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'use strict'; var test = require('tape'); var qs = require('../'); var utils = require('../lib/utils'); var iconv = require('iconv-lite'); var SaferBuffer = require('safer-buffer').Buffer; test('stringify()', function (t) { t.test('stringifies a querystring object', function (st) { st.equal(qs.stringify({...
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JavaScript
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describe('Matchers (Integration)', function() { let env; beforeEach(function() { env = new privateUnderTest.Env(); }); afterEach(function() { env.cleanup_(); }); function verifyPasses(expectations) { it('passes', async function() { env.it('a spec', function() { expectations(env)...
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JavaScript
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const stream = require('stream') const util = require('util') const debug = require('debug')('serialport/stream') // VALIDATION const DATABITS = Object.freeze([5, 6, 7, 8]) const STOPBITS = Object.freeze([1, 1.5, 2]) const PARITY = Object.freeze(['none', 'even', 'mark', 'odd', 'space']) const FLOWCONTROLS = Object.fr...
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JavaScript
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(function(f){if(typeof exports==="object"&&typeof module!=="undefined"){module.exports=f()}else if(typeof define==="function"&&define.amd){define([],f)}else{var g;if(typeof window!=="undefined"){g=window}else if(typeof global!=="undefined"){g=global}else if(typeof self!=="undefined"){g=self}else{g=this}g.Qs = f()}})(fu...
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'use strict'; const EventEmitter = require('events'); const https = require('https'); const http = require('http'); const net = require('net'); const tls = require('tls'); const { randomBytes, createHash } = require('crypto'); const { URL } = require('url'); const PerMessageDeflate = require('./permessage-deflate'); ...
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"use strict"; // Fix back button cache problem window.onunload = function () { }; // Global variable, shared between modules function playground_text(playground) { let code_block = playground.querySelector("code"); if (window.ace && code_block.classList.contains("editable")) { let editor = window.ace...
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describe('GlobalErrors', function() { it('calls the added handler on error', function() { const globals = browserGlobals(); const handler = jasmine.createSpy('errorHandler'); const errors = new privateUnderTest.GlobalErrors( globals.global, () => ({}) ); errors.install(); errors.p...
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'use strict'; const EventEmitter = require('events'); const https = require('https'); const http = require('http'); const net = require('net'); const tls = require('tls'); const { randomBytes, createHash } = require('crypto'); const { URL } = require('url'); const PerMessageDeflate = require('./permessage-deflate'); ...
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describe('TreeRunner', function() { describe('spec execution', function() { it('starts the timer, reports the spec started, and updates run state at the start of the queue', async function() { const timer = jasmine.createSpyObj('timer', ['start']); const spec = new privateUnderTest.Spec({ id: ...
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module.exports = minimatch minimatch.Minimatch = Minimatch var path = { sep: '/' } try { path = require('path') } catch (er) {} var GLOBSTAR = minimatch.GLOBSTAR = Minimatch.GLOBSTAR = {} var expand = require('brace-expansion') var plTypes = { '!': { open: '(?:(?!(?:', close: '))[^/]*?)'}, '?': { open: '(?:', ...
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'use strict'; const constants = require('./constants'); const utils = require('./utils'); /** * Constants */ const { MAX_LENGTH, POSIX_REGEX_SOURCE, REGEX_NON_SPECIAL_CHARS, REGEX_SPECIAL_CHARS_BACKREF, REPLACEMENTS } = constants; /** * Helpers */ const expandRange = (args, options) => { if (typeof...
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/*! * express * Copyright(c) 2009-2013 TJ Holowaychuk * Copyright(c) 2014-2015 Douglas Christopher Wilson * MIT Licensed */ 'use strict'; /** * Module dependencies. * @private */ var Buffer = require('safe-buffer').Buffer var contentDisposition = require('content-disposition'); var deprecate = require('depd'...
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JavaScript
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getJasmineRequireObj().Env = function(j$, private$) { 'use strict'; const DEFAULT_IT_DESCRIBE_STACK_DEPTH = 3; /** * @class Env * @since 2.0.0 * @classdesc The Jasmine environment.<br> * _Note:_ Do not construct this directly. You can obtain the Env instance by * calling {@link jasmine.getEnv}. ...
