--- loncom/homework/convertjme.pl 2003/10/16 19:46:36 1.1 +++ loncom/homework/convertjme.pl 2003/10/16 21:52:27 1.3 @@ -3,27 +3,53 @@ # 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 PostScript::Simple; +use LONCAPA::loncgi(); -# read the width and the JME string from the cgi query -%data = &read_input; -@JMEstring = split (/ /,$data{JME}); -$width = $data{WIDTH}; +if (! &LONCAPA::loncgi::check_cookie_and_load_env()) { + print < +Bad Cookie + +Your cookie information is incorrect. + + +END + exit; +} -#print "Content-type: text/plain\n\n"; +sub unescape { + my $str=shift; + $str =~ s/%([a-fA-F0-9][a-fA-F0-9])/pack("C",hex($1))/eg; + return $str; +} -# parse JME string +# 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'}; +my $png = $ENV{'cgi.'.$id.'.PNG'}; +my $ps = $ENV{'cgi.'.$id.'.PS'}; +if (!$width) { $width = 200; } -$natoms= shift @JMEstring; -$nbonds= shift @JMEstring; +# parse JME string -for ($i = 0; $i < $natoms; $i++) { +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; } -for ($i = 0; $i < $nbonds; $i++) { +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; @@ -31,11 +57,11 @@ for ($i = 0; $i < $nbonds; $i++) { # Find border and move lower left corner to (1.5,1.0) -$xmin = $xmax = @x[0]; -$ymin = $ymax = $y[0]; -$maxName = 0; +my $xmin = my $xmax = @x[0]; +my $ymin = my $ymax = $y[0]; +my $maxName = 0; -for ($i = 1; $i < $natoms; $i++) { +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] > $ymax); @@ -44,24 +70,23 @@ for ($i = 1; $i < $natoms; $i++) { $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-$ymin+2); -$scale = $width / ($xmax-$xmin+3+$maxName); -$height = $scale * ($ymax-$ymin+2); - -for ($i = 0; $i < $natoms; $i++) { +for (my $i = 0; $i < $natoms; $i++) { @x[$i] += (1.5+$maxName/2-$xmin); - @x[$i] *= $scale; + if ($png) { @x[$i] *= $scale; } @y[$i] += (1.0-$ymin); - @y[$i] *= $scale; + if ($png) { @y[$i] *= $scale; } } # Count bonds -@bonds = map {0} 0..$natoms-1; -@adjacent = map {0} 0..$natoms-1; -@bondsx = map {0} 0..$natoms-1; -@bondsy = map {0} 0..$natoms-1; -for ($i = 0; $i < $nbonds; $i++) { +my @bonds = map {0} 0..$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[$i] : 1; @@ -75,105 +100,160 @@ for ($i = 0; $i < $nbonds; $i++) { } # Create a new PostScript object -$im = new GD::Image($width,$height); -$white = $im->colorAllocate(255,255,255); -$black = $im->colorAllocate(0,0,0); -$gray = $im->colorAllocate(200,200,200); +my ($im,$white,$black,$gray); +if ($png) { + $im = new GD::Image($width,$height); + $white = $im->colorAllocate(255,255,255); + $black = $im->colorAllocate(0,0,0); + $gray = $im->colorAllocate(200,200,200); #$gdAntiAliased = $im->colorAllocate(1,1,1); -$im->setAntiAliased($black); + $im->setAntiAliased($black); +} elsif ($ps) { + $im = new PostScript::Simple(xsize => $xmax-$xmin+3+$maxName, + ysize => $ymax-$ymin+2, + clip => 