Current Dev State

static/js/ketcher2/node_modules/shelljs/src/cat.js

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+var common = require('./common');
+var fs = require('fs');
+
+common.register('cat', _cat, {
+  canReceivePipe: true,
+});
+
+//@
+//@ ### cat(file [, file ...])
+//@ ### cat(file_array)
+//@
+//@ Examples:
+//@
+//@ ```javascript
+//@ var str = cat('file*.txt');
+//@ var str = cat('file1', 'file2');
+//@ var str = cat(['file1', 'file2']); // same as above
+//@ ```
+//@
+//@ Returns a string containing the given file, or a concatenated string
+//@ containing the files if more than one file is given (a new line character is
+//@ introduced between each file).
+function _cat(options, files) {
+  var cat = common.readFromPipe();
+
+  if (!files && !cat) common.error('no paths given');
+
+  files = [].slice.call(arguments, 1);
+
+  files.forEach(function (file) {
+    if (!fs.existsSync(file)) {
+      common.error('no such file or directory: ' + file);
+    } else if (fs.statSync(file).isDirectory()) {
+      common.error(file + ': Is a directory');
+    }
+
+    cat += fs.readFileSync(file, 'utf8');
+  });
+
+  return cat;
+}
+module.exports = _cat;

static/js/ketcher2/node_modules/shelljs/src/cd.js

@@ -0,0 +1,38 @@
+var fs = require('fs');
+var common = require('./common');
+
+common.register('cd', _cd, {});
+
+//@
+//@ ### cd([dir])
+//@ Changes to directory `dir` for the duration of the script. Changes to home
+//@ directory if no argument is supplied.
+function _cd(options, dir) {
+  if (!dir) dir = common.getUserHome();
+
+  if (dir === '-') {
+    if (!process.env.OLDPWD) {
+      common.error('could not find previous directory');
+    } else {
+      dir = process.env.OLDPWD;
+    }
+  }
+
+  try {
+    var curDir = process.cwd();
+    process.chdir(dir);
+    process.env.OLDPWD = curDir;
+  } catch (e) {
+    // something went wrong, let's figure out the error
+    var err;
+    try {
+      fs.statSync(dir); // if this succeeds, it must be some sort of file
+      err = 'not a directory: ' + dir;
+    } catch (e2) {
+      err = 'no such file or directory: ' + dir;
+    }
+    if (err) common.error(err);
+  }
+  return '';
+}
+module.exports = _cd;

static/js/ketcher2/node_modules/shelljs/src/chmod.js

@@ -0,0 +1,216 @@
+var common = require('./common');
+var fs = require('fs');
+var path = require('path');
+
+var PERMS = (function (base) {
+  return {
+    OTHER_EXEC: base.EXEC,
+    OTHER_WRITE: base.WRITE,
+    OTHER_READ: base.READ,
+
+    GROUP_EXEC: base.EXEC << 3,
+    GROUP_WRITE: base.WRITE << 3,
+    GROUP_READ: base.READ << 3,
+
+    OWNER_EXEC: base.EXEC << 6,
+    OWNER_WRITE: base.WRITE << 6,
+    OWNER_READ: base.READ << 6,
+
+    // Literal octal numbers are apparently not allowed in "strict" javascript.
+    STICKY: parseInt('01000', 8),
+    SETGID: parseInt('02000', 8),
+    SETUID: parseInt('04000', 8),
+
+    TYPE_MASK: parseInt('0770000', 8),
+  };
+}({
+  EXEC: 1,
+  WRITE: 2,
+  READ: 4,
+}));
+
+common.register('chmod', _chmod, {
+});
+
+//@
+//@ ### chmod([options,] octal_mode || octal_string, file)
+//@ ### chmod([options,] symbolic_mode, file)
+//@
+//@ Available options:
+//@
+//@ + `-v`: output a diagnostic for every file processed//@
+//@ + `-c`: like verbose but report only when a change is made//@
+//@ + `-R`: change files and directories recursively//@
+//@
+//@ Examples:
+//@
+//@ ```javascript
+//@ chmod(755, '/Users/brandon');
+//@ chmod('755', '/Users/brandon'); // same as above
+//@ chmod('u+x', '/Users/brandon');
+//@ chmod('-R', 'a-w', '/Users/brandon');
+//@ ```
+//@
+//@ Alters the permissions of a file or directory by either specifying the
+//@ absolute permissions in octal form or expressing the changes in symbols.
+//@ This command tries to mimic the POSIX behavior as much as possible.
+//@ Notable exceptions:
+//@
+//@ + In symbolic modes, 'a-r' and '-r' are identical.  No consideration is
+//@   given to the umask.
+//@ + There is no "quiet" option since default behavior is to run silent.
+function _chmod(options, mode, filePattern) {
+  if (!filePattern) {
+    if (options.length > 0 && options.charAt(0) === '-') {
+      // Special case where the specified file permissions started with - to subtract perms, which
+      // get picked up by the option parser as command flags.
+      // If we are down by one argument and options starts with -, shift everything over.
+      [].unshift.call(arguments, '');
+    } else {
+      common.error('You must specify a file.');
+    }
+  }
+
+  options = common.parseOptions(options, {
+    'R': 'recursive',
+    'c': 'changes',
+    'v': 'verbose',
+  });
+
+  filePattern = [].slice.call(arguments, 2);
+
+  var files;
+
+  // TODO: replace this with a call to common.expand()
+  if (options.recursive) {
+    files = [];
+    filePattern.forEach(function addFile(expandedFile) {
+      var stat = fs.lstatSync(expandedFile);
+
+      if (!stat.isSymbolicLink()) {
+        files.push(expandedFile);
+
+        if (stat.isDirectory()) {  // intentionally does not follow symlinks.
+          fs.readdirSync(expandedFile).forEach(function (child) {
+            addFile(expandedFile + '/' + child);
+          });
+        }
+      }
+    });
+  } else {
+    files = filePattern;
+  }
+
+  files.forEach(function innerChmod(file) {
+    file = path.resolve(file);
+    if (!fs.existsSync(file)) {
+      common.error('File not found: ' + file);
+    }
+
+    // When recursing, don't follow symlinks.
+    if (options.recursive && fs.lstatSync(file).isSymbolicLink()) {
+      return;
+    }
+
+    var stat = fs.statSync(file);
+    var isDir = stat.isDirectory();
+    var perms = stat.mode;
+    var type = perms & PERMS.TYPE_MASK;
+
+    var newPerms = perms;
+
+    if (isNaN(parseInt(mode, 8))) {
+      // parse options
+      mode.split(',').forEach(function (symbolicMode) {
+        var pattern = /([ugoa]*)([=\+-])([rwxXst]*)/i;
+        var matches = pattern.exec(symbolicMode);
+
+        if (matches) {
+          var applyTo = matches[1];
+          var operator = matches[2];
+          var change = matches[3];
+
+          var changeOwner = applyTo.indexOf('u') !== -1 || applyTo === 'a' || applyTo === '';
+          var changeGroup = applyTo.indexOf('g') !== -1 || applyTo === 'a' || applyTo === '';
+          var changeOther = applyTo.indexOf('o') !== -1 || applyTo === 'a' || applyTo === '';
+
+          var changeRead = change.indexOf('r') !== -1;
+          var changeWrite = change.indexOf('w') !== -1;
+          var changeExec = change.indexOf('x') !== -1;
+          var changeExecDir = change.indexOf('X') !== -1;
+          var changeSticky = change.indexOf('t') !== -1;
+          var changeSetuid = change.indexOf('s') !== -1;
+
+          if (changeExecDir && isDir) {
+            changeExec = true;
+          }
+
+          var mask = 0;
+          if (changeOwner) {
+            mask |= (changeRead ? PERMS.OWNER_READ : 0) + (changeWrite ? PERMS.OWNER_WRITE : 0) + (changeExec ? PERMS.OWNER_EXEC : 0) + (changeSetuid ? PERMS.SETUID : 0);
+          }
+          if (changeGroup) {
+            mask |= (changeRead ? PERMS.GROUP_READ : 0) + (changeWrite ? PERMS.GROUP_WRITE : 0) + (changeExec ? PERMS.GROUP_EXEC : 0) + (changeSetuid ? PERMS.SETGID : 0);
+          }
+          if (changeOther) {
+            mask |= (changeRead ? PERMS.OTHER_READ : 0) + (changeWrite ? PERMS.OTHER_WRITE : 0) + (changeExec ? PERMS.OTHER_EXEC : 0);
+          }
+
+          // Sticky bit is special - it's not tied to user, group or other.
+          if (changeSticky) {
+            mask |= PERMS.STICKY;
+          }
+
+          switch (operator) {
+            case '+':
+              newPerms |= mask;
+              break;
+
+            case '-':
+              newPerms &= ~mask;
+              break;
+
+            case '=':
+              newPerms = type + mask;
+
+              // According to POSIX, when using = to explicitly set the
+              // permissions, setuid and setgid can never be cleared.
+              if (fs.statSync(file).isDirectory()) {
+                newPerms |= (PERMS.SETUID + PERMS.SETGID) & perms;
+              }
+              break;
+            default:
+              common.error('Could not recognize operator: `' + operator + '`');
+          }
+
+          if (options.verbose) {
+            console.log(file + ' -> ' + newPerms.toString(8));
+          }
+
+          if (perms !== newPerms) {
+            if (!options.verbose && options.changes) {
+              console.log(file + ' -> ' + newPerms.toString(8));
+            }
+            fs.chmodSync(file, newPerms);
+            perms = newPerms; // for the next round of changes!
+          }
+        } else {
+          common.error('Invalid symbolic mode change: ' + symbolicMode);
+        }
+      });
+    } else {
+      // they gave us a full number
+      newPerms = type + parseInt(mode, 8);
+
+      // POSIX rules are that setuid and setgid can only be added using numeric
+      // form, but not cleared.
+      if (fs.statSync(file).isDirectory()) {
+        newPerms |= (PERMS.SETUID + PERMS.SETGID) & perms;
+      }
+
+      fs.chmodSync(file, newPerms);
+    }
+  });
+  return '';
+}
+module.exports = _chmod;

