molli 0.99.1

Molecular toolbox library

molli 1.0: Molecular Toolbox Library

https://github.com/SEDenmarkLab/molli

Developed by:

• Alexander S. Shved
• Blake E. Ocampo
• Elena S. Burlova
• Casey L. Olen
• N. Ian Rinehart

S. E. Denmark Laboratory, University of Illinois, Urbana-Champaign

Copyright 2022-2023 The Board of Trustees of the University of Illinois. All Rights Reserved.

Installation and Building

Molli is designed to serve as both a pip package and a conda package. The main difference comes from the fact that several required components are unavailable from a normal pip distribution (openbabel, xtb/crest, etc).

Molli is both a pip and conda package. Technically, it is installable with both, but there are large differences described below. They boil down to pip's inability to install certain secondary dependencies.

Install as a pip package

This mode is not preferred, but allows easier debugging in certain cases. Please note that this installation may leave your conda environment (if you have one) in a broken state.

1. Download or clone the source code to <path_to_molli_src>
2. pip install <path_to_molli_src>

This way of installing also compiles molli external C++ code correctly.

Install as a conda package

TBD when conda channel becomes functional

Building

1. Create a new environment

conda config --set channel_priority flexible
conda config --append channels conda-forge

Testing installation

1. Run the following command from your terminal.

molli info

2. Perform unit tests (-v for verbose mode is optional):

python -m unittest molli_test -v

Install in development mode

pip install -e . --config-settings editable_mode=compat

Hello, World!

This section describes your first steps in molli package

Package structure

Benchmarks