Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/benevolentAI/guacamol
Benchmarks for generative chemistry
https://github.com/benevolentAI/guacamol
Last synced: 3 months ago
JSON representation
Benchmarks for generative chemistry
- Host: GitHub
- URL: https://github.com/benevolentAI/guacamol
- Owner: BenevolentAI
- License: mit
- Created: 2018-11-16T12:45:21.000Z (almost 6 years ago)
- Default Branch: master
- Last Pushed: 2024-02-11T08:59:38.000Z (9 months ago)
- Last Synced: 2024-03-15T05:06:40.004Z (8 months ago)
- Language: Python
- Size: 95.7 KB
- Stars: 373
- Watchers: 15
- Forks: 81
- Open Issues: 14
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- top-life-sciences - **benevolentAI/guacamol** - 02-11 08:59:38 | (Ranked by starred repositories)
README
# GuacaMol
[](https://travis-ci.com/BenevolentAI/guacamol)
**GuacaMol** is an open source Python package for benchmarking of models for
*de novo* molecular design.
For an in-depth explanation of the types of benchmarks and baseline scores,
please consult our paper
[Benchmarking Models for De Novo Molecular Design](https://arxiv.org/abs/1811.09621)
## Installation
The easiest way to install `guacamol` is with `pip`:
```bash
pip install guacamol
```
Dependencies:
- `guacamol` requires the [RDKit library](http://rdkit.org/) (version `2018.09.1.0` or newer).
- We also depend on the [FCD](https://github.com/bioinf-jku/FCD) library (version `1.1`) for the calculation of the Fréchet ChemNet Distance.
#### Unit testing suite
You can test your installation of the guacamol benchmarking library by running the unit tests from this directory:
```bash
pytest .
```
## Benchmarking models
For the distribution-learning benchmarks, specialize `DistributionMatchingGenerator`
(from `guacamol.distribution_matching_generator`) for your model.
Instances of this class must be able to generate molecules similar to the training set.
For the actual benchmarks, call `assess_distribution_learning`
(from `guacamol.assess_distribution_learning`) with an instance of your class.
You must also provide the location of the training set file (See section "Data" below).
For the goal-directed benchmarks, specialize `GoalDirectedGenerator`
(from `guacamol.goal_directed_generator`) for your model.
Instances of this class must be able to generate a specified number of molecules
that achieve high scores for a given scoring function.
For the actual benchmarks, call `assess_goal_directed_generation`
(from `guacamol.assess_goal_directed_generation`) with an instance of your class.
Example implementations for baseline methods are available from https://github.com/BenevolentAI/guacamol_baselines.
In [guacamol_baselines](https://github.com/BenevolentAI/guacamol_baselines),
we provide a `Dockerfile` with an example environment for developing generative models and running guacamol.
## Data
For fairness in the evaluation of the benchmarks and comparability of the results,
you should use a training set containing molecules from the ChEMBL dataset.
Follow the procedure described below to get standardized datasets.
### Download
You can download pre-built datasets [here](https://figshare.com/projects/GuacaMol/56639):
md5 `05ad85d871958a05c02ab51a4fde8530` [training](https://ndownloader.figshare.com/files/13612760 )
md5 `e53db4bff7dc4784123ae6df72e3b1f0` [validation](https://ndownloader.figshare.com/files/13612766)
md5 `677b757ccec4809febd83850b43e1616` [test](https://ndownloader.figshare.com/files/13612757)
md5 `7d45bc95c33c10cb96ef5e78c38ac0b6` [all](https://ndownloader.figshare.com/files/13612745)
### Generation
To generate the training data yourself, run
```
python -m guacamol.data.get_data -o [output_directory]
```
which will download and process ChEMBL for you in your current folder.
This script will use the molecules from
[`holdout_set_gcm_v1.smiles`](https://github.com/BenevolentAI/guacamol/blob/master/guacamol/data/holdout_set_gcm_v1.smiles)
as a holdout set, and will exclude molecules very similar to these.
Different versions of your Python packages may lead to differences in the generated dataset, which will cause the script to fail.
See the section below ("Docker") to reproducibly generate the standardized dataset with the hashes given above.
### Docker
To be sure that you have the right dependencies you can build a Docker image, run from the top-level directory:
```
docker build -t guacamol-deps -f dockers/Dockerfile .
```
Then you can run:
```
docker run --rm -it -v `pwd`:/guacamol -w /guacamol guacamol-deps python -m guacamol.data.get_data -o guacamol/data
```
## Change log
- 1 May 2020: update version of FCD dependency
- 15 Oct 2020: pin dependencies since FCD does not
- 10 Nov 2021: relax pinned versions of keras, tensorflow & h5py dependencies
- 20 Dec 2021: expose forbidden symbols argument for custom smiles dataset filtering
## Leaderboard
See [https://www.benevolent.com/guacamol](https://www.benevolent.com/guacamol).