cs481-ekh · matthew-oberg · Apr 23, 2024 · Apr 20, 2024 · Apr 20, 2024 · Apr 20, 2024
diff --git a/README.md b/README.md
@@ -8,7 +8,7 @@ GoVizzy will work on any system with a supported version on Python and Pip insta
 Simply run the build.sh script, which will install all dependencies in a virtual environment, and launch GoVizzy.
 
 ## Documentation
-All of the documentation for GoVizzy can be found in the docs directory. See the [intro page](docs/intro.md).
+All of the documentation for GoVizzy can be found in the docs/manual directory. See the [intro page](docs/manual/intro.md).
 
 ## Testing
 

diff --git a/docs/_config.yml b/docs/_config.yml
@@ -0,0 +1,6 @@
+title: GoVizzy
+logo: gv.png
+description: GoVizzy is a program that generates interactive 3D renderings and 2D slices of molecules.
+remote_theme: pages-themes/minimal@v0.2.0
+plugins:
+- jekyll-remote-theme
diff --git a/docs/gv.png b/docs/gv.png
diff --git a/docs/index.md b/docs/index.md
@@ -1,14 +1,58 @@
-# GoVizzy Documentation
+---
+layout: default
+---
 
-## Intro
-All GoVizzy documentation takes the form of markdown files found in this directory.
+# GoVizzy - 2D and 3D Molecule Vizualization
 
-For a general overview of GoVizzy, see [intro](intro.md).
+## Abstract
 
-## Table of Contents
+Computational chemistry, as the name suggests, relies heavily on software. Displaying sets
+of molecules rendered in 3D and as 2D slices is a common method used by scientists to interpret
+and comprehend their data. Molecular visualization programs available today are outdated, have
+limited feature sets, and are not extensible due to their designs and the languages used.
+GoVizzy is a modern, user and developer friendly application for molecular visualization,
+built atop JupyterLab using standard Python libraries. GoVizzy is easily installed, used,
+tweaked, and expanded by chemists, many of whom already use and are familiar with
+Python and Jupyter. GoVizzy takes in data as standard .cube files, used by existing
+applications today. The data is displayed in a manipulatable 3D graph; it can be moved,
+zoomed, colored, and have elements made selectively visible. 2D slices of the visualizations
+can be made as well. GoVizzy’s modern design and user interface (UI), combined with a powerful
+featureset, make it an indispensable tool for computational chemistry research.
 
- - [Intro](intro.md)
- - [Build and Run](build.md)
- - [Basic Usage](usage.md)
- - [Data Import](data.md)
- - [Testing](testing.md)
+## Project Description
+
+GoVizzy is a Python module wrapped in a Jupyter Notebook UI that allows users to view multiple
+types of 3D renderings and 2D slices of molecules and atoms.
+
+Data is entered into GoVizzy in the standard .cube file format. The user is first presented with
+the slicing screen. This screen shows the 3D render of their .cube data, which can be interacted
+with in real time.
+
+![slicing screen](slice1.png "Slicing Screen")
+
+The user can then create and view 2D slices of the data. A slice plane exists for each axis, and
+each plane's visibility and location can be toggled individually. A set of three plots show the
+selected slice on each axis.
+
+![slicing screen](slice2.png "Slicing Screen")
+
+GoVizzy also supports mesh renderings of .cube files. In mesh mode, each individual atom can have
+its visibility and color set; chemical bonds are also configurable in the same way.
+
+![mesh screen](mesh.png "Mesh Screen")
+
+## Manual
+
+The user manual for GoVizzy can be found [here](manual/index.md).
+
+## GoVizzy Development
+
+GoVizzy was developed in the spring of 2024 as a Senior Design Project by four Boise State
+University Computer Science students. The project was sponsored by Dr. Oliviero Andreussi of
+the Boise State University Chemistry Department.
+
+### The Team
+ - Digno Teogalbo
+ - Brayden Thompson
+ - Rylie Walsh
+ - Matthew Oberg
diff --git a/docs/build.md → docs/manual/build.md b/docs/build.md → docs/manual/build.md
diff --git a/docs/data.md → docs/manual/data.md b/docs/data.md → docs/manual/data.md
diff --git a/docs/manual/index.md b/docs/manual/index.md
@@ -0,0 +1,14 @@
+# GoVizzy Documentation
+
+## Intro
+All GoVizzy documentation takes the form of markdown files found in this directory.
+
+For a general overview of GoVizzy, see [intro](intro.md).
+
+## Table of Contents
+
+ - [Intro](intro.md)
+ - [Build and Run](build.md)
+ - [Basic Usage](usage.md)
+ - [Data Import](data.md)
+ - [Testing](testing.md)
diff --git a/docs/intro.md → docs/manual/intro.md b/docs/intro.md → docs/manual/intro.md
diff --git a/docs/testing.md → docs/manual/testing.md b/docs/testing.md → docs/manual/testing.md
diff --git a/docs/usage.md → docs/manual/usage.md b/docs/usage.md → docs/manual/usage.md
diff --git a/docs/mesh.png b/docs/mesh.png
diff --git a/docs/slice1.png b/docs/slice1.png
diff --git a/docs/slice2.png b/docs/slice2.png