static/js/ketcher2/node_modules/shelljs/src/common.js

@@ -0,0 +1,466 @@
+// Ignore warning about 'new String()'
+/* eslint no-new-wrappers: 0 */
+'use strict';
+
+var os = require('os');
+var fs = require('fs');
+var glob = require('glob');
+var shell = require('..');
+
+var shellMethods = Object.create(shell);
+
+// objectAssign(target_obj, source_obj1 [, source_obj2 ...])
+// "Ponyfill" for Object.assign
+//    objectAssign({A:1}, {b:2}, {c:3}) returns {A:1, b:2, c:3}
+var objectAssign = typeof Object.assign === 'function' ?
+  Object.assign :
+  function objectAssign(target) {
+    var sources = [].slice.call(arguments, 1);
+    sources.forEach(function (source) {
+      Object.keys(source).forEach(function (key) {
+        target[key] = source[key];
+      });
+    });
+
+    return target;
+  };
+exports.extend = objectAssign;
+
+// Check if we're running under electron
+var isElectron = Boolean(process.versions.electron);
+
+// Module globals (assume no execPath by default)
+var DEFAULT_CONFIG = {
+  fatal: false,
+  globOptions: {},
+  maxdepth: 255,
+  noglob: false,
+  silent: false,
+  verbose: false,
+  execPath: null,
+  bufLength: 64 * 1024, // 64KB
+};
+
+var config = {
+  reset: function () {
+    objectAssign(this, DEFAULT_CONFIG);
+    if (!isElectron) {
+      this.execPath = process.execPath;
+    }
+  },
+  resetForTesting: function () {
+    this.reset();
+    this.silent = true;
+  },
+};
+
+config.reset();
+exports.config = config;
+
+var state = {
+  error: null,
+  errorCode: 0,
+  currentCmd: 'shell.js',
+  tempDir: null,
+};
+exports.state = state;
+
+delete process.env.OLDPWD; // initially, there's no previous directory
+
+// This is populated by calls to commonl.wrap()
+var pipeMethods = [];
+
+// Reliably test if something is any sort of javascript object
+function isObject(a) {
+  return typeof a === 'object' && a !== null;
+}
+exports.isObject = isObject;
+
+function log() {
+  /* istanbul ignore next */
+  if (!config.silent) {
+    console.error.apply(console, arguments);
+  }
+}
+exports.log = log;
+
+// Converts strings to be equivalent across all platforms. Primarily responsible
+// for making sure we use '/' instead of '\' as path separators, but this may be
+// expanded in the future if necessary
+function convertErrorOutput(msg) {
+  if (typeof msg !== 'string') {
+    throw new TypeError('input must be a string');
+  }
+  return msg.replace(/\\/g, '/');
+}
+exports.convertErrorOutput = convertErrorOutput;
+
+// Shows error message. Throws if config.fatal is true
+function error(msg, _code, options) {
+  // Validate input
+  if (typeof msg !== 'string') throw new Error('msg must be a string');
+
+  var DEFAULT_OPTIONS = {
+    continue: false,
+    code: 1,
+    prefix: state.currentCmd + ': ',
+    silent: false,
+  };
+
+  if (typeof _code === 'number' && isObject(options)) {
+    options.code = _code;
+  } else if (isObject(_code)) { // no 'code'
+    options = _code;
+  } else if (typeof _code === 'number') { // no 'options'
+    options = { code: _code };
+  } else if (typeof _code !== 'number') { // only 'msg'
+    options = {};
+  }
+  options = objectAssign({}, DEFAULT_OPTIONS, options);
+
+  if (!state.errorCode) state.errorCode = options.code;
+
+  var logEntry = convertErrorOutput(options.prefix + msg);
+  state.error = state.error ? state.error + '\n' : '';
+  state.error += logEntry;
+
+  // Throw an error, or log the entry
+  if (config.fatal) throw new Error(logEntry);
+  if (msg.length > 0 && !options.silent) log(logEntry);
+
+  if (!options.continue) {
+    throw {
+      msg: 'earlyExit',
+      retValue: (new ShellString('', state.error, state.errorCode)),
+    };
+  }
+}
+exports.error = error;
+
+//@
+//@ ### ShellString(str)
+//@
+//@ Examples:
+//@
+//@ ```javascript
+//@ var foo = ShellString('hello world');
+//@ ```
+//@
+//@ Turns a regular string into a string-like object similar to what each
+//@ command returns. This has special methods, like `.to()` and `.toEnd()`
+function ShellString(stdout, stderr, code) {
+  var that;
+  if (stdout instanceof Array) {
+    that = stdout;
+    that.stdout = stdout.join('\n');
+    if (stdout.length > 0) that.stdout += '\n';
+  } else {
+    that = new String(stdout);
+    that.stdout = stdout;
+  }
+  that.stderr = stderr;
+  that.code = code;
+  // A list of all commands that can appear on the right-hand side of a pipe
+  // (populated by calls to common.wrap())
+  pipeMethods.forEach(function (cmd) {
+    that[cmd] = shellMethods[cmd].bind(that);
+  });
+  return that;
+}
+
+exports.ShellString = ShellString;
+
+// Return the home directory in a platform-agnostic way, with consideration for
+// older versions of node
+function getUserHome() {
+  var result;
+  if (os.homedir) {
+    result = os.homedir(); // node 3+
+  } else {
+    result = process.env[(process.platform === 'win32') ? 'USERPROFILE' : 'HOME'];
+  }
+  return result;
+}
+exports.getUserHome = getUserHome;
+
+// Returns {'alice': true, 'bob': false} when passed a string and dictionary as follows:
+//   parseOptions('-a', {'a':'alice', 'b':'bob'});
+// Returns {'reference': 'string-value', 'bob': false} when passed two dictionaries of the form:
+//   parseOptions({'-r': 'string-value'}, {'r':'reference', 'b':'bob'});
+function parseOptions(opt, map, errorOptions) {
+  // Validate input
+  if (typeof opt !== 'string' && !isObject(opt)) {
+    throw new Error('options must be strings or key-value pairs');
+  } else if (!isObject(map)) {
+    throw new Error('parseOptions() internal error: map must be an object');
+  } else if (errorOptions && !isObject(errorOptions)) {
+    throw new Error('parseOptions() internal error: errorOptions must be object');
+  }
+
+  // All options are false by default
+  var options = {};
+  Object.keys(map).forEach(function (letter) {
+    var optName = map[letter];
+    if (optName[0] !== '!') {
+      options[optName] = false;
+    }
+  });
+
+  if (opt === '') return options; // defaults
+
+  if (typeof opt === 'string') {
+    if (opt[0] !== '-') {
+      error("Options string must start with a '-'", errorOptions || {});
+    }
+
+    // e.g. chars = ['R', 'f']
+    var chars = opt.slice(1).split('');
+
+    chars.forEach(function (c) {
+      if (c in map) {
+        var optionName = map[c];
+        if (optionName[0] === '!') {
+          options[optionName.slice(1)] = false;
+        } else {
+          options[optionName] = true;
+        }
+      } else {
+        error('option not recognized: ' + c, errorOptions || {});
+      }
+    });
+  } else { // opt is an Object
+    Object.keys(opt).forEach(function (key) {
+      // key is a string of the form '-r', '-d', etc.
+      var c = key[1];
+      if (c in map) {
+        var optionName = map[c];
+        options[optionName] = opt[key]; // assign the given value
+      } else {
+        error('option not recognized: ' + c, errorOptions || {});
+      }
+    });
+  }
+  return options;
+}
+exports.parseOptions = parseOptions;
+
+// Expands wildcards with matching (ie. existing) file names.
+// For example:
+//   expand(['file*.js']) = ['file1.js', 'file2.js', ...]
+//   (if the files 'file1.js', 'file2.js', etc, exist in the current dir)
+function expand(list) {
+  if (!Array.isArray(list)) {
+    throw new TypeError('must be an array');
+  }
+  var expanded = [];
+  list.forEach(function (listEl) {
+    // Don't expand non-strings
+    if (typeof listEl !== 'string') {
+      expanded.push(listEl);
+    } else {
+      var ret;
+      try {
+        ret = glob.sync(listEl, config.globOptions);
+        // if nothing matched, interpret the string literally
+        ret = ret.length > 0 ? ret : [listEl];
+      } catch (e) {
+        // if glob fails, interpret the string literally
+        ret = [listEl];
+      }
+      expanded = expanded.concat(ret);
+    }
+  });
+  return expanded;
+}
+exports.expand = expand;
+
+// Normalizes Buffer creation, using Buffer.alloc if possible.
+// Also provides a good default buffer length for most use cases.
+var buffer = typeof Buffer.alloc === 'function' ?
+  function (len) {
+    return Buffer.alloc(len || config.bufLength);
+  } :
+  function (len) {
+    return new Buffer(len || config.bufLength);
+  };
+exports.buffer = buffer;
+
+// Normalizes _unlinkSync() across platforms to match Unix behavior, i.e.
+// file can be unlinked even if it's read-only, see https://github.com/joyent/node/issues/3006
+function unlinkSync(file) {
+  try {
+    fs.unlinkSync(file);
+  } catch (e) {
+    // Try to override file permission
+    /* istanbul ignore next */
+    if (e.code === 'EPERM') {
+      fs.chmodSync(file, '0666');
+      fs.unlinkSync(file);
+    } else {
+      throw e;
+    }
+  }
+}
+exports.unlinkSync = unlinkSync;
+
+// e.g. 'shelljs_a5f185d0443ca...'
+function randomFileName() {
+  function randomHash(count) {
+    if (count === 1) {
+      return parseInt(16 * Math.random(), 10).toString(16);
+    }
+    var hash = '';
+    for (var i = 0; i < count; i++) {
+      hash += randomHash(1);
+    }
+    return hash;
+  }
+
+  return 'shelljs_' + randomHash(20);
+}
+exports.randomFileName = randomFileName;
+
+// Common wrapper for all Unix-like commands that performs glob expansion,
+// command-logging, and other nice things
+function wrap(cmd, fn, options) {
+  options = options || {};
+  if (options.canReceivePipe) {
+    pipeMethods.push(cmd);
+  }
+  return function () {
+    var retValue = null;
+
+    state.currentCmd = cmd;
+    state.error = null;
+    state.errorCode = 0;
+
+    try {
+      var args = [].slice.call(arguments, 0);
+
+      // Log the command to stderr, if appropriate
+      if (config.verbose) {
+        console.error.apply(console, [cmd].concat(args));
+      }
+
+      // If this is coming from a pipe, let's set the pipedValue (otherwise, set
+      // it to the empty string)
+      state.pipedValue = (this && typeof this.stdout === 'string') ? this.stdout : '';
+
+      if (options.unix === false) { // this branch is for exec()
+        retValue = fn.apply(this, args);
+      } else { // and this branch is for everything else
+        if (isObject(args[0]) && args[0].constructor.name === 'Object') {
+          // a no-op, allowing the syntax `touch({'-r': file}, ...)`
+        } else if (args.length === 0 || typeof args[0] !== 'string' || args[0].length <= 1 || args[0][0] !== '-') {
+          args.unshift(''); // only add dummy option if '-option' not already present
+        }
+
+        // flatten out arrays that are arguments, to make the syntax:
+        //    `cp([file1, file2, file3], dest);`
+        // equivalent to:
+        //    `cp(file1, file2, file3, dest);`
+        args = args.reduce(function (accum, cur) {
+          if (Array.isArray(cur)) {
+            return accum.concat(cur);
+          }
+          accum.push(cur);
+          return accum;
+        }, []);
+
+        // Convert ShellStrings (basically just String objects) to regular strings
+        args = args.map(function (arg) {
+          if (isObject(arg) && arg.constructor.name === 'String') {
+            return arg.toString();
+          }
+          return arg;
+        });
+
+        // Expand the '~' if appropriate
+        var homeDir = getUserHome();
+        args = args.map(function (arg) {
+          if (typeof arg === 'string' && arg.slice(0, 2) === '~/' || arg === '~') {
+            return arg.replace(/^~/, homeDir);
+          }
+          return arg;
+        });
+
+        // Perform glob-expansion on all arguments after globStart, but preserve
+        // the arguments before it (like regexes for sed and grep)
+        if (!config.noglob && options.allowGlobbing === true) {
+          args = args.slice(0, options.globStart).concat(expand(args.slice(options.globStart)));
+        }
+
+        try {
+          // parse options if options are provided
+          if (isObject(options.cmdOptions)) {
+            args[0] = parseOptions(args[0], options.cmdOptions);
+          }
+
+          retValue = fn.apply(this, args);
+        } catch (e) {
+          /* istanbul ignore else */
+          if (e.msg === 'earlyExit') {
+            retValue = e.retValue;
+          } else {
+            throw e; // this is probably a bug that should be thrown up the call stack
+          }
+        }
+      }
+    } catch (e) {
+      /* istanbul ignore next */
+      if (!state.error) {
+        // If state.error hasn't been set it's an error thrown by Node, not us - probably a bug...
+        console.error('ShellJS: internal error');
+        console.error(e.stack || e);
+        process.exit(1);
+      }
+      if (config.fatal) throw e;
+    }
+
+    if (options.wrapOutput &&
+        (typeof retValue === 'string' || Array.isArray(retValue))) {
+      retValue = new ShellString(retValue, state.error, state.errorCode);
+    }
+
+    state.currentCmd = 'shell.js';
+    return retValue;
+  };
+} // wrap
+exports.wrap = wrap;
+
+// This returns all the input that is piped into the current command (or the
+// empty string, if this isn't on the right-hand side of a pipe
+function _readFromPipe() {
+  return state.pipedValue;
+}
+exports.readFromPipe = _readFromPipe;
+
+var DEFAULT_WRAP_OPTIONS = {
+  allowGlobbing: true,
+  canReceivePipe: false,
+  cmdOptions: false,
+  globStart: 1,
+  pipeOnly: false,
+  unix: true,
+  wrapOutput: true,
+  overWrite: false,
+};
+
+// Register a new ShellJS command
+function _register(name, implementation, wrapOptions) {
+  wrapOptions = wrapOptions || {};
+  // If an option isn't specified, use the default
+  wrapOptions = objectAssign({}, DEFAULT_WRAP_OPTIONS, wrapOptions);
+
+  if (shell[name] && !wrapOptions.overWrite) {
+    throw new Error('unable to overwrite `' + name + '` command');
+  }
+
+  if (wrapOptions.pipeOnly) {
+    wrapOptions.canReceivePipe = true;
+    shellMethods[name] = wrap(name, implementation, wrapOptions);
+  } else {
+    shell[name] = wrap(name, implementation, wrapOptions);
+  }
+}
+exports.register = _register;

