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Diff for /loncom/homework/convertjme.pl between versions 1.4 and 1.17

version 1.4, 2003/10/17 22:24:51 version 1.17, 2024/06/02 10:52:01
Line 28 Line 28
 # Coded by Guy Ashkenazi, guy@fh.huji.ac.il  # Coded by Guy Ashkenazi, guy@fh.huji.ac.il
 # Based on the work of Peter Ertl, peter.ertl@pharma.novartis.com  # Based on the work of Peter Ertl, peter.ertl@pharma.novartis.com
   
   
   
 use strict;  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 lib '/home/httpd/lib/perl';
   use LONCAPA::loncgi;
   use LONCAPA;
   
 use GD;  use GD;
 use PostScript::Simple;  use PostScript::Simple;
 use LONCAPA::loncgi();  
   
 if (! &LONCAPA::loncgi::check_cookie_and_load_env()) {  if ($loncapa) {
     print <<END;      if (! &LONCAPA::loncgi::check_cookie_and_load_env()) {
    print <<END;
 Content-type: text/html  Content-type: text/html
   
 <html>  <html>
Line 47  Your cookie information is incorrect. Line 52  Your cookie information is incorrect.
 </body>  </body>
 </html>  </html>
 END  END
     exit;          exit;
       }
 }  }
   
 sub unescape {  sub unescape {
Line 57  sub unescape { Line 63  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 ($id,$width,$ps,$png,@JMEstring);
 my @JMEstring = split(/ /,&unescape($ENV{'cgi.'.$id.'.JME'}));  if ($loncapa) {
 my $width = $ENV{'cgi.'.$id.'.WIDTH'};      $id=$ENV{'QUERY_STRING'};
 my $png = $ENV{'cgi.'.$id.'.PNG'};      $width = $Apache::lonnet::env{'cgi.'.$id.'.WIDTH'};
 my $ps = $ENV{'cgi.'.$id.'.PS'};      if (!$width) { $width = 400; }
 if (!$width) { $width = 200; }      $png = $Apache::lonnet::env{'cgi.'.$id.'.PNG'};
       $ps = $Apache::lonnet::env{'cgi.'.$id.'.PS'};
 # parse JME string      @JMEstring=&unescape($Apache::lonnet::env{'cgi.'.$id.'.JME'});
   } else {
 my $natoms= shift @JMEstring;      @JMEstring = @ARGV;
 my $nbonds= shift @JMEstring;      $width = shift @JMEstring;
 my (@name,@x,@y);      $png = 1;
 for (my $i = 0; $i < $natoms; $i++) {      $ps = 1;
     @name[$i] = shift @JMEstring;  }
     @x[$i] = shift @JMEstring;  
     @y[$i] = shift @JMEstring;  #get objects
 }  my ($reactants,$modulators,$products)=split('>',$JMEstring[0]);
   
 my (@atomA,@atomB,@bondType);  my @reactant_structs=split(/\|/,$reactants);
 for (my $i = 0; $i < $nbonds; $i++) {  my @modulator_structs=split(/\|/,$modulators);
     @atomA[$i] = (shift @JMEstring)-1;  my @product_structs=split(/\|/,$products);
     @atomB[$i] = (shift @JMEstring)-1;  
     @bondType[$i] = shift @JMEstring;  
 }  my @all_structs=(@reactant_structs,@modulator_structs,@product_structs);
   
