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<?php
//
// +----------------------------------------------------------------------+
// | PHP Version 4 |
// +----------------------------------------------------------------------+
// | Copyright (c) 1997-2003 The PHP Group |
// +----------------------------------------------------------------------+
// | This source file is subject to version 2.0 of the PHP license, |
// | that is bundled with this package in the file LICENSE, and is |
// | 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 <jmcastagnetto@php.net> |
// +----------------------------------------------------------------------+
//
// $Id: Atom.php,v 1.4 2003/05/13 01:18:17 jmcastagnetto Exp $
//
require_once "Science/Chemistry.php";
/**
* Base class representing an Atom
*
* @author Jesus M. Castagnetto <jmcastagnetto@php.net>
* @version 1.0
* @access public
* @package Science_Chemistry
*/
class Science_Chemistry_Atom {
/**
* Element symbol
*
* @var string
* @access private
*
* @see getElement();
*/
var $element="";
/**
* Science_Chemistry_Coordinates object
*
* @var object Science_Chemistry_Coordinates
* @access private
*
* @see getCoordinates();
*/
var $xyz;
/**
* Constructor for the class, requires the element symbol
* and an optional array of coordinates
*
* @param string $element chemical symbol
* @param optional array $coords array of coordinates (x, y, z)
* @access public
* @return object Science_Chemistry_Atom
*
* @see setCoordinates()
*/
function Science_Chemistry_Atom($element, $coords="") {
if ($element && ereg("[[:alpha:]]{1,2}", $element))
$this->element = $element;
else
return null;
if (is_array($coords) && count($coords) == 3)
if (!$this->xyz = new Science_Chemistry_Coordinates($coords))
return null;
}
/**
* Sets the coordinates for the atom object
*
* @param array $coords array of coordinates (x, y, z)
* @return boolean
* @access public
*/
function setCoordinates($coords) {
$this->xyz = new Science_Chemistry_Coordinates($coords);
return (is_object($this->xyz) && !empty($this->xyz));
}
/**
* Returns the chemical symbol for the atom
*
* @return string
* @access public
*
* @see $element;
*/
function getElement() {
return $this->element;
}
/**
* Returns the coordinates object for the atom
*
* @return object Science_Chemistry_Coordinates
* @access public
*
* @see $xyz;
*/
function getCoordinates() {
return $this->xyz;
}
/**
* 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;
}
/**
* Checks if the object is an instance of Science_Chemistry_Atom
*
* @param object Science_Chemistry_Atom $obj
* @return boolean
* @access public
*/
function isAtom($obj) {
return (is_object($obj) &&
(strtolower(get_class($obj)) == strtolower("Science_Chemistry_Atom")
|| is_subclass_of($obj, strtolower("Science_Chemistry_Atom")))
);
}
/**
* Returns a string representation of the Science_Chemistry_Atom object
* Alias of toXYZ()
*
* @return string
* @access public
* @see toXYZ()
*/
function toString() {
return $this->toXYZ();
}
/**
* Returns a XYZ representation of the Science_Chemistry_Atom object
*
* @return string
* @access public
* @see toString()
*/
function toXYZ() {
if ($this->element && $this->xyz)
return sprintf("%2s",$this->element)." ".$this->xyz->toString();
}
/**
* Returns a CML representation of the Science_Chemistry_Atom object
* Accepts an optional id
*
* @param optional string $id
* @return string
* @access public
*/
function toCML($id=1) {
$out = " <atom title=\"atom\" id=\"$id\">\n";
$out .= " <string title=\"name\">".$this->element."</string>\n";
$out .= " ".$this->xyz->toCML();
$out .= " </atom>\n";
return $out;
}
} // end of class Science_Chemistry_Atom
// vim: expandtab: ts=4: sw=4
?>
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