jingqiong / ChemTSv2

Refined and extended version of ChemTS

ChemTSv2

ChemTSv2 is a refined and extended version of ChemTS[1]. The original implementation is available at https://github.com/tsudalab/ChemTS.

It provides:

• easy-to-run interface by using only a configuration file
• easy-to-define framework for users' any reward function, molecular filter, and tree policy
• various usage examples in the GitHub repository

[1] X. Yang, J. Zhang, K. Yoshizoe, K. Terayama, and K. Tsuda, "ChemTS: An Efficient Python Library for de novo Molecular Generation", Science and Technology of Advanced Materials, Vol.18, No.1, pp.972-976, 2017.

Requirements

1. python: 3.7
2. rdkit: 2021.03.5
3. tensorflow: 2.5.0
4. pyyaml
5. pandas
6. joblib
7. mpi4py: 3.0.3 (for massive parallel mode)

How to setup

Case 1: ChemTSv2 with single process mode

cd YOUR_WORKSPACE
python3.7 -m venv .venv
source .venv/bin/activate
pip install --upgrade chemtsv2

Case 2: ChemTSv2 with massive parallel mode

NOTE: You need to run ChemTSv2-MP on a server where OpenMPI or MPICH is installed. If you can't find mpiexec command, please consult your server administrator to install such an MPI library.

If you can use/prepare a server with MPI environment, please follow the (a) instruction; otherwise, please follow the (b) instruction.

(a) Installation on a server WITH a MPI environment

cd YOUR_WORKSPACE
python3.7 -m venv .venv
source .venv/bin/activate
pip install --upgrade chemtsv2
pip install mpi4py==3.0.3

(b) Installation on a server WITHOUT a MPI environment

conda create -n mpchem python=3.7
# swith to the `mpchem` environment
conda install -c conda-forge openmpi cxx-compiler mpi mpi4py=3.0.3
pip install --upgrade chemtsv2

How to run ChemTSv2

1. Clone this repository and move into it

git clone [e-mail]:molecule-generator-collection/ChemTSv2.git
cd ChemTSv2

2. (Optional) Train the RNN model

cd train_RNN
python train_RNN.py -c model_setting.yaml

If you want to use your trained model, please update chemtsv2/misc/load_model:loaded_model based on your model architecture.

3. (Optional) Create a config file for ChemTSv2

Please refer to the sample file (config/setting.yaml). If you want to pass any value to calc_reward_from_objective_values (e.g., weights for each value), add it in the config file.

4. Generate molecules

ChemTSv2 with single process mode

chemtsv2 -c config/setting.yaml

If you want to use GPU, run ChemTS with --gpu GPU_ID argument as follows.

chemtsv2 -c config/setting.yaml --gpu 0

ChemTSv2 with massive parallel mode

mpiexec -n 4 chemtsv2-mp --config config/setting_mp.yaml

Advanced usege

Extend user-specified SMILES

You can extend the SMILES string you input. In this case, you need to put the atom you want to extend at the end of the string and run ChemTS with --input_smiles argument as follows.

chemtsv2 -c config/setting.yaml --input_smiles 'C1=C(C)N=CC(N)=C1C'

Usage examples

1. Multiobjective optimization using Dscore

2. AutoDock Vina as reward function

License

This package is distributed under the MIT License.

Contact

• Shoichi Ishida ([e-mail])
• Kei Terayama ([e-mail]).