<?php
class AminoAcid {
var $name; // aa name
var $symbol; // three letter symbol
var $code; // one letter code
var $type; // hydrophobic, charged or neutral
function AminoAcid ($aa)
{
foreach ($aa as $k=>$v)
$this->$k = $aa[$k];
}
}
function readDatabase($filename)
{
// read the XML database of aminoacids
$data = implode("", file($filename));
$parser = xml_parser_create();
xml_parser_set_option($parser, XML_OPTION_CASE_FOLDING, 0);
xml_parser_set_option($parser, XML_OPTION_SKIP_WHITE, 1);
xml_parse_into_struct($parser, $data, $values, $tags);
xml_parser_free($parser);
// loop through the structures
foreach ($tags as $key=>$val) {
if ($key == "molecule") {
$molranges = $val;
// each contiguous pair of array entries are the
// lower and upper range for each molecule definition
for ($i=0; $i < count($molranges); $i+=2) {
$offset = $molranges[$i] + 1;
$len = $molranges[$i + 1] - $offset;
$tdb[] = parseMol(array_slice($values, $offset, $len));
}
} else {
continue;
}
}
return $tdb;
}
function parseMol($mvalues)
{
for ($i=0; $i < count($mvalues); $i++) {
$mol[$mvalues[$i]["tag"]] = $mvalues[$i]["value"];
}
return new AminoAcid($mol);
}
$db = readDatabase("moldb.xml");
echo "** Database of AminoAcid objects:\n";
print_r($db);
?>