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ChemEnzyRetroPlanner_metadata
xiaoruiwang/ChemEnzyRetroPlanner_metadata
ChemEnzyRetroPlanner_metadata is a machine learning model from xiaoruiwang. Use it for the machine learning task on the model card, and read the license before you ship it in a product. The card lists the license as mit.
This repository hosts the model metadata and environment packages for the ChemEnzy-RetroPlanner platform — a hybrid organic–enzymatic synthesis planning system integrating multi-step retrosynthesis, enzyme recommendat…
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Updated Oct 10, 2025
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At a glance
- License
- mit
- Access
- Public
- Created
- Jan 14, 2025
- Updated
- Oct 10, 2025
- SHA
- b9ef6049
Model card
From the Hugging Face model README
🧪 ChemEnzy-RetroPlanner Metadata Repository
This repository hosts the model metadata and environment packages for the ChemEnzy-RetroPlanner platform — a hybrid organic–enzymatic synthesis planning system integrating multi-step retrosynthesis, enzyme recommendation, and active-site annotation.
The files here are required to fully reproduce the computational environment and pretrained models for the system’s various modules.
📦 Repository Contents
| File Name | Description | Size |
|---|---|---|
retro_planner_env.tar.gz | Prebuilt conda environment for the ChemEnzyRetroPlanner | 3.6 GB |
parrot_env.tar.gz | Prebuilt conda environment for the reaction condition predictor (Parrot) | 5.7 GB |
building_block_dataset.zip | Chemical building block dataset | 401 MB |
condition_predictor_metadata.zip | Metadata for the reaction condition predictor (RCR) | 144 MB |
easifa_metadata.zip | Metadata for the enzyme active site annotator (EasIFA) | 2.5 GB |
enzyme_cls_metadata.zip | Metadata for enzyme classification module (Enzymatic Reaction Identification Model & Enzyme Recommender) | 25.8 MB |
graph_retrosyn_metadata.zip | Graph-based single-step retrosynthesis metadata (Trained on USPTO-all-remapped) | 1.3 GB |
onmt_metadata.zip | Template-based retrosynthesis metadata (BioNavi-NP) | 549 MB |
rxn_filter_metadata.zip | Reaction filtering model metadata (Reaction Plausibility Evaluator) | 31 MB |
value_fun_metadata.zip | Value function for synthesis planning (Depth-based guiding function model) | 2 MB |
USPTO_condition.mar | Trained reaction condition predictor (Parrot) | 101 MB |
⚙️ Quick Installation Guide
1️⃣ Clone and Configure
git clone https://github.com/wangxr0526/ChemEnzyRetroPlanner.git
cd ChemEnzyRetroPlanner
chmod +x ./setup_ChemEnzyRetroPlanner.sh
./setup_ChemEnzyRetroPlanner.sh
Alternatively, you may use the provided auto-installation script (see below).
🧰 Automatic Setup Script
The repository includes a Bash script to automatically:
- Configure environment variables
- Download and unpack all required
.tar.gzand.zipfiles - Verify model existence before download
- Install ESM-2 pretrained weights (for enzyme feature extraction)
- Prepare the conda environment for immediate use
To execute:
bash setup_environment.sh
The script will:
- Create necessary directories under
$CONDA_HOME/envs - Unpack the prebuilt conda environment
retro_planner_env.tar.gz - Activate the environment
- Download and place metadata under
./metadata/ - Retrieve
structures.csv.gzfrom ChEBI for EasIFA integration
🧾 Dependencies
- Conda ≥ 23.0
- gdown, curl, wget, tar, unzip
All dependencies are pre-packaged within retro_planner_env.tar.gz.
🪄 Notes
- Some
.zipfiles contain large model weights; ensure sufficient disk space (>15 GB). - Certain files (e.g.,
onmt_metadata.zip) may be flagged as unsafe due topickleserialization — these are safe if used within the provided environment.
📬 Contact
For technical support or collaborative inquiries: 📧 [email protected] 🧩 Maintainer: Xiaorui Wang, Postdoctoral Research Fellow in Zhejiang University
- License
- mit
- Created
- Jan 14, 2025
- Updated
- Oct 10, 2025