static/js/ketcher2/node_modules/shelljs/src/cp.js

@@ -0,0 +1,299 @@
+var fs = require('fs');
+var path = require('path');
+var common = require('./common');
+
+common.register('cp', _cp, {
+  cmdOptions: {
+    'f': '!no_force',
+    'n': 'no_force',
+    'u': 'update',
+    'R': 'recursive',
+    'r': 'recursive',
+    'L': 'followsymlink',
+    'P': 'noFollowsymlink',
+  },
+  wrapOutput: false,
+});
+
+// Buffered file copy, synchronous
+// (Using readFileSync() + writeFileSync() could easily cause a memory overflow
+//  with large files)
+function copyFileSync(srcFile, destFile, options) {
+  if (!fs.existsSync(srcFile)) {
+    common.error('copyFileSync: no such file or directory: ' + srcFile);
+  }
+
+  var isWindows = process.platform === 'win32';
+
+  // Check the mtimes of the files if the '-u' flag is provided
+  try {
+    if (options.update && fs.statSync(srcFile).mtime < fs.statSync(destFile).mtime) {
+      return;
+    }
+  } catch (e) {
+    // If we're here, destFile probably doesn't exist, so just do a normal copy
+  }
+
+  if (fs.lstatSync(srcFile).isSymbolicLink() && !options.followsymlink) {
+    try {
+      fs.lstatSync(destFile);
+      common.unlinkSync(destFile); // re-link it
+    } catch (e) {
+      // it doesn't exist, so no work needs to be done
+    }
+
+    var symlinkFull = fs.readlinkSync(srcFile);
+    fs.symlinkSync(symlinkFull, destFile, isWindows ? 'junction' : null);
+  } else {
+    var buf = common.buffer();
+    var bufLength = buf.length;
+    var bytesRead = bufLength;
+    var pos = 0;
+    var fdr = null;
+    var fdw = null;
+
+    try {
+      fdr = fs.openSync(srcFile, 'r');
+    } catch (e) {
+      /* istanbul ignore next */
+      common.error('copyFileSync: could not read src file (' + srcFile + ')');
+    }
+
+    try {
+      fdw = fs.openSync(destFile, 'w');
+    } catch (e) {
+      /* istanbul ignore next */
+      common.error('copyFileSync: could not write to dest file (code=' + e.code + '):' + destFile);
+    }
+
+    while (bytesRead === bufLength) {
+      bytesRead = fs.readSync(fdr, buf, 0, bufLength, pos);
+      fs.writeSync(fdw, buf, 0, bytesRead);
+      pos += bytesRead;
+    }
+
+    fs.closeSync(fdr);
+    fs.closeSync(fdw);
+
+    fs.chmodSync(destFile, fs.statSync(srcFile).mode);
+  }
+}
+
+// Recursively copies 'sourceDir' into 'destDir'
+// Adapted from https://github.com/ryanmcgrath/wrench-js
+//
+// Copyright (c) 2010 Ryan McGrath
+// Copyright (c) 2012 Artur Adib
+//
+// Licensed under the MIT License
+// http://www.opensource.org/licenses/mit-license.php
+function cpdirSyncRecursive(sourceDir, destDir, currentDepth, opts) {
+  if (!opts) opts = {};
+
+  // Ensure there is not a run away recursive copy
+  if (currentDepth >= common.config.maxdepth) return;
+  currentDepth++;
+
+  var isWindows = process.platform === 'win32';
+
+  // Create the directory where all our junk is moving to; read the mode of the
+  // source directory and mirror it
+  try {
+    var checkDir = fs.statSync(sourceDir);
+    fs.mkdirSync(destDir, checkDir.mode);
+  } catch (e) {
+    // if the directory already exists, that's okay
+    if (e.code !== 'EEXIST') throw e;
+  }
+
+  var files = fs.readdirSync(sourceDir);
+
+  for (var i = 0; i < files.length; i++) {
+    var srcFile = sourceDir + '/' + files[i];
+    var destFile = destDir + '/' + files[i];
+    var srcFileStat = fs.lstatSync(srcFile);
+
+    var symlinkFull;
+    if (opts.followsymlink) {
+      if (cpcheckcycle(sourceDir, srcFile)) {
+        // Cycle link found.
+        console.error('Cycle link found.');
+        symlinkFull = fs.readlinkSync(srcFile);
+        fs.symlinkSync(symlinkFull, destFile, isWindows ? 'junction' : null);
+        continue;
+      }
+    }
+    if (srcFileStat.isDirectory()) {
+      /* recursion this thing right on back. */
+      cpdirSyncRecursive(srcFile, destFile, currentDepth, opts);
+    } else if (srcFileStat.isSymbolicLink() && !opts.followsymlink) {
+      symlinkFull = fs.readlinkSync(srcFile);
+      try {
+        fs.lstatSync(destFile);
+        common.unlinkSync(destFile); // re-link it
+      } catch (e) {
+        // it doesn't exist, so no work needs to be done
+      }
+      fs.symlinkSync(symlinkFull, destFile, isWindows ? 'junction' : null);
+    } else if (srcFileStat.isSymbolicLink() && opts.followsymlink) {
+      srcFileStat = fs.statSync(srcFile);
+      if (srcFileStat.isDirectory()) {
+        cpdirSyncRecursive(srcFile, destFile, currentDepth, opts);
+      } else {
+        copyFileSync(srcFile, destFile, opts);
+      }
+    } else {
+      /* At this point, we've hit a file actually worth copying... so copy it on over. */
+      if (fs.existsSync(destFile) && opts.no_force) {
+        common.log('skipping existing file: ' + files[i]);
+      } else {
+        copyFileSync(srcFile, destFile, opts);
+      }
+    }
+  } // for files
+} // cpdirSyncRecursive
+
+// Checks if cureent file was created recently
+function checkRecentCreated(sources, index) {
+  var lookedSource = sources[index];
+  return sources.slice(0, index).some(function (src) {
+    return path.basename(src) === path.basename(lookedSource);
+  });
+}
+
+function cpcheckcycle(sourceDir, srcFile) {
+  var srcFileStat = fs.lstatSync(srcFile);
+  if (srcFileStat.isSymbolicLink()) {
+    // Do cycle check. For example:
+    //   $ mkdir -p 1/2/3/4
+    //   $ cd  1/2/3/4
+    //   $ ln -s ../../3 link
+    //   $ cd ../../../..
+    //   $ cp -RL 1 copy
+    var cyclecheck = fs.statSync(srcFile);
+    if (cyclecheck.isDirectory()) {
+      var sourcerealpath = fs.realpathSync(sourceDir);
+      var symlinkrealpath = fs.realpathSync(srcFile);
+      var re = new RegExp(symlinkrealpath);
+      if (re.test(sourcerealpath)) {
+        return true;
+      }
+    }
+  }
+  return false;
+}
+
+//@
+//@ ### cp([options,] source [, source ...], dest)
+//@ ### cp([options,] source_array, dest)
+//@ Available options:
+//@
+//@ + `-f`: force (default behavior)
+//@ + `-n`: no-clobber
+//@ + `-u`: only copy if source is newer than dest
+//@ + `-r`, `-R`: recursive
+//@ + `-L`: follow symlinks
+//@ + `-P`: don't follow symlinks
+//@
+//@ Examples:
+//@
+//@ ```javascript
+//@ cp('file1', 'dir1');
+//@ cp('-R', 'path/to/dir/', '~/newCopy/');
+//@ cp('-Rf', '/tmp/*', '/usr/local/*', '/home/tmp');
+//@ cp('-Rf', ['/tmp/*', '/usr/local/*'], '/home/tmp'); // same as above
+//@ ```
+//@
+//@ Copies files.
+function _cp(options, sources, dest) {
+  // If we're missing -R, it actually implies -L (unless -P is explicit)
+  if (options.followsymlink) {
+    options.noFollowsymlink = false;
+  }
+  if (!options.recursive && !options.noFollowsymlink) {
+    options.followsymlink = true;
+  }
+
+  // Get sources, dest
+  if (arguments.length < 3) {
+    common.error('missing <source> and/or <dest>');
+  } else {
+    sources = [].slice.call(arguments, 1, arguments.length - 1);
+    dest = arguments[arguments.length - 1];
+  }
+
+  var destExists = fs.existsSync(dest);
+  var destStat = destExists && fs.statSync(dest);
+
+  // Dest is not existing dir, but multiple sources given
+  if ((!destExists || !destStat.isDirectory()) && sources.length > 1) {
+    common.error('dest is not a directory (too many sources)');
+  }
+
+  // Dest is an existing file, but -n is given
+  if (destExists && destStat.isFile() && options.no_force) {
+    return new common.ShellString('', '', 0);
+  }
+
+  sources.forEach(function (src, srcIndex) {
+    if (!fs.existsSync(src)) {
+      if (src === '') src = "''"; // if src was empty string, display empty string
+      common.error('no such file or directory: ' + src, { continue: true });
+      return; // skip file
+    }
+    var srcStat = fs.statSync(src);
+    if (!options.noFollowsymlink && srcStat.isDirectory()) {
+      if (!options.recursive) {
+        // Non-Recursive
+        common.error("omitting directory '" + src + "'", { continue: true });
+      } else {
+        // Recursive
+        // 'cp /a/source dest' should create 'source' in 'dest'
+        var newDest = (destStat && destStat.isDirectory()) ?
+            path.join(dest, path.basename(src)) :
+            dest;
+
+        try {
+          fs.statSync(path.dirname(dest));
+          cpdirSyncRecursive(src, newDest, 0, { no_force: options.no_force, followsymlink: options.followsymlink });
+        } catch (e) {
+          /* istanbul ignore next */
+          common.error("cannot create directory '" + dest + "': No such file or directory");
+        }
+      }
+    } else {
+      // If here, src is a file
+
+      // When copying to '/path/dir':
+      //    thisDest = '/path/dir/file1'
+      var thisDest = dest;
+      if (destStat && destStat.isDirectory()) {
+        thisDest = path.normalize(dest + '/' + path.basename(src));
+      }
+
+      var thisDestExists = fs.existsSync(thisDest);
+      if (thisDestExists && checkRecentCreated(sources, srcIndex)) {
+        // cannot overwrite file created recently in current execution, but we want to continue copying other files
+        if (!options.no_force) {
+          common.error("will not overwrite just-created '" + thisDest + "' with '" + src + "'", { continue: true });
+        }
+        return;
+      }
+
+      if (thisDestExists && options.no_force) {
+        return; // skip file
+      }
+
+      if (path.relative(src, thisDest) === '') {
+        // a file cannot be copied to itself, but we want to continue copying other files
+        common.error("'" + thisDest + "' and '" + src + "' are the same file", { continue: true });
+        return;
+      }
+
+      copyFileSync(src, thisDest, options);
+    }
+  }); // forEach(src)
+
+  return new common.ShellString('', common.state.error, common.state.errorCode);
+}
+module.exports = _cp;

static/js/ketcher2/node_modules/shelljs/src/dirs.js

@@ -0,0 +1,200 @@
+var common = require('./common');
+var _cd = require('./cd');
+var path = require('path');
+
+common.register('dirs', _dirs, {
+  wrapOutput: false,
+});
+common.register('pushd', _pushd, {
+  wrapOutput: false,
+});
+common.register('popd', _popd, {
+  wrapOutput: false,
+});
+
+// Pushd/popd/dirs internals
+var _dirStack = [];
+
+function _isStackIndex(index) {
+  return (/^[\-+]\d+$/).test(index);
+}
+
+function _parseStackIndex(index) {
+  if (_isStackIndex(index)) {
+    if (Math.abs(index) < _dirStack.length + 1) { // +1 for pwd
+      return (/^-/).test(index) ? Number(index) - 1 : Number(index);
+    }
+    common.error(index + ': directory stack index out of range');
+  } else {
+    common.error(index + ': invalid number');
+  }
+}
+
+function _actualDirStack() {
+  return [process.cwd()].concat(_dirStack);
+}
+
+//@
+//@ ### pushd([options,] [dir | '-N' | '+N'])
+//@
+//@ Available options:
+//@
+//@ + `-n`: Suppresses the normal change of directory when adding directories to the stack, so that only the stack is manipulated.
+//@
+//@ Arguments:
+//@
+//@ + `dir`: Makes the current working directory be the top of the stack, and then executes the equivalent of `cd dir`.
+//@ + `+N`: Brings the Nth directory (counting from the left of the list printed by dirs, starting with zero) to the top of the list by rotating the stack.
+//@ + `-N`: Brings the Nth directory (counting from the right of the list printed by dirs, starting with zero) to the top of the list by rotating the stack.
+//@
+//@ Examples:
+//@
+//@ ```javascript
+//@ // process.cwd() === '/usr'
+//@ pushd('/etc'); // Returns /etc /usr
+//@ pushd('+1');   // Returns /usr /etc
+//@ ```
+//@
+//@ Save the current directory on the top of the directory stack and then cd to `dir`. With no arguments, pushd exchanges the top two directories. Returns an array of paths in the stack.
+function _pushd(options, dir) {
+  if (_isStackIndex(options)) {
+    dir = options;
+    options = '';
+  }
+
+  options = common.parseOptions(options, {
+    'n': 'no-cd',
+  });
+
+  var dirs = _actualDirStack();
+
+  if (dir === '+0') {
+    return dirs; // +0 is a noop
+  } else if (!dir) {
+    if (dirs.length > 1) {
+      dirs = dirs.splice(1, 1).concat(dirs);
+    } else {
+      return common.error('no other directory');
+    }
+  } else if (_isStackIndex(dir)) {
+    var n = _parseStackIndex(dir);
+    dirs = dirs.slice(n).concat(dirs.slice(0, n));
+  } else {
+    if (options['no-cd']) {
+      dirs.splice(1, 0, dir);
+    } else {
+      dirs.unshift(dir);
+    }
+  }
+
+  if (options['no-cd']) {
+    dirs = dirs.slice(1);
+  } else {
+    dir = path.resolve(dirs.shift());
+    _cd('', dir);
+  }
+
+  _dirStack = dirs;
+  return _dirs('');
+}
+exports.pushd = _pushd;
+
+//@
+//@ ### popd([options,] ['-N' | '+N'])
+//@
+//@ Available options:
+//@
+//@ + `-n`: Suppresses the normal change of directory when removing directories from the stack, so that only the stack is manipulated.
+//@
+//@ Arguments:
+//@
+//@ + `+N`: Removes the Nth directory (counting from the left of the list printed by dirs), starting with zero.
+//@ + `-N`: Removes the Nth directory (counting from the right of the list printed by dirs), starting with zero.
+//@
+//@ Examples:
+//@
+//@ ```javascript
+//@ echo(process.cwd()); // '/usr'
+//@ pushd('/etc');       // '/etc /usr'
+//@ echo(process.cwd()); // '/etc'
+//@ popd();              // '/usr'
+//@ echo(process.cwd()); // '/usr'
+//@ ```
+//@
+//@ When no arguments are given, popd removes the top directory from the stack and performs a cd to the new top directory. The elements are numbered from 0 starting at the first directory listed with dirs; i.e., popd is equivalent to popd +0. Returns an array of paths in the stack.
+function _popd(options, index) {
+  if (_isStackIndex(options)) {
+    index = options;
+    options = '';
+  }
+
+  options = common.parseOptions(options, {
+    'n': 'no-cd',
+  });
+
+  if (!_dirStack.length) {
+    return common.error('directory stack empty');
+  }
+
+  index = _parseStackIndex(index || '+0');
+
+  if (options['no-cd'] || index > 0 || _dirStack.length + index === 0) {
+    index = index > 0 ? index - 1 : index;
+    _dirStack.splice(index, 1);
+  } else {
+    var dir = path.resolve(_dirStack.shift());
+    _cd('', dir);
+  }
+
+  return _dirs('');
+}
+exports.popd = _popd;
+
+//@
+//@ ### dirs([options | '+N' | '-N'])
+//@
+//@ Available options:
+//@
+//@ + `-c`: Clears the directory stack by deleting all of the elements.
+//@
+//@ Arguments:
+//@
+//@ + `+N`: Displays the Nth directory (counting from the left of the list printed by dirs when invoked without options), starting with zero.
+//@ + `-N`: Displays the Nth directory (counting from the right of the list printed by dirs when invoked without options), starting with zero.
+//@
+//@ Display the list of currently remembered directories. Returns an array of paths in the stack, or a single path if +N or -N was specified.
+//@
+//@ See also: pushd, popd
+function _dirs(options, index) {
+  if (_isStackIndex(options)) {
+    index = options;
+    options = '';
+  }
+
+  options = common.parseOptions(options, {
+    'c': 'clear',
+  });
+
+  if (options.clear) {
+    _dirStack = [];
+    return _dirStack;
+  }
+
+  var stack = _actualDirStack();
+
+  if (index) {
+    index = _parseStackIndex(index);
+
+    if (index < 0) {
+      index = stack.length + index;
+    }
+
+    common.log(stack[index]);
+    return stack[index];
+  }
+
+  common.log(stack.join(' '));
+
+  return stack;
+}
+exports.dirs = _dirs;

