├── .gitattributes ├── .gitignore ├── README.md ├── dataset_pipeline.py ├── img ├── architecture_main.png ├── cas study.jpg └── result.png ├── metrics.py ├── src ├── args.py ├── data │ ├── CATH.py │ ├── build_vocab.py │ ├── cath_2nd.py │ ├── colabfold_output_process.py │ ├── data_proc.py │ ├── data_utils.py │ ├── dataloader.py │ ├── esmfold.py │ ├── extract_ss_embedding.py │ ├── foldseek_web.py │ └── protein_utils.py ├── decoder │ ├── diff_decoder.py │ ├── modules.py │ ├── multihead_attention.py │ ├── rotary_embedding.py │ ├── tokenizer.py │ └── vocab.txt ├── diffusion │ └── model_diffusion.py ├── embedding_pooling │ └── embedding_pooling.py ├── encoder_decoder │ └── encoder_decoder.py └── module │ └── egnn │ ├── egnn.py │ └── model.py ├── train_diff.py └── train_encoder_decoder.py /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ai4protein/CPDiffusion-SS/HEAD/.gitattributes -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ai4protein/CPDiffusion-SS/HEAD/.gitignore -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ai4protein/CPDiffusion-SS/HEAD/README.md -------------------------------------------------------------------------------- /dataset_pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ai4protein/CPDiffusion-SS/HEAD/dataset_pipeline.py -------------------------------------------------------------------------------- /img/architecture_main.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ai4protein/CPDiffusion-SS/HEAD/img/architecture_main.png -------------------------------------------------------------------------------- /img/cas study.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ai4protein/CPDiffusion-SS/HEAD/img/cas study.jpg -------------------------------------------------------------------------------- /img/result.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ai4protein/CPDiffusion-SS/HEAD/img/result.png -------------------------------------------------------------------------------- /metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ai4protein/CPDiffusion-SS/HEAD/metrics.py -------------------------------------------------------------------------------- /src/args.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ai4protein/CPDiffusion-SS/HEAD/src/args.py -------------------------------------------------------------------------------- /src/data/CATH.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ai4protein/CPDiffusion-SS/HEAD/src/data/CATH.py -------------------------------------------------------------------------------- /src/data/build_vocab.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ai4protein/CPDiffusion-SS/HEAD/src/data/build_vocab.py -------------------------------------------------------------------------------- /src/data/cath_2nd.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ai4protein/CPDiffusion-SS/HEAD/src/data/cath_2nd.py -------------------------------------------------------------------------------- /src/data/colabfold_output_process.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ai4protein/CPDiffusion-SS/HEAD/src/data/colabfold_output_process.py -------------------------------------------------------------------------------- /src/data/data_proc.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ai4protein/CPDiffusion-SS/HEAD/src/data/data_proc.py -------------------------------------------------------------------------------- /src/data/data_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ai4protein/CPDiffusion-SS/HEAD/src/data/data_utils.py -------------------------------------------------------------------------------- /src/data/dataloader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ai4protein/CPDiffusion-SS/HEAD/src/data/dataloader.py -------------------------------------------------------------------------------- /src/data/esmfold.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ai4protein/CPDiffusion-SS/HEAD/src/data/esmfold.py -------------------------------------------------------------------------------- /src/data/extract_ss_embedding.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ai4protein/CPDiffusion-SS/HEAD/src/data/extract_ss_embedding.py -------------------------------------------------------------------------------- /src/data/foldseek_web.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ai4protein/CPDiffusion-SS/HEAD/src/data/foldseek_web.py -------------------------------------------------------------------------------- /src/data/protein_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ai4protein/CPDiffusion-SS/HEAD/src/data/protein_utils.py -------------------------------------------------------------------------------- /src/decoder/diff_decoder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ai4protein/CPDiffusion-SS/HEAD/src/decoder/diff_decoder.py -------------------------------------------------------------------------------- /src/decoder/modules.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ai4protein/CPDiffusion-SS/HEAD/src/decoder/modules.py -------------------------------------------------------------------------------- /src/decoder/multihead_attention.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ai4protein/CPDiffusion-SS/HEAD/src/decoder/multihead_attention.py -------------------------------------------------------------------------------- /src/decoder/rotary_embedding.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ai4protein/CPDiffusion-SS/HEAD/src/decoder/rotary_embedding.py -------------------------------------------------------------------------------- /src/decoder/tokenizer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ai4protein/CPDiffusion-SS/HEAD/src/decoder/tokenizer.py -------------------------------------------------------------------------------- /src/decoder/vocab.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ai4protein/CPDiffusion-SS/HEAD/src/decoder/vocab.txt -------------------------------------------------------------------------------- /src/diffusion/model_diffusion.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ai4protein/CPDiffusion-SS/HEAD/src/diffusion/model_diffusion.py -------------------------------------------------------------------------------- /src/embedding_pooling/embedding_pooling.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ai4protein/CPDiffusion-SS/HEAD/src/embedding_pooling/embedding_pooling.py -------------------------------------------------------------------------------- /src/encoder_decoder/encoder_decoder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ai4protein/CPDiffusion-SS/HEAD/src/encoder_decoder/encoder_decoder.py -------------------------------------------------------------------------------- /src/module/egnn/egnn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ai4protein/CPDiffusion-SS/HEAD/src/module/egnn/egnn.py -------------------------------------------------------------------------------- /src/module/egnn/model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ai4protein/CPDiffusion-SS/HEAD/src/module/egnn/model.py -------------------------------------------------------------------------------- /train_diff.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ai4protein/CPDiffusion-SS/HEAD/train_diff.py -------------------------------------------------------------------------------- /train_encoder_decoder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ai4protein/CPDiffusion-SS/HEAD/train_encoder_decoder.py --------------------------------------------------------------------------------