Magento - How to assign simple products to configurable programmatically?

Some of our simple products were not correctly assigned to a configurable product. And, some of them were visible independently in the front end. My task was to assign simple products to correct configurable product and make associated products to not visible individually. It was easy to find configurable product and associated simple products because of the SKU they had. All simple products had sku configurableSKU__*.

So after some trials this code worked for me.

<?php
/**
 * Associate simple products to configurable products
 * Re-written By Damodar because of memory issue with previous code.
 *
 * @category   	Technooze
 * @package     Add simple products to configurable products
 * @copyright  	Copyright (c) 2012 Technooze.com
 * @author		Damodar Bashyal
 * @license    	http://opensource.org/licenses/osl-3.0.php  Open Software License (OSL 3.0)
 *
 */
require_once dirname(__FILE__) . '/../app/Mage.php';
class Mage_Shell_setChildren {
    public function run() {
		// because of the memory issue, i need to use cache file
        $cacheFile = 'configurable.txt';
        // display a startup message
        echo "\n\rOpening file...";
        // check to see if file exists, if not attempt to create it
        if(!file_exists($cacheFile)){
            $fh = fopen($cacheFile, 'w+') or die("can't open file - {$cacheFile}");
            fclose($fh);
        }
        // read file into array
        $file_contents = file($cacheFile, FILE_IGNORE_NEW_LINES | FILE_SKIP_EMPTY_LINES);
        // if the file content is empty, then look into database and write into file
        if(empty($file_contents)){
            echo "\n\rNo Ids found in file, so looking into database";
            $collectionConfigurable = Mage::getResourceModel('catalog/product_collection')
                ->addAttributeToFilter('type_id', array('eq' => 'configurable'))
                //->addAttributeToFilter('has_been_fixed', array('eq' => '0'))
                //->addAttributeToFilter('sku', array('eq' => '10SOC04RD'))
            ;
            $configurableIds = array();
            if($total = count($collectionConfigurable)){
                foreach ($collectionConfigurable as $parent) {
                    $configurableIds[] = $parent->getId();
                }
            }
            // write in a file, so we can read file instead of quering database later
            file_put_contents($cacheFile, implode("\n",$configurableIds));
        } else {
            $total = count($file_contents);
            $configurableIds = $file_contents;
            echo "\n\rIds found in cache file, so using those Ids";
        }
        // free some memory
        unset($file_contents);
        $loop = 1;
        echo "\n\rFound total: {$total} configurable product IDs";
        // now iterate through the ids and update products.
        foreach ($configurableIds as $k => $id) {
            $parent = Mage::getModel('catalog/product')->load($id);
            echo "\n\r" . $loop++ . '. Processing SKU - ' . $parent->getSku() . ' - ' . $parent->getId() . "\n\r";
            // get existing associated product ids
            $childIds = $parent->getTypeInstance()->getUsedProductIds();
            // look for simple products that could be associated products of this configurable product
            $collectionPosChildren = Mage::getResourceModel('catalog/product_collection')
                ->addAttributeToFilter('type_id', array('eq' => 'simple'))
                ->addAttributeToFilter('sku', array('like' => $parent->getSku() . "__%"));
				// get ids of associated products and set the as not visible individually
            foreach ($collectionPosChildren as $product) {
                $childIds[] = $product->getId();
                $product = $product->load($product->getId());
                echo "\n\rsetting simple product ({$product->getSku()}) as not visible individually!";
                $product->setVisibility(Mage_Catalog_Model_Product_Visibility::VISIBILITY_NOT_VISIBLE);
                $product->save();
            }
            // we don't need this $product variable, so unset it to free memory
            unset($product);
            // make the array of associated products ids unique
            $childIds = array_unique($childIds);
            // save parent id on variable as it's lost after next step, not sure why
            $parentId = $parent->getId();
            // now load the resource model for this configurable product and save it with associated product ids
            $product = Mage::getResourceModel( 'catalog/product_type_configurable' )->load( $parent, $parent->getId() );
            echo "\n\rSaving configurable product...\n\r";
            $product->saveProducts( $parentId, $childIds );
            // now lets remove this id from our cache file and overwrite with remaining ids
            unset($configurableIds[$k]);
            echo "\n\rUpdating cache file...\n\r";
            file_put_contents($cacheFile, implode("\n",$configurableIds));
            $k++;
            echo "\n\r{$k} of {$total} completed!!!\n\r\n\r\n\r";
        }
        echo "\n\r\n\rDone!!!\n\r\n\r";
    }
}
umask(0);
/* not Mage::run(); */
Mage::app()->setCurrentStore(Mage_Core_Model_App::ADMIN_STORE_ID);
error_reporting(E_ALL ^ E_NOTICE);
$shell = new Mage_Shell_setChildren();
$shell->run();
//end of file: shell/associateSimples.php

This is how i run in the php command line:

shell > php associateSimples.php

Sample output:

1. Processing SKU - SOC22WH - 420
	ID - 420
2. Processing SKU - FOK22WH - 469
	ID - 469