synfrag 1.0.0
SynFrag: A Synthetic Accessibility Predictor based Fragment Assembly autoRegressive pretrain
License: MIT
Requires Python: >=3.8
Keywords: chemistry, molecular, synthesizability, synthetic accessibility, fragment assembly, deep learning, graph neural networks, cheminformatics, drug discovery, SMILES

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# SynFrag: Synthetic Accessibility via Fragment Assembly Generation
> Predict the synthetic accessibility of molecules like an experienced synthetic chemist
## 🎯 What Makes SynFrag Different
SynFrag revolutionizes synthetic accessibility prediction through **Pre-training strategy for generating molecules via fragment autoregressive assembly**. Unlike traditional approaches that directly learn synthesis patterns, SynFrag first masters molecular construction fundamentals—understanding how molecules are assembled from fragments—then applies this knowledge to predict synthetic accessibility.
### Two-Stage Learning:
* **Stage 1**: Pretrain on 9.2M unlabeled molecules to learn molecular assembly patterns
* **Stage 2**: Finetune on 800K labeled molecules for synthetic accessibility prediction

This mirrors human chemical intuition: experienced chemists understand molecular construction before assessing synthetic difficulty.

## ✨ Key Features
* Easy Integration - Simple CSV input/output format
* Batch Prediction - One-click synthetic accessibility scoring
* High Accuracy - Achieves SOTA performance on multiple test sets with key metrics including accuracy, AUROC and specificity.

## 🌐 Online Service
**Instant molecular synthesis prediction in the cloud.** Simply upload your CSV file with SMILES and receive AI-powered synthetic accessibility scores in seconds.

## 🚀 Quick Start
### 1. Installation
```python
    # Clone repository
    git clone https://github.com/simmzx/SynFrag.git
    cd ../SynFrag

    # Create environment and install dependencies
    conda create -n SynFrag python=3.8
    conda activate SynFrag
    pip install -r requirements.txt
```
### 2. Prepare Data
Create CSV file with "smiles" field:
molecule_id  | smiles|
:---------: | :--------:|
Palbociclib  | CC1=C(C(=O)N(C2=NC(=NC=C12)NC3=NC=C(C=C3)N4CCNCC4)C5CCCC5)C(=O)C |
(+)-Eburnamonine  | [C@]12(C3=C4CCN1CCC[C@@]2(CC(=O)N3C1C4=CC=CC=1)CC)[H] |
### 3. Run Prediction
CSV File Mode
```python
    python synfrag.py --input_file example.csv
```
Direct SMILES Mode
```python
    # Single molecule
    python synfrag.py --smiles "CCO"
    # Multiple molecules
    python synfrag.py --smiles "CCO" "CC(=O)O" "c1ccccc1"
```
### 4. View Results
Output file will contain SynFrag values:
| molecule_id | smiles  | synfrag |
| :------------: |:---------------:|:-----:|
| Palbociclib      | CC1=C(C(=O)N(C2=NC(=NC=C12)NC3=NC=C(C=C3)N4CCNCC4)C5CCCC5)C(=O)C | 0.9453 |
| (+)-Eburnamonine | [C@]12(C3=C4CCN1CCC[C@@]2(CC(=O)N3C1C4=CC=CC=1)CC)[H]        |    0.0286 |

**SynFrag Interpretation:**
* Close to 1: Easy to synthesize
- Close to 0: Hard to synthesize
* Threshold 0.5: Binary classification cutoff

## 📖 Advanced Usage
Custom Pretraining and Finetuning task
### Pretrain Model
```python
    python synfrag_pretrain.py \
        --dataset smiles.txt \
        --vocab fragment.txt 
```
Note: `smiles.txt` contains unlabeled molecules, `fragment.txt` is a fragment vocabulary generated by `./scripts/utils/mol/cls.py` from `smiles.txt` for fragment assembly autoregressive pretrain.

### Finetune Model
```python
    python synfrag_finetune.py \
        --input_model_file gnn_pretrained.pth \
        --dataset dataset.csv
```
Note: `gnn_pretrained.pth` is a model saved in pretraining stage, `dataset.csv` contains labeled molecules for finetune on specific downstream task.

## 🔧 Requirements
* Python 3.8-3.10
* CUDA-enabled GPU (recommended)
* Key dependencies: PyTorch, RDKit, DGL, DeepChem

## 📄 Citation
If this program is useful to you, please cite our paper:


## 📧 Contact
For questions, please contact: Xiang Zhang (Email: zhangxiang@simm.ac.cn)
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