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SAFE is the deep learning molecular representation. It's an encoding leveraging a peculiarity in the decoding schemes of SMILES, to allow representation of molecules as a contiguous sequence of connected fragments. SAFE strings are valid SMILES strings, and thus are able to preserve the same amount of information. The intuitive representation of molecules as an ordered sequence of connected fragments greatly simplifies the following tasks often encountered in molecular design:

• de novo design
• superstructure generation
• scaffold decoration
• motif extension
• linker generation
• scaffold morphing.

The construction of a SAFE strings requires defining a molecular fragmentation algorithm. By default, we use [BRICS], but any other fragmentation algorithm can be used. The image below illustrates the process of building a SAFE string. The resulting string is a valid SMILES that can be read by datamol or RDKit.

You can install safe using pip:

pip install safe-mol

You can use conda/mamba:

mamba install -c conda-forge safe-mol

Please refer to the documentation, which contains tutorials for getting started with safe and detailed descriptions of the functions provided, as well as an example of how to get started with SAFE-GPT.

We summarize some key functions provided by the safe package below.

import safe

ibuprofen = "CC(Cc1ccc(cc1)C(C(=O)O)C)C"

# SMILES -> SAFE -> SMILES translation
try:
    ibuprofen_sf = safe.encode(ibuprofen)  # c12ccc3cc1.C3(C)C(=O)O.CC(C)C2
    ibuprofen_smi = safe.decode(ibuprofen_sf, canonical=True)  # CC(C)Cc1ccc(C(C)C(=O)O)cc1
except safe.EncoderError:
    pass
except safe.DecoderError:
    pass

ibuprofen_tokens = list(safe.split(ibuprofen_sf))

A command line interface is available to train a new model, please run safe-train --help. You can also provide an existing checkpoint to continue training or finetune on you own dataset.

For example:

safe-train --config <path to config> \
    --model-path <path to model> \
    --tokenizer  <path to tokenizer> \
    --dataset <path to dataset> \
    --num_labels 9 \
    --torch_compile True \
    --optim "adamw_torch" \
    --learning_rate 1e-5 \
    --prop_loss_coeff 1e-3 \
    --gradient_accumulation_steps 1 \
    --output_dir "<path to outputdir>" \
    --max_steps 5

If you use this repository, please cite the following related paper:

@misc{noutahi2023gotta,
      title={Gotta be SAFE: A New Framework for Molecular Design},
      author={Emmanuel Noutahi and Cristian Gabellini and Michael Craig and Jonathan S. C Lim and Prudencio Tossou},
      year={2023},
      eprint={2310.10773},
      archivePrefix={arXiv},
      primaryClass={cs.LG}
}

Note that all data and model weights of SAFE are exclusively licensed for research purposes. The accompanying dataset is licensed under CC BY 4.0, which permits solely non-commercial usage. See DATA_LICENSE for details.

This code base is licensed under the Apache-2.0 license. See LICENSE for details.

mamba create -n safe -f env.yml
mamba activate safe

pip install --no-deps -e .

You can run tests locally with:

pytest