* Used to trigger all of the circle atoms within a molecule and all of the molecules within it to update their value. Used when the number of segments

* Sends the output of this molecule to be displayed in the 3D view.

* Send the value of this atom to the 3D display.

* Runs when a gitHub molecule menu option is clicked to show search bar.

* Stops nest and changes flag to not working

* Add a button to trigger the evolution process

* Generate a layered outline of the part where the tool will cut

* Grab values from the inputs and push them out to the input atoms.

* Add a constant to the list. Used as a callback from passing up the tree.

* Animation loop. Runs with every frame to draw the program on the display.

* Attaches a new connector to this ap * @param {object} connector - The connector to attach

* Defines bin which will be used to place parts for nested svg

* Starts propagation from this atom if it is not waiting for anything up stream.

* Breed the best performers in the population, cull the rest

* Take two individuals and breed them to form a new individual with a mix of their genes and mutations

* Walks through each of the atoms in this molecule and takes a census of how many there are and how many are currently waiting to be processed.

* Returns an array of length two indicating that this is one atom and if it is waiting to be computed

* Updates the value of the selected color and then the value.

* Creates the checkbox hidden menu when viewer is active. These really shouldn't be regenerated every time. They should just be hidden.

* When mouse moves and Ctrl is down updates value for box width and height

* Handles mouse click and move to expand the AP. Could this be done with a call to expand out? * @param {number} x - The x coordinate of the clic

* Gives this molecule inputs with the same names as all of it's parent's inputs

* Creates an editable UI representation of the bom list. * @param {Object} list - list is an object to which the generated HTML element will be

* Creates file upload button. Used in the sidebar. * @param {object} list - The HTML object to attach the new item to. * @param {object} par

* Creates a html representation of the passed text. Used in the sidebar. * @param {object} list - The HTML object to attach the new item to.

* Creates segment length slider and passes value to Global Variables

* Override super delete function to prevent output from being deleted

* A function to allow you to still call the delete function if needed.

* Creates markdown version of the readme content for this atom in the sidebar * @param {object} list - The HTML object to append the created elem

* Creates a simple BOM list which cannot be edited. The generated element is added to the passed list. * @param {object} list - The HTML object t

* Edit the atom's code when it is double clicked * @param {number} x - The X coordinate of the click * @param {number} y - The Y coordinate

* The function which is called when you press the download button.

* The function which is called when you press the download button.

* The function which is called when you press the download button. * Stops nest in progress and downloads file to computer. Only enabled if svg h

* Add the center dot to the molecule

* Draws the atom on the screen

* Draws the attachment point on the screen. Called with each frame.

* Draw the connector as a bezier curve on the screen

* Handles mouse click down. If the click is inside the AP it's connectors are selected if it is an input. * @param {number} cursorDistance - The

* Generate a random number between min and max

* Replace the currently displayed molecule with the parent of this molecule...moves the user up one level.

* Runs once when the program begins to initialize variables.

* Generate an initial population

* Set the atom's response to a key press. Is used to delete the atom if it is selected. * @param {string} key - The key which has been pressed.

* Sets all the input and output values to match their associated atoms.

* Triggers the loadTree process from this molecules output

* Checks if menu is open and changes class to trigger hiding of individual buttons

* Places a new connector within the molecule * @param {object} connectorObj - An object representation of the connector specifying its inputs and

* Runs when a menu option is clicked to place a new atom from searching on GitHub. * @param {object} ev - The event triggered by clicking on a me

* Runs when a menu option is clicked to place a new atom from the local atoms list. * @param {object} ev - The event triggered by click event on

* Selects a random color from an array. Where is this used? Can this be deleted? * @param {array} colors - An array of possible colors.

* Reload this github molecule from github

* Check to see if any of this molecules children have contributions to make to the README file. Children closer to the top left will be applied first.

* Return any contribution from this atom to the README file

* I'm not sure what this does. Can it be deleted?

* Runs when enter key is clicked and the input is focused to show results from search.

* Delineates bounds for selection box.

* Generates and returns a object representation of this molecule and all of its children.

* Restores the ap to it's default value.

* Set the current equation to be a new value.

* Called when the simplify check box is checked or unchecked.

* Starts the timer to retract the menu

* Starts nesting, replaces html svg for nested svg

* Turns geometry values into svg then starts nest and returns nested SVG

* Runs with each frame to draw the atom.

* Regenerate the list of constants we are evolving