1, + eps => 1, + color => 0, + units => "cm"); +} # Draw bonds -$doubleWidth = 0.10*$scale; -$tripleWidth = 0.15*$scale; - -for ($i = 0; $i < $nbonds; $i++) { - $xa = @x[@atomA[$i]]; - $ya = @y[@atomA[$i]]; - $xb = @x[@atomB[$i]]; - $yb = @y[@atomB[$i]]; +my $doubleWidth; +my $tripleWidth; +if ($png) { + $doubleWidth = 0.10*$scale; + $tripleWidth = 0.15*$scale; +} elsif ($ps) { + $doubleWidth = 0.10; + $tripleWidth = 0.15; +} + +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; - $dd = sqrt($dx*$dx + $dy*$dy); + my $dd = sqrt($dx*$dx + $dy*$dy); $sina=$dy/$dd; $cosa=$dx/$dd; } if (@bondType[$i] == -2) { - for ($t = 0; $t <= 1; $t += 0.1) { - $xab = $xa + $t*$dx; - $yab = $ya + $t*$dy; - $xperp = $tripleWidth*$sina*$t; - $yperp = $tripleWidth*$cosa*$t; - $im->line($xab+$xperp,$height-($yab-$yperp), - $xab-$xperp,$height-($yab+$yperp), - gdAntiAliased); + 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*$t; + if ($png) { + $im->line($xab+$xperp,$height-($yab-$yperp), + $xab-$xperp,$height-($yab+$yperp), + gdAntiAliased); + } elsif ($ps) { + $im->line($xab+$xperp,$yab-$yperp,$xab-$xperp,$yab+$yperp); + } } } elsif (@bondType[$i] == -1) { - $xperp = $tripleWidth*$sina; - $yperp = $tripleWidth*$cosa; - $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); + my $xperp = $tripleWidth*$sina; + my $yperp = $tripleWidth*$cosa; + if ($png) { + 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,$black); + } elsif ($ps) { + $im->polygon({filled=>1}, + $xa,$ya, + $xb+$xperp,$yb-$yperp, + $xb-$xperp,$yb+$yperp); + } } elsif (@bondType[$i] == 1) { - $im->line($xa,$height-$ya,$xb,$height-$yb,gdAntiAliased); + if ($png) { + $im->line($xa,$height-$ya,$xb,$height-$yb,gdAntiAliased); + } elsif ($ps) { + $im->line($xa,$ya,$xb,$yb); + } } elsif (@bondType[$i] == 2 && ((@adjacent[@atomA[$i]] == 1 && @adjacent[@atomB[$i]] > 2)|| (@adjacent[@atomB[$i]] == 1 && @adjacent[@atomA[$i]] > 2))) { # centered bond - $xperp = $doubleWidth*$sina; - $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); + my $xperp = $doubleWidth*$sina; + my $yperp = $doubleWidth*$cosa; + if ($png) { + $im->line($xa+$xperp,$height-($ya-$yperp), + $xb+$xperp,$height-($yb-$yperp), + gdAntiAliased); + $im->line($xa-$xperp,$height-($ya+$yperp), + $xb-$xperp,$height-($yb+$yperp), + gdAntiAliased); + } elsif ($ps) { + $im->line($xa+$xperp,$ya-$yperp,$xb+$xperp,$yb-$yperp); + $im->line($xa-$xperp,$ya+$yperp,$xb-$xperp,$yb+$yperp); + } } elsif (@bondType[$i] == 2) { - $xperp = 2*$doubleWidth*$sina; - $yperp = 2*$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); + my $xperp = 2*$doubleWidth*$sina; + my $yperp = 2*$doubleWidth*$cosa; + if ($png) { + $im->line($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+$yperp), + gdAntiAliased); + } elsif ($ps) { + $im->line($xa,$ya,$xb,$yb); + $im->line($xa+0.1*$dx-$xperp,$ya+0.1*$dy+$yperp, + $xb-0.1*$dx-$xperp,$yb-0.1*$dy+$yperp); + + } } elsif (@bondType[$i] == 3) { - $xperp = $tripleWidth*$sina; - $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); + my $xperp = $tripleWidth*$sina; + my $yperp = $tripleWidth*$cosa; + if ($png) { + $im->line($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+$yperp), + gdAntiAliased); + } elsif ($ps) { + $im->line($xa,$ya,$xb,$yb); + $im->line($xa+$xperp,$ya-$yperp,$xb+$xperp,$yb-$yperp); + $im->line($xa-$xperp,$ya+$yperp,$xb-$xperp,$yb+$yperp); + } } } # Write labels -%valence = ("C",4,"N",3,"P",3,"O",2,"S",2); - -$font = '/usr/share/fonts/default/Type1/n021003l.pfb'; -$pointsize = 20; -@bounds = GD::Image->stringTTF($black,$font,100,0,0,0,"H"); -$ptsize = 100*0.662*$pointsize*(2.54/72)*$scale/(@bounds[3]-@bounds[5]); +my %valence = ("C",4,"N",3,"P",3,"O",2,"S",2); +my %font_width = (" ",250,"+",564,"-",500,"0",500,"1",500,"2",500,"3",500,"4",500,"5",500,"6",500,"7",500,"8",500,"9",500,"A",722,"B",667,"C",667,"D",722,"E",611,"F",556,"G",722,"H",722,"I",333,"J",389,"K",722,"L",611,"M",889,"N",722,"O",722,"P",556,"Q",722,"R",667,"S",556,"T",611,"U",722,"V",722,"W",944,"X",722,"Y",722,"Z",611,"a",444,"b",500,"c",444,"d",500,"e",444,"f",333,"g",500,"h",500,"i",278,"j",278,"k",500,"l",278,"m",778,"n",500,"o",500,"p",500,"q",500,"r",333,"s",389,"t",278,"u",500,"v",500,"w",722,"x",500,"y",500,"z",444); +my $font = '/usr/share/fonts/default/Type1/n021003l.pfb'; +my $pointsize = 20; +my ($ptsize,@bounds); +if ($png) { + @bounds = GD::Image->stringTTF($black,$font,100,0,0,0,"H"); + $ptsize = 100*0.662*$pointsize*(2.54/72)*$scale/(@bounds[3]-@bounds[5]); +} -for ($i = 0; $i < $natoms; $i++) { +for (my $i = 0; $i < $natoms; $i++) { my ($formula,$sign,$charge) = (@name[$i] =~ /(\w+)([\+|\-])?(\d)?/); - $sign = "–" if ($sign eq "-"); # replace by n-dash - + if ($png) { + $sign = "–" if ($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 - $nH = 0; + my $nH = 0; if (exists $valence{$formula}) { $nH = $valence{$formula} - @bonds[$i]; $nH += (($charge eq "")? 1 : $charge) if ($sign eq "+"); @@ -181,9 +261,10 @@ for ($i = 0; $i < $natoms; $i++) { } $formula .= "H" if ($nH > 0); $formula .= $nH if ($nH > 1); - @formula = $formula=~ /[A-Z][a-z]?\d*/g; + my @formula = $formula=~ /[A-Z][a-z]?\d*/g; - $PI = 3.1415; + my $PI = 3.1415; + my $bondAngle; if (abs(@bondsy[$i]) < 0.01 && abs(@bondsx[$i]) < 0.01) { $bondAngle = -$PI; } @@ -191,6 +272,7 @@ for ($i = 0; $i < $natoms; $i++) { $bondAngle = atan2(@bondsy[$i],@bondsx[$i]); } + my $direction; if (@adjacent[$i] < 2) { $direction = (@bondsx[$i] < 0.01) ? "r" : "l"; } @@ -211,7 +293,7 @@ for ($i = 0; $i < $natoms; $i++) { if ($direction eq "r") { # direction = right @formula[0] =~ /([A-Z][a-z]?)(\d*)/; - $carrige = @x[$i]-stringWidth($1)/2; + my $carrige = @x[$i]-stringWidth($1)/2; foreach (@formula) { $_ =~ /([A-Z][a-z]?)