static/js/ketcher2/node_modules/shelljs/src/echo.js

@@ -0,0 +1,34 @@
+var common = require('./common');
+
+common.register('echo', _echo, {
+  allowGlobbing: false,
+});
+
+//@
+//@ ### echo([options,] string [, string ...])
+//@ Available options:
+//@
+//@ + `-e`: interpret backslash escapes (default)
+//@
+//@ Examples:
+//@
+//@ ```javascript
+//@ echo('hello world');
+//@ var str = echo('hello world');
+//@ ```
+//@
+//@ Prints string to stdout, and returns string with additional utility methods
+//@ like `.to()`.
+function _echo(opts, messages) {
+  // allow strings starting with '-', see issue #20
+  messages = [].slice.call(arguments, opts ? 0 : 1);
+
+  if (messages[0] === '-e') {
+    // ignore -e
+    messages.shift();
+  }
+
+  console.log.apply(console, messages);
+  return messages.join(' ');
+}
+module.exports = _echo;

static/js/ketcher2/node_modules/shelljs/src/error.js

@@ -0,0 +1,14 @@
+var common = require('./common');
+
+//@
+//@ ### error()
+//@ Tests if error occurred in the last command. Returns a truthy value if an
+//@ error returned and a falsy value otherwise.
+//@
+//@ **Note**: do not rely on the
+//@ return value to be an error message. If you need the last error message, use
+//@ the `.stderr` attribute from the last command's return value instead.
+function error() {
+  return common.state.error;
+}
+module.exports = error;

static/js/ketcher2/node_modules/shelljs/src/exec.js

@@ -0,0 +1,295 @@
+var common = require('./common');
+var _tempDir = require('./tempdir');
+var _pwd = require('./pwd');
+var path = require('path');
+var fs = require('fs');
+var child = require('child_process');
+
+var DEFAULT_MAXBUFFER_SIZE = 20 * 1024 * 1024;
+
+common.register('exec', _exec, {
+  unix: false,
+  canReceivePipe: true,
+  wrapOutput: false,
+});
+
+// Hack to run child_process.exec() synchronously (sync avoids callback hell)
+// Uses a custom wait loop that checks for a flag file, created when the child process is done.
+// (Can't do a wait loop that checks for internal Node variables/messages as
+// Node is single-threaded; callbacks and other internal state changes are done in the
+// event loop).
+function execSync(cmd, opts, pipe) {
+  if (!common.config.execPath) {
+    common.error('Unable to find a path to the node binary. Please manually set config.execPath');
+  }
+
+  var tempDir = _tempDir();
+  var stdoutFile = path.resolve(tempDir + '/' + common.randomFileName());
+  var stderrFile = path.resolve(tempDir + '/' + common.randomFileName());
+  var codeFile = path.resolve(tempDir + '/' + common.randomFileName());
+  var scriptFile = path.resolve(tempDir + '/' + common.randomFileName());
+  var sleepFile = path.resolve(tempDir + '/' + common.randomFileName());
+
+  opts = common.extend({
+    silent: common.config.silent,
+    cwd: _pwd().toString(),
+    env: process.env,
+    maxBuffer: DEFAULT_MAXBUFFER_SIZE,
+  }, opts);
+
+  var previousStdoutContent = '';
+  var previousStderrContent = '';
+  // Echoes stdout and stderr changes from running process, if not silent
+  function updateStream(streamFile) {
+    if (opts.silent || !fs.existsSync(streamFile)) {
+      return;
+    }
+
+    var previousStreamContent;
+    var procStream;
+    if (streamFile === stdoutFile) {
+      previousStreamContent = previousStdoutContent;
+      procStream = process.stdout;
+    } else { // assume stderr
+      previousStreamContent = previousStderrContent;
+      procStream = process.stderr;
+    }
+
+    var streamContent = fs.readFileSync(streamFile, 'utf8');
+    // No changes since last time?
+    if (streamContent.length <= previousStreamContent.length) {
+      return;
+    }
+
+    procStream.write(streamContent.substr(previousStreamContent.length));
+    previousStreamContent = streamContent;
+  }
+
+  if (fs.existsSync(scriptFile)) common.unlinkSync(scriptFile);
+  if (fs.existsSync(stdoutFile)) common.unlinkSync(stdoutFile);
+  if (fs.existsSync(stderrFile)) common.unlinkSync(stderrFile);
+  if (fs.existsSync(codeFile)) common.unlinkSync(codeFile);
+
+  var execCommand = JSON.stringify(common.config.execPath) + ' ' + JSON.stringify(scriptFile);
+  var script;
+
+  opts.cwd = path.resolve(opts.cwd);
+  var optString = JSON.stringify(opts);
+
+  if (typeof child.execSync === 'function') {
+    script = [
+      "var child = require('child_process')",
+      "  , fs = require('fs');",
+      'var childProcess = child.exec(' + JSON.stringify(cmd) + ', ' + optString + ', function(err) {',
+      '  var fname = ' + JSON.stringify(codeFile) + ';',
+      '  if (!err) {',
+      '    fs.writeFileSync(fname, "0");',
+      '  } else if (err.code === undefined) {',
+      '    fs.writeFileSync(fname, "1");',
+      '  } else {',
+      '    fs.writeFileSync(fname, err.code.toString());',
+      '  }',
+      '});',
+      'var stdoutStream = fs.createWriteStream(' + JSON.stringify(stdoutFile) + ');',
+      'var stderrStream = fs.createWriteStream(' + JSON.stringify(stderrFile) + ');',
+      'childProcess.stdout.pipe(stdoutStream, {end: false});',
+      'childProcess.stderr.pipe(stderrStream, {end: false});',
+      'childProcess.stdout.pipe(process.stdout);',
+      'childProcess.stderr.pipe(process.stderr);',
+    ].join('\n') +
+      (pipe ? '\nchildProcess.stdin.end(' + JSON.stringify(pipe) + ');\n' : '\n') +
+      [
+        'var stdoutEnded = false, stderrEnded = false;',
+        'function tryClosingStdout(){ if(stdoutEnded){ stdoutStream.end(); } }',
+        'function tryClosingStderr(){ if(stderrEnded){ stderrStream.end(); } }',
+        "childProcess.stdout.on('end', function(){ stdoutEnded = true; tryClosingStdout(); });",
+        "childProcess.stderr.on('end', function(){ stderrEnded = true; tryClosingStderr(); });",
+      ].join('\n');
+
+    fs.writeFileSync(scriptFile, script);
+
+    if (opts.silent) {
+      opts.stdio = 'ignore';
+    } else {
+      opts.stdio = [0, 1, 2];
+    }
+
+    // Welcome to the future
+    try {
+      child.execSync(execCommand, opts);
+    } catch (e) {
+      // Clean up immediately if we have an exception
+      try { common.unlinkSync(scriptFile); } catch (e2) {}
+      try { common.unlinkSync(stdoutFile); } catch (e2) {}
+      try { common.unlinkSync(stderrFile); } catch (e2) {}
+      try { common.unlinkSync(codeFile); } catch (e2) {}
+      throw e;
+    }
+  } else {
+    cmd += ' > ' + stdoutFile + ' 2> ' + stderrFile; // works on both win/unix
+
+    script = [
+      "var child = require('child_process')",
+      "  , fs = require('fs');",
+      'var childProcess = child.exec(' + JSON.stringify(cmd) + ', ' + optString + ', function(err) {',
+      '  var fname = ' + JSON.stringify(codeFile) + ';',
+      '  if (!err) {',
+      '    fs.writeFileSync(fname, "0");',
+      '  } else if (err.code === undefined) {',
+      '    fs.writeFileSync(fname, "1");',
+      '  } else {',
+      '    fs.writeFileSync(fname, err.code.toString());',
+      '  }',
+      '});',
+    ].join('\n') +
+      (pipe ? '\nchildProcess.stdin.end(' + JSON.stringify(pipe) + ');\n' : '\n');
+
+    fs.writeFileSync(scriptFile, script);
+
+    child.exec(execCommand, opts);
+
+    // The wait loop
+    // sleepFile is used as a dummy I/O op to mitigate unnecessary CPU usage
+    // (tried many I/O sync ops, writeFileSync() seems to be only one that is effective in reducing
+    // CPU usage, though apparently not so much on Windows)
+    while (!fs.existsSync(codeFile)) { updateStream(stdoutFile); fs.writeFileSync(sleepFile, 'a'); }
+    while (!fs.existsSync(stdoutFile)) { updateStream(stdoutFile); fs.writeFileSync(sleepFile, 'a'); }
+    while (!fs.existsSync(stderrFile)) { updateStream(stderrFile); fs.writeFileSync(sleepFile, 'a'); }
+    try { common.unlinkSync(sleepFile); } catch (e) {}
+  }
+
+  // At this point codeFile exists, but it's not necessarily flushed yet.
+  // Keep reading it until it is.
+  var code = parseInt('', 10);
+  while (isNaN(code)) {
+    code = parseInt(fs.readFileSync(codeFile, 'utf8'), 10);
+  }
+
+  var stdout = fs.readFileSync(stdoutFile, 'utf8');
+  var stderr = fs.readFileSync(stderrFile, 'utf8');
+
+  // No biggie if we can't erase the files now -- they're in a temp dir anyway
+  try { common.unlinkSync(scriptFile); } catch (e) {}
+  try { common.unlinkSync(stdoutFile); } catch (e) {}
+  try { common.unlinkSync(stderrFile); } catch (e) {}
+  try { common.unlinkSync(codeFile); } catch (e) {}
+
+  if (code !== 0) {
+    common.error('', code, { continue: true });
+  }
+  var obj = common.ShellString(stdout, stderr, code);
+  return obj;
+} // execSync()
+
+// Wrapper around exec() to enable echoing output to console in real time
+function execAsync(cmd, opts, pipe, callback) {
+  var stdout = '';
+  var stderr = '';
+
+  opts = common.extend({
+    silent: common.config.silent,
+    cwd: _pwd().toString(),
+    env: process.env,
+    maxBuffer: DEFAULT_MAXBUFFER_SIZE,
+  }, opts);
+
+  var c = child.exec(cmd, opts, function (err) {
+    if (callback) {
+      if (!err) {
+        callback(0, stdout, stderr);
+      } else if (err.code === undefined) {
+        // See issue #536
+        callback(1, stdout, stderr);
+      } else {
+        callback(err.code, stdout, stderr);
+      }
+    }
+  });
+
+  if (pipe) c.stdin.end(pipe);
+
+  c.stdout.on('data', function (data) {
+    stdout += data;
+    if (!opts.silent) process.stdout.write(data);
+  });
+
+  c.stderr.on('data', function (data) {
+    stderr += data;
+    if (!opts.silent) process.stderr.write(data);
+  });
+
+  return c;
+}
+
+//@
+//@ ### exec(command [, options] [, callback])
+//@ Available options (all `false` by default):
+//@
+//@ + `async`: Asynchronous execution. If a callback is provided, it will be set to
+//@   `true`, regardless of the passed value.
+//@ + `silent`: Do not echo program output to console.
+//@ + and any option available to Node.js's
+//@   [child_process.exec()](https://nodejs.org/api/child_process.html#child_process_child_process_exec_command_options_callback)
+//@
+//@ Examples:
+//@
+//@ ```javascript
+//@ var version = exec('node --version', {silent:true}).stdout;
+//@
+//@ var child = exec('some_long_running_process', {async:true});
+//@ child.stdout.on('data', function(data) {
+//@   /* ... do something with data ... */
+//@ });
+//@
+//@ exec('some_long_running_process', function(code, stdout, stderr) {
+//@   console.log('Exit code:', code);
+//@   console.log('Program output:', stdout);
+//@   console.log('Program stderr:', stderr);
+//@ });
+//@ ```
+//@
+//@ Executes the given `command` _synchronously_, unless otherwise specified.  When in synchronous
+//@ mode, this returns a ShellString (compatible with ShellJS v0.6.x, which returns an object
+//@ of the form `{ code:..., stdout:... , stderr:... }`). Otherwise, this returns the child process
+//@ object, and the `callback` gets the arguments `(code, stdout, stderr)`.
+//@
+//@ Not seeing the behavior you want? `exec()` runs everything through `sh`
+//@ by default (or `cmd.exe` on Windows), which differs from `bash`. If you
+//@ need bash-specific behavior, try out the `{shell: 'path/to/bash'}` option.
+//@
+//@ **Note:** For long-lived processes, it's best to run `exec()` asynchronously as
+//@ the current synchronous implementation uses a lot of CPU. This should be getting
+//@ fixed soon.
+function _exec(command, options, callback) {
+  options = options || {};
+  if (!command) common.error('must specify command');
+
+  var pipe = common.readFromPipe();
+
+  // Callback is defined instead of options.
+  if (typeof options === 'function') {
+    callback = options;
+    options = { async: true };
+  }
+
+  // Callback is defined with options.
+  if (typeof options === 'object' && typeof callback === 'function') {
+    options.async = true;
+  }
+
+  options = common.extend({
+    silent: common.config.silent,
+    async: false,
+  }, options);
+
+  try {
+    if (options.async) {
+      return execAsync(command, options, pipe, callback);
+    } else {
+      return execSync(command, options, pipe);
+    }
+  } catch (e) {
+    common.error('internal error');
+  }
+}
+module.exports = _exec;

