Advanced Science [Paper] [arXiv]
Official github of Molecular generative model via retrosynthetically prepared chemical building block assembly by Seonghwan Seo*, Jaechang Lim, Woo Youn Kim. (Advanced Science)
This repository is improved version(BBARv2) of jaechang-hits/BBAR-pytorch which contains codes and model weights to reproduce the results in paper. You can find the updated architectures at architecture
.
If you have any problems or need help with the code, please add an issue or contact shwan0106@kaist.ac.kr.
@article{seo2023bbar,
title = {Molecular Generative Model via Retrosynthetically Prepared Chemical Building Block Assembly},
author = {Seo, Seonghwan and Lim, Jaechang and Kim, Woo Youn},
journal = {Advanced Science},
volume = {10},
number = {8},
pages = {2206674},
doi = {https://doi.org/10.1002/advs.202206674},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/advs.202206674},
}
- python=3.9
- PyTorch=1.12
- Tensorboard=2.11.0
- PyTorch Geometric=2.1.0
- Pandas=1.5.1
- RDKit=2022.3.5
- Parmap=1.6.0
Move to data/
directory. Initially, the structure of directory data/
is as follows.
├── data/
├── ZINC/ (ZINC15 Database)
│ ├── smiles/
│ │ ├── train.smi (https://github.com/wengong-jin/icml18-jtnn/tree/master/data/zinc/train.txt)
│ │ ├── valid.smi (https://github.com/wengong-jin/icml18-jtnn/tree/master/data/zinc/valid.txt)
│ │ └── test.smi (https://github.com/wengong-jin/icml18-jtnn/tree/master/data/zinc/test.txt)
│ ├── get_data.py
│ └── library.csv
└── 3CL_ZINC/ (Smina calculation result. (ligands: ZINC15, receptor: 7L13))
├── data.csv
├── split.csv
└── library.csv (Same to data/ZINC/library.csv)
data/ZINC/
,data/3CL_ZINC/
: Dataset which used in our paper.
Move to data/ZINC
directory, and run python get_data.py
. And then, data.csv
and split.csv
will be created. The dataset for 3CL docking is already prepared.
├── data/
├── ZINC/
├── smiles/
├── get_data.py
├── data.csv new!
├── split.csv new!
└── library.csv
For your own dataset, you need to prepare data.csv
and split.csv
as follows.
-
./data/<OWN-DATA>/data.csv
SMILES,Property1,Property2,... c1ccccc1,10.25,32.21,... C1CCCC1,35.1,251.2,... ...
- SMILES must be RDKit-readable.
- If you want to train a single molecule set with different properties, you don't have to configure datasets separately for each property. You need to configure just one dataset file which contains all of property information. For example,
ZINC/data.csv
contains information aboutmw
,logp
,tpsa
,qed
, and you can train the model with property or properties, e.g.mw
,[mw, logp, tpsa]
.
-
./data/<OWN-DATA>/split.csv
train,0 train,1 ... val,125 ... test,163 ...
- First column is data type (train, val, test), and second column is index of
data.csv
.
- First column is data type (train, val, test), and second column is index of
And then, you need to create a building block library. Go to root directory and run ./script/get_library.py
.
cd <ROOT-DIR>
python ./script/get_library.py \
--data_dir ./data/<OWN-DATA> \
--cpus <N-CPUS>
After this step, the structure of directory data/
is as follows.
├── data/
├── <OWN-DATA>/
├── data.csv
├── split.csv
└── library.csv new!
The model training requires less than 12 hours with 1 GPU(RTX2080) and 4 CPUs(Intel Xeon Gold 6234).
You can skip data processing during train by pre-processing data with ./script/preprocess.py
.
cd <ROOT-DIR>
python ./script/preprocess.py \
--data_dir ./data/<DATA-DIR> \
--cpus <N-CPUS>
After preprocessing step, the structure of directory data/
is as follows. data.csv
, split.csv
and library.csv
are required, and data.pkl
is optional.
├── data/
├── <DATA-DIR>/
├── data.csv
├── data.pkl new!
├── split.csv
└── library.csv
cd <ROOT-DIR>
python ./script/train.py -h
Training Script Format Example
Our training script reads model config files ./config/model.yaml
. You can change model size by modifying or creating new config files. You can find another arguments through running with -h
flag.
python ./script/train.py \
--name <exp-name> \
--exp_dir <exp-dir-name> \ # default: ./result/
--property <property1> <property2> ... \
--data_dir <DATA-DIR> \ # default: ./data/ZINC/
--model_config <model-config-path> # default: ./config/model.yaml
Example running script
python ./script/train.py \
--name 'logp-tpsa' \
--exp_dir ./result/ZINC/ \
--data_dir ./data/ZINC/ \
--property logp tpsa
python ./script/train.py \
--name '3cl_affinity' \
--exp_dir ./result/3cl_affinity/ \
--data_dir ./data/3CL_ZINC/ \
--property affinity
The model generates 20 to 30 molecules per 1 second with 1 CPU(Intel Xeon E5-2667 v4).
# Download Weights of pretrained models. (mw, logp, tpsa, qed, 3cl-affinity)
# Path: ./test/pretrained_model/
cd <ROOT-DIR>
sh ./download-weights.sh
cd <ROOT-DIR>
python ./script/sample.py -h
Example running script.
# Output directory path
mkdir ./result_sample
# Scaffold-based generation. => use `-s` or `--scaffold`
python sample.py \
-g ./test/generation_config/tpsa.yaml \
-s "c1ccccc1" \
--num_samples 100 \
--logp 6 \
-o ./result_sample/logp\=6.smi
# Scaffold-based generation. (From File) => use `-S` or `--scaffold_path`
python sample.py \
--generator_config ./test/generation_config/mw.yaml \
--scaffold_path ./test/start_scaffolds.smi \
--num_samples 100 \
--mw 300 \
--o ./result_sample/mw\=300.smi \
--seed 0 -q
Generator config (Yaml)
-
generator config format (
./config/generator.yaml
)# If library_builtin_model_path is not null, generator save or load library-builtin model. # The library-builtin model contains model parameters and library information. # (library information: SMILES and latent vector of building block) # During configuration process of generator, model vectorizes all building blocks in library. # This process requires about 30 seconds. With library-builtin model, this process is skipped. # When the file `library_builtin_model_path` exists, upper two parameters (`model_path`, `library_path`) are not needed. model_path: <MODEL_PATH> library_path: <LIBRARY_PATH> library_builtin_model_path: <LIBRARY_BUILTIN_MODEL_PATH> # optional # Required window_size: 2000 alpha: 0.75 max_iteration: 10
-
Example (
./test/generation_config/logp.yaml
)model_path: ./test/pretrained_model/logp.tar library_path: ./data/ZINC/library.csv library_builtin_model_path: ./test/builtin_model/logp.tar window_size: 2000 alpha: 0.75 max_iteration: 10