Awesome
MolFrag
Our web server is freely available at https://dpai.ccnu.edu.cn/MolFrag/
Requirements
torch 1.13.1
dgl 1.0.1
dgllife 0.3.2
rdkit 2022.9.5
igraph 0.10.6
Usage
If you want to use DigFrag to segment drug (or pesticde) molecules, run these commands:
python segment_Drug.pyc --pred_path=mol.csv --model_path=BEST_DF_Drug.pth --frag_path=frag_drug.csv --image_path=./image_drugfrag
or
python segment_Pesticide.pyc --pred_path=mol.csv --model_path=BEST_DF_Pesticide.pth --frag_path=frag_pesticide.csv --image_path=./image_pesticidefrag
Where the first parameter is the molecules you want to segment, the second parameter is the trained model(which has been provided), the third parameter is the file where the results will be stored, and the fourth parameter is the folder where the fragment images will be generated.
If you want to use other methods to segment molecules, run these commands:
# BRICS
python main.py --smi_path=mol.smi --output=brics.csv --methods=Brics
or
# RECAP
python main.py --smi_path=mol.smi --output=recap.csv --methods=Recap
or
# MacFrag
python MacFrag.py -i mol.smi -o macfrag.csv -maxBlocks 6 -maxSR 8 -asMols False -minFragAtoms 1
Please note that the MacFrag code is sourced from Diao et al.