File:  [LON-CAPA] / loncom / homework / convertjme.pl
Revision 1.16: download - view: text, annotated - select for diffs
Mon Jul 4 09:24:54 2011 UTC (10 years, 10 months ago) by foxr
Branches: MAIN
CVS tags: version_2_12_X, version_2_11_X, version_2_11_4_uiuc, version_2_11_4_msu, version_2_11_4, version_2_11_3_uiuc, version_2_11_3_msu, version_2_11_3, version_2_11_2_uiuc, version_2_11_2_msu, version_2_11_2_educog, version_2_11_2, version_2_11_1, version_2_11_0_RC3, version_2_11_0_RC2, version_2_11_0_RC1, version_2_11_0, language_hyphenation_merge, language_hyphenation, HEAD, BZ4492-merge, BZ4492-feature_horizontal_radioresponse, BZ4492-feature_Support_horizontal_radioresponse, BZ4492-Support_horizontal_radioresponse
Centralize knowledge of where the tmp directory is within LONCAPA.pm

#!/usr/bin/perl
# The LearningOnline Network with CAPA
# Dynamically converts JME strings into either a png or ps file.
#
# $Id: convertjme.pl,v 1.16 2011/07/04 09:24:54 foxr Exp $
#
# Copyright Michigan State University Board of Trustees
#
# This file is part of the LearningOnline Network with CAPA (LON-CAPA).
#
# LON-CAPA 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.
#
# LON-CAPA 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 LON-CAPA; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
#
# /home/httpd/html/adm/gpl.txt
#
# http://www.lon-capa.org/
# Coded by Guy Ashkenazi, guy@fh.huji.ac.il
# Based on the work of Peter Ertl, peter.ertl@pharma.novartis.com

use strict;

### FOR LON-CAPA set $loncapa to 1 and uncomment both uses
### For standalone operation, set $loncapa to 0, and comment out both uses
my $loncapa=1;
use lib '/home/httpd/lib/perl';
use LONCAPA::loncgi;
use LONCAPA;

use GD;
use PostScript::Simple;

if ($loncapa) {
    if (! &LONCAPA::loncgi::check_cookie_and_load_env()) {
	print <<END;
Content-type: text/html

<html>
<head><title>Bad Cookie</title></head>
<body>
Your cookie information is incorrect. 
</body>
</html>
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 ($id,$width,$ps,$png,@JMEstring);
if ($loncapa) {
    $id=$ENV{'QUERY_STRING'};
    $width = $Apache::lonnet::env{'cgi.'.$id.'.WIDTH'};
    if (!$width) { $width = 400; }
    $png = $Apache::lonnet::env{'cgi.'.$id.'.PNG'};
    $ps = $Apache::lonnet::env{'cgi.'.$id.'.PS'};
    @JMEstring=&unescape($Apache::lonnet::env{'cgi.'.$id.'.JME'});
} else {
    @JMEstring = @ARGV;
    $width = shift @JMEstring;
    $png = 1;
    $ps = 1;
}

#get objects
my ($reactants,$modulators,$products)=split('>',$JMEstring[0]);

my @reactant_structs=split(/\|/,$reactants);
my @modulator_structs=split(/\|/,$modulators);
my @product_structs=split(/\|/,$products);


my @all_structs=(@reactant_structs,@modulator_structs,@product_structs);

#get size of image and initialize image and globals
my ($xmin,$xmax,$ymin,$ymax,$maxName,$height,$scale) =
    &determine_size(@all_structs);

my $draw_arrow;
if (@modulator_structs || @product_structs) { $draw_arrow=1; }
my ($arrow_x1,$arrow_x2,$arrow_y) = (-1e20,1e20,0);
if ($draw_arrow) {
    foreach my $struct (@reactant_structs) {
	my @bounds =  &determine_size($struct);
	if ($arrow_x1 < $bounds[1]) {
	    $arrow_x1 = $bounds[1];
	    $arrow_y = ($bounds[2] + $bounds[3]) / 2;
	}
    }
    foreach my $struct (@product_structs) {
	my @bounds =  &determine_size($struct);
	$arrow_x2 = $bounds[0] if ($arrow_x2 > $bounds[0]);
    }

