--- loncom/homework/convertjme.pl	2003/12/08 18:36:58	1.9
+++ loncom/homework/convertjme.pl	2005/01/25 14:55:15	1.10
@@ -2,7 +2,7 @@
 # The LearningOnline Network with CAPA
 # Dynamically converts JME strings into either a png or ps file.
 #
-# $Id: convertjme.pl,v 1.9 2003/12/08 18:36:58 albertel Exp $
+# $Id: convertjme.pl,v 1.10 2005/01/25 14:55:15 albertel Exp $
 #
 # Copyright Michigan State University Board of Trustees
 #
@@ -135,7 +135,7 @@ if ($png) {
 				 units => "cm");
 }
 
-my %valence = ("C",4,"N",3,"P",3,"O",2,"S",2);
+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 = '/usr/share/fonts/default/Type1/n021003l.pfb';
 my $pointsize = 20;
@@ -333,14 +333,16 @@ foreach my $struct (@all_structs) {
 	if ($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
-	    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 "-");
+	    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);
 	    }
-	    $formula .= "H" if ($nH > 0);
-	    $formula .= $nH if ($nH > 1);
 	    my @formula = $formula=~ /[A-Z][a-z]?\d*/g;
 	    
 	    my $PI = 3.1415;