 # Find border and move lower left corner to (1.5,1.0)  #get size of image and initialize image and globals
   my ($xmin,$xmax,$ymin,$ymax,$maxName,$height,$scale) =
 my $xmin = my $xmax = @x[0];      &determine_size(@all_structs);
 my $ymin = my $ymax = $y[0];  
 my $maxName = 0;  my $draw_arrow;
   if (@modulator_structs || @product_structs) { $draw_arrow=1; }
 for (my $i = 1; $i < $natoms; $i++) {  my ($arrow_x1,$arrow_x2,$arrow_y) = (-1e20,1e20,0);
     $xmax = @x[$i] if (@x[$i] > $xmax);  if ($draw_arrow) {
     $xmin = @x[$i] if (@x[$i] < $xmin);      foreach my $struct (@reactant_structs) {
     $ymax = @y[$i] if (@y[$i] > $ymax);   my @bounds =  &determine_size($struct);
     $ymin = @y[$i] if (@y[$i] < $ymin);   if ($arrow_x1 < $bounds[1]) {
     @name[$i] =~ /(\@{1,2})?(\w+)([\+|\-])?(\d)?/;      $arrow_x1 = $bounds[1];
     $maxName = length $2 if (length $2 > $maxName);      $arrow_y = ($bounds[2] + $bounds[3]) / 2;
 }   }
 $maxName = ($maxName-3 < 0) ? 0 : $maxName-3;      }
 my $scale = $width / ($xmax-$xmin+3+$maxName);      foreach my $struct (@product_structs) {
 my $height = $scale * ($ymax-$ymin+2);   my @bounds =  &determine_size($struct);
    $arrow_x2 = $bounds[0] if ($arrow_x2 > $bounds[0]);
 for (my $i = 0; $i < $natoms; $i++) {      }
     @x[$i] += (1.5+$maxName/2-$xmin);  
     if ($png) {  @x[$i] *= $scale; }      $arrow_x1 += (1.5+$maxName/2-$xmin);
     @y[$i] += (1.0-$ymin);      $arrow_x1 *= $scale;
     if ($png) { @y[$i] *= $scale; }      $arrow_x2 += (1.5+$maxName/2-$xmin);
 }      $arrow_x2 *= $scale; 
       $arrow_y += (1.0-$ymin);
 # Count bonds      $arrow_y *= $scale;
   
 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);
   my $gdAntiAliased;
 if ($png) {  if ($png) {
     $im = new GD::Image($width,$height);       $im = new GD::Image($width,$height); 
     $white = $im->colorAllocate(255,255,255);      $white = $im->colorAllocate(255,255,255);
     $black = $im->colorAllocate(0,0,0);      $black = $im->colorAllocate(0,0,0);
     $gray = $im->colorAllocate(200,200,200);      $gray = $im->colorAllocate(200,200,200);
 #$gdAntiAliased = $im->colorAllocate(1,1,1);      $gdAntiAliased = $im->colorAllocate(1,1,1);
     $im->setAntiAliased($black);      # $im->setAntiAliased($black);
 } elsif ($ps) {  } elsif ($ps) {
     $im = new PostScript::Simple(xsize => $xmax-$xmin+3+$maxName,      $im = new PostScript::Simple(xsize => $xmax-$xmin+3+$maxName,
  ysize => $ymax-$ymin+2,   ysize => $ymax-$ymin+2,
  clip => 1,   clip => 1,
  eps => 1,   eps => 1,
  color => 0,   colour => 1,
  units => "cm");   units => "cm");
 }  }
   
 # Draw bonds  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 $doubleWidth;
 my $tripleWidth;  my $tripleWidth;
 if ($png) {  $doubleWidth = 0.10*$scale;
     $doubleWidth = 0.10*$scale;  $tripleWidth = 0.15*$scale;
     $tripleWidth = 0.15*$scale;  
 } elsif ($ps) {  # Draw arrow
     $doubleWidth = 0.10;  
     $tripleWidth = 0.15;  if ($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));
       }
 }  }
   
