enqueue isotope js and custom js functions file.

gistfile1.txt

<?php
/**
 * Theme Directories & Paths
 * ===================================
 */
if (!defined('FRAMEWORK_DIR'))
    define('FRAMEWORK_DIR', trailingslashit(get_template_directory()));

if (!defined('FRAMEWORK_URI'))
    define('FRAMEWORK_URI', trailingslashit(get_template_directory_uri()));

define('INC_DIR', trailingslashit( FRAMEWORK_DIR . 'inc'));
define('ASSETS_URI', trailingslashit( FRAMEWORK_URI . 'assets'));

/**
 * Enqueue scripts and styles.
 */
function sperry_scripts() {
    // isotopes js
    wp_enqueue_script( 'isotope-js', ASSETS_URI . 'js/jquery.isotope.min.js', array('jquery'), null, true );
    // custom functions
    wp_enqueue_script( 'custom-functions', ASSETS_URI . 'js/custom-functions.js', array('jquery'), null, true );
}
add_action( 'wp_enqueue_scripts', 'sperry_scripts' );