mindlessgen 0.4.0

Mindless Molecule GENerator

Mindless Molecule Generator

mindlessgen is a Python-based program for semi-automated generation of "mindless" small molecules, as described here. The rule-based algorithm places atoms randomly within the coordinate space and applies several optimization, fragment detection, and sanity check steps. The program is mainly controlled via a TOML configuration file, see below for details.

Installation

[!IMPORTANT] xtb (see here) has to be available on your machine, either via a conda-forge installation, a release binary, or compiled from source. If post-processing with DFT is desired, also orca (see here) has to be available.

Non-development purposes

The project can be simply installed in an existing virtual environment (by, e.g., conda or mamba (see also here and here)) with

pip install .

A matching Python environment can be set up and activated via the following command using the tools above:

mamba create -n mindlessgen python=3.12
mamba activate mindlessgen

Development purposes

For working on the code of mindlessgen, the following setup is recommended:

mamba create -n mindlessgen python=3.12
mamba activate mindlessgen
pip install -e '.[dev]'

Thereby, all necessary development tools (e.g., ruff, mypy, tox, pytest, and pre-commit) are installed. Before start to make changes in the code, activate the pre-commit hooks via:

pre-commit install

Before pushing a commit to the repository, please run also the optional tests, which depend on external dependencies like xtb, via

pytest -vv --optional

Further information on how to contribute to this project can also be found in the contribution guidelines.

Usage

[!WARNING] mindlessgen may still be subject to API changes.

mindlessgen can be executed after installation in the desired environment via:

mindlessgen -h

This command displays all command line options in the terminal. In addition, all commands are accessible via the TOML configuration file. The template configuration file in the root directory of the repository contains comprehensive explanations for each of the available configuration keys. If its path is not given via -c/--config, the configuration file "mindlessgen.toml" is searched in the following paths in ascending order:

1. Current working directory (e.g., $CWD)
2. Home directory (e.g., $USER/)

The active configuration can be printed using --print-config.

When using the program for academic purposes, please cite:

J. Chem. Theory Comput. 2009, 5, 4, 993–1003

or in BibTeX format:

@article{doi:10.1021/ct800511q,
author = {Korth, Martin and Grimme, Stefan},
title = {“Mindless” DFT Benchmarking},
journal = {Journal of Chemical Theory and Computation},
volume = {5},
number = {4},
pages = {993-1003},
year = {2009},
doi = {10.1021/ct800511q},
note ={PMID: 26609608},
URL = {https://doi.org/10.1021/ct800511q},
eprint = {https://doi.org/10.1021/ct800511q}
}

One-page overview

Acknowdledgements

T. Gasevic for creating an initial GitHub migration of the code and providing important adjustments to the workflow. S. Grimme and M. Korth for the original code written in Fortran associated to the publication in J. Chem. Theory Comput..