static/js/ketcher2/node_modules/shelljs/src/find.js

@@ -0,0 +1,61 @@
+var fs = require('fs');
+var path = require('path');
+var common = require('./common');
+var _ls = require('./ls');
+
+common.register('find', _find, {});
+
+//@
+//@ ### find(path [, path ...])
+//@ ### find(path_array)
+//@ Examples:
+//@
+//@ ```javascript
+//@ find('src', 'lib');
+//@ find(['src', 'lib']); // same as above
+//@ find('.').filter(function(file) { return file.match(/\.js$/); });
+//@ ```
+//@
+//@ Returns array of all files (however deep) in the given paths.
+//@
+//@ The main difference from `ls('-R', path)` is that the resulting file names
+//@ include the base directories, e.g. `lib/resources/file1` instead of just `file1`.
+function _find(options, paths) {
+  if (!paths) {
+    common.error('no path specified');
+  } else if (typeof paths === 'string') {
+    paths = [].slice.call(arguments, 1);
+  }
+
+  var list = [];
+
+  function pushFile(file) {
+    if (process.platform === 'win32') {
+      file = file.replace(/\\/g, '/');
+    }
+    list.push(file);
+  }
+
+  // why not simply do ls('-R', paths)? because the output wouldn't give the base dirs
+  // to get the base dir in the output, we need instead ls('-R', 'dir/*') for every directory
+
+  paths.forEach(function (file) {
+    var stat;
+    try {
+      stat = fs.statSync(file);
+    } catch (e) {
+      common.error('no such file or directory: ' + file);
+    }
+
+    pushFile(file);
+
+    if (stat.isDirectory()) {
+      _ls({ recursive: true, all: true }, file).forEach(function (subfile) {
+        pushFile(path.join(file, subfile));
+      });
+    }
+  });
+
+  return list;
+}
+module.exports = _find;

static/js/ketcher2/node_modules/shelljs/src/grep.js

@@ -0,0 +1,67 @@
+var common = require('./common');
+var fs = require('fs');
+
+common.register('grep', _grep, {
+  globStart: 2, // don't glob-expand the regex
+  canReceivePipe: true,
+  cmdOptions: {
+    'v': 'inverse',
+    'l': 'nameOnly',
+  },
+});
+
+//@
+//@ ### grep([options,] regex_filter, file [, file ...])
+//@ ### grep([options,] regex_filter, file_array)
+//@ Available options:
+//@
+//@ + `-v`: Inverse the sense of the regex and print the lines not matching the criteria.
+//@ + `-l`: Print only filenames of matching files
+//@
+//@ Examples:
+//@
+//@ ```javascript
+//@ grep('-v', 'GLOBAL_VARIABLE', '*.js');
+//@ grep('GLOBAL_VARIABLE', '*.js');
+//@ ```
+//@
+//@ Reads input string from given files and returns a string containing all lines of the
+//@ file that match the given `regex_filter`.
+function _grep(options, regex, files) {
+  // Check if this is coming from a pipe
+  var pipe = common.readFromPipe();
+
+  if (!files && !pipe) common.error('no paths given', 2);
+
+  files = [].slice.call(arguments, 2);
+
+  if (pipe) {
+    files.unshift('-');
+  }
+
+  var grep = [];
+  files.forEach(function (file) {
+    if (!fs.existsSync(file) && file !== '-') {
+      common.error('no such file or directory: ' + file, 2, { continue: true });
+      return;
+    }
+
+    var contents = file === '-' ? pipe : fs.readFileSync(file, 'utf8');
+    var lines = contents.split(/\r*\n/);
+    if (options.nameOnly) {
+      if (contents.match(regex)) {
+        grep.push(file);
+      }
+    } else {
+      lines.forEach(function (line) {
+        var matched = line.match(regex);
+        if ((options.inverse && !matched) || (!options.inverse && matched)) {
+          grep.push(line);
+        }
+      });
+    }
+  });
+
+  return grep.join('\n') + '\n';
+}
+module.exports = _grep;

static/js/ketcher2/node_modules/shelljs/src/head.js

@@ -0,0 +1,111 @@
+var common = require('./common');
+var fs = require('fs');
+
+common.register('head', _head, {
+  canReceivePipe: true,
+  cmdOptions: {
+    'n': 'numLines',
+  },
+});
+
+// This reads n or more lines, or the entire file, whichever is less.
+function readSomeLines(file, numLines) {
+  var buf = common.buffer();
+  var bufLength = buf.length;
+  var bytesRead = bufLength;
+  var pos = 0;
+  var fdr = null;
+
+  try {
+    fdr = fs.openSync(file, 'r');
+  } catch (e) {
+    common.error('cannot read file: ' + file);
+  }
+
+  var numLinesRead = 0;
+  var ret = '';
+  while (bytesRead === bufLength && numLinesRead < numLines) {
+    bytesRead = fs.readSync(fdr, buf, 0, bufLength, pos);
+    var bufStr = buf.toString('utf8', 0, bytesRead);
+    numLinesRead += bufStr.split('\n').length - 1;
+    ret += bufStr;
+    pos += bytesRead;
+  }
+
+  fs.closeSync(fdr);
+  return ret;
+}
+//@
+//@ ### head([{'-n': \<num\>},] file [, file ...])
+//@ ### head([{'-n': \<num\>},] file_array)
+//@ Available options:
+//@
+//@ + `-n <num>`: Show the first `<num>` lines of the files
+//@
+//@ Examples:
+//@
+//@ ```javascript
+//@ var str = head({'-n': 1}, 'file*.txt');
+//@ var str = head('file1', 'file2');
+//@ var str = head(['file1', 'file2']); // same as above
+//@ ```
+//@
+//@ Read the start of a file.
+function _head(options, files) {
+  var head = [];
+  var pipe = common.readFromPipe();
+
+  if (!files && !pipe) common.error('no paths given');
+
+  var idx = 1;
+  if (options.numLines === true) {
+    idx = 2;
+    options.numLines = Number(arguments[1]);
+  } else if (options.numLines === false) {
+    options.numLines = 10;
+  }
+  files = [].slice.call(arguments, idx);
+
+  if (pipe) {
+    files.unshift('-');
+  }
+
+  var shouldAppendNewline = false;
+  files.forEach(function (file) {
+    if (file !== '-') {
+      if (!fs.existsSync(file)) {
+        common.error('no such file or directory: ' + file, { continue: true });
+        return;
+      } else if (fs.statSync(file).isDirectory()) {
+        common.error("error reading '" + file + "': Is a directory", {
+          continue: true,
+        });
+        return;
+      }
+    }
+
+    var contents;
+    if (file === '-') {
+      contents = pipe;
+    } else if (options.numLines < 0) {
+      contents = fs.readFileSync(file, 'utf8');
+    } else {
+      contents = readSomeLines(file, options.numLines);
+    }
+
+    var lines = contents.split('\n');
+    var hasTrailingNewline = (lines[lines.length - 1] === '');
+    if (hasTrailingNewline) {
+      lines.pop();
+    }
+    shouldAppendNewline = (hasTrailingNewline || options.numLines < lines.length);
+
+    head = head.concat(lines.slice(0, options.numLines));
+  });
+
+  if (shouldAppendNewline) {
+    head.push(''); // to add a trailing newline once we join
+  }
+  return head.join('\n');
+}
+module.exports = _head;

static/js/ketcher2/node_modules/shelljs/src/ln.js

@@ -0,0 +1,72 @@
+var fs = require('fs');
+var path = require('path');
+var common = require('./common');
+
+common.register('ln', _ln, {
+  cmdOptions: {
+    's': 'symlink',
+    'f': 'force',
+  },
+});
+
+//@
+//@ ### ln([options,] source, dest)
+//@ Available options:
+//@
+//@ + `-s`: symlink
+//@ + `-f`: force
+//@
+//@ Examples:
+//@
+//@ ```javascript
+//@ ln('file', 'newlink');
+//@ ln('-sf', 'file', 'existing');
+//@ ```
+//@
+//@ Links source to dest. Use -f to force the link, should dest already exist.
+function _ln(options, source, dest) {
+  if (!source || !dest) {
+    common.error('Missing <source> and/or <dest>');
+  }
+
+  source = String(source);
+  var sourcePath = path.normalize(source).replace(RegExp(path.sep + '$'), '');
+  var isAbsolute = (path.resolve(source) === sourcePath);
+  dest = path.resolve(process.cwd(), String(dest));
+
+  if (fs.existsSync(dest)) {
+    if (!options.force) {
+      common.error('Destination file exists', { continue: true });
+    }
+
+    fs.unlinkSync(dest);
+  }
+
+  if (options.symlink) {
+    var isWindows = process.platform === 'win32';
+    var linkType = isWindows ? 'file' : null;
+    var resolvedSourcePath = isAbsolute ? sourcePath : path.resolve(process.cwd(), path.dirname(dest), source);
+    if (!fs.existsSync(resolvedSourcePath)) {
+      common.error('Source file does not exist', { continue: true });
+    } else if (isWindows && fs.statSync(resolvedSourcePath).isDirectory()) {
+      linkType = 'junction';
+    }
+
+    try {
+      fs.symlinkSync(linkType === 'junction' ? resolvedSourcePath : source, dest, linkType);
+    } catch (err) {
+      common.error(err.message);
+    }
+  } else {
+    if (!fs.existsSync(source)) {
+      common.error('Source file does not exist', { continue: true });
+    }
+    try {
+      fs.linkSync(source, dest);
+    } catch (err) {
+      common.error(err.message);
+    }
+  }
+  return '';
+}
+module.exports = _ln;

static/js/ketcher2/node_modules/shelljs/src/ls.js

@@ -0,0 +1,126 @@
+var path = require('path');
+var fs = require('fs');
+var common = require('./common');
+var glob = require('glob');
+
+var globPatternRecursive = path.sep + '**';
+
+common.register('ls', _ls, {
+  cmdOptions: {
+    'R': 'recursive',
+    'A': 'all',
+    'L': 'link',
+    'a': 'all_deprecated',
+    'd': 'directory',
+    'l': 'long',
+  },
+});
+
+//@
+//@ ### ls([options,] [path, ...])
+//@ ### ls([options,] path_array)
+//@ Available options:
+//@
+//@ + `-R`: recursive
+//@ + `-A`: all files (include files beginning with `.`, except for `.` and `..`)
+//@ + `-L`: follow symlinks
+//@ + `-d`: list directories themselves, not their contents
+//@ + `-l`: list objects representing each file, each with fields containing `ls
+//@         -l` output fields. See
+//@         [fs.Stats](https://nodejs.org/api/fs.html#fs_class_fs_stats)
+//@         for more info
+//@
+//@ Examples:
+//@
+//@ ```javascript
+//@ ls('projs/*.js');
+//@ ls('-R', '/users/me', '/tmp');
+//@ ls('-R', ['/users/me', '/tmp']); // same as above
+//@ ls('-l', 'file.txt'); // { name: 'file.txt', mode: 33188, nlink: 1, ...}
+//@ ```
+//@
+//@ Returns array of files in the given path, or in current directory if no path provided.
+function _ls(options, paths) {
+  if (options.all_deprecated) {
+    // We won't support the -a option as it's hard to image why it's useful
+    // (it includes '.' and '..' in addition to '.*' files)
+    // For backwards compatibility we'll dump a deprecated message and proceed as before
+    common.log('ls: Option -a is deprecated. Use -A instead');
+    options.all = true;
+  }
+
+  if (!paths) {
+    paths = ['.'];
+  } else {
+    paths = [].slice.call(arguments, 1);
+  }
+
+  var list = [];
+
+  function pushFile(abs, relName, stat) {
+    if (process.platform === 'win32') {
+      relName = relName.replace(/\\/g, '/');
+    }
+    if (options.long) {
+      stat = stat || (options.link ? fs.statSync(abs) : fs.lstatSync(abs));
+      list.push(addLsAttributes(relName, stat));
+    } else {
+      // list.push(path.relative(rel || '.', file));
+      list.push(relName);
+    }
+  }
+
+  paths.forEach(function (p) {
+    var stat;
+
+    try {
+      stat = options.link ? fs.statSync(p) : fs.lstatSync(p);
+    } catch (e) {
+      common.error('no such file or directory: ' + p, 2, { continue: true });
+      return;
+    }
+
+    // If the stat succeeded
+    if (stat.isDirectory() && !options.directory) {
+      if (options.recursive) {
+        // use glob, because it's simple
+        glob.sync(p + globPatternRecursive, { dot: options.all, follow: options.link })
+          .forEach(function (item) {
+            // Glob pattern returns the directory itself and needs to be filtered out.
+            if (path.relative(p, item)) {
+              pushFile(item, path.relative(p, item));
+            }
+          });
+      } else if (options.all) {
+        // use fs.readdirSync, because it's fast
+        fs.readdirSync(p).forEach(function (item) {
+          pushFile(path.join(p, item), item);
+        });
+      } else {
+        // use fs.readdirSync and then filter out secret files
+        fs.readdirSync(p).forEach(function (item) {
+          if (item[0] !== '.') {
+            pushFile(path.join(p, item), item);
+          }
+        });
+      }
+    } else {
+      pushFile(p, p, stat);
+    }
+  });
+
+  // Add methods, to make this more compatible with ShellStrings
+  return list;
+}
+
+function addLsAttributes(pathName, stats) {
+  // Note: this object will contain more information than .toString() returns
+  stats.name = pathName;
+  stats.toString = function () {
+    // Return a string resembling unix's `ls -l` format
+    return [this.mode, this.nlink, this.uid, this.gid, this.size, this.mtime, this.name].join(' ');
+  };
+  return stats;
+}
+
+module.exports = _ls;