    $arrow_x1 += (1.5+$maxName/2-$xmin);
    $arrow_x1 *= $scale;
    $arrow_x2 += (1.5+$maxName/2-$xmin);
    $arrow_x2 *= $scale; 
    $arrow_y += (1.0-$ymin);
    $arrow_y *= $scale;
}

# Create a new PostScript object
my ($im,$white,$black,$gray);
my $gdAntiAliased;
if ($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);
} elsif ($ps) {
    $im = new PostScript::Simple(xsize => $xmax-$xmin+3+$maxName,
				 ysize => $ymax-$ymin+2,
				 clip => 1,
				 eps => 1,
				 color => 0,
				 units => "cm");
}

my %electrons = ("C",4,"N",5,"P",5,"O",6,"S",6);
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 = '/home/httpd/html/adm/fonts/DejaVuSerif-Roman.ttf';
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]);
}

#set bond sizes
my $doubleWidth;
my $tripleWidth;
$doubleWidth = 0.10*$scale;
$tripleWidth = 0.15*$scale;

# Draw arrow

if ($draw_arrow) {
    my $dx = $arrow_x2 - $arrow_x1;
    if ($png) {
	$im->line($arrow_x1+0.25*$dx,$height-$arrow_y,
		  $arrow_x2-0.25*$dx,$height-$arrow_y,
		  $gdAntiAliased);
	$im->line($arrow_x2-0.25*$dx,$height-$arrow_y,
		  $arrow_x2-0.25*$dx-fm2cm(500),$height-$arrow_y-fm2cm(300),
		  $gdAntiAliased);
	$im->line($arrow_x2-0.25*$dx,$height-$arrow_y,
		  $arrow_x2-0.25*$dx-fm2cm(500),$height-$arrow_y+fm2cm(300),
		  $gdAntiAliased);
	
    } elsif ($ps) {
	$im->line($arrow_x1+0.25*$dx,$arrow_y,
		  $arrow_x2-0.25*$dx,$arrow_y);
	$im->line($arrow_x2-0.25*$dx,$arrow_y,
		  $arrow_x2-0.25*$dx-fm2cm(500),$arrow_y-fm2cm(250));
	$im->line($arrow_x2-0.25*$dx,$arrow_y,
		  $arrow_x2-0.25*$dx-fm2cm(500),$arrow_y+fm2cm(250));
    }
}


foreach my $struct (@all_structs) {

    my (@name,@x,@y,@atomA,@atomB,@bondType,$natoms,$nbonds);
    &parse_struct($struct,\@name,\@x,\@y,\@atomA,\@atomB,\@bondType);
    $natoms=scalar(@x);
    $nbonds=scalar(@bondType);

# Scale and move lower left corner to (1.5,1.0)

    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;
    my @aldehyde = 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]];

	if ( @bondType[$i] == 2) {
	    @aldehyde[@atomA[$i]] ++ if (@name[@atomB[$i]] eq "O");
	    @aldehyde[@atomB[$i]] ++ if (@name[@atomA[$i]] eq "O");
	}

    }

   
# Draw bonds
    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*$t;
		if ($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) {
	    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) {
	    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[$i]] > 2)||
		@name[@atomA[$i]] eq "O" || @name[@atomB[$i]] eq "O")) {
	    # centered bond
	    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) {
	    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) {
	    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

    for (my $i = 0; $i < $natoms; $i++) {
	my ($formula,$sign,$charge) =
	    ($name[$i] =~ /(\w+)([\+|\-])?(\d)?/);
	if ($formula ne "C" || $sign ne ""||
	    $adjacent[$i] < 2 || ($adjacent[$i] == 2 && $bonds[$i] == 4) || (@aldehyde[$i] == 1 && @bonds[$i] == 3)) {
	    # don't show C, unless charged, terminal, or linear
	    if (exists $electrons{$formula}) {
		# add H atoms to satisfy minimum valence
		my $e = $electrons{$formula};
		$e -= (($charge eq "")? 1 : $charge) if ($sign eq "+");
		$e += (($charge eq "")? 1 : $charge) if ($sign eq "-");
		my $valence = 4 - abs($e-4);
		my $nH = $valence - @bonds[$i];
		$formula .= "H" if ($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(900) : $y[$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(-900) : $y[$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 ""); 
	    }
	}
    }
}