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'use strict'; var test = require('tape'); var qs = require('../'); var utils = require('../lib/utils'); var iconv = require('iconv-lite'); var SaferBuffer = require('safer-buffer').Buffer; test('parse()', function (t) { t.test('parses a simple string', function (st) { st.deepEqual(qs.parse('0=foo'), { 0: ...
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"use strict"; let chartInstance = null; let playgroundData = null; let renderDebounceTimer = null; const els = { version: document.getElementById("versionSelect"), batch: document.getElementById("batchInput"), hiddenFrac: document.getElementById("hiddenFracSelect"), difficulty: document.getElementById("diffic...
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'use strict'; const { EventEmitter } = require('events'); const fs = require('fs'); const sysPath = require('path'); const { promisify } = require('util'); const readdirp = require('readdirp'); const anymatch = require('anymatch').default; const globParent = require('glob-parent'); const isGlob = require('is-glob'); c...
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/** * @author qiao / https://github.com/qiao * @author mrdoob / http://mrdoob.com * @author alteredq / http://alteredqualia.com/ * @author WestLangley / http://github.com/WestLangley * @author erich666 / http://erichaines.com */ // This set of controls performs orbiting, dollying (zooming), and panning. // Unlik...
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describe('Env', function() { let env; beforeEach(function() { env = new privateUnderTest.Env(); }); afterEach(function() { env.cleanup_(); }); describe('#pending', function() { it('throws a PendingSpecException', function() { expect(function() { env.pending(); }).toThrowErr...
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// Copyright Joyent, Inc. and other Node contributors. // // Permission is hereby granted, free of charge, to any person obtaining a // copy of this software and associated documentation files (the // "Software"), to deal in the Software without restriction, including // without limitation the rights to use, copy, modi...
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describe('QueueRunner', function() { it('validates that queueableFns are truthy', function() { expect(function() { new privateUnderTest.QueueRunner({ queueableFns: [undefined] }); }).toThrowError('Received a falsy queueableFn'); }); it('validates that queueableFns have fn properties',...
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"use strict"; // Generated data for sbcs codec. Don't edit manually. Regenerate using generation/gen-sbcs.js script. module.exports = { "437": "cp437", "737": "cp737", "775": "cp775", "850": "cp850", "852": "cp852", "855": "cp855", "856": "cp856", "857": "cp857", "858": "cp858", "860": "cp860", "...
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// Underscore.js 1.3.1 // (c) 2009-2012 Jeremy Ashkenas, DocumentCloud Inc. // Underscore is freely distributable under the MIT license. // Portions of Underscore are inspired or borrowed from Prototype, // Oliver Steele's Functional, and John Resig's Micro-Templating. // For all details and doc...
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// Copyright Joyent, Inc. and other Node contributors. // // Permission is hereby granted, free of charge, to any person obtaining a // copy of this software and associated documentation files (the // "Software"), to deal in the Software without restriction, including // without limitation the rights to use, copy, modi...
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/*@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ * WEBGL 2.0 : 2D 3-Variable Model * * PROGRAMMER : ABOUZAR KABOUDIAN * DATE : Thu 28 Sep 2017 11:33:48 AM EDT * PLACE : Chaos Lab @ GaTech, Atlanta, GA *@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@...
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describe('matchersUtil', function() { it('exposes the injected pretty-printer as .pp', function() { const pp = function() {}; const matchersUtil = new privateUnderTest.MatchersUtil({ pp: pp }); expect(matchersUtil.pp).toBe(pp); }); describe('equals', function() { it('passes for literals that are...
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Search.setIndex({"alltitles": {"API Usage:": [[6, "api-usage"], [6, "id2"], [8, "api-usage"], [8, "id1"], [9, "api-usage"], [9, "id1"], [10, "api-usage"], [10, "id2"], [11, "api-usage"], [11, "id2"], [12, "api-usage"], [12, "id2"], [13, "api-usage"], [13, "id2"], [14, "api-usage"], [14, "id2"], [15, "api-usage"], [15, ...
