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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: Macromolecule.php,v 1.5 2003/05/13 01:18:17 jmcastagnetto Exp $
//
require_once "Science/Chemistry.php";
require_once "Science/Chemistry/Atom.php";
require_once "Science/Chemistry/Molecule.php";
/**
* Represents a macromolecule, composed of several
* Science_Chemistry_Molecule objects
*
* @author Jesus M. Castagnetto <jmcastagnetto@php.net>
* @version 1.0
* @access public
* @package Science_Chemistry
*/
class Science_Chemistry_Macromolecule {
/**
* Macromolecule's name
*
* @var string
* @access private
*/
var $name;
/**
* Array of molecular objects
*
* @var array
* @access private
*/
var $molecules;
/**
* Number of molecules/subunits
*
* @var int
* @access private
*/
var $num_molecules;
/**
* Constructor for the class, requires a macromolecule name
* and an optional array of Science_Chemistry_Molecule objects
*
* @param string $name
* @param optional array $molecules
* @return object Science_Chemistry_Macromolecule
* @access public
* @see $name
* @see initMacromolecule()
*/
function Science_Chemistry_Macromolecule($name, $molecules="") {
$this->name = $name;
if (!empty($molecules))
if (!$this->initMacromolecule($molecules))
return null;
}
/**
* Initializes the array of Science_Chemistry_Molecule objects
*
* @param array $molecules
* @return boolean
* @access public
* @see $num_molecules
* @see $molecules
* @see addMolecule()
*/
function initMacromolecule($molecules) {
if (!is_array)
return false;
for ($i=0; $i < count($molecules); $i++)
if(!$this->addMolecule($molecules[$i]))
return false;
return 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;
}
}
/**
* Returns an array of Science_Chemistry_Molecule objects
*
* @return array
* @access public
* @see $molecules
*/
function getMolecules() {
return $this->molecules;
}
/**
* Checks if the object is an instance of Science_Chemistry_Macromolecule
*
* @param object Science_Chemistry_Macromolecule $obj
* @return boolean
* @access public
*/
function isMacromolecule($obj) {
return (is_object($obj) &&
(strtolower(get_class($obj)) == strtolower("Science_Chemistry_Macromolecule") ||
is_subclass_of($obj, strtolower("Science_Chemistry_Macromolecule")))
);
}
/**
* Returns a string representation of the macromolecule
* as a multiple molecule XYZ-format file
*
* @return string
* @access public
* @see toString()
*/
function toXYZ() {
$out = "# Number of molecules: ".$this->num_molecules."\n";
for ($i=0; $i < $this->num_molecules; $i++)
$out .= "# Molecule ".($i+1)."\n".$this->molecules[$i]->toString()."\n";
return $out;
}
/**
* Returns a string representation of the macromolecule
* as a multiple molecule XYZ-format file
* Alias of toXYZ()
*
* @return string
* @access public
* @see toString()
*/
function toString() {
return $this->toXYZ();
}
/**
* Returns a CML representation of the molecule
* Accepts an optional id, and a flag to signal
* printing of the connection table
*
* @param optional string $id
* @param optional boolean $connect
* @return string
* @access public
*/
function toCML($title="macromolecule", $id="macromol1", $connect=false) {
$out = "<molecule title=\"$title\" id=\"$id\">\n";
$out .= "<list title=\"molecules\">\n";
for ($i=0; $i < $this->num_molecules; $i++) {
$mol =& $this->molecules[$i];
$out .= $mol->toCML($mol->name, ($i+1), $connect);
}
$out .= "</list>\n</molecule>\n";
return $out;
}
} // end of Science_Chemistry_Macromolecule
// vim: expandtab: ts=4: sw=4
?>
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