├── .gitignore ├── README.md ├── deepec ├── data_loader.py ├── homology.py ├── model.py ├── process_data.py ├── train.py └── utils.py ├── environment.yml ├── example ├── mdh_ecoli.fa └── output │ ├── DeepECv2_result.txt │ └── tmp │ └── DL_prediction_result.txt ├── model ├── model.pth └── swissprot_enzyme_diamond.dmnd ├── run_DeepECtransformer_in_colab.ipynb └── run_deepectransformer.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kaistsystemsbiology/DeepProZyme/HEAD/.gitignore -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kaistsystemsbiology/DeepProZyme/HEAD/README.md -------------------------------------------------------------------------------- /deepec/data_loader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kaistsystemsbiology/DeepProZyme/HEAD/deepec/data_loader.py -------------------------------------------------------------------------------- /deepec/homology.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kaistsystemsbiology/DeepProZyme/HEAD/deepec/homology.py -------------------------------------------------------------------------------- /deepec/model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kaistsystemsbiology/DeepProZyme/HEAD/deepec/model.py -------------------------------------------------------------------------------- /deepec/process_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kaistsystemsbiology/DeepProZyme/HEAD/deepec/process_data.py -------------------------------------------------------------------------------- /deepec/train.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kaistsystemsbiology/DeepProZyme/HEAD/deepec/train.py -------------------------------------------------------------------------------- /deepec/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kaistsystemsbiology/DeepProZyme/HEAD/deepec/utils.py -------------------------------------------------------------------------------- /environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kaistsystemsbiology/DeepProZyme/HEAD/environment.yml -------------------------------------------------------------------------------- /example/mdh_ecoli.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kaistsystemsbiology/DeepProZyme/HEAD/example/mdh_ecoli.fa -------------------------------------------------------------------------------- /example/output/DeepECv2_result.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kaistsystemsbiology/DeepProZyme/HEAD/example/output/DeepECv2_result.txt -------------------------------------------------------------------------------- /example/output/tmp/DL_prediction_result.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kaistsystemsbiology/DeepProZyme/HEAD/example/output/tmp/DL_prediction_result.txt -------------------------------------------------------------------------------- /model/model.pth: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kaistsystemsbiology/DeepProZyme/HEAD/model/model.pth -------------------------------------------------------------------------------- /model/swissprot_enzyme_diamond.dmnd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kaistsystemsbiology/DeepProZyme/HEAD/model/swissprot_enzyme_diamond.dmnd -------------------------------------------------------------------------------- /run_DeepECtransformer_in_colab.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kaistsystemsbiology/DeepProZyme/HEAD/run_DeepECtransformer_in_colab.ipynb -------------------------------------------------------------------------------- /run_deepectransformer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kaistsystemsbiology/DeepProZyme/HEAD/run_deepectransformer.py --------------------------------------------------------------------------------