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exports = module.exports = SemVer var debug /* istanbul ignore next */ if (typeof process === 'object' && process.env && process.env.NODE_DEBUG && /\bsemver\b/i.test(process.env.NODE_DEBUG)) { debug = function () { var args = Array.prototype.slice.call(arguments, 0) args.unshift('SEMVER') con...
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describe('Clock', function() { const NODE_JS = typeof process !== 'undefined' && process.versions && typeof process.versions.node === 'string'; it('does not replace setTimeout until it is installed', function() { const fakeSetTimeout = jasmine.createSpy('global setTimeout'); const fakeGlobal = ...
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describe('toEqual', function() { 'use strict'; function compareEquals(actual, expected) { const matchersUtil = new privateUnderTest.MatchersUtil({ pp: privateUnderTest.makePrettyPrinter() }); const matcher = privateUnderTest.matchers.toEqual(matchersUtil); const result = matcher.compare(actu...
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describe('spec running', function() { let env; beforeEach(function() { specHelpers.registerIntegrationMatchers(); env = new privateUnderTest.Env(); env.configure({ random: false }); }); afterEach(function() { env.cleanup_(); }); it('should assign spec ids sequentially', function() { l...
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describe('Global error handling (integration)', function() { const isBrowser = typeof window !== 'undefined'; let env; beforeEach(function() { specHelpers.registerIntegrationMatchers(); env = new privateUnderTest.Env(); }); afterEach(function() { env.cleanup_(); }); function mockGlobal() { ...
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/* Copyright (c) 2008-2019 Pivotal Labs Copyright (c) 2008-2026 The Jasmine developers Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights ...
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exports = module.exports = SemVer var debug /* istanbul ignore next */ if (typeof process === 'object' && process.env && process.env.NODE_DEBUG && /\bsemver\b/i.test(process.env.NODE_DEBUG)) { debug = function () { var args = Array.prototype.slice.call(arguments, 0) args.unshift('SEMVER') con...
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describe('HtmlReporterV2', function() { let env, container, location; beforeEach(function() { container = document.createElement('div'); env = new privateUnderTest.Env(); location = { search: '' }; }); afterEach(function() { env.cleanup_(); }); function setup(options = {}) { return ne...
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/*! * Shuffle.js by @Vestride * Categorize, sort, and filter a responsive grid of items. * Dependencies: jQuery 1.9+, Modernizr 2.6.2+ * @license MIT license * @version 3.0.0 */ /* Modernizr 2.6.2 (Custom Build) | MIT & BSD * Build: http://modernizr.com/download/#-csstransforms-csstransforms3d-csstransitions-cs...
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/*! * The buffer module from node.js, for the browser. * * @author Feross Aboukhadijeh <https://feross.org> * @license MIT */ /* eslint-disable no-proto */ 'use strict' var base64 = require('base64-js') var ieee754 = require('ieee754') var customInspectSymbol = (typeof Symbol === 'function' && typeof Symbol...
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/*! * Socket.IO v3.1.2 * (c) 2014-2021 Guillermo Rauch * Released under the MIT License. */ !function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.io=e():t.io=e()}(this,(function(){return function(t){var...
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/*! * Socket.IO v3.1.2 * (c) 2014-2021 Guillermo Rauch * Released under the MIT License. */ !function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.io=e():t.io=e()}(this,(function(){return function(t){var...
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/* * /MathJax.js * * Copyright (c) 2009-2018 The MathJax Consortium * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Un...
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/*! * Socket.IO v4.0.1 * (c) 2014-2021 Guillermo Rauch * Released under the MIT License. */ !function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.io=e():t.io=e()}(self,(function(){return function(t){var...
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/*! * Socket.IO v4.0.1 * (c) 2014-2021 Guillermo Rauch * Released under the MIT License. */ !function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.io=e():t.io=e()}(self,(function(){return function(t){var...
