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Diff for /loncom/homework/convertjme.pl between versions 1.4 and 1.5

version 1.4, 2003/10/17 22:24:51 version 1.5, 2003/10/18 06:51:08
Line 58  sub unescape { Line 58  sub unescape {
   
 # read the width and the JME string from the cgi query  # read the width and the JME string from the cgi query
 my $id=$ENV{'QUERY_STRING'};  my $id=$ENV{'QUERY_STRING'};
 my @JMEstring = split(/ /,&unescape($ENV{'cgi.'.$id.'.JME'}));  
 my $width = $ENV{'cgi.'.$id.'.WIDTH'};  my $width = $ENV{'cgi.'.$id.'.WIDTH'};
   if (!$width) { $width = 400; }
 my $png = $ENV{'cgi.'.$id.'.PNG'};  my $png = $ENV{'cgi.'.$id.'.PNG'};
 my $ps = $ENV{'cgi.'.$id.'.PS'};  my $ps = $ENV{'cgi.'.$id.'.PS'};
 if (!$width) { $width = 200; }  
   
 # parse JME string  #get objects
   my ($reactants,$solution,$products)=split('>',&unescape($ENV{'cgi.'.$id.'.JME'}));
   
 my $natoms= shift @JMEstring;  my @reactant_structs=split(/\|/,$reactants);
 my $nbonds= shift @JMEstring;  my @solution_structs=split(/\|/,$solution);
 my (@name,@x,@y);  my @product_structs=split(/\|/,$products);
 for (my $i = 0; $i < $natoms; $i++) {  
     @name[$i] = shift @JMEstring;  
     @x[$i] = shift @JMEstring;  
     @y[$i] = shift @JMEstring;  
 }  
   
 my (@atomA,@atomB,@bondType);  my $draw_arrow;
 for (my $i = 0; $i < $nbonds; $i++) {  if (@solution_structs || @product_structs) { $draw_arrow=1; }
     @atomA[$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 @all_structs=(@reactant_structs,@solution_structs,@product_structs);
   
 my $xmin = my $xmax = @x[0];  #get size of image and initialize image and globals
 my $ymin = my $ymax = $y[0];  my ($xmin,$xmax,$ymin,$ymax,$maxName,$height,$scale) =
 my $maxName = 0;      &determine_size(@all_structs);
   
 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);  
     if ($png) {  @x[$i] *= $scale; }  
     @y[$i] += (1.0-$ymin);  
     if ($png) { @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  # Create a new PostScript object
 my ($im,$white,$black,$gray);  my ($im,$white,$black,$gray);
Line 144  if ($png) { Line 98  if ($png) {
  units => "cm");   units => "cm");
 }  }
   
 # Draw bonds  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]);
   }
   
   #set bond sizes
 my $doubleWidth;  my $doubleWidth;
 my $tripleWidth;  my $tripleWidth;
 if ($png) {  if ($png) {
Line 155  if ($png) { Line 119  if ($png) {
     $tripleWidth = 0.15;      $tripleWidth = 0.15;
 }  }
   
 for (my $i = 0; $i < $nbonds; $i++) {  
     my $xa = @x[@atomA[$i]];  foreach my $struct (@all_structs) {
     my $ya = @y[@atomA[$i]];  
     my $xb = @x[@atomB[$i]];      my (@name,@x,@y,@atomA,@atomB,@bondType,$natoms,$nbonds);
     my $yb = @y[@atomB[$i]];      &parse_struct($struct,\@name,\@x,\@y,\@atomA,\@atomB,\@bondType);
       $natoms=scalar(@x);
     my ($sina,$cosa,$dx,$dy);      $nbonds=scalar(@bondType);
     if (@bondType[$i] != 1) {  
         $dx = $xb-$xa;      for (my $i = 0; $i < $natoms; $i++) {
  $dy = $yb-$ya;   @x[$i] += (1.5+$maxName/2-$xmin);
         my $dd = sqrt($dx*$dx + $dy*$dy);   if ($png) {  @x[$i] *= $scale; }
         $sina=$dy/$dd;   @y[$i] += (1.0-$ymin);
         $cosa=$dx/$dd;   if ($png) { @y[$i] *= $scale; }
     }      }
     if    (@bondType[$i] == -2) {  
  for (my $t = 0; $t <= 1; $t += 0.1) {  # Count bonds
     my $xab = $xa + $t*$dx;   
     my $yab = $ya + $t*$dy;       my @bonds = map {0} 0..$natoms-1;
     my $xperp = $tripleWidth*$sina*$t;      my @adjacent = map {0} 0..$natoms-1;
     my $yperp = $tripleWidth*$cosa*$t;      my @bondsx = map {0} 0..$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]];
       }
   