static/js/ketcher2/node_modules/shelljs/src/mkdir.js

@@ -0,0 +1,99 @@
+var common = require('./common');
+var fs = require('fs');
+var path = require('path');
+
+common.register('mkdir', _mkdir, {
+  cmdOptions: {
+    'p': 'fullpath',
+  },
+});
+
+// Recursively creates 'dir'
+function mkdirSyncRecursive(dir) {
+  var baseDir = path.dirname(dir);
+
+  // Prevents some potential problems arising from malformed UNCs or
+  // insufficient permissions.
+  /* istanbul ignore next */
+  if (baseDir === dir) {
+    common.error('dirname() failed: [' + dir + ']');
+  }
+
+  // Base dir exists, no recursion necessary
+  if (fs.existsSync(baseDir)) {
+    fs.mkdirSync(dir, parseInt('0777', 8));
+    return;
+  }
+
+  // Base dir does not exist, go recursive
+  mkdirSyncRecursive(baseDir);
+
+  // Base dir created, can create dir
+  fs.mkdirSync(dir, parseInt('0777', 8));
+}
+
+//@
+//@ ### mkdir([options,] dir [, dir ...])
+//@ ### mkdir([options,] dir_array)
+//@ Available options:
+//@
+//@ + `-p`: full path (will create intermediate dirs if necessary)
+//@
+//@ Examples:
+//@
+//@ ```javascript
+//@ mkdir('-p', '/tmp/a/b/c/d', '/tmp/e/f/g');
+//@ mkdir('-p', ['/tmp/a/b/c/d', '/tmp/e/f/g']); // same as above
+//@ ```
+//@
+//@ Creates directories.
+function _mkdir(options, dirs) {
+  if (!dirs) common.error('no paths given');
+
+  if (typeof dirs === 'string') {
+    dirs = [].slice.call(arguments, 1);
+  }
+  // if it's array leave it as it is
+
+  dirs.forEach(function (dir) {
+    try {
+      var stat = fs.lstatSync(dir);
+      if (!options.fullpath) {
+        common.error('path already exists: ' + dir, { continue: true });
+      } else if (stat.isFile()) {
+        common.error('cannot create directory ' + dir + ': File exists', { continue: true });
+      }
+      return; // skip dir
+    } catch (e) {
+      // do nothing
+    }
+
+    // Base dir does not exist, and no -p option given
+    var baseDir = path.dirname(dir);
+    if (!fs.existsSync(baseDir) && !options.fullpath) {
+      common.error('no such file or directory: ' + baseDir, { continue: true });
+      return; // skip dir
+    }
+
+    try {
+      if (options.fullpath) {
+        mkdirSyncRecursive(path.resolve(dir));
+      } else {
+        fs.mkdirSync(dir, parseInt('0777', 8));
+      }
+    } catch (e) {
+      var reason;
+      if (e.code === 'EACCES') {
+        reason = 'Permission denied';
+      } else if (e.code === 'ENOTDIR' || e.code === 'ENOENT') {
+        reason = 'Not a directory';
+      } else {
+        /* istanbul ignore next */
+        throw e;
+      }
+      common.error('cannot create directory ' + dir + ': ' + reason, { continue: true });
+    }
+  });
+  return '';
+} // mkdir
+module.exports = _mkdir;

static/js/ketcher2/node_modules/shelljs/src/mv.js

@@ -0,0 +1,117 @@
+var fs = require('fs');
+var path = require('path');
+var common = require('./common');
+var cp = require('./cp');
+var rm = require('./rm');
+
+common.register('mv', _mv, {
+  cmdOptions: {
+    'f': '!no_force',
+    'n': 'no_force',
+  },
+});
+
+// Checks if cureent file was created recently
+function checkRecentCreated(sources, index) {
+  var lookedSource = sources[index];
+  return sources.slice(0, index).some(function (src) {
+    return path.basename(src) === path.basename(lookedSource);
+  });
+}
+
+//@
+//@ ### mv([options ,] source [, source ...], dest')
+//@ ### mv([options ,] source_array, dest')
+//@ Available options:
+//@
+//@ + `-f`: force (default behavior)
+//@ + `-n`: no-clobber
+//@
+//@ Examples:
+//@
+//@ ```javascript
+//@ mv('-n', 'file', 'dir/');
+//@ mv('file1', 'file2', 'dir/');
+//@ mv(['file1', 'file2'], 'dir/'); // same as above
+//@ ```
+//@
+//@ Moves files.
+function _mv(options, sources, dest) {
+  // Get sources, dest
+  if (arguments.length < 3) {
+    common.error('missing <source> and/or <dest>');
+  } else if (arguments.length > 3) {
+    sources = [].slice.call(arguments, 1, arguments.length - 1);
+    dest = arguments[arguments.length - 1];
+  } else if (typeof sources === 'string') {
+    sources = [sources];
+  } else {
+    // TODO(nate): figure out if we actually need this line
+    common.error('invalid arguments');
+  }
+
+  var exists = fs.existsSync(dest);
+  var stats = exists && fs.statSync(dest);
+
+  // Dest is not existing dir, but multiple sources given
+  if ((!exists || !stats.isDirectory()) && sources.length > 1) {
+    common.error('dest is not a directory (too many sources)');
+  }
+
+  // Dest is an existing file, but no -f given
+  if (exists && stats.isFile() && options.no_force) {
+    common.error('dest file already exists: ' + dest);
+  }
+
+  sources.forEach(function (src, srcIndex) {
+    if (!fs.existsSync(src)) {
+      common.error('no such file or directory: ' + src, { continue: true });
+      return; // skip file
+    }
+
+    // If here, src exists
+
+    // When copying to '/path/dir':
+    //    thisDest = '/path/dir/file1'
+    var thisDest = dest;
+    if (fs.existsSync(dest) && fs.statSync(dest).isDirectory()) {
+      thisDest = path.normalize(dest + '/' + path.basename(src));
+    }
+
+    var thisDestExists = fs.existsSync(thisDest);
+
+    if (thisDestExists && checkRecentCreated(sources, srcIndex)) {
+      // cannot overwrite file created recently in current execution, but we want to continue copying other files
+      if (!options.no_force) {
+        common.error("will not overwrite just-created '" + thisDest + "' with '" + src + "'", { continue: true });
+      }
+      return;
+    }
+
+    if (fs.existsSync(thisDest) && options.no_force) {
+      common.error('dest file already exists: ' + thisDest, { continue: true });
+      return; // skip file
+    }
+
+    if (path.resolve(src) === path.dirname(path.resolve(thisDest))) {
+      common.error('cannot move to self: ' + src, { continue: true });
+      return; // skip file
+    }
+
+    try {
+      fs.renameSync(src, thisDest);
+    } catch (e) {
+      /* istanbul ignore next */
+      if (e.code === 'EXDEV') {
+        // If we're trying to `mv` to an external partition, we'll actually need
+        // to perform a copy and then clean up the original file. If either the
+        // copy or the rm fails with an exception, we should allow this
+        // exception to pass up to the top level.
+        cp('-r', src, thisDest);
+        rm('-rf', src);
+      }
+    }
+  }); // forEach(src)
+  return '';
+} // mv
+module.exports = _mv;

static/js/ketcher2/node_modules/shelljs/src/popd.js

@@ -0,0 +1 @@
+// see dirs.js

static/js/ketcher2/node_modules/shelljs/src/pushd.js

@@ -0,0 +1 @@
+// see dirs.js

static/js/ketcher2/node_modules/shelljs/src/pwd.js

@@ -0,0 +1,15 @@
+var path = require('path');
+var common = require('./common');
+
+common.register('pwd', _pwd, {
+  allowGlobbing: false,
+});
+
+//@
+//@ ### pwd()
+//@ Returns the current directory.
+function _pwd() {
+  var pwd = path.resolve(process.cwd());
+  return pwd;
+}
+module.exports = _pwd;

static/js/ketcher2/node_modules/shelljs/src/rm.js

@@ -0,0 +1,200 @@
+var common = require('./common');
+var fs = require('fs');
+
+common.register('rm', _rm, {
+  cmdOptions: {
+    'f': 'force',
+    'r': 'recursive',
+    'R': 'recursive',
+  },
+});
+
+// Recursively removes 'dir'
+// Adapted from https://github.com/ryanmcgrath/wrench-js
+//
+// Copyright (c) 2010 Ryan McGrath
+// Copyright (c) 2012 Artur Adib
+//
+// Licensed under the MIT License
+// http://www.opensource.org/licenses/mit-license.php
+function rmdirSyncRecursive(dir, force, fromSymlink) {
+  var files;
+
+  files = fs.readdirSync(dir);
+
+  // Loop through and delete everything in the sub-tree after checking it
+  for (var i = 0; i < files.length; i++) {
+    var file = dir + '/' + files[i];
+    var currFile = fs.lstatSync(file);
+
+    if (currFile.isDirectory()) { // Recursive function back to the beginning
+      rmdirSyncRecursive(file, force);
+    } else { // Assume it's a file - perhaps a try/catch belongs here?
+      if (force || isWriteable(file)) {
+        try {
+          common.unlinkSync(file);
+        } catch (e) {
+          /* istanbul ignore next */
+          common.error('could not remove file (code ' + e.code + '): ' + file, {
+            continue: true,
+          });
+        }
+      }
+    }
+  }
+
+  // if was directory was referenced through a symbolic link,
+  // the contents should be removed, but not the directory itself
+  if (fromSymlink) return;
+
+  // Now that we know everything in the sub-tree has been deleted, we can delete the main directory.
+  // Huzzah for the shopkeep.
+
+  var result;
+  try {
+    // Retry on windows, sometimes it takes a little time before all the files in the directory are gone
+    var start = Date.now();
+
+    // TODO: replace this with a finite loop
+    for (;;) {
+      try {
+        result = fs.rmdirSync(dir);
+        if (fs.existsSync(dir)) throw { code: 'EAGAIN' };
+        break;
+      } catch (er) {
+        /* istanbul ignore next */
+        // In addition to error codes, also check if the directory still exists and loop again if true
+        if (process.platform === 'win32' && (er.code === 'ENOTEMPTY' || er.code === 'EBUSY' || er.code === 'EPERM' || er.code === 'EAGAIN')) {
+          if (Date.now() - start > 1000) throw er;
+        } else if (er.code === 'ENOENT') {
+          // Directory did not exist, deletion was successful
+          break;
+        } else {
+          throw er;
+        }
+      }
+    }
+  } catch (e) {
+    common.error('could not remove directory (code ' + e.code + '): ' + dir, { continue: true });
+  }
+
+  return result;
+} // rmdirSyncRecursive
+
+// Hack to determine if file has write permissions for current user
+// Avoids having to check user, group, etc, but it's probably slow
+function isWriteable(file) {
+  var writePermission = true;
+  try {
+    var __fd = fs.openSync(file, 'a');
+    fs.closeSync(__fd);
+  } catch (e) {
+    writePermission = false;
+  }
+
+  return writePermission;
+}
+
+function handleFile(file, options) {
+  if (options.force || isWriteable(file)) {
+    // -f was passed, or file is writable, so it can be removed
+    common.unlinkSync(file);
+  } else {
+    common.error('permission denied: ' + file, { continue: true });
+  }
+}
+
+function handleDirectory(file, options) {
+  if (options.recursive) {
+    // -r was passed, so directory can be removed
+    rmdirSyncRecursive(file, options.force);
+  } else {
+    common.error('path is a directory', { continue: true });
+  }
+}
+
+function handleSymbolicLink(file, options) {
+  var stats;
+  try {
+    stats = fs.statSync(file);
+  } catch (e) {
+    // symlink is broken, so remove the symlink itself
+    common.unlinkSync(file);
+    return;
+  }
+
+  if (stats.isFile()) {
+    common.unlinkSync(file);
+  } else if (stats.isDirectory()) {
+    if (file[file.length - 1] === '/') {
+      // trailing separator, so remove the contents, not the link
+      if (options.recursive) {
+        // -r was passed, so directory can be removed
+        var fromSymlink = true;
+        rmdirSyncRecursive(file, options.force, fromSymlink);
+      } else {
+        common.error('path is a directory', { continue: true });
+      }
+    } else {
+      // no trailing separator, so remove the link
+      common.unlinkSync(file);
+    }
+  }
+}
+
+function handleFIFO(file) {
+  common.unlinkSync(file);
+}
+
+//@
+//@ ### rm([options,] file [, file ...])
+//@ ### rm([options,] file_array)
+//@ Available options:
+//@
+//@ + `-f`: force
+//@ + `-r, -R`: recursive
+//@
+//@ Examples:
+//@
+//@ ```javascript
+//@ rm('-rf', '/tmp/*');
+//@ rm('some_file.txt', 'another_file.txt');
+//@ rm(['some_file.txt', 'another_file.txt']); // same as above
+//@ ```
+//@
+//@ Removes files.
+function _rm(options, files) {
+  if (!files) common.error('no paths given');
+
+  // Convert to array
+  files = [].slice.call(arguments, 1);
+
+  files.forEach(function (file) {
+    var lstats;
+    try {
+      var filepath = (file[file.length - 1] === '/')
+        ? file.slice(0, -1) // remove the '/' so lstatSync can detect symlinks
+        : file;
+      lstats = fs.lstatSync(filepath); // test for existence
+    } catch (e) {
+      // Path does not exist, no force flag given
+      if (!options.force) {
+        common.error('no such file or directory: ' + file, { continue: true });
+      }
+      return; // skip file
+    }
+
+    // If here, path exists
+    if (lstats.isFile()) {
+      handleFile(file, options);
+    } else if (lstats.isDirectory()) {
+      handleDirectory(file, options);
+    } else if (lstats.isSymbolicLink()) {
+      handleSymbolicLink(file, options);
+    } else if (lstats.isFIFO()) {
+      handleFIFO(file);
+    }
+  }); // forEach(file)
+  return '';
+} // rm
+module.exports = _rm;