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/*! Select2 4.0.13 | https://github.com/select2/select2/blob/master/LICENSE.md */ !function(n){"function"==typeof define&&define.amd?define(["jquery"],n):"object"==typeof module&&module.exports?module.exports=function(e,t){return void 0===t&&(t="undefined"!=typeof window?require("jquery"):require("jquery")(e)),n(t),t}:...
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/** vim: et:ts=4:sw=4:sts=4 * @license RequireJS 2.3.1 Copyright jQuery Foundation and other contributors. * Released under MIT license, https://github.com/requirejs/requirejs/blob/master/LICENSE */ //Not using strict: uneven strict support in browsers, #392, and causes //problems with requirejs.exec()/transpiler pl...
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/*! jQuery v3.4.1 | (c) JS Foundation and other contributors | jquery.org/license */ !function(e,t){"use strict";"object"==typeof module&&"object"==typeof module.exports?module.exports=e.document?t(e,!0):function(e){if(!e.document)throw new Error("jQuery requires a window with a document");return t(e)}:t(e)}("undefined...
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/*! jQuery v3.6.0 | (c) OpenJS Foundation and other contributors | jquery.org/license */ !function(e,t){"use strict";"object"==typeof module&&"object"==typeof module.exports?module.exports=e.document?t(e,!0):function(e){if(!e.document)throw new Error("jQuery requires a window with a document");return t(e)}:t(e)}("undef...
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/*! jQuery v3.6.4 | (c) OpenJS Foundation and other contributors | jquery.org/license */ !function(e,t){"use strict";"object"==typeof module&&"object"==typeof module.exports?module.exports=e.document?t(e,!0):function(e){if(!e.document)throw new Error("jQuery requires a window with a document");return t(e)}:t(e)}("undef...
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describe('Env integration', function() { let env; const isBrowser = typeof window !== 'undefined'; beforeEach(function() { specHelpers.registerIntegrationMatchers(); env = new privateUnderTest.Env(); }); afterEach(function() { env.cleanup_(); }); it('Suites execute as expected (no nesting)'...
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/* XRegExp.build 3.2.0 <xregexp.com> Steven Levithan (c) 2012-2017 MIT License Inspired by Lea Verou's RegExp.create <lea.verou.me> XRegExp.matchRecursive 3.2.0 <xregexp.com> Steven Levithan (c) 2009-2017 MIT License XRegExp Unicode Base 3.2.0 <xregexp.com> Steven Levithan (c) 2008-2017 MIT License XRegExp U...
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/* Highlight.js 10.1.1 (93fd0d73) License: BSD-3-Clause Copyright (c) 2006-2020, Ivan Sagalaev */ var hljs=function(){"use strict";function e(n){Object.freeze(n);var t="function"==typeof n;return Object.getOwnPropertyNames(n).forEach((function(r){!Object.hasOwnProperty.call(n,r)||null===n[r]||"object"!=typeof n[r...
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/*! * Select2 4.0.13 * https://select2.github.io * * Released under the MIT license * https://github.com/select2/select2/blob/master/LICENSE.md */ ;(function (factory) { if (typeof define === 'function' && define.amd) { // AMD. Register as an anonymous module. define(['jquery'], factory); } else if (t...
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/** * @fileoverview gl-matrix - High performance matrix and vector operations * @author Brandon Jones * @author Colin MacKenzie IV * @version 2.4.0 */ /* Copyright (c) 2015, Brandon Jones, Colin MacKenzie IV. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associ...
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/*! * Socket.IO v3.1.2 * (c) 2014-2021 Guillermo Rauch * Released under the MIT License. */ (function webpackUniversalModuleDefinition(root, factory) { if(typeof exports === 'object' && typeof module === 'object') module.exports = factory(); else if(typeof define === 'function' && define.amd) define([], facto...
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/*! * Socket.IO v4.0.1 * (c) 2014-2021 Guillermo Rauch * Released under the MIT License. */ (function webpackUniversalModuleDefinition(root, factory) { if(typeof exports === 'object' && typeof module === 'object') module.exports = factory(); else if(typeof define === 'function' && define.amd) define([], facto...
