remove dependencies from master and move to separate branches

Author: andrewjmcgehee

LICENSE

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+![polyfold](src/resources/readme/thumb.png)
+
+PolyFold is an interactive visual simulator for distance-based protein folding 
+dynamics. The goal of PolyFold is to give citizen scientists and academic 
+scientists alike an intuitive and visually appealing tool which elucidates the
+process of folding proteins with common machine learning optimization 
+techniques in real time. It is the hope of the PolyFold team that this tool will 
+serve to fill out the gaps in the user's intuition and understanding of the way 
+certain types of proteins respond to certain types of optimization strategies.
+
+No prior scientific background is needed to work with PolyFold. It is built
+entirely with human intuition in mind.
+
+### How to Compile and Run the Source Code
+
+#### Using Make
+1. Run the following line to compile the code:
+```
+$ make
+```
+2. Run the following line to run the application:
+```
+$ make run
+```
+
+#### Using the JRE
+1. Run the following line to compile the code:
+```
+$ javac PolyFold.java
+```
+2. Run the following line to run the application:
+```
+$ java PolyFold
+```
+### Manual
+
+Upon opening PolyFold you will be greeted by a screen which looks similar to this:
+
+![polyfold splash screen](src/resources/readme/splash.png)
+
+You will notice that there is a menu bar and a tool bar at the top of the screen. Let's go through each item of the menu bar. 
+
+#### Menu Bar
+
+##### File Menu
+![file menu](src/resources/readme/file.png)
+
+The file menu contains options for opening ".rr" files and saving the current state of a folded protein in PolyFold as a ".pdb" file. 
+
+##### Edit Menu
+![edit menu](src/resources/readme/edit.png)
+
+The edit menu contains options to Undo and Redo changes made within PolyFold, as well as to Save or Load a named save state of a folded protein from the current PolyFold session.
+
+##### Window Menu
+![window menu](src/resources/readme/window.png)
+
+The window menu contains options for minimizing the current window or making it full screen.
+
+##### Configure Menu
+![configure menu](src/resources/readme/configure.png)
+
+The configure window contains options for changing the configuration of either the gradient descent or the Monte Carlo optimization strategies.
+
+##### Help Menu
+![help menu](src/resources/readme/help.png)
+
+The help menu contains an option for opening PolyFold's "About" window. This contains information about the application, authors, and license of PolyFold. It can also redirect you to PolyFold's website hosted on GitHub.
+
+Now let's explore the tool bar.
+
+#### Tool Bar
+
+![auto zoom button](src/resources/readme/autozoom.png)
+##### AutoZoom Button
+
+The AutoZoom button attempts to move the PolyFold camera such that the majority of the protein structure is rendered in the current frame. It can also be activated by pressing the "A" key. 
+
+![gradient descent button](src/resources/readme/gd.png)
+##### Gradient Descent Button
+
+The Gradient Descent button will start a gradient descent optimization on the current protein structure.
+
+![monte carlo button](src/resources/readme/mc.png)
+##### Monte Carlo Button
+
+The Monte Carlo button will start a Monte Carlo optimization on the current protein structure. 
+
+![undo button](src/resources/readme/undo.png)
+##### Undo Button
+
+The Undo button will undo the previous change that was applied to the current protein structure.
+
+![redo button](src/resources/readme/redo.png)
+##### Redo Button
+
+The Redo button will redo the previous change that was applied to the current protein structure.
+
+![info button](src/resources/readme/info.png)
+##### Info Button
+
+The Info button opens PolyFold's "About" window. This contains information about the application, authors, and license of PolyFold. It can also redirect you to PolyFold's website hosted on GitHub.

README.md

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+title: PolyFold
+description: An interactive visual simulator for distance-based protein folding dynamics
+logo: /src/resources/logo.png
+theme: jekyll-theme-slate
+google_analytics:
+show_downloads: true

_config.yml

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+/**************************** JAVA IMPORTS ************************************/
+import java.io.IOException;
+/*************************** JAVAFX IMPORTS ***********************************/
+import javafx.application.Application;
+import javafx.fxml.FXMLLoader;
+import javafx.scene.*;
+import javafx.stage.Stage;
+/***************************** PF IMPORTS *************************************/
+import pf.controllers.Controller;
+
+public class PolyFold extends Application {
+  /* Main function for FX apps */
+  @Override
+  public void start(Stage stage) throws IOException {
+    FXMLLoader loader = new FXMLLoader(
+        getClass().getResource("/fxml/main.fxml"));
+    Controller controller = new Controller(stage);
+    loader.setController(controller);
+    // Build main window
+    Parent root = loader.load();
+    Scene scene = new Scene(root, 1024, 768, true);
+    scene.getStylesheets().add("style/style.css");
+    stage.setTitle("PolyFold (Beta Version)");
+    stage.setScene(scene);
+    stage.show();
+    // Min dimensions must be set after stage is shown
+    stage.setMinWidth(stage.getWidth());
+    stage.setMinHeight(stage.getHeight());
+    // Show splash screen
+    controller.showSplash();
+  }
+
+  /* Ignored but necessary in FX apps */
+  public static void main(String[] args) { launch(args); }
+}

src/PolyFold.java

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+- Clean CSS
+- Clean FXML