   # 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 ($png) {      if ($png) {
  $im->line($xab+$xperp,$height-($yab-$yperp),   my $poly = new GD::Polygon;
   $xab-$xperp,$height-($yab+$yperp),   $poly->addPt($xa,$height-$ya);
   gdAntiAliased);   $poly->addPt($xb+$xperp,$height-($yb-$yperp));
    $poly->addPt($xb-$xperp,$height-($yb+$yperp));
    $im->filledPolygon($poly,$black);
     } elsif ($ps) {      } elsif ($ps) {
  $im->line($xab+$xperp,$yab-$yperp,$xab-$xperp,$yab+$yperp);   $im->polygon({filled=>1},
        $xa,$ya,
        $xb+$xperp,$yb-$yperp,
        $xb-$xperp,$yb+$yperp);
     }      }
  }   }
     }   elsif (@bondType[$i] == 1) {
     elsif (@bondType[$i] == -1) {      if ($png) {
  my $xperp = $tripleWidth*$sina;   $im->line($xa,$height-$ya,$xb,$height-$yb,gdAntiAliased);
  my $yperp = $tripleWidth*$cosa;      } elsif ($ps) {
  if ($png) {   $im->line($xa,$ya,$xb,$yb);
     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 &&
     elsif (@bondType[$i] == 2 &&         ((@adjacent[@atomA[$i]] == 1 && @adjacent[@atomB[$i]] > 2)||
    ((@adjacent[@atomA[$i]] == 1 && @adjacent[@atomB[$i]] > 2)||   (@adjacent[@atomB[$i]] == 1 && @adjacent[@atomA[$i]] > 2))) {
     (@adjacent[@atomB[$i]] == 1 && @adjacent[@atomA[$i]] > 2))) {      # centered bond
  # centered bond      my $xperp = $doubleWidth*$sina;
  my $xperp = $doubleWidth*$sina;      my $yperp = $doubleWidth*$cosa;
  my $yperp = $doubleWidth*$cosa;      if ($png) {
  if ($png) {   $im->line($xa+$xperp,$height-($ya-$yperp),
     $im->line($xa+$xperp,$height-($ya-$yperp),    $xb+$xperp,$height-($yb-$yperp),
       $xb+$xperp,$height-($yb-$yperp),    gdAntiAliased);
       gdAntiAliased);   $im->line($xa-$xperp,$height-($ya+$yperp),
     $im->line($xa-$xperp,$height-($ya+$yperp),    $xb-$xperp,$height-($yb+$yperp),
       $xb-$xperp,$height-($yb+$yperp),    gdAntiAliased);
       gdAntiAliased);      } elsif ($ps) {
  } elsif ($ps) {   $im->line($xa+$xperp,$ya-$yperp,$xb+$xperp,$yb-$yperp);
     $im->line($xa+$xperp,$ya-$yperp,$xb+$xperp,$yb-$yperp);   $im->line($xa-$xperp,$ya+$yperp,$xb-$xperp,$yb+$yperp);
     $im->line($xa-$xperp,$ya+$yperp,$xb-$xperp,$yb+$yperp);      }
  }   }
     }   elsif (@bondType[$i] == 2) {
     elsif (@bondType[$i] == 2) {      my $xperp = 2*$doubleWidth*$sina;
  my $xperp = 2*$doubleWidth*$sina;      my $yperp = 2*$doubleWidth*$cosa;
  my $yperp = 2*$doubleWidth*$cosa;      if ($png) {
  if ($png) {   $im->line($xa,$height-$ya,$xb,$height-$yb,gdAntiAliased);
     $im->line($xa,$height-$ya,$xb,$height-$yb,gdAntiAliased);   $im->line($xa+0.1*$dx-$xperp,$height-($ya+0.1*$dy+$yperp),
     $im->line($xa+0.1*$dx-$xperp,$height-($ya+0.1*$dy+$yperp),    $xb-0.1*$dx-$xperp,$height-($yb-0.1*$dy+$yperp),
       $xb-0.1*$dx-$xperp,$height-($yb-0.1*$dy+$yperp),    gdAntiAliased);
       gdAntiAliased);      } elsif ($ps) {
  } elsif ($ps) {   $im->line($xa,$ya,$xb,$yb);
     $im->line($xa,$ya,$xb,$yb);   $im->line($xa+0.1*$dx-$xperp,$ya+0.1*$dy+$yperp,
     $im->line($xa+0.1*$dx-$xperp,$ya+0.1*$dy+$yperp,    $xb-0.1*$dx-$xperp,$yb-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+$yperp);
       }
    }   
     }      }
     elsif (@bondType[$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  # Write labels
   