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(function webpackUniversalModuleDefinition(root, factory) { if(typeof exports === 'object' && typeof module === 'object') module.exports = factory(); else if(typeof define === 'function' && define.amd) define([], factory); else if(typeof exports === 'object') exports["dat"] = factory(); else root["dat"] = f...
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Search.setIndex({"alltitles":{"1. Convert your features to the default WORC format":[[70,"convert-your-features-to-the-default-worc-format"]],"1.0.0rc1 - 2017-05-08":[[66,"rc1-2017-05-08"]],"2. Alter feature selection on the feature labels":[[70,"alter-feature-selection-on-the-feature-labels"]],"2.0.0 - 2018-02-13":[[6...
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// Auto-generated for landing_page_2 from the corrected GP_Hard_Fix pipeline results. // Structure: [hiddenFrac][difficulty][protocol][batch][surrogate][dataset][optimizer] // (adds the 'surrogate' level the original landing page lacked.) window.playgroundData = {"0.95":{"Regular":{"Hide_The_Label":{"1":{"BNN":{"T_Cell...
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/*! * jQuery JavaScript Library v3.6.4 * https://jquery.com/ * * Includes Sizzle.js * https://sizzlejs.com/ * * Copyright OpenJS Foundation and other contributors * Released under the MIT license * https://jquery.org/license * * Date: 2023-03-08T15:28Z */ ( function( global, factory ) { "use strict"; if...
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/*@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ * Abubu.js : library for computational work * * PROGRAMMER : ABOUZAR KABOUDIAN * DATE : Wed 28 Nov 2018 10:42:36 (EST) * PLACE : Chaos Lab @ GaTech, Atlanta, GA *@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@...
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(function (global, factory) { typeof exports === 'object' && typeof module !== 'undefined' ? factory(exports) : typeof define === 'function' && define.amd ? define(['exports'], factory) : (factory((global.THREE = global.THREE || {}))); }(this, (function (exports) { 'use strict'; // Polyfills if ( Number.EPSILON ...
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/*@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ * Abubu.js : library for computational work * * PROGRAMMER : ABOUZAR KABOUDIAN * DATE : Wed 28 Aug 2019 16:54:47 (EDT) * PLACE : Chaos Lab @ GaTech, Atlanta, GA *@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@...
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/*! * jQuery JavaScript Library v3.2.1 * https://jquery.com/ * * Includes Sizzle.js * https://sizzlejs.com/ * * Copyright JS Foundation and other contributors * Released under the MIT license * https://jquery.org/license * * Date: 2017-03-20T18:59Z */ ( function( global, factory ) { "use strict"; if ( t...
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// threejs.org/license (function(l,xa){"object"===typeof exports&&"undefined"!==typeof module?xa(exports):"function"===typeof define&&define.amd?define(["exports"],xa):xa(l.THREE=l.THREE||{})})(this,function(l){function xa(){}function C(a,b){this.x=a||0;this.y=b||0}function ba(a,b,c,d,e,f,g,h,k,m){Object.defineProperty...
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(function(f){if(typeof exports==="object"&&typeof module!=="undefined"){module.exports=f()}else if(typeof define==="function"&&define.amd){define([],f)}else{var g;if(typeof window!=="undefined"){g=window}else if(typeof global!=="undefined"){g=global}else if(typeof self!=="undefined"){g=self}else{g=this}g.XRegExp = f()}...
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/* Copyright (c) 2008-2019 Pivotal Labs Copyright (c) 2008-2026 The Jasmine developers Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights ...
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/*@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ * Abubu.js : library for computational work * * PROGRAMMER : ABOUZAR KABOUDIAN * DATE : Wed 28 Nov 2018 10:42:36 (EST) * PLACE : Chaos Lab @ GaTech, Atlanta, GA *@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@...
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/* peartree v1.3.0 — single-file bundle */ (function(){var s=document.createElement("style");s.textContent="@charset \"UTF-8\";@import\"https://fonts.googleapis.com/css2?family=Source+Sans+Pro:wght@400;600;700&display=swap\";:root,[data-bs-theme=light]{--bs-blue: #b58900;--bs-indigo: #6610f2;--bs-purple: #6f42c1;--bs-p...
