$ptsize,0, $x,$height-($y+fm2cm(0.2*$yy)),$charge); $im->filledRectangle( @bounds[6]-1,@bounds[7]-fm2cm(45), @bounds[2]+1,@bounds[3]+fm2cm(45),$white); $im->stringTTF($black,$font,0.6*$ptsize,0,$x,$height-($y+fm2cm(0.2*$yy)),$charge); $x = @bounds[2] + 1; }