 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;  # Scale and move lower left corner to (1.5,1.0)
  $dy = $yb-$ya;  
         my $dd = sqrt($dx*$dx + $dy*$dy);      for (my $i = 0; $i < $natoms; $i++) {
         $sina=$dy/$dd;   $x[$i] += (1.5+$maxName/2-$xmin);
         $cosa=$dx/$dd;   $x[$i] *= $scale; 
     }   $y[$i] += (1.0-$ymin);
     if    (@bondType[$i] == -2) {   $y[$i] *= $scale;
  for (my $t = 0; $t <= 1; $t += 0.1) {      }
     my $xab = $xa + $t*$dx;       
     my $yab = $ya + $t*$dy;   # Count bonds
     my $xperp = $tripleWidth*$sina*$t;  
     my $yperp = $tripleWidth*$cosa*$t;      my @bonds = map {0} 0..$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 ($png) {      if ($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[$i]] > 2))) {   @name[@atomA[$i]] eq "O" || @name[@atomB[$i]] eq "O")) {
  # 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 $pointsize = 20;   if ($formula ne "C" || $sign ne ""||
 my ($ptsize,@bounds);      $adjacent[$i] < 2 || ($adjacent[$i] == 2 && $bonds[$i] == 4) || (@aldehyde[$i] == 1 && @bonds[$i] == 3)) {
 if ($png) {      # don't show C, unless charged, terminal, or linear
     @bounds = GD::Image->stringTTF($black,$font,100,0,0,0,"H");      if (exists $electrons{$formula}) {
     $ptsize = 100*0.662*$pointsize*(2.54/72)*$scale/(@bounds[3]-@bounds[5]);   # add H atoms to satisfy minimum valence
 }   my $e = $electrons{$formula};
    $e -= (($charge eq "")? 1 : $charge) if ($sign eq "+");
 for (my $i = 0; $i < $natoms; $i++) {   $e += (($charge eq "")? 1 : $charge) if ($sign eq "-");
     my ($formula,$sign,$charge) =   my $valence = 4 - abs($e-4);
  (@name[$i] =~ /(\w+)([\+|\-])?(\d)?/);   my $nH = $valence - @bonds[$i];
     if ($png) {   $formula .= "H" if ($nH > 0);
  $sign = "&#8211;" if ($sign eq "-");  # replace by n-dash   $formula .= $nH if ($nH > 1);
     }      }
     if ($formula ne "C" || $sign ne ""||      my @formula = $formula=~ /[A-Z][a-z]?\d*/g;
  @adjacent[$i] < 2 || (@adjacent[$i] == 2 && @bonds[$i] == 4)) {      
  # don't show C, unless charged, terminal, or linear      my $PI = 3.1415;
  my $nH = 0;      my $bondAngle;
  if (exists $valence{$formula}) {      if (abs($bondsy[$i]) < 0.01 && abs($bondsx[$i]) < 0.01) {
     $nH = $valence{$formula} - @bonds[$i];   $bondAngle = -$PI;
     $nH += (($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) {      else {
  $direction = "d";   $bondAngle = atan2($bondsy[$i],$bondsx[$i]);
     }      }
     elsif ($bondAngle < -$PI/4 && $bondAngle > -3*$PI/4) {  
  $direction = "u";      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      elsif ($direction eq "l") {  # direction = left, reverse hydrogens
     @formula[0] =~ /([A-Z][a-z]?)(\d*)/;   $formula[0] =~ /([A-Z][a-z]?)(\d*)/;
     my $carrige = @x[$i]+   my $carrige = $x[$i]+
  stringWidth($1)/2+stringWidth($2)-stringWidth($formula);      stringWidth($1)/2+stringWidth($2)-stringWidth($formula);
     foreach (reverse @formula) {   foreach (reverse @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 "u") { # direction = up      elsif ($direction eq "u") { # direction = up
     (shift @formula) =~ /([A-Z][a-z]?)(\d*)/;   (shift @formula) =~ /([A-Z][a-z]?)(\d*)/;
     my $carrige = @x[$i]-stringWidth($1)/2;   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];   my $y = (@formula > 0) ? $y[$i] + fm2cm(900) : $y[$i];
     $carrige =   $carrige =
  (@formula > 0) ? @x[$i]-stringWidth($1)/2 : $carrige;      (@formula > 0) ? $x[$i]-stringWidth($1)/2 : $carrige;
     foreach (@formula) {   foreach (@formula) {
  $_ =~ /([A-Z][a-z]?)(\d*)/;      $_ =~ /([A-Z][a-z]?)(\d*)/;
  $carrige = printElement ($1,$2,$carrige,$y);      $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      else { # direction = down
     (shift @formula) =~ /([A-Z][a-z]?)(\d*)/;   (shift @formula) =~ /([A-Z][a-z]?)(\d*)/;
     my $carrige = @x[$i]-stringWidth($1)/2;   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];   my $y = (@formula > 0) ? $y[$i] + fm2cm(-900) : $y[$i];
     $carrige =   $carrige =
  (@formula > 0) ? @x[$i]-stringWidth($1)/2 : $carrige;      (@formula > 0) ? $x[$i]-stringWidth($1)/2 : $carrige;
     foreach (@formula) {   foreach (@formula) {
  $_ =~ /([A-Z][a-z]?)(\d*)/;      $_ =~ /([A-Z][a-z]?)(\d*)/;
  $carrige = printElement ($1,$2,$carrige,$y);      $carrige = printElement ($1,$2,$carrige,$y);
    }
    printCharge ($sign,$charge,$carrige,$y) if ($sign ne ""); 
     }      }
     printCharge ($sign,$charge,$carrige,$y) if ($sign ne "");   
  }   }
     }      }
 }  }
   
