$use_cmmmsrv = "n";
}
$pos = 0;
}
// remove CR if present (IE, Mozilla et al.) and add it again (for Opera)
$mol = str_replace("\r\n", "\n", $mol);
$mol = str_replace("\n", "\r\n", $mol);
//$saferxn = escapeshellcmd($mol);
$saferxn = str_replace(";", " ", $mol);
$saferxn = str_replace("\"", " ", $saferxn);
$saferxn = str_replace("\\'", " ", $saferxn);
$saferxn = str_replace("\\´", " ", $saferxn);
$saferxn = str_replace("\\`", " ", $saferxn);
$saferxn = str_replace("\\|", " ", $saferxn);
$rxndescr = analyze_rxnfile($saferxn);
$nrmol = get_nrmol($rxndescr);
$npmol = get_npmol($rxndescr);
//echo "there are $nrmol reactants and $npmol products<br>\n";
if ($nrmol == 0 || $npmol == 0) {
echo "incomplete reaction file!\n";
echo "</body></html>\n";
die;
}
$allmol = array();
$rmol = array();
$pmol = array();
$label_list = array();
$map_list = array();
$n_labels = 0;
$n_maps = 0;
$mapstr = "";
function apply_maps($myrxn, $mymap)
{
$result = "";
$rxndescr = analyze_rxnfile($myrxn);
$nrmol = get_nrmol($rxndescr);
$npmol = get_npmol($rxndescr);
$allmol = array();
$allmol = explode("\$MOL\r\n", $myrxn);
$ca = count($allmol);
$header = $allmol[0];
$rlabel_list = array();
$plabel_list = array();
$map_list = array();
$n_rlabels = 0;
$n_plabels = 0;
$n_maps = 0;
if (strlen($mymap) > 0) {
$map_list = explode(",", $mymap);
$n_maps = count($map_list);
}
if ($nrmol > 0 && $npmol > 0) {
if ($nrmol > 0) {
for ($i = 0; $i < $nrmol; $i++) {
$rmol[$i] = $allmol[$i + 1];
$mnum = $i + 1;
$mid = "r" . $mnum;
}
}
if ($npmol > 0) {
for ($i = 0; $i < $npmol; $i++) {
$pmol[$i] = $allmol[$i + 1 + $nrmol];
$mnum = $i + 1;
$labels = get_atomlabels($pmol[$i]);
$mid = "p" . $mnum;
}
}
$l = 1;
foreach ($map_list as $item) {
$marr1 = explode("=", $item);
$rpart = $marr1[0];
$rarr1 = explode(":", $rpart);
$rm = $rarr1[0];
$rm = intval(str_replace("r", "", $rm));
$ra = $rarr1[1];
$rl = $l;
$ppart = $marr1[1];
$parr1 = explode(":", $ppart);
$pm = $parr1[0];
$pm = intval(str_replace("p", "", $pm));
$pa = $parr1[1];
$pl = $l;
@($rlbl = $rlabel_list[$rm - 1]);
if (strlen($rlbl) > 0) {
$rlbl .= ",";
}
$rlbl .= $ra . "-" . $rl;
$rlabel_list[$rm - 1] = $rlbl;
@($plbl = $plabel_list[$pm - 1]);
if (strlen($plbl) > 0) {
$plbl .= ",";
}
$plbl .= $pa . "-" . $pl;
$plabel_list[$pm - 1] = $plbl;
$l++;
}
for ($i = 0; $i < $nrmol; $i++) {
$lbl = $rlabel_list[$i];
}
for ($i = 0; $i < $npmol; $i++) {
$lbl = $plabel_list[$i];
}
$newrxn = $header;
for ($i = 0; $i < $nrmol; $i++) {
$rmol[$i] = apply_labels($rmol[$i], $rlabel_list[$i]);
$newrxn .= "\$MOL\r\n" . $rmol[$i];
}
for ($i = 0; $i < $npmol; $i++) {
$pmol[$i] = apply_labels($pmol[$i], $plabel_list[$i]);
$newrxn .= "\$MOL\r\n" . $pmol[$i];
}
$result = $newrxn;
}
// end if there are both reactants and products
return $result;
}