static/js/ketcher2/node_modules/shelljs/src/sed.js

@@ -0,0 +1,86 @@
+var common = require('./common');
+var fs = require('fs');
+
+common.register('sed', _sed, {
+  globStart: 3, // don't glob-expand regexes
+  canReceivePipe: true,
+  cmdOptions: {
+    'i': 'inplace',
+  },
+});
+
+//@
+//@ ### sed([options,] search_regex, replacement, file [, file ...])
+//@ ### sed([options,] search_regex, replacement, file_array)
+//@ Available options:
+//@
+//@ + `-i`: Replace contents of 'file' in-place. _Note that no backups will be created!_
+//@
+//@ Examples:
+//@
+//@ ```javascript
+//@ sed('-i', 'PROGRAM_VERSION', 'v0.1.3', 'source.js');
+//@ sed(/.*DELETE_THIS_LINE.*\n/, '', 'source.js');
+//@ ```
+//@
+//@ Reads an input string from `files` and performs a JavaScript `replace()` on the input
+//@ using the given search regex and replacement string or function. Returns the new string after replacement.
+//@
+//@ Note:
+//@
+//@ Like unix `sed`, ShellJS `sed` supports capture groups. Capture groups are specified
+//@ using the `$n` syntax:
+//@
+//@ ```javascript
+//@ sed(/(\w+)\s(\w+)/, '$2, $1', 'file.txt');
+//@ ```
+function _sed(options, regex, replacement, files) {
+  // Check if this is coming from a pipe
+  var pipe = common.readFromPipe();
+
+  if (typeof replacement !== 'string' && typeof replacement !== 'function') {
+    if (typeof replacement === 'number') {
+      replacement = replacement.toString(); // fallback
+    } else {
+      common.error('invalid replacement string');
+    }
+  }
+
+  // Convert all search strings to RegExp
+  if (typeof regex === 'string') {
+    regex = RegExp(regex);
+  }
+
+  if (!files && !pipe) {
+    common.error('no files given');
+  }
+
+  files = [].slice.call(arguments, 3);
+
+  if (pipe) {
+    files.unshift('-');
+  }
+
+  var sed = [];
+  files.forEach(function (file) {
+    if (!fs.existsSync(file) && file !== '-') {
+      common.error('no such file or directory: ' + file, 2, { continue: true });
+      return;
+    }
+
+    var contents = file === '-' ? pipe : fs.readFileSync(file, 'utf8');
+    var lines = contents.split(/\r*\n/);
+    var result = lines.map(function (line) {
+      return line.replace(regex, replacement);
+    }).join('\n');
+
+    sed.push(result);
+
+    if (options.inplace) {
+      fs.writeFileSync(file, result, 'utf8');
+    }
+  });
+
+  return sed.join('\n');
+}
+module.exports = _sed;

static/js/ketcher2/node_modules/shelljs/src/set.js

@@ -0,0 +1,55 @@
+var common = require('./common');
+
+common.register('set', _set, {
+  allowGlobbing: false,
+  wrapOutput: false,
+});
+
+//@
+//@ ### set(options)
+//@ Available options:
+//@
+//@ + `+/-e`: exit upon error (`config.fatal`)
+//@ + `+/-v`: verbose: show all commands (`config.verbose`)
+//@ + `+/-f`: disable filename expansion (globbing)
+//@
+//@ Examples:
+//@
+//@ ```javascript
+//@ set('-e'); // exit upon first error
+//@ set('+e'); // this undoes a "set('-e')"
+//@ ```
+//@
+//@ Sets global configuration variables
+function _set(options) {
+  if (!options) {
+    var args = [].slice.call(arguments, 0);
+    if (args.length < 2) common.error('must provide an argument');
+    options = args[1];
+  }
+  var negate = (options[0] === '+');
+  if (negate) {
+    options = '-' + options.slice(1); // parseOptions needs a '-' prefix
+  }
+  options = common.parseOptions(options, {
+    'e': 'fatal',
+    'v': 'verbose',
+    'f': 'noglob',
+  });
+
+  if (negate) {
+    Object.keys(options).forEach(function (key) {
+      options[key] = !options[key];
+    });
+  }
+
+  Object.keys(options).forEach(function (key) {
+    // Only change the global config if `negate` is false and the option is true
+    // or if `negate` is true and the option is false (aka negate !== option)
+    if (negate !== options[key]) {
+      common.config[key] = options[key];
+    }
+  });
+  return;
+}
+module.exports = _set;

static/js/ketcher2/node_modules/shelljs/src/sort.js

@@ -0,0 +1,98 @@
+var common = require('./common');
+var fs = require('fs');
+
+common.register('sort', _sort, {
+  canReceivePipe: true,
+  cmdOptions: {
+    'r': 'reverse',
+    'n': 'numerical',
+  },
+});
+
+// parse out the number prefix of a line
+function parseNumber(str) {
+  var match = str.match(/^\s*(\d*)\s*(.*)$/);
+  return { num: Number(match[1]), value: match[2] };
+}
+
+// compare two strings case-insensitively, but examine case for strings that are
+// case-insensitive equivalent
+function unixCmp(a, b) {
+  var aLower = a.toLowerCase();
+  var bLower = b.toLowerCase();
+  return (aLower === bLower ?
+      -1 * a.localeCompare(b) : // unix sort treats case opposite how javascript does
+      aLower.localeCompare(bLower));
+}
+
+// compare two strings in the fashion that unix sort's -n option works
+function numericalCmp(a, b) {
+  var objA = parseNumber(a);
+  var objB = parseNumber(b);
+  if (objA.hasOwnProperty('num') && objB.hasOwnProperty('num')) {
+    return ((objA.num !== objB.num) ?
+        (objA.num - objB.num) :
+        unixCmp(objA.value, objB.value));
+  } else {
+    return unixCmp(objA.value, objB.value);
+  }
+}
+
+//@
+//@ ### sort([options,] file [, file ...])
+//@ ### sort([options,] file_array)
+//@ Available options:
+//@
+//@ + `-r`: Reverse the result of comparisons
+//@ + `-n`: Compare according to numerical value
+//@
+//@ Examples:
+//@
+//@ ```javascript
+//@ sort('foo.txt', 'bar.txt');
+//@ sort('-r', 'foo.txt');
+//@ ```
+//@
+//@ Return the contents of the files, sorted line-by-line. Sorting multiple
+//@ files mixes their content, just like unix sort does.
+function _sort(options, files) {
+  // Check if this is coming from a pipe
+  var pipe = common.readFromPipe();
+
+  if (!files && !pipe) common.error('no files given');
+
+  files = [].slice.call(arguments, 1);
+
+  if (pipe) {
+    files.unshift('-');
+  }
+
+  var lines = [];
+  files.forEach(function (file) {
+    if (file !== '-') {
+      if (!fs.existsSync(file)) {
+        common.error('no such file or directory: ' + file, { continue: true });
+        return;
+      } else if (fs.statSync(file).isDirectory()) {
+        common.error('read failed: ' + file + ': Is a directory', {
+          continue: true,
+        });
+        return;
+      }
+    }
+
+    var contents = file === '-' ? pipe : fs.readFileSync(file, 'utf8');
+    lines = lines.concat(contents.trimRight().split(/\r*\n/));
+  });
+
+  var sorted;
+  sorted = lines.sort(options.numerical ? numericalCmp : unixCmp);
+
+  if (options.reverse) {
+    sorted = sorted.reverse();
+  }
+
+  return sorted.join('\n') + '\n';
+}
+
+module.exports = _sort;

static/js/ketcher2/node_modules/shelljs/src/tail.js

@@ -0,0 +1,79 @@
+var common = require('./common');
+var fs = require('fs');
+
+common.register('tail', _tail, {
+  canReceivePipe: true,
+  cmdOptions: {
+    'n': 'numLines',
+  },
+});
+
+//@
+//@ ### tail([{'-n': \<num\>},] file [, file ...])
+//@ ### tail([{'-n': \<num\>},] file_array)
+//@ Available options:
+//@
+//@ + `-n <num>`: Show the last `<num>` lines of the files
+//@
+//@ Examples:
+//@
+//@ ```javascript
+//@ var str = tail({'-n': 1}, 'file*.txt');
+//@ var str = tail('file1', 'file2');
+//@ var str = tail(['file1', 'file2']); // same as above
+//@ ```
+//@
+//@ Read the end of a file.
+function _tail(options, files) {
+  var tail = [];
+  var pipe = common.readFromPipe();
+
+  if (!files && !pipe) common.error('no paths given');
+
+  var idx = 1;
+  if (options.numLines === true) {
+    idx = 2;
+    options.numLines = Number(arguments[1]);
+  } else if (options.numLines === false) {
+    options.numLines = 10;
+  }
+  options.numLines = -1 * Math.abs(options.numLines);
+  files = [].slice.call(arguments, idx);
+
+  if (pipe) {
+    files.unshift('-');
+  }
+
+  var shouldAppendNewline = false;
+  files.forEach(function (file) {
+    if (file !== '-') {
+      if (!fs.existsSync(file)) {
+        common.error('no such file or directory: ' + file, { continue: true });
+        return;
+      } else if (fs.statSync(file).isDirectory()) {
+        common.error("error reading '" + file + "': Is a directory", {
+          continue: true,
+        });
+        return;
+      }
+    }
+
+    var contents = file === '-' ? pipe : fs.readFileSync(file, 'utf8');
+
+    var lines = contents.split('\n');
+    if (lines[lines.length - 1] === '') {
+      lines.pop();
+      shouldAppendNewline = true;
+    } else {
+      shouldAppendNewline = false;
+    }
+
+    tail = tail.concat(lines.slice(options.numLines));
+  });
+
+  if (shouldAppendNewline) {
+    tail.push(''); // to add a trailing newline once we join
+  }
+  return tail.join('\n');
+}
+module.exports = _tail;

static/js/ketcher2/node_modules/shelljs/src/tempdir.js

@@ -0,0 +1,60 @@
+var common = require('./common');
+var os = require('os');
+var fs = require('fs');
+
+common.register('tempdir', _tempDir, {
+  allowGlobbing: false,
+  wrapOutput: false,
+});
+
+// Returns false if 'dir' is not a writeable directory, 'dir' otherwise
+function writeableDir(dir) {
+  if (!dir || !fs.existsSync(dir)) return false;
+
+  if (!fs.statSync(dir).isDirectory()) return false;
+
+  var testFile = dir + '/' + common.randomFileName();
+  try {
+    fs.writeFileSync(testFile, ' ');
+    common.unlinkSync(testFile);
+    return dir;
+  } catch (e) {
+    /* istanbul ignore next */
+    return false;
+  }
+}
+
+
+//@
+//@ ### tempdir()
+//@
+//@ Examples:
+//@
+//@ ```javascript
+//@ var tmp = tempdir(); // "/tmp" for most *nix platforms
+//@ ```
+//@
+//@ Searches and returns string containing a writeable, platform-dependent temporary directory.
+//@ Follows Python's [tempfile algorithm](http://docs.python.org/library/tempfile.html#tempfile.tempdir).
+function _tempDir() {
+  var state = common.state;
+  if (state.tempDir) return state.tempDir; // from cache
+
+  state.tempDir = writeableDir(os.tmpdir && os.tmpdir()) || // node 0.10+
+                  writeableDir(os.tmpDir && os.tmpDir()) || // node 0.8+
+                  writeableDir(process.env.TMPDIR) ||
+                  writeableDir(process.env.TEMP) ||
+                  writeableDir(process.env.TMP) ||
+                  writeableDir(process.env.Wimp$ScrapDir) || // RiscOS
+                  writeableDir('C:\\TEMP') || // Windows
+                  writeableDir('C:\\TMP') || // Windows
+                  writeableDir('\\TEMP') || // Windows
+                  writeableDir('\\TMP') || // Windows
+                  writeableDir('/tmp') ||
+                  writeableDir('/var/tmp') ||
+                  writeableDir('/usr/tmp') ||
+                  writeableDir('.'); // last resort
+
+  return state.tempDir;
+}
+module.exports = _tempDir;