 if ($png) {  if ($loncapa) {
       if ($png) {
 # make sure we are writing to a binary stream  # make sure we are writing to a binary stream
     binmode STDOUT;   binmode STDOUT;
   
 # Convert the image to PNG and print it on standard output  # Convert the image to PNG and print it on standard output
     print "Content-type: image/png\n\n";   print "Content-type: image/png\n\n";
     print $im->png;   print $im->png;
 } elsif ($ps) {      } elsif ($ps) {
     my $psfile = "/home/httpd/perl/tmp/".$id.'.eps';   my $psfile = LONCAPA::tempdir().$id.'.eps';
     $im->output($psfile);   $im->output($psfile);
     print "Content-type: text/html\n\n";   print "Content-type: text/html\n\n";
     print (<<HTML)   print (<<HTML)
 <html>      <html>
 <body>      <body>
 Wrote eps file $psfile      Wrote eps file $psfile
 </body>      </body>
 </html>      </html>
 HTML  HTML
       }
   } else {
       if ($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 {  sub stringWidth {
Line 392  sub stringWidth { Line 459  sub stringWidth {
     while ($string =~ /[A-Za-z]/g) {      while ($string =~ /[A-Za-z]/g) {
  if ($png) {   if ($png) {
     my @bounds = GD::Image->stringTTF($black,$font,$ptsize,0,0,0,$&);      my @bounds = GD::Image->stringTTF($black,$font,$ptsize,0,0,0,$&);
     $width += @bounds[2]-@bounds[0]+2;      $width += $bounds[2]-$bounds[0]+2;
  } elsif ($ps) {   } elsif ($ps) {
     $width += $font_width{$&};      $width += fm2cm($font_width{$&});
  }   }
     }      }
     while ($string =~ /[\d+-]/g) {      while ($string =~ /[\d+-]/g) {
  if ($png) {   if ($png) {
     my @bounds=GD::Image->stringTTF($black,$font,0.6*$ptsize,0,0,0,$&);      my @bounds=GD::Image->stringTTF($black,$font,0.6*$ptsize,0,0,0,$&);
     $width += @bounds[2]-@bounds[0]+2;      $width += $bounds[2]-$bounds[0]+2;
  } elsif ($ps) {   } elsif ($ps) {
     $width += 0.6*$font_width{$&};      $width += fm2cm(0.6*$font_width{$&});
  }   }
     }      }
           