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/*! p5.js v1.7.0 July 10, 2023 */ !function(e){"object"==typeof exports&&"undefined"!=typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):("undefined"!=typeof window?window:"undefined"!=typeof global?global:"undefined"!=typeof self?self:this).p5=e()}(function(){var s,t,r;return function ...
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if VERSION < v"1.12-" # AtomType has missing union, PeriodicTorsion has NTuple Aqua.test_all(Molly; unbound_args=false) else Aqua.test_all(Molly) end
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export TSSHistoryForgetting, TSSState, TSSSimulation, tss_grid_graph, tss_free_energy_uncertainties, tss_free_energies include("TSS/common.jl") include("TSS/history.jl") include("TSS/observables.jl") include("TSS/single_window.jl") include("TSS/windows.jl") include("TSS/global_estimators.jl") i...
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using Documenter using Molly makedocs( sitename="Molly.jl", format=Documenter.HTML( prettyurls=(get(ENV, "CI", nothing) == "true"), size_threshold_ignore=["api.md"], ), modules=[Molly], pages=[ "Home" => "index.md", "Documentation" =>...
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# ACEmd test # See https://acesuit.github.io/ACEmd.jl/stable/molly # Separate since ACEmd is not in the general registry using Molly import ACEmd using ExtXYZ using Test @testset "ACEmd" begin fname_ace = joinpath(pkgdir(ACEmd), "data", "TiAl.json") fname_xyz = joinpath(pkgdir(ACEmd), "data", "TiAl-big.xyz")...
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export HarmonicBond @doc raw""" HarmonicBond(; k, r0) A harmonic bond between two atoms. The potential energy is defined as ```math V(r) = \frac{1}{2} k (r - r_0)^2 ``` """ @kwdef struct HarmonicBond{K, D} k::K r0::D end Base.zero(::Type{HarmonicBond{K, D}}) where {K, D} = HarmonicBond(k=zero(K), r0=zer...
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# Extract water clusters from MACE-OFF data function extract() prev_line = "" atom_counter, conf_counter, n_atoms = 0, 0, 0 writing = false of = nothing for line in Iterators.flatten(( eachline("train_large_neut_no_bad_clean.xyz"), eachline("test_large_neut_all.xyz"...
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# Radial distribution function # This file is only loaded when KernelDensity is imported module MollyKernelDensityExt using Molly using KernelDensity function Molly.rdf(coords, boundary::Molly.AbstractBoundary{D, T}; npoints::Integer=200) where {D, T} n_atoms = length(coords) dists = dista...
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export MorseBond @doc raw""" MorseBond(; D, a, r0) A Morse potential bond between two atoms. The potential energy is defined as ```math V(r) = D(1 - e^{-a(r - r_0)})^2 ``` """ @kwdef struct MorseBond{T, A, R} D::T a::A r0::R end Base.zero(::Type{MorseBond{T, A, R}}) where {T, A, R} = MorseBond(D=zer...
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# Check all force field XML files in openmm/openmmforcefields repositories read in okay using Molly using EzXML using Suppressor const suppress_warnings = true const prefix = "." const projects = ["openmm", "openmmforcefields"] function read_all_xml() c_fine, c_err = 0, 0 for project in projects for ...
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export HarmonicPositionRestraint @doc raw""" HarmonicPositionRestraint(; k, x0) A harmonic position restraint on an atom to coordinate `x0`. The potential energy is defined as ```math V(\boldsymbol{x}) = \frac{1}{2} k |\boldsymbol{x} - \boldsymbol{x}_0|^2 ``` Does not contribute to the virial. """ @kwdef struct...
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# Generate features for MACE-OFF water data training # Assumes all formal charges are zero, since charges are not spread to equivalent atoms out_fp = "features_maceoff.tsv" data_dir = "../data_maceoff/water" n_confs = length(readdir(data_dir)) open(out_fp, "w") do of for conf_i in 1:n_confs n_molecules =...
