├── LICENSE ├── README.md ├── antibody_scripts ├── antibody_finetune.py ├── antibody_finetune.sh ├── antibody_run.sh ├── antibody_train.py ├── humab25_eval.py ├── patent_eval.py ├── sample.py └── sample_for_anti_cdr.py ├── configs ├── antibody_finetune.yml ├── antibody_test.yml ├── antibody_train.yml ├── heavy_test.yml ├── heavy_train.yml └── training_nano_framework.yml ├── data ├── antibody_eval_data │ ├── HuAb348_data │ │ ├── humanization_pair_data_filter.csv │ │ ├── only_h_lab.fasta │ │ ├── only_l_lab.fasta │ │ ├── only_lk_lab.fasta │ │ ├── only_ll_lab.fasta │ │ ├── sample_t20_mouse_score.csv │ │ └── sample_t20_score.csv │ ├── Humab25_data │ │ ├── parental_mouse.csv │ │ ├── sample_experimental_t20_score.csv │ │ └── sample_mouse_t20_score.csv │ └── putative_data │ │ └── humanization_pair152.csv ├── fasta_file │ ├── 7k9i.fasta │ └── 7x2l.fasta ├── nanobody_eval_data │ ├── abnativ_select_vhh.csv │ └── nanobert_exp.csv └── train_sh_file │ ├── camel_data │ └── nano_download.sh │ ├── heavy_data │ └── unpair_download_selected.sh │ └── pair_data │ └── bulk_download.sh ├── dataset ├── abnativ_alignment │ ├── __init__.py │ ├── aho_consensus.py │ ├── align_and_clean.py │ ├── blossum.py │ ├── csv_dict.py │ ├── misc.py │ ├── mybio.py │ ├── parse_pdb.py │ ├── plotter.py │ └── structs.py ├── oas_dataset.py ├── oas_pair_dataset_new.py ├── oas_unpair_dataset_new.py └── preprocess.py ├── doc └── process.svg ├── environment.yaml ├── evaluation ├── ABLSTM_eval.py ├── Biophi_eval.py ├── T20_eval.py ├── Zscore_eval.py └── humab_eval.py ├── model ├── encoder │ ├── __init__.py │ ├── cross_attention.py │ ├── diffusion.py │ ├── model.py │ ├── modules.py │ ├── multihead_attention.py │ └── rotary_embedding.py └── nanoencoder │ ├── abnativ_model.py │ ├── abnativ_onehot.py │ ├── abnativ_scoring.py │ ├── abnativ_utils.py │ ├── abnativ_vq.py │ ├── attention.py │ └── model.py ├── nanobody_scripts ├── nano_eval.py ├── nanofinetune.py ├── nanofinetune_run.sh ├── nanosample.py ├── nanotrain.py ├── nanotrain_run.sh └── sample_for_nano_cdr.py ├── start_docker.sh └── utils ├── anti_numbering.py ├── evaluation.py ├── loss.py ├── misc.py ├── tokenizer.py ├── train_utils.py └── warmup.py /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TencentAI4S/HuDiff/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TencentAI4S/HuDiff/HEAD/README.md -------------------------------------------------------------------------------- /antibody_scripts/antibody_finetune.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TencentAI4S/HuDiff/HEAD/antibody_scripts/antibody_finetune.py -------------------------------------------------------------------------------- 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