├── .gitignore ├── LICENSE ├── README.md ├── assets └── 8ac8.cif ├── checkpoints ├── SaProt │ ├── config.json │ └── vocab.txt ├── flan-t5-large │ ├── config.json │ ├── special_tokens_map.json │ ├── spiece.model │ ├── tokenizer.json │ └── tokenizer_config.json ├── flan-t5-xxl │ ├── config.json │ ├── special_tokens_map.json │ ├── spiece.model │ ├── tokenizer.json │ └── tokenizer_config.json ├── microsoft-BiomedNLP-PubMedBERT-base-uncased-abstract-v2 │ ├── config.json │ ├── tokenizer_config.json │ └── vocab.txt ├── microsoft-BiomedNLP-PubMedBERT-base-uncased-abstract │ ├── config.json │ ├── tokenizer_config.json │ └── vocab.txt ├── models--gpt2-huge │ ├── .no_exist │ │ └── 15ea56dee5df4983c59b2538573817e1667135e2 │ │ │ ├── adapter_config.json │ │ │ ├── added_tokens.json │ │ │ └── special_tokens_map.json │ ├── blobs │ │ └── 932bdee9f4b3878f7f285187564b46f256243aff │ ├── refs │ │ └── main │ └── snapshots │ │ └── 15ea56dee5df4983c59b2538573817e1667135e2 │ │ ├── config.json │ │ ├── model.safetensors │ │ └── vocab.json ├── models--gpt2-large │ ├── .no_exist │ │ └── 32b71b12589c2f8d625668d2335a01cac3249519 │ │ │ └── adapter_config.json │ ├── blobs │ │ └── 31587029033088429a7e344901883fa792f75bcc │ ├── refs │ │ └── main │ └── snapshots │ │ └── 32b71b12589c2f8d625668d2335a01cac3249519 │ │ ├── config.json │ │ └── vocab.json └── structure_tokenizer │ ├── tokenizer_config.json │ └── vocab.txt ├── models ├── SaProtIF.py ├── StructureTokenPredictionModel.py ├── __init__.py ├── abs_model.py ├── esm2 │ ├── __init__.py │ └── modeling_esm.py └── gpt2 │ ├── __init__.py │ ├── configuration_gpt2.py │ └── modeling_gpt2.py ├── requirements.txt └── utils ├── design_utils.py └── foldseek_utils.py /.gitignore: -------------------------------------------------------------------------------- 1 | __pycache__ 2 | assets/bin 3 | weights -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/README.md -------------------------------------------------------------------------------- /assets/8ac8.cif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/assets/8ac8.cif -------------------------------------------------------------------------------- /checkpoints/SaProt/config.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/checkpoints/SaProt/config.json -------------------------------------------------------------------------------- /checkpoints/SaProt/vocab.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/checkpoints/SaProt/vocab.txt -------------------------------------------------------------------------------- /checkpoints/flan-t5-large/config.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/checkpoints/flan-t5-large/config.json -------------------------------------------------------------------------------- /checkpoints/flan-t5-large/special_tokens_map.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/checkpoints/flan-t5-large/special_tokens_map.json -------------------------------------------------------------------------------- /checkpoints/flan-t5-large/spiece.model: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/checkpoints/flan-t5-large/spiece.model -------------------------------------------------------------------------------- /checkpoints/flan-t5-large/tokenizer.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/checkpoints/flan-t5-large/tokenizer.json -------------------------------------------------------------------------------- /checkpoints/flan-t5-large/tokenizer_config.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/checkpoints/flan-t5-large/tokenizer_config.json -------------------------------------------------------------------------------- /checkpoints/flan-t5-xxl/config.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/checkpoints/flan-t5-xxl/config.json -------------------------------------------------------------------------------- /checkpoints/flan-t5-xxl/special_tokens_map.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/checkpoints/flan-t5-xxl/special_tokens_map.json -------------------------------------------------------------------------------- /checkpoints/flan-t5-xxl/spiece.model: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/checkpoints/flan-t5-xxl/spiece.model -------------------------------------------------------------------------------- /checkpoints/flan-t5-xxl/tokenizer.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/checkpoints/flan-t5-xxl/tokenizer.json -------------------------------------------------------------------------------- /checkpoints/flan-t5-xxl/tokenizer_config.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/checkpoints/flan-t5-xxl/tokenizer_config.json -------------------------------------------------------------------------------- /checkpoints/microsoft-BiomedNLP-PubMedBERT-base-uncased-abstract-v2/config.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/checkpoints/microsoft-BiomedNLP-PubMedBERT-base-uncased-abstract-v2/config.json -------------------------------------------------------------------------------- /checkpoints/microsoft-BiomedNLP-PubMedBERT-base-uncased-abstract-v2/tokenizer_config.json: -------------------------------------------------------------------------------- 1 | { 2 | "do_lower_case": true 3 | } 4 | -------------------------------------------------------------------------------- /checkpoints/microsoft-BiomedNLP-PubMedBERT-base-uncased-abstract-v2/vocab.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/checkpoints/microsoft-BiomedNLP-PubMedBERT-base-uncased-abstract-v2/vocab.txt -------------------------------------------------------------------------------- /checkpoints/microsoft-BiomedNLP-PubMedBERT-base-uncased-abstract/config.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/checkpoints/microsoft-BiomedNLP-PubMedBERT-base-uncased-abstract/config.json -------------------------------------------------------------------------------- /checkpoints/microsoft-BiomedNLP-PubMedBERT-base-uncased-abstract/tokenizer_config.json: -------------------------------------------------------------------------------- 1 | { 2 | "do_lower_case": true 3 | } 4 | -------------------------------------------------------------------------------- /checkpoints/microsoft-BiomedNLP-PubMedBERT-base-uncased-abstract/vocab.