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using Pkg #Pkg.add("DataFrames") #Pkg.add("CSV") using DataFrames,CSV df=DataFrame(CSV.File("L:/promec/Elite/LARS/2021/april/olej/second run SAX 2/210408_FT_SAX_urt3_210416151908.raw.intensityThreshold1000.errTolDecimalPlace3.MZ1R.csv.combined.csv",normalizenames=true)) names(df) #Pkg.add("Plots") using Plots #Pkg.add(...
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export CosineAngle @doc raw""" CosineAngle(; k, θ0) A cosine bond angle between three atoms. `θ0` is in radians. The potential energy is defined as ```math V(\theta) = k(1 + \cos(\theta - \theta_0)) ``` """ @kwdef struct CosineAngle{K, D} k::K θ0::D end Base.zero(::Type{CosineAngle{K, D}}) where {K, D} ...
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### A Pluto.jl notebook ### # v0.14.0 using Markdown using InteractiveUtils # ╔═╡ 3f1c5cd3-2020-45e1-b4e7-8cbb967ef092 using WAV # ╔═╡ 1b1f4b61-9e97-4cbb-acec-5f7f36ac80c5 using Plots # ╔═╡ 234cbb60-9547-11eb-3d9c-739a1958d633 #youtube-dl -i --extract-audio --audio-format wav --audio-quality 0 "https://www.youtube.com...
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export HarmonicAngle @doc raw""" HarmonicAngle(; k, θ0) A harmonic bond angle between three atoms. `θ0` is in radians. The second atom is the middle atom. The potential energy is defined as ```math V(\theta) = \frac{1}{2} k (\theta - \theta_0)^2 ``` """ @kwdef struct HarmonicAngle{K, D} k::K θ0::D end B...
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export Gravity @doc raw""" Gravity(; cutoff, G, use_neighbors) The gravitational interaction between two atoms. The potential energy is defined as ```math V(r_{ij}) = -\frac{G m_i m_j}{r_{ij}} ``` """ @kwdef struct Gravity{T, C} <: PairwiseInteraction cutoff::C = NoCutoff() G::T = Unitful.G use_neigh...
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export HarmonicTorsion @doc raw""" HarmonicTorsion(; k, θ0) A harmonic torsion angle between four atoms, often used for improper torsions. `θ0` is in radians. The potential energy is defined as ```math V(\theta) = k (\theta - \theta_0)^2 ``` where `θ` is the angle between the planes defined by atoms (i, j, k) an...
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export EnsembleSystem, read_frame! """ EnsembleSystem(coordinate_file, trajectory_file, force_field; <keyword arguments>) EnsembleSystem(system, trajectory_file) An object allowing data to be read from a trajectory or ensemble associated with a [`System`](@ref). The keyword arguments are the same as ...
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# Python ASE calculator test # Test values from ASE v3.22.1 ENV["JULIA_CONDAPKG_BACKEND"] = "Null" using Molly using PythonCall using Test @testset "Python ASE MACE" begin mc = pyimport("mace.calculators") ase_calc = mc.mace_off(model="medium", device="cuda") atoms = fill(Atom(mass=(14.0 / Unitful.Na)u...
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export FENEBond @doc raw""" FENEBond(; k, r0, σ, ϵ) A finitely extensible non-linear elastic (FENE) bond between two atoms, see [Kremer and Grest 1990](https://doi.org/10.1063/1.458541). The potential energy is defined as ```math V(r) = -\frac{1}{2} k r^2_0 \ln \left( 1 - \left( \frac{r}{r_0} \right) ^2 \right) ...
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# Protein simulation benchmark using Molly using CUDA using DelimitedFiles const n_steps = 1_000 const n_threads = Threads.nthreads() const data_dir = normpath(dirname(pathof(Molly)), "..", "data") const ff_dir = joinpath(data_dir, "force_fields") const openmm_dir = joinpath(data_dir, "openmm_6mrr") function setup_...
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export UreyBradley @doc raw""" UreyBradley(; kangle, θ0, kbond, r0) An interaction between three atoms consisting of a harmonic bond angle and a harmonic bond between the outer atoms. `θ0` is in radians. The second atom is the middle atom. The potential energy is defined as ```math V(\theta, r) = \frac{1}{2} k_a...