Line 411  sub stringWidth { Line 478  sub stringWidth {
   
 sub fm2cm {  #font metrics to cm  sub fm2cm {  #font metrics to cm
     my ($fm) = @_;      my ($fm) = @_;
     if ($png) {      return $scale*(2.54/72)*$pointsize*$fm/1000;
  return $scale*(2.54/72)*$pointsize*$fm/1000;  
     } elsif ($ps) {  
  return (2.54/72)*$pointsize*$fm/1000;  
     }  
 }  }
   
 sub printElement {  sub printElement {
Line 433  sub printElement_png {  #element symbol Line 496  sub printElement_png {  #element symbol
     my @bounds = GD::Image->stringTTF($black,$font,$ptsize,0,      my @bounds = GD::Image->stringTTF($black,$font,$ptsize,0,
    $x,$height-($y+fm2cm(-$yy/2)),$element);     $x,$height-($y+fm2cm(-$yy/2)),$element);
     $im->filledRectangle(      $im->filledRectangle(
  @bounds[6]-1,@bounds[7]-fm2cm(135),   $bounds[6]-1,$bounds[7]-fm2cm(135),
  @bounds[2]+1,@bounds[3]+fm2cm(135),$white);   $bounds[2]+1,$bounds[3]+fm2cm(135),$white);
   
     $im->stringTTF($black,$font,$ptsize,0,      $im->stringTTF($black,$font,$ptsize,0,
    $x,$height-($y+fm2cm(-$yy/2)),$element);     $x,$height-($y+fm2cm(-$yy/2)),$element);
     $x = @bounds[2] + 1;      $x = $bounds[2] + 1;
   
     if ($subscript ne "") {      if ($subscript ne "") {
  @bounds = GD::Image->stringTTF($black,$font,0.6*$ptsize,0,   @bounds = GD::Image->stringTTF($black,$font,0.6*$ptsize,0,
    $x,$height-($y+fm2cm(-0.8*$yy)),$subscript);     $x,$height-($y+fm2cm(-0.8*$yy)),$subscript);
  $im->filledRectangle(   $im->filledRectangle(
      @bounds[6]-1,@bounds[7]-fm2cm(45),       $bounds[6]-1,$bounds[7]-fm2cm(45),
      @bounds[2]+1,@bounds[3]+fm2cm(45),$white);       $bounds[2]+1,$bounds[3]+fm2cm(45),$white);
  $im->stringTTF($black,$font,0.6*$ptsize,0,   $im->stringTTF($black,$font,0.6*$ptsize,0,
  $x,$height-($y+fm2cm(-0.8*$yy)),$subscript);   $x,$height-($y+fm2cm(-0.8*$yy)),$subscript);
     }      }
     $x = @bounds[2] + 1;      $x = $bounds[2] + 1;
 }  }
   
 sub printElement_ps {  #element symbol + optional subscript  sub printElement_ps {  #element symbol + optional subscript
     my ($element,$subscript,$x,$y) = @_;      my ($element,$subscript,$x,$y) = @_;
     $height = 662;      $height = 662;
       
     $im->setcolour("white");      $im->setcolour("white");
     $im->box({filled=>1},      $im->box({filled=>1},
     $x+fm2cm(-30),$y+fm2cm(-$height/2-150),      $x+fm2cm(-30),$y+fm2cm(-$height/2-150),
     $x+fm2cm(stringWidth($element)+50),$y+fm2cm(+$height/2+150));      $x+stringWidth($element)+fm2cm(50),$y+fm2cm(+$height/2+150));
     $im->setcolour("black");      $im->setcolour("black");
     $im->setfont("Times-Roman",$pointsize);      $im->setfont("Times-Roman",$pointsize);
     $im->text($x,$y+fm2cm(-$height/2),$element);      $im->text($x,$y+fm2cm(-$height/2),$element);
     $x += fm2cm(stringWidth($element));      $x += stringWidth($element);
   