static/js/ketcher2/node_modules/shelljs/src/test.js

@@ -0,0 +1,84 @@
+var common = require('./common');
+var fs = require('fs');
+
+common.register('test', _test, {
+  cmdOptions: {
+    'b': 'block',
+    'c': 'character',
+    'd': 'directory',
+    'e': 'exists',
+    'f': 'file',
+    'L': 'link',
+    'p': 'pipe',
+    'S': 'socket',
+  },
+  wrapOutput: false,
+  allowGlobbing: false,
+});
+
+
+//@
+//@ ### test(expression)
+//@ Available expression primaries:
+//@
+//@ + `'-b', 'path'`: true if path is a block device
+//@ + `'-c', 'path'`: true if path is a character device
+//@ + `'-d', 'path'`: true if path is a directory
+//@ + `'-e', 'path'`: true if path exists
+//@ + `'-f', 'path'`: true if path is a regular file
+//@ + `'-L', 'path'`: true if path is a symbolic link
+//@ + `'-p', 'path'`: true if path is a pipe (FIFO)
+//@ + `'-S', 'path'`: true if path is a socket
+//@
+//@ Examples:
+//@
+//@ ```javascript
+//@ if (test('-d', path)) { /* do something with dir */ };
+//@ if (!test('-f', path)) continue; // skip if it's a regular file
+//@ ```
+//@
+//@ Evaluates expression using the available primaries and returns corresponding value.
+function _test(options, path) {
+  if (!path) common.error('no path given');
+
+  var canInterpret = false;
+  Object.keys(options).forEach(function (key) {
+    if (options[key] === true) {
+      canInterpret = true;
+    }
+  });
+
+  if (!canInterpret) common.error('could not interpret expression');
+
+  if (options.link) {
+    try {
+      return fs.lstatSync(path).isSymbolicLink();
+    } catch (e) {
+      return false;
+    }
+  }
+
+  if (!fs.existsSync(path)) return false;
+
+  if (options.exists) return true;
+
+  var stats = fs.statSync(path);
+
+  if (options.block) return stats.isBlockDevice();
+
+  if (options.character) return stats.isCharacterDevice();
+
+  if (options.directory) return stats.isDirectory();
+
+  if (options.file) return stats.isFile();
+
+  /* istanbul ignore next */
+  if (options.pipe) return stats.isFIFO();
+
+  /* istanbul ignore next */
+  if (options.socket) return stats.isSocket();
+
+  /* istanbul ignore next */
+  return false; // fallback
+} // test
+module.exports = _test;

static/js/ketcher2/node_modules/shelljs/src/to.js

@@ -0,0 +1,37 @@
+var common = require('./common');
+var fs = require('fs');
+var path = require('path');
+
+common.register('to', _to, {
+  pipeOnly: true,
+  wrapOutput: false,
+});
+
+//@
+//@ ### ShellString.prototype.to(file)
+//@
+//@ Examples:
+//@
+//@ ```javascript
+//@ cat('input.txt').to('output.txt');
+//@ ```
+//@
+//@ Analogous to the redirection operator `>` in Unix, but works with
+//@ ShellStrings (such as those returned by `cat`, `grep`, etc). _Like Unix
+//@ redirections, `to()` will overwrite any existing file!_
+function _to(options, file) {
+  if (!file) common.error('wrong arguments');
+
+  if (!fs.existsSync(path.dirname(file))) {
+    common.error('no such file or directory: ' + path.dirname(file));
+  }
+
+  try {
+    fs.writeFileSync(file, this.stdout || this.toString(), 'utf8');
+    return this;
+  } catch (e) {
+    /* istanbul ignore next */
+    common.error('could not write to file (code ' + e.code + '): ' + file, { continue: true });
+  }
+}
+module.exports = _to;

static/js/ketcher2/node_modules/shelljs/src/toEnd.js

@@ -0,0 +1,36 @@
+var common = require('./common');
+var fs = require('fs');
+var path = require('path');
+
+common.register('toEnd', _toEnd, {
+  pipeOnly: true,
+  wrapOutput: false,
+});
+
+//@
+//@ ### ShellString.prototype.toEnd(file)
+//@
+//@ Examples:
+//@
+//@ ```javascript
+//@ cat('input.txt').toEnd('output.txt');
+//@ ```
+//@
+//@ Analogous to the redirect-and-append operator `>>` in Unix, but works with
+//@ ShellStrings (such as those returned by `cat`, `grep`, etc).
+function _toEnd(options, file) {
+  if (!file) common.error('wrong arguments');
+
+  if (!fs.existsSync(path.dirname(file))) {
+    common.error('no such file or directory: ' + path.dirname(file));
+  }
+
+  try {
+    fs.appendFileSync(file, this.stdout || this.toString(), 'utf8');
+    return this;
+  } catch (e) {
+    /* istanbul ignore next */
+    common.error('could not append to file (code ' + e.code + '): ' + file, { continue: true });
+  }
+}
+module.exports = _toEnd;

static/js/ketcher2/node_modules/shelljs/src/touch.js

@@ -0,0 +1,110 @@
+var common = require('./common');
+var fs = require('fs');
+
+common.register('touch', _touch, {
+  cmdOptions: {
+    'a': 'atime_only',
+    'c': 'no_create',
+    'd': 'date',
+    'm': 'mtime_only',
+    'r': 'reference',
+  },
+});
+
+//@
+//@ ### touch([options,] file [, file ...])
+//@ ### touch([options,] file_array)
+//@ Available options:
+//@
+//@ + `-a`: Change only the access time
+//@ + `-c`: Do not create any files
+//@ + `-m`: Change only the modification time
+//@ + `-d DATE`: Parse DATE and use it instead of current time
+//@ + `-r FILE`: Use FILE's times instead of current time
+//@
+//@ Examples:
+//@
+//@ ```javascript
+//@ touch('source.js');
+//@ touch('-c', '/path/to/some/dir/source.js');
+//@ touch({ '-r': FILE }, '/path/to/some/dir/source.js');
+//@ ```
+//@
+//@ Update the access and modification times of each FILE to the current time.
+//@ A FILE argument that does not exist is created empty, unless -c is supplied.
+//@ This is a partial implementation of *[touch(1)](http://linux.die.net/man/1/touch)*.
+function _touch(opts, files) {
+  if (!files) {
+    common.error('no files given');
+  } else if (typeof files === 'string') {
+    files = [].slice.call(arguments, 1);
+  } else {
+    common.error('file arg should be a string file path or an Array of string file paths');
+  }
+
+  files.forEach(function (f) {
+    touchFile(opts, f);
+  });
+  return '';
+}
+
+function touchFile(opts, file) {
+  var stat = tryStatFile(file);
+
+  if (stat && stat.isDirectory()) {
+    // don't error just exit
+    return;
+  }
+
+  // if the file doesn't already exist and the user has specified --no-create then
+  // this script is finished
+  if (!stat && opts.no_create) {
+    return;
+  }
+
+  // open the file and then close it. this will create it if it doesn't exist but will
+  // not truncate the file
+  fs.closeSync(fs.openSync(file, 'a'));
+
+  //
+  // Set timestamps
+  //
+
+  // setup some defaults
+  var now = new Date();
+  var mtime = opts.date || now;
+  var atime = opts.date || now;
+
+  // use reference file
+  if (opts.reference) {
+    var refStat = tryStatFile(opts.reference);
+    if (!refStat) {
+      common.error('failed to get attributess of ' + opts.reference);
+    }
+    mtime = refStat.mtime;
+    atime = refStat.atime;
+  } else if (opts.date) {
+    mtime = opts.date;
+    atime = opts.date;
+  }
+
+  if (opts.atime_only && opts.mtime_only) {
+    // keep the new values of mtime and atime like GNU
+  } else if (opts.atime_only) {
+    mtime = stat.mtime;
+  } else if (opts.mtime_only) {
+    atime = stat.atime;
+  }
+
+  fs.utimesSync(file, atime, mtime);
+}
+
+module.exports = _touch;
+
+function tryStatFile(filePath) {
+  try {
+    return fs.statSync(filePath);
+  } catch (e) {
+    return null;
+  }
+}

static/js/ketcher2/node_modules/shelljs/src/uniq.js

@@ -0,0 +1,91 @@
+var common = require('./common');
+var fs = require('fs');
+
+// add c spaces to the left of str
+function lpad(c, str) {
+  var res = '' + str;
+  if (res.length < c) {
+    res = Array((c - res.length) + 1).join(' ') + res;
+  }
+  return res;
+}
+
+common.register('uniq', _uniq, {
+  canReceivePipe: true,
+  cmdOptions: {
+    'i': 'ignoreCase',
+    'c': 'count',
+    'd': 'duplicates',
+  },
+});
+
+//@
+//@ ### uniq([options,] [input, [output]])
+//@ Available options:
+//@
+//@ + `-i`: Ignore case while comparing
+//@ + `-c`: Prefix lines by the number of occurrences
+//@ + `-d`: Only print duplicate lines, one for each group of identical lines
+//@
+//@ Examples:
+//@
+//@ ```javascript
+//@ uniq('foo.txt');
+//@ uniq('-i', 'foo.txt');
+//@ uniq('-cd', 'foo.txt', 'bar.txt');
+//@ ```
+//@
+//@ Filter adjacent matching lines from input
+function _uniq(options, input, output) {
+  // Check if this is coming from a pipe
+  var pipe = common.readFromPipe();
+
+  if (!pipe) {
+    if (!input) common.error('no input given');
+
+    if (!fs.existsSync(input)) {
+      common.error(input + ': No such file or directory');
+    } else if (fs.statSync(input).isDirectory()) {
+      common.error("error reading '" + input + "'");
+    }
+  }
+  if (output && fs.existsSync(output) && fs.statSync(output).isDirectory()) {
+    common.error(output + ': Is a directory');
+  }
+
+  var lines = (input ? fs.readFileSync(input, 'utf8') : pipe).
+              trimRight().
+              split(/\r*\n/);
+
+  var compare = function (a, b) {
+    return options.ignoreCase ?
+           a.toLocaleLowerCase().localeCompare(b.toLocaleLowerCase()) :
+           a.localeCompare(b);
+  };
+  var uniqed = lines.reduceRight(function (res, e) {
+    // Perform uniq -c on the input
+    if (res.length === 0) {
+      return [{ count: 1, ln: e }];
+    } else if (compare(res[0].ln, e) === 0) {
+      return [{ count: res[0].count + 1, ln: e }].concat(res.slice(1));
+    } else {
+      return [{ count: 1, ln: e }].concat(res);
+    }
+  }, []).filter(function (obj) {
+                 // Do we want only duplicated objects?
+    return options.duplicates ? obj.count > 1 : true;
+  }).map(function (obj) {
+                 // Are we tracking the counts of each line?
+    return (options.count ? (lpad(7, obj.count) + ' ') : '') + obj.ln;
+  }).join('\n') + '\n';
+
+  if (output) {
+    (new common.ShellString(uniqed)).to(output);
+    // if uniq writes to output, nothing is passed to the next command in the pipeline (if any)
+    return '';
+  } else {
+    return uniqed;
+  }
+}
+
+module.exports = _uniq;

static/js/ketcher2/node_modules/shelljs/src/which.js

@@ -0,0 +1,99 @@
+var common = require('./common');
+var fs = require('fs');
+var path = require('path');
+
+common.register('which', _which, {
+  allowGlobbing: false,
+  cmdOptions: {
+    'a': 'all',
+  },
+});
+
+// XP's system default value for PATHEXT system variable, just in case it's not
+// set on Windows.
+var XP_DEFAULT_PATHEXT = '.com;.exe;.bat;.cmd;.vbs;.vbe;.js;.jse;.wsf;.wsh';
+
+// Cross-platform method for splitting environment PATH variables
+function splitPath(p) {
+  return p ? p.split(path.delimiter) : [];
+}
+
+function checkPath(pathName) {
+  return fs.existsSync(pathName) && !fs.statSync(pathName).isDirectory();
+}
+
+//@
+//@ ### which(command)
+//@
+//@ Examples:
+//@
+//@ ```javascript
+//@ var nodeExec = which('node');
+//@ ```
+//@
+//@ Searches for `command` in the system's PATH. On Windows, this uses the
+//@ `PATHEXT` variable to append the extension if it's not already executable.
+//@ Returns string containing the absolute path to the command.
+function _which(options, cmd) {
+  if (!cmd) common.error('must specify command');
+
+  var isWindows = process.platform === 'win32';
+  var pathEnv = process.env.path || process.env.Path || process.env.PATH;
+  var pathArray = splitPath(pathEnv);
+
+  var queryMatches = [];
+
+  // No relative/absolute paths provided?
+  if (cmd.indexOf('/') === -1) {
+    // Assume that there are no extensions to append to queries (this is the
+    // case for unix)
+    var pathExtArray = [''];
+    if (isWindows) {
+      // In case the PATHEXT variable is somehow not set (e.g.
+      // child_process.spawn with an empty environment), use the XP default.
+      var pathExtEnv = process.env.PATHEXT || XP_DEFAULT_PATHEXT;
+      pathExtArray = splitPath(pathExtEnv.toUpperCase());
+    }
+
+    // Search for command in PATH
+    for (var k = 0; k < pathArray.length; k++) {
+      // already found it
+      if (queryMatches.length > 0 && !options.all) break;
+
+      var attempt = path.resolve(pathArray[k], cmd);
+
+      if (isWindows) {
+        attempt = attempt.toUpperCase();
+      }
+
+      var match = attempt.match(/\.[^<>:"/\|?*.]+$/);
+      if (match && pathExtArray.indexOf(match[0]) >= 0) { // this is Windows-only
+        // The user typed a query with the file extension, like
+        // `which('node.exe')`
+        if (checkPath(attempt)) {
+          queryMatches.push(attempt);
+          break;
+        }
+      } else { // All-platforms
+        // Cycle through the PATHEXT array, and check each extension
+        // Note: the array is always [''] on Unix
+        for (var i = 0; i < pathExtArray.length; i++) {
+          var ext = pathExtArray[i];
+          var newAttempt = attempt + ext;
+          if (checkPath(newAttempt)) {
+            queryMatches.push(newAttempt);
+            break;
+          }
+        }
+      }
+    }
+  } else if (checkPath(cmd)) { // a valid absolute or relative path
+    queryMatches.push(path.resolve(cmd));
+  }
+
+  if (queryMatches.length > 0) {
+    return options.all ? queryMatches : queryMatches[0];
+  }
+  return options.all ? [] : null;
+}
+module.exports = _which;