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export optimize_cuda_launch_config! const CUDA_LAUNCH_AUTOTUNE_CACHE_RESET_HOOK = Ref{Any}(nothing) #= cuda_launch_config(system) Return the stored CUDA launch overrides for `system`. The returned [`CUDALaunchConfig`](@ref) is consulted by Molly's tiled CUDA pairwise kernels whenever they choose launch para...
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export RBTorsion @doc raw""" RBTorsion(; c0, c1, c2, c3, c4, c5) A Ryckaert-Bellemans torsion angle between four atoms. The potential energy is defined as ```math V(\phi) = \sum_{n=0}^{5} C_n \cos^n(\psi) ``` where ``\psi = \phi - 180^{\circ}`` and ``\phi`` is the angle between the planes defined by atoms (i, j,...
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@testset "Energy minimization" begin coords = [ SVector(1.0, 1.0, 1.0)u"nm", SVector(1.6, 1.0, 1.0)u"nm", SVector(1.4, 1.6, 1.0)u"nm", ] sys = System( atoms=[Atom(σ=(0.4 / (2 ^ (1 / 6)))u"nm", ϵ=1.0u"kJ * mol^-1") for i in 1:3], coords=coords, boundary=CubicBo...
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export SoftSphere @doc raw""" SoftSphere(; cutoff, use_neighbors, shortcut, σ_mixing, ϵ_mixing) The soft-sphere potential. The potential energy is defined as ```math V(r_{ij}) = 4\varepsilon_{ij} \left(\frac{\sigma_{ij}}{r_{ij}}\right)^{12} ``` """ @kwdef struct SoftSphere{C, H, S, E} <: PairwiseInteraction ...
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module Molly using Reexport @reexport using StaticArrays @reexport using Unitful using AcceleratedKernels using Atomix import AtomsBase import AtomsCalculators import BioStructures import CellListMap import Chemfiles using Combinatorics using DataStructures using Distances using Distributions using EzXML using FFTW u...
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struct StatisticalInefficiency{I, S, L, E, LG} inefficiency::I stride::S input_length::L effective_size::E lag::LG end # statistical_inefficiency(series::AbstractVector; maxlag::Union{Nothing, Int}=nothing) # # Integrated autocorrelation time estimator with IPS truncation and # finite-sample taper....
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export MullerBrown @doc raw""" MullerBrown(; A, a, b, c, x0, y0, force_units, energy_units) The Müller-Brown potential energy surface implemented as an AtomsCalculators.jl calculator. The potential energy is defined as ```math V(x,y) = \sum_{n=1}^{4} A_k \exp[a_k(x-x_k^0)^2 + b_k(x-x_k^0)(y-y_k^0) + c_k(y-y_k^0)...
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tss_count(n::Integer, singular::AbstractString, plural::AbstractString=string(singular, "s")) = string(n, " ", n == 1 ? singular : plural) mutable struct TSSStats{T} iterations::Vector{Int} active_state::Vector{Int} sampled_next_state::Vector{Int} max_abs_delta_f::Vector{T} f_history::Vector{Ve...
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# Energy conservation test using Molly using AMDGPU using CUDA using GPUArrays using Test @testset "Lennard-Jones energy conservation" begin function test_energy_conservation(nl::Bool, ::Type{AT}, n_threads::Integer, n_steps::Integer) where AT n_atoms = 2_000 ...
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export Buckingham @doc raw""" Buckingham(; cutoff, use_neighbors, shortcut, A_mixing, B_mixing, C_mixing, weight_special) The Buckingham interaction between two atoms. The potential energy is defined as ```math V(r_{ij}) = A_{ij} \exp(-B_{ij} r_{ij}) - \frac{C_{ij}}{r_{ij}^6} ``` and the force on ...
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const AlchemicalRole = Int32 const CoreRole::AlchemicalRole = Int32(0) const InsertRole::AlchemicalRole = Int32(1) const DeleteRole::AlchemicalRole = Int32(2) #= The logic found in this file is a reinterpretation of how OpenFE deals with alchemical transformations. The original logic can be found in: https://gith...