 my %valence = ("C",4,"N",3,"P",3,"O",2,"S",2);      for (my $i = 0; $i < $natoms; $i++) {
 my %font_width = (" ",250,"+",564,"-",500,"0",500,"1",500,"2",500,"3",500,"4",500,"5",500,"6",500,"7",500,"8",500,"9",500,"A",722,"B",667,"C",667,"D",722,"E",611,"F",556,"G",722,"H",722,"I",333,"J",389,"K",722,"L",611,"M",889,"N",722,"O",722,"P",556,"Q",722,"R",667,"S",556,"T",611,"U",722,"V",722,"W",944,"X",722,"Y",722,"Z",611,"a",444,"b",500,"c",444,"d",500,"e",444,"f",333,"g",500,"h",500,"i",278,"j",278,"k",500,"l",278,"m",778,"n",500,"o",500,"p",500,"q",500,"r",333,"s",389,"t",278,"u",500,"v",500,"w",722,"x",500,"y",500,"z",444);   my ($formula,$sign,$charge) =
 my $font = '/usr/share/fonts/default/Type1/n021003l.pfb';      (@name[$i] =~ /(\w+)([\+|\-])?(\d)?/);
 my $pointsize = 20;   if ($png) {
 my ($ptsize,@bounds);      $sign = "&#8211;" if ($sign eq "-");  # replace by n-dash
 if ($png) {   }
     @bounds = GD::Image->stringTTF($black,$font,100,0,0,0,"H");   if ($formula ne "C" || $sign ne ""||
     $ptsize = 100*0.662*$pointsize*(2.54/72)*$scale/(@bounds[3]-@bounds[5]);      @adjacent[$i] < 2 || (@adjacent[$i] == 2 && @bonds[$i] == 4)) {
 }      # don't show C, unless charged, terminal, or linear
       my $nH = 0;
 for (my $i = 0; $i < $natoms; $i++) {      if (exists $valence{$formula}) {
     my ($formula,$sign,$charge) =   $nH = $valence{$formula} - @bonds[$i];
  (@name[$i] =~ /(\w+)([\+|\-])?(\d)?/);   $nH += (($charge eq "")? 1 : $charge) if ($sign eq "+");
     if ($png) {   $nH -= (($charge eq "")? 1 : $charge) if ($sign eq "-");
  $sign = "&#8211;" if ($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) {      $formula .= "H" if ($nH > 0);
  $direction = "d";      $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;
     }      }
     elsif ($bondAngle < -$PI/4 && $bondAngle > -3*$PI/4) {      else {
  $direction = "u";   $bondAngle = atan2(@bondsy[$i],@bondsx[$i]);
       }
   