     if ($subscript ne "") {      if ($subscript ne "") {
  $im->setcolour("white");   $im->setcolour("white");
  $im->box({filled=>1},   $im->box({filled=>1},
  $x,$y+fm2cm(-0.8*$height-45),   $x,$y+fm2cm(-0.8*$height-45),
  $x+fm2cm(stringWidth($subscript)+50),$y+fm2cm(-0.2*$height+45));   $x+stringWidth($subscript)+fm2cm(50),$y+fm2cm(-0.2*$height+45));
  $im->setcolour("black");   $im->setcolour("black");
  $im->setfont("Times-Roman",0.6*$pointsize);   $im->setfont("Times-Roman",0.6*$pointsize);
  $im->text($x,$y+fm2cm(-0.8*$height),$subscript);   $im->text($x,$y+fm2cm(-0.8*$height),$subscript);
     }      }
     $x += fm2cm(stringWidth($subscript));      $x += stringWidth($subscript);
 }  }
   
 sub printCharge {  sub printCharge {
Line 489  sub printCharge_png { Line 552  sub printCharge_png {
     my ($sign,$charge,$x,$y) = @_;      my ($sign,$charge,$x,$y) = @_;
     my $yy = 662;      my $yy = 662;
   
       $sign = "&#8722;" if ($sign eq "-");  # replace by n-dash
     $charge = "" if ($charge == 1);      $charge = "" if ($charge == 1);
     $charge .= $sign;      $charge .= $sign;
           
     my @bounds = GD::Image->stringTTF($black,$font,0.6*$ptsize,0,      my @bounds = GD::Image->stringTTF($black,$font,0.6*$ptsize,0,
        $x,$height-($y+fm2cm(0.2*$yy)),$charge);         $x,$height-($y+fm2cm(0.2*$yy)),$charge);
     $im->filledRectangle(      $im->filledRectangle(
  @bounds[6]-1,@bounds[7]-fm2cm(45),   $bounds[6]-1,$bounds[7]-fm2cm(45),
  @bounds[2]+1,@bounds[3]+fm2cm(45),$white);   $bounds[2]+1,$bounds[3]+fm2cm(45),$white);
   
     $im->stringTTF($black,$font,0.6*$ptsize,0,$x,$height-($y+fm2cm(0.2*$yy)),$charge);      $im->stringTTF($black,$font,0.6*$ptsize,0,$x,$height-($y+fm2cm(0.2*$yy)),$charge);
     $x = @bounds[2] + 1;      $x = $bounds[2] + 1;
 }  }
   
 sub printCharge_ps {  sub printCharge_ps {
Line 512  sub printCharge_ps { Line 576  sub printCharge_ps {
     $im->setcolour("white");      $im->setcolour("white");
     $im->box({filled=>1},      $im->box({filled=>1},
     $x,$y+fm2cm(0.2*$height-45),      $x,$y+fm2cm(0.2*$height-45),
     $x+fm2cm(stringWidth($charge)+50),$y+fm2cm(0.8*$height+45));      $x+stringWidth($charge)+fm2cm(50),$y+fm2cm(0.8*$height+45));
   
     if ($sign eq "-") { # replace by n-dash      if ($sign eq "-") { # replace by n-dash
  chop $charge;   chop $charge;
Line 521  sub printCharge_ps { Line 585  sub printCharge_ps {
     $im->setcolour("black");      $im->setcolour("black");
     $im->setfont("Times-Roman",0.6*$pointsize);      $im->setfont("Times-Roman",0.6*$pointsize);
     $im->text($x,$y+fm2cm(0.2*$height),$charge);      $im->text($x,$y+fm2cm(0.2*$height),$charge);
     $x += fm2cm(stringWidth($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;
       }
   }
   
Removed from v.1.4  
changed lines
  Added in v.1.17

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