//
require_once "Science/Chemistry.php";
require_once "Science/Chemistry/Molecule_XYZ.php";
require_once "Science/Chemistry/Macromolecule.php";
echo "Creating and printing an atom\n";
$a = new Science_Chemistry_Atom("N", array(2.3, 4.5, -2.1));
echo $a->toString() . "\n";
echo "Creating a second atom and calculating distance to first one\n";
$b = new Science_Chemistry_Atom("C", array(1.2, 3.4, -1.6));
echo $b->toString() . "\n";
echo "\nDistance N to C: " . sprintf("%.4f", $a->distance($b)) . " Angstroms\n";
//print_r($a);
//print_r($b);
echo "\n=====\nReading a molecule:\n";
$m = new Science_Chemistry_Molecule_XYZ("his.xyz");
echo "\$m is a molecule: " . (int) Science_Chemistry_Molecule::isMolecule($m) . "\n";
echo $m->toString();
//echo "Calculating Distance Matrix\n";
//$m->printDistanceMatrix();
//echo "Calculating Connection Table\n";
//$m->printConnectionTable();
//echo $m->toCML("Histidine","His", true);
//print_r($m);
//print_r($m->getConnectionTable());
//$start=time();
$n = new Science_Chemistry_Molecule_XYZ("lys.xyz");
$mols = array($m, $n);
$big = new Science_Chemistry_Macromolecule("big one", $mols);
echo $big->toString();
echo $big->toCML("biggie", "big", true);
?>
/**
* Adds a Science_Chemistry_Molecule object to the list of molecules in the macromolecule
*
* @param object Science_Chemistry_Molecule $mol
* @return boolean
* @access public
* @see initMacromolecule()
*/
function addMolecule($mol)
{
if (Science_Chemistry_Molecule::isMolecule($mol)) {
$this->molecules[] = $mol;
$this->num_molecules++;
return true;
} else {
return false;
}
}