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/checkpoints/microsoft-BiomedNLP-PubMedBERT-base-uncased-abstract/vocab.txt -------------------------------------------------------------------------------- /checkpoints/models--gpt2-huge/.no_exist/15ea56dee5df4983c59b2538573817e1667135e2/adapter_config.json: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /checkpoints/models--gpt2-huge/.no_exist/15ea56dee5df4983c59b2538573817e1667135e2/added_tokens.json: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /checkpoints/models--gpt2-huge/.no_exist/15ea56dee5df4983c59b2538573817e1667135e2/special_tokens_map.json: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /checkpoints/models--gpt2-huge/blobs/932bdee9f4b3878f7f285187564b46f256243aff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/checkpoints/models--gpt2-huge/blobs/932bdee9f4b3878f7f285187564b46f256243aff -------------------------------------------------------------------------------- /checkpoints/models--gpt2-huge/refs/main: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/checkpoints/models--gpt2-huge/refs/main -------------------------------------------------------------------------------- /checkpoints/models--gpt2-huge/snapshots/15ea56dee5df4983c59b2538573817e1667135e2/config.json: -------------------------------------------------------------------------------- 1 | ../../blobs/932bdee9f4b3878f7f285187564b46f256243aff -------------------------------------------------------------------------------- /checkpoints/models--gpt2-huge/snapshots/15ea56dee5df4983c59b2538573817e1667135e2/model.safetensors: -------------------------------------------------------------------------------- 1 | ../../blobs/0f8b28eb05a8075f48b61b6f35332978c74fc7763fa9fb4051a1c30511736a6a -------------------------------------------------------------------------------- /checkpoints/models--gpt2-huge/snapshots/15ea56dee5df4983c59b2538573817e1667135e2/vocab.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/checkpoints/models--gpt2-huge/snapshots/15ea56dee5df4983c59b2538573817e1667135e2/vocab.json -------------------------------------------------------------------------------- /checkpoints/models--gpt2-large/.no_exist/32b71b12589c2f8d625668d2335a01cac3249519/adapter_config.json: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /checkpoints/models--gpt2-large/blobs/31587029033088429a7e344901883fa792f75bcc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/checkpoints/models--gpt2-large/blobs/31587029033088429a7e344901883fa792f75bcc -------------------------------------------------------------------------------- /checkpoints/models--gpt2-large/refs/main: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/checkpoints/models--gpt2-large/refs/main -------------------------------------------------------------------------------- /checkpoints/models--gpt2-large/snapshots/32b71b12589c2f8d625668d2335a01cac3249519/config.json: -------------------------------------------------------------------------------- 1 | ../../blobs/31587029033088429a7e344901883fa792f75bcc -------------------------------------------------------------------------------- /checkpoints/models--gpt2-large/snapshots/32b71b12589c2f8d625668d2335a01cac3249519/vocab.json: -------------------------------------------------------------------------------- 1 | ../../blobs/1f1d9aaca301414e7f6c9396df506798ff4eb9a6 -------------------------------------------------------------------------------- /checkpoints/structure_tokenizer/tokenizer_config.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/checkpoints/structure_tokenizer/tokenizer_config.json -------------------------------------------------------------------------------- /checkpoints/structure_tokenizer/vocab.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/checkpoints/structure_tokenizer/vocab.txt -------------------------------------------------------------------------------- /models/SaProtIF.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/models/SaProtIF.py -------------------------------------------------------------------------------- /models/StructureTokenPredictionModel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/models/StructureTokenPredictionModel.py -------------------------------------------------------------------------------- /models/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/models/__init__.py -------------------------------------------------------------------------------- /models/abs_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/models/abs_model.py -------------------------------------------------------------------------------- /models/esm2/__init__.py: -------------------------------------------------------------------------------- 1 | from .modeling_esm import EsmForMaskedLM -------------------------------------------------------------------------------- /models/esm2/modeling_esm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/models/esm2/modeling_esm.py -------------------------------------------------------------------------------- /models/gpt2/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/models/gpt2/__init__.py -------------------------------------------------------------------------------- /models/gpt2/configuration_gpt2.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/models/gpt2/configuration_gpt2.py -------------------------------------------------------------------------------- /models/gpt2/modeling_gpt2.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/models/gpt2/modeling_gpt2.py -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/requirements.txt -------------------------------------------------------------------------------- /utils/design_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/utils/design_utils.py -------------------------------------------------------------------------------- /utils/foldseek_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/Denovo-Pinal/HEAD/utils/foldseek_utils.py --------------------------------------------------------------------------------