Update README.md

README.md

@@ -1,8 +1,14 @@
-Megladon: The Protoss Shark AI here to challenge!
-=================================================
+Cocktail Shaker: Drug Expansion and Enumeration for Peptides!
+=============================================================
 
-[![License: MPL 2.0](https://img.shields.io/badge/License-MPL%202.0-brightgreen.svg)](https://opensource.org/licenses/MPL-2.0))
+[![Build](https://travis-ci.org/Sulstice/Cocktail-Shaker.svg?branch=master)](https://travis-ci.org/Sulstice/Cocktail-Shaker)
+[![License: MPL 2.0](https://img.shields.io/badge/License-MPL%202.0-brightgreen.svg)](https://opensource.org/licenses/MPL-2.0)
+[![Coverage](https://coveralls.io/repos/github/Sulstice/Cocktail-Shaker/badge.svg?branch=master)](https://coveralls.io/github/Sulstice/Cocktail-Shaker?branch=master)
 ![Python](https://img.shields.io/badge/python-3.6-blue.svg)
+[![Gitter](https://badges.gitter.im/Cocktail-Shaker/community.svg)](https://gitter.im/Cocktail-Shaker/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
+[![Zenodo](https://zenodo.org/badge/170644606.svg)](https://zenodo.org/badge/latestdoi/170644606)
+[![Documentation Status](https://readthedocs.org/projects/cocktail-shaker/badge/?version=latest)](https://cocktail-shaker.readthedocs.io/en/latest/?badge=latest)
+[![status](https://joss.theoj.org/papers/c2e1d3c408a5729d832b34ac680d6305/status.svg)](https://joss.theoj.org/papers/c2e1d3c408a5729d832b34ac680d6305)
 
 <p align="center">
   <img width="200" height="300" src="images/logoshaker.png">
@@ -15,44 +21,99 @@ library**. cocktail-shaker leverages the computational power of
 Announcements
 =============
 
--   Work has began! March 2020
+-   **Release!** Version 1.0.0-beta, August 26, 2019
+-   **RDkit UGM 2019**: talk at September 25th at the University of
+    Hamburg, Germany.
 
-Using Megladon
+Using Cocktail Shaker
 =====================
 
-Megladon will be my starcraft 2 ai that will be publically avaliable for people to use freely in building their AI. As the project evolves and the megladon gains more power and success certain features of the bot will be non-disclosed (I expect it to go pro - high expectations for my bot). 
+cocktail-shaker is a young library under heavy development at this time.
+It targets two categories of users:
 
-Megladon's goals:
+1.  **Users familiar with RDKit**, or those willing to learn RDKit, who want to
+    create fast sets of data for high throughput screening or machine
+    learning.
+2.  **Open-Science Scientists without any knowledge of RDKit** who are
+    seeking a a high-level wrapper to create chemical files for their
+    software.
 
-- Become a grandmaster of the protoss race
+If you're in the first category, then you can already start using RDKit.
+cocktail-shaker offers a Pythonic, easy-to-use library and you can start
+channeling molecules in the expansion library. Instead of validating the
+sanity of the data, cocktail-shaker takes care of that for you. With
+each molecule being generated it will head into a 1D and/or 2D
+validation check (3D not supported yet).
+
+If you're in the second category, we're starting to build experimental
+high-level python code to take care a lot of the underpinnings of RDKit.
 
 Installation 
-============
+==================
+
+Cocktail-shaker runs on Python 3.5+ and within a conda environment due to the RDKit dependency. A conda installation is coming soon (as soon as I figure it out). 
+
+For the time being, here is the following:
+
+- [Anaconda](https://docs.anaconda.com/anaconda/install/)
+- [RDKit](https://www.rdkit.org/docs/Install.html) Version: 2019.09.1
+
+Cocktail shaker is distributed through PyPi and can be installed via:
+
+`your_env/bin/python -m pip install cocktail-shaker`
 
-Megladon will be running primarily with python 3.5+. As for now if you want to submit any PRs then please clone/fork this repository and follow the contribution guidelines. 
 
-The project will be under heavy development as I find the time to code it (response may be slow). 
+
+Development Installation
+========================
+
+As cocktail-shaker is under heavy development at this time, we highly
+recommend developers to use the development version on Github (master
+branch). You need to clone the repository and install cocktail-shaker with
+
+`python setup.py install`.
+
+As a one-liner, assuming git is installed:
 
     git clone https://github.com/Sulstice/Cocktail-Shaker.git
 
+This will automatically install the latest version of cocktail-shaker.
 
 Structure of cocktail-shaker
 ============================
 
 Currently, the main subpackages are:
 
--   **megladon**: starcraft 2 main ai package 
+-   **cocktail_shaker**: Contains a lot of the high level functionality; request
+    handling, file parsing/writing, enumeration, and expansion.
+-   **docs**: An access point for the readthedocs implementation.
+-   **cocktail_shaker/datasources**: This is where the system stores its data on
+    predfined functional groups and/or shapes (coming soon).
+-   **tests**: Tests that are for the file handling, requests, and
+    testing molecule pattern recognition.
+
+The API of all public interfaces are subject to change in the future,
+although **datasources** are *relatively* stable at this point.
 
 Genesis
 =======
 
-Megladon has started because I needed projects away from life sciences.
+cocktail-shaker began when one developer/scientist wanted an open source
+drug library.
 
 - Lead Developer [Suliman sharif](http://sulstice.github.io/)
+- Artwork [Elena Chow](http://www.chowelena.com/)
+- Technical Documentation [Rose Gierth](https://www.linkedin.com/in/rose-gierth-69a4a083/)
+- QA Tester [Marvin Corro](https://www.linkedin.com/in/marvincorro/)
+
+Now cocktail-shaker looks to build on the expertise of these
+developers/scientists and the broader open-science community to build an
+effective drug library.
 
 * * * * *
 
 External links
 ==============
 
+-   [Documentation](http://cocktail-shaker.readthedocs.org)