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auto-qchem installation instructions

Prerequisite for Windows users only

Install openbabel binaries (comes with a GUI) https://github.com/openbabel/openbabel/releases/download/openbabel-2-4-1/OpenBabel-2.4.1.exe

Installation with Miniconda (Windows, MacOS)

Install the miniconda with python=3.7 suitable for your OS: miniconda installation webpage

In anaconda prompt (Windows) or terminal (MacOS) create a conda environment. You can use a different environment name, in this instructions we will use autoqchem. For Windows 'Anaconda Powershell Prompt' has more functionality than 'Anaconda Prompt', e.g. tab-completion, but either one works fine.

conda create --name autoqchem python=3.7

Activate the environment

conda activate autoqchem

Install mainstream python packages

conda install jupyter pandas scipy matplotlib pymongo pyyaml fabric xlrd appdirs openpyxl

Answer "y" to the questions. If you'd like to automatically say yes to all question you can add -y at the end of the command, e.g. conda install jupyter -y

Install openbabel v2.4.1 (v3.0.0 is available, but crashes on many structures) and rdkit

conda install -c conda-forge openbabel=2.4.1
conda install -c rdkit rdkit

Install imolecule (allows 3d rotateable renderings within jupyter), a specific version is required here

python -m pip install imolecule==0.1.13

Clone autoqchem from github. If you don't have git, please install git for your OS git installation webpage. Note that the last argument to the command below is a local directory to which auto-qchem will be installed, please update it to a suitable one. It can be anywhere, but it needs to either be empty or not yet existing. For the purpose of this instructions I will use some_directory. A good example would be ~/software/github/auto-qchem.

git clone https://github.com/PrincetonUniversity/auto-qchem.git some_directory

Navigate to the directory where auto-qchem github repository is installed (a file setup.py should be present in that directory) and run the setup script

cd some_directory
python setup.py install

That's it!

Verify the installation

Verify the installation by running a special template notebook framework_functionality_test.ipynb. It doesn't do a whole lot, but runs through some key functions.

Navigate to notebooks directory

cd some_directory/notebooks

Fire up jupyter-notebook

jupyter-notebook framework_functionality_test.ipynb

Run the notebook!