├── README.md ├── all_checkpoints └── stage1 │ └── .gitignore ├── data ├── ChEBI-20_data │ ├── test.txt │ ├── test_filter.txt │ ├── train.txt │ └── validation.txt ├── PubChem324k │ ├── test.txt │ ├── train.txt │ └── valid.txt └── kv_data │ ├── test.txt │ ├── test_kv.txt │ ├── train.txt │ └── validation.txt ├── environment.yml ├── model ├── blip2.py ├── blip2_llama.py ├── blip2_opt.py ├── blip2_stage1.py ├── blip2_stage1_2.py ├── blip2qformer.py ├── blip2qformer_2.py ├── gin_model.py ├── gin_model_2.py └── help_funcs.py └── polymers ├── ckpt └── tmp-chebi-clip │ └── .gitignore ├── diffusion ├── __init__.py ├── constant.py ├── denoising_diffusion.py ├── evaluate_metric.py ├── optimizer.py └── torch_utils.py ├── evaluate_diffusion.py ├── get_vocab.py ├── gin_pretrained └── .gitignore ├── main.py ├── poly_hgraph ├── __init__.py ├── chemutils.py ├── dataset.py ├── decoder.py ├── encoder.py ├── gine_diffusion.py ├── hgnn.py ├── hgnn_clip.py ├── inc_graph.py ├── mol_graph.py ├── nnutils.py ├── rnn.py ├── transformer │ ├── diffusion_transformer.py │ └── x_transformer.py └── vocab.py ├── preprocess.py ├── preprocess_filter.py ├── results_chebi └── model-winoise100_train_decoder.pt ├── vae_train.py └── vocab_chebi_30 ├── fragment.txt └── vocab.txt /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huaishengzhu/3MDiffusion/HEAD/README.md -------------------------------------------------------------------------------- /all_checkpoints/stage1/.gitignore: -------------------------------------------------------------------------------- 1 | * 2 | !.gitignore 3 | *.ckpt -------------------------------------------------------------------------------- /data/ChEBI-20_data/test.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huaishengzhu/3MDiffusion/HEAD/data/ChEBI-20_data/test.txt 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