/**
* Adds a Science_Chemistry_Atom object to the list of atoms in the molecule
*
* @param object Science_Chemistry_Atom $atom
* @return boolean
* @access public
* @see initMolecule()
*/
function addAtom($atom)
{
if (Science_Chemistry_Atom::isAtom($atom)) {
$this->atoms[] = $atom;
$this->num_atoms++;
// unset the distance matrix and
// connection table if they are not empty
// so next time either one is requested
// it gets calculated anew
if (!empty($this->dist_matrix)) {
$this->dist_matrix = array();
}
if (!empty($this->conn_table)) {
$this->conn_table = array();
}
return true;
} else {
return false;
}
}
// | available at through the world-wide-web at |
// | http://www.php.net/license/2_02.txt. |
// | If you did not receive a copy of the PHP license and are unable to |
// | obtain it through the world-wide-web, please send a note to |
// | license@php.net so we can mail you a copy immediately. |
// +----------------------------------------------------------------------+
// | Authors: Jesus M. Castagnetto <*****@*****.**> |
// +----------------------------------------------------------------------+
//
// $Id: testChem.php,v 1.3 2003/01/04 11:56:25 mj Exp $
//
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();
/**
* Calculates the cartesian distance from this atom
* instance to another
*
* @param object Science_Chemistry_Atom $atom2
* @return float distance
* @access public
*/
function distance($atom2)
{
if (!empty($this->xyz) && Science_Chemistry_Coordinates::areCoordinates($this->xyz) && Science_Chemistry_Atom::isAtom($atom2)) {
return $this->xyz->distance($atom2->xyz);
} else {
return -1.0;
}
}