       my $direction;
       if (@adjacent[$i] < 2) {
    $direction = (@bondsx[$i] < 0.01) ? "r" : "l";
     }      }
     else {      else {
  $direction = "r";   if  ($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 ($direction eq "r") {  # direction = right      if ($direction eq "r") {  # direction = right
     @formula[0] =~ /([A-Z][a-z]?)(\d*)/;   @formula[0] =~ /([A-Z][a-z]?)(\d*)/;
     my $carrige = @x[$i]-stringWidth($1)/2;   my $carrige = @x[$i]-stringWidth($1)/2;
     foreach (@formula) {   foreach (@formula) {
  $_ =~ /([A-Z][a-z]?)(\d*)/;      $_ =~ /([A-Z][a-z]?)(\d*)/;
  $carrige = printElement ($1,$2,$carrige,@y[$i]);      $carrige = printElement ($1,$2,$carrige,@y[$i]);
    }
    printCharge ($sign,$charge,$carrige,@y[$i]) if ($sign ne ""); 
     }      }
     printCharge ($sign,$charge,$carrige,@y[$i]) if ($sign ne "");       elsif ($direction eq "l") {  # direction = left, reverse hydrogens
  }   @formula[0] =~ /([A-Z][a-z]?)(\d*)/;
  elsif ($direction eq "l") {  # direction = left, reverse hydrogens   my $carrige = @x[$i]+
     @formula[0] =~ /([A-Z][a-z]?)(\d*)/;      stringWidth($1)/2+stringWidth($2)-stringWidth($formula);
     my $carrige = @x[$i]+   foreach (reverse @formula) {
  stringWidth($1)/2+stringWidth($2)-stringWidth($formula);      $_ =~ /([A-Z][a-z]?)(\d*)/;
     foreach (reverse @formula) {      $carrige = printElement ($1,$2,$carrige,@y[$i]);
  $_ =~ /([A-Z][a-z]?)(\d*)/;   }
    printCharge ($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]);   $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 ""); 
     }      }
     printCharge ($sign,$charge,$carrige,@y[$i]) if ($sign ne "");       else { # direction = down
  }   (shift @formula) =~ /([A-Z][a-z]?)(\d*)/;
  elsif ($direction eq "u") { # direction = up   my $carrige = @x[$i]-stringWidth($1)/2;
     (shift @formula) =~ /([A-Z][a-z]?)(\d*)/;   $carrige = printElement ($1,$2,$carrige,@y[$i]);
     my $carrige = @x[$i]-stringWidth($1)/2;   my $y = (@formula > 0) ? @y[$i] + fm2cm(-800) : @y[$i];
     $carrige = printElement ($1,$2,$carrige,@y[$i]);   $carrige =
     my $y = (@formula > 0) ? @y[$i] + fm2cm(800) : @y[$i];      (@formula > 0) ? @x[$i]-stringWidth($1)/2 : $carrige;
     $carrige =   foreach (@formula) {
  (@formula > 0) ? @x[$i]-stringWidth($1)/2 : $carrige;      $_ =~ /([A-Z][a-z]?)(\d*)/;
     foreach (@formula) {      $carrige = printElement ($1,$2,$carrige,$y);
  $_ =~ /([A-Z][a-z]?)(\d*)/;   }
  $carrige = printElement ($1,$2,$carrige,$y);   printCharge ($sign,$charge,$carrige,$y) if ($sign ne ""); 
     }  
     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 "");   
  }   }
     }      }
 }  }
   
 if ($png) {  if ($png) {
 # make sure we are writing to a binary stream  # make sure we are writing to a binary stream
     binmode STDOUT;      binmode STDOUT;
Line 524  sub printCharge_ps { Line 512  sub printCharge_ps {
     $x += fm2cm(stringWidth($charge));      $x += fm2cm(stringWidth($charge));
 }  }
   
   sub determine_size {
   # Find border and move lower left corner to (1.5,1.0)
       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 = 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);
   
       return ($xmin,$xmax,$ymin,$ymax,$maxName,$height,$scale);
   
   }
   
   sub parse_struct {
       my ($struct,$name,$x,$y,$atomA,$atomB,$bondType)=@_;
       my @JMEstring = split(/ /,$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;
       }
   }
   
Removed from v.1.4  
changed lines
  Added in v.1.5

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