(\d*)/; $carrige = printElement ($1,$2,$carrige,@y[$i]); @@ -220,7 +302,7 @@ for ($i = 0; $i < $natoms; $i++) { } elsif ($direction eq "l") { # direction = left, reverse hydrogens @formula[0] =~ /([A-Z][a-z]?)(\d*)/; - $carrige = @x[$i]+ + my $carrige = @x[$i]+ stringWidth($1)/2+stringWidth($2)-stringWidth($formula); foreach (reverse @formula) { $_ =~ /([A-Z][a-z]?)(\d*)/; @@ -230,9 +312,9 @@ for ($i = 0; $i < $natoms; $i++) { } elsif ($direction eq "u") { # direction = up (shift @formula) =~ /([A-Z][a-z]?)(\d*)/; - $carrige = @x[$i]-stringWidth($1)/2; + my $carrige = @x[$i]-stringWidth($1)/2; $carrige = printElement ($1,$2,$carrige,@y[$i]); - $y = (@formula > 0) ? @y[$i] + fm2cm(800) : @y[$i]; + my $y = (@formula > 0) ? @y[$i] + fm2cm(800) : @y[$i]; $carrige = (@formula > 0) ? @x[$i]-stringWidth($1)/2 : $carrige; foreach (@formula) { @@ -243,9 +325,9 @@ for ($i = 0; $i < $natoms; $i++) { } else { # direction = down (shift @formula) =~ /([A-Z][a-z]?)(\d*)/; - $carrige = @x[$i]-stringWidth($1)/2; + my $carrige = @x[$i]-stringWidth($1)/2; $carrige = printElement ($1,$2,$carrige,@y[$i]); - $y = (@formula > 0) ? @y[$i] + fm2cm(-800) : @y[$i]; + my $y = (@formula > 0) ? @y[$i] + fm2cm(-800) : @y[$i]; $carrige = (@formula > 0) ? @x[$i]-stringWidth($1)/2 : $carrige; foreach (@formula) { @@ -255,25 +337,46 @@ for ($i = 0; $i < $natoms; $i++) { printCharge ($sign,$charge,$carrige,$y) if ($sign ne ""); } } - } +if ($png) { # make sure we are writing to a binary stream -binmode STDOUT; + binmode STDOUT; # Convert the image to PNG and print it on standard output -print "Content-type: image/png\n\n"; -print $im->png; + print "Content-type: image/png\n\n"; + print $im->png; +} elsif ($ps) { + my $psfile = "/home/httpd/perl/tmp/".$id.'.eps'; + $im->output($psfile); + print "Content-type: text/html\n\n"; + print (< + +Wrote eps file $psfile + + +HTML +} + sub stringWidth { my ($string) = @_; my $width = 0; while ($string =~ /[A-Za-z]/g) { - my @bounds = GD::Image->stringTTF($black,$font,$ptsize,0,0,0,$&); - $width += @bounds[2]-@bounds[0]+2; + if ($png) { + my @bounds = GD::Image->stringTTF($black,$font,$ptsize,0,0,0,$&); + $width += @bounds[2]-@bounds[0]+2; + } elsif ($ps) { + $width += $font_width{$&}; + } } while ($string =~ /[\d+-]/g) { - my @bounds = GD::Image->stringTTF($black,$font,0.6*$ptsize,0,0,0,$&); - $width += @bounds[2]-@bounds[0]+2; + if ($png) { + my @bounds=GD::Image->stringTTF($black,$font,0.6*$ptsize,0,0,0,$&); + $width += @bounds[2]-@bounds[0]+2; + } elsif ($ps) { + $width += 0.6*$font_width{$&}; + } } return $width; @@ -281,12 +384,24 @@ sub stringWidth { sub fm2cm { #font metrics to cm my ($fm) = @_; - return $scale*(2.54/72)*$pointsize*$fm/1000; + if ($png) { + return $scale*(2.54/72)*$pointsize*$fm/1000; + } elsif ($ps) { + return (2.54/72)*$pointsize*$fm/1000; + } +} + +sub printElement { + if ($png) { + return &printElement_png(@_); + } elsif ($ps) { + return &printElement_ps(@_); + } } -sub printElement { #element symbol + optional subscript +sub printElement_png { #element symbol + optional subscript my ($element,$subscript,$x,$y) = @_; - $yy = 662; + my $yy = 662; my @bounds = GD::Image->stringTTF($black,$font,$ptsize,0, $x,$height-($y+fm2cm(-$yy/2)),$element); @@ -310,9 +425,42 @@ sub printElement { #element symbol + op $x = @bounds[2] + 1; } +sub printElement_ps { #element symbol + optional subscript + my ($element,$subscript,$x,$y) = @_; + $height = 662; + + $im->setcolour("white"); + $im->box({filled=>1}, + $x+fm2cm(-30),$y+fm2cm(-$height/2-150), + $x+fm2cm(stringWidth($element)+50),$y+fm2cm(+$height/2+150)); + $im->setcolour("black"); + $im->setfont("Times-Roman",$pointsize); + $im->text($x,$y+fm2cm(-$height/2),$element); + $x += fm2cm(stringWidth($element)); + + if ($subscript ne "") { + $im->setcolour("white"); + $im->box({filled=>1}, + $x,$y+fm2cm(-0.8*$height-45), + $x+fm2cm(stringWidth($subscript)+50),$y+fm2cm(-0.2*$height+45)); + $im->setcolour("black"); + $im->setfont("Times-Roman",0.6*$pointsize); + $im->text($x,$y+fm2cm(-0.8*$height),$subscript); + } + $x += fm2cm(stringWidth($subscript)); +} + sub printCharge { + if ($png) { + return &printCharge_png(@_); + } elsif ($ps) { + return &printCharge_ps(@_); + } +} + +sub printCharge_png { my ($sign,$charge,$x,$y) = @_; - $yy = 662; + my $yy = 662; $charge = "" if ($charge == 1); $charge .= $sign; @@ -327,41 +475,26 @@ sub printCharge { $x = @bounds[2] + 1; } -sub dienice { - my($errmsg) = @_; - print "Content-type: text/html\n\n"; - print "

Error

\n"; - print "$errmsg

\n"; - print "\n"; - system("/bin/rm temp/$SNUM.*"); - exit; +sub printCharge_ps { + my ($sign,$charge,$x,$y) = @_; + $height = 662; + + $charge = "" if ($charge == 1); + $charge .= $sign; + + $im->setcolour("white"); + $im->box({filled=>1}, + $x,$y+fm2cm(0.2*$height-45), + $x+fm2cm(stringWidth($charge)+50),$y+fm2cm(0.8*$height+45)); + + if ($sign eq "-") { # replace by n-dash + chop $charge; + $charge .= "\xb1"; + } + $im->setcolour("black"); + $im->setfont("Times-Roman",0.6*$pointsize); + $im->text($x,$y+fm2cm(0.2*$height),$charge); + $x += fm2cm(stringWidth($charge)); } -sub read_input -{ - local ($buffer, @pairs, $pair, $name, $value, %FORM); - # Read in text - $ENV{'REQUEST_METHOD'} =~ tr/a-z/A-Z/; - if ($ENV{'REQUEST_METHOD'} eq "POST") - { - read(STDIN, $buffer, $ENV{'CONTENT_LENGTH'}); - } else - { - $buffer = $ENV{'QUERY_STRING'}; - } - # Split information into name/value pairs - @pairs = split(/&/, $buffer); - foreach $pair (@pairs) - { - ($name, $value) = split(/=/, $pair); - $value =~ tr/+/ /; - $value =~ s/%(..)/pack("C", hex($1))/eg; - $FORM{$name} = $value; - } - %FORM; -} - -#while (($key,$value) = each %ENV) { -# print "$key = $value
\n"; -#} -#open(STDERR,">errorlog"); +