if ($loncapa) {
    if ($png) {
# 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 $im->png;
    } elsif ($ps) {
	my $psfile = LONCAPA::tempdir().$id.'.eps';
	$im->output($psfile);
	print "Content-type: text/html\n\n";
	print (<<HTML)
	    <html>
	    <body>
	    Wrote eps file $psfile
	    </body>
	    </html>
HTML
    }
} else {
    if ($png) {
# make sure we are writing to a binary stream
	binmode STDOUT;
# Convert the image to PNG and print it on standard output
	print $im->png;
    } elsif ($ps) {
	$im->output("file.ps");
    }
}

sub stringWidth {
    my ($string) = @_;
    my $width = 0;
    while ($string =~ /[A-Za-z]/g) {
	if ($png) {
	    my @bounds = GD::Image->stringTTF($black,$font,$ptsize,0,0,0,$&);
	    $width += $bounds[2]-$bounds[0]+2;
	} elsif ($ps) {
	    $width += fm2cm($font_width{$&});
	}
    }
    while ($string =~ /[\d+-]/g) {
	if ($png) {
	    my @bounds=GD::Image->stringTTF($black,$font,0.6*$ptsize,0,0,0,$&);
	    $width += $bounds[2]-$bounds[0]+2;
	} elsif ($ps) {
	    $width += fm2cm(0.6*$font_width{$&});
	}
    }
    
    return $width;
}

sub fm2cm {  #font metrics to cm
    my ($fm) = @_;
    return $scale*(2.54/72)*$pointsize*$fm/1000;
}

sub printElement {
    if ($png) {
	return &printElement_png(@_);
    } elsif ($ps) {
	return &printElement_ps(@_);
    }
}

sub printElement_png {  #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 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),
	    $x+stringWidth($element)+fm2cm(50),$y+fm2cm(+$height/2+150));
    $im->setcolour("black");
    $im->setfont("Times-Roman",$pointsize);
    $im->text($x,$y+fm2cm(-$height/2),$element);
    $x += stringWidth($element);

    if ($subscript ne "") {
	$im->setcolour("white");
	$im->box({filled=>1},
		$x,$y+fm2cm(-0.8*$height-45),
		$x+stringWidth($subscript)+fm2cm(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);
    }
    $x += stringWidth($subscript);
}

sub printCharge {
    if ($png) {
	return &printCharge_png(@_);
    } elsif ($ps) {
	return &printCharge_ps(@_);
    }
}

sub printCharge_png {
    my ($sign,$charge,$x,$y) = @_;
    my $yy = 662;

    $sign = "&#8722;" if ($sign eq "-");  # replace by n-dash
    $charge = "" if ($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;
}

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),
	    $x+stringWidth($charge)+fm2cm(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);
    $x += stringWidth($charge);
}

sub determine_size {
# Find border 
    my (@all_structs)=@_;
    my $xmin = my $ymin = 1e20;
    my $xmax = my $ymax = -1e20;
    my $maxName = 0;
    foreach my $struct (@all_structs) {
	my (@name,@x,@y,@atomA,@atomB,@bondType,$natoms,$nbonds);
	&parse_struct($struct,\@name,\@x,\@y,\@atomA,\@atomB,\@bondType);
	$natoms=scalar(@x);
	$nbonds=scalar(@bondType);
	for (my $i = 0; $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 $scale;
    if ($png) {
	$scale = $width / ($xmax-$xmin+3+$maxName);
    } elsif ($ps) {
	$scale = 1;
    }
    my $height = $scale * ($ymax-$ymin+2);

    return ($xmin,$xmax,$ymin,$ymax,$maxName,$height,$scale);

}

sub parse_struct {
    my ($struct,$name,$x,$y,$atomA,$atomB,$bondType)=@_;
    $struct=~s/^\s*//;
    $struct=~s/\s*$//;
    my @JMEstring = split(/ +/,$struct);
# parse JME string
    my $natoms= shift @JMEstring;
    my $nbonds= shift @JMEstring;
    for (my $i = 0; $i < $natoms; $i++) {
	$$name[$i] = shift @JMEstring;
	$$x[$i] = shift @JMEstring;
	$$y[$i] = shift @JMEstring;
    }

    for (my $i = 0; $i < $nbonds; $i++) {
	$$atomA[$i] = (shift @JMEstring)-1;
	$$atomB[$i] = (shift @JMEstring)-1;
	$$bondType[$i] = shift @JMEstring;
    }
}


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