diff --git a/README.md b/README.md index ec547d8..46c3cee 100644 --- 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 new file mode 100644 index 0000000..36cf921 --- /dev/null +++ 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 new file mode 100644 index 0000000..5019dc0 Binary files /dev/null and b/docs/gv.png differ diff --git a/docs/index.md b/docs/index.md index 09a55b4..1f0bff0 100644 --- 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 Molecular visualization programs available today are outdated, have +limited feature sets, and are not extensible due to their designs and the languages used.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 b/docs/manual/build.md similarity index 100% rename from docs/build.md rename to docs/manual/build.md diff --git a/docs/data.md b/docs/manual/data.md similarity index 100% rename from docs/data.md rename to docs/manual/data.md diff --git a/docs/manual/index.md b/docs/manual/index.md new file mode 100644 index 0000000..09a55b4 --- /dev/null +++ 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 b/docs/manual/intro.md similarity index 100% rename from docs/intro.md rename to docs/manual/intro.md diff --git a/docs/testing.md b/docs/manual/testing.md similarity index 100% rename from docs/testing.md rename to docs/manual/testing.md diff --git a/docs/usage.md b/docs/manual/usage.md similarity index 100% rename from docs/usage.md rename to docs/manual/usage.md diff --git a/docs/mesh.png b/docs/mesh.png new file mode 100644 index 0000000..6052909 Binary files /dev/null and b/docs/mesh.png differ diff --git a/docs/slice1.png b/docs/slice1.png new file mode 100644 index 0000000..5e3d47c Binary files /dev/null and b/docs/slice1.png differ diff --git a/docs/slice2.png b/docs/slice2.png new file mode 100644 index 0000000..4c99ebe Binary files /dev/null and b/docs/slice2.png differ