This repository contains the code for Direct Molecular Conformation Generation (DMCG).

Related tags

Deep LearningDMCG
Overview

Direct Molecular Conformation Generation

This repository contains the code for Direct Molecular Conformation Generation (DMCG).

Dataset

Download rdkit_folder.tar.gz from this url.

tar -xvf rdkit_folder.tar.gz

Requirements and Installation

  • PyTorch
  • Torch-Geometric

You can build a Docker image with the Dockerfile. To install DMCG and develop it locally

pip install -e . 

Train

The first time you run this code, you should specify the data path with --base-path, and the code will binarize data into binarized format.

bash run_training.sh --dropout 0.1 --use-bn --no-3drot  \
    --aux-loss 0.2 --num-layers 6 --lr 2e-4 --batch-size 128 --vae-beta-min 0.0001 --vae-beta-max 0.03 \
    --reuse-prior --node-attn --data-split confgf --pred-pos-residual \
    --dataset-name qm9 --remove-hs --shared-output  --base-path $yourdatapath

Test

python evaluate.py --dropout 0.1 --use-bn --lr-warmup --use-adamw --train-subset \
    --num-layers 6 --eval-from  $yourcktpath --workers 20 --batch-size 128 \
    --reuse-prior --node-attn --data-split confgf --dataset-name qm9 --remove-hs \
    --shared-output --pred-pos-residual --sample-beta 1.2
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