/**
* 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;
}
}
/**
* 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;
}
}