├── .gitignore ├── LICENSE ├── README.md ├── assets ├── acs.joc.5b01703-Scheme-c1.png ├── acs.oprd.5b00209-Scheme-c4.png ├── acs.orglett.5b01044-Table-c1.png ├── acs.orglett.6b01181-Scheme-c4.png ├── jacs.5b12989-Table-c3.png ├── model.png └── output │ ├── output0.png │ └── output1.png ├── data └── parse │ ├── dev.json │ ├── dois.txt │ ├── splits │ ├── dev0.json │ ├── dev1.json │ ├── dev2.json │ ├── dev3.json │ ├── dev4.json │ ├── test0.json │ ├── test1.json │ ├── test2.json │ ├── test3.json │ ├── test4.json │ ├── train0.json │ ├── train1.json │ ├── train2.json │ ├── train3.json │ └── train4.json │ └── train.json ├── evaluate.py ├── main.py ├── notebook ├── predict.ipynb └── visualize_data.ipynb ├── predict.py ├── requirements.txt ├── rxnscribe ├── __init__.py ├── data.py ├── dataset.py ├── evaluate.py ├── inference │ ├── __init__.py │ ├── beam_search.py │ ├── decode_strategy.py │ └── greedy_search.py ├── interface.py ├── loss.py ├── model.py ├── pix2seq │ ├── __init__.py │ ├── attention_layer.py │ ├── backbone.py │ ├── misc.py │ ├── pix2seq.py │ ├── position_encoding.py │ └── transformer.py ├── tokenizer.py ├── transformer │ ├── __init__.py │ ├── decoder.py │ ├── embedding.py │ └── swin_transformer.py ├── transforms.py └── utils.py ├── scripts ├── train_pix2seq_cv.sh └── train_pix2seq_full.sh └── setup.py /.gitignore: -------------------------------------------------------------------------------- 1 | scripts/*.sh 2 | **/__pycache__ 3 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/README.md -------------------------------------------------------------------------------- /assets/acs.joc.5b01703-Scheme-c1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/assets/acs.joc.5b01703-Scheme-c1.png -------------------------------------------------------------------------------- /assets/acs.oprd.5b00209-Scheme-c4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/assets/acs.oprd.5b00209-Scheme-c4.png -------------------------------------------------------------------------------- /assets/acs.orglett.5b01044-Table-c1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/assets/acs.orglett.5b01044-Table-c1.png -------------------------------------------------------------------------------- /assets/acs.orglett.6b01181-Scheme-c4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/assets/acs.orglett.6b01181-Scheme-c4.png -------------------------------------------------------------------------------- /assets/jacs.5b12989-Table-c3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/assets/jacs.5b12989-Table-c3.png -------------------------------------------------------------------------------- /assets/model.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/assets/model.png -------------------------------------------------------------------------------- /assets/output/output0.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/assets/output/output0.png -------------------------------------------------------------------------------- /assets/output/output1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/assets/output/output1.png -------------------------------------------------------------------------------- /data/parse/dev.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/data/parse/dev.json -------------------------------------------------------------------------------- /data/parse/dois.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/data/parse/dois.txt -------------------------------------------------------------------------------- /data/parse/splits/dev0.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/data/parse/splits/dev0.json -------------------------------------------------------------------------------- /data/parse/splits/dev1.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/data/parse/splits/dev1.json -------------------------------------------------------------------------------- /data/parse/splits/dev2.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/data/parse/splits/dev2.json -------------------------------------------------------------------------------- /data/parse/splits/dev3.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/data/parse/splits/dev3.json -------------------------------------------------------------------------------- /data/parse/splits/dev4.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/data/parse/splits/dev4.json -------------------------------------------------------------------------------- /data/parse/splits/test0.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/data/parse/splits/test0.json -------------------------------------------------------------------------------- /data/parse/splits/test1.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/data/parse/splits/test1.json -------------------------------------------------------------------------------- /data/parse/splits/test2.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/data/parse/splits/test2.json -------------------------------------------------------------------------------- /data/parse/splits/test3.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/data/parse/splits/test3.json -------------------------------------------------------------------------------- /data/parse/splits/test4.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/data/parse/splits/test4.json -------------------------------------------------------------------------------- /data/parse/splits/train0.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/data/parse/splits/train0.json -------------------------------------------------------------------------------- /data/parse/splits/train1.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/data/parse/splits/train1.json -------------------------------------------------------------------------------- /data/parse/splits/train2.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/data/parse/splits/train2.json -------------------------------------------------------------------------------- /data/parse/splits/train3.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/data/parse/splits/train3.json -------------------------------------------------------------------------------- /data/parse/splits/train4.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/data/parse/splits/train4.json -------------------------------------------------------------------------------- /data/parse/train.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/data/parse/train.json -------------------------------------------------------------------------------- /evaluate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/evaluate.py -------------------------------------------------------------------------------- /main.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/main.py -------------------------------------------------------------------------------- /notebook/predict.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/notebook/predict.ipynb -------------------------------------------------------------------------------- /notebook/visualize_data.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/notebook/visualize_data.ipynb -------------------------------------------------------------------------------- /predict.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/predict.py -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/requirements.txt -------------------------------------------------------------------------------- /rxnscribe/__init__.py: -------------------------------------------------------------------------------- 1 | from .interface import RxnScribe 2 | -------------------------------------------------------------------------------- /rxnscribe/data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/rxnscribe/data.py -------------------------------------------------------------------------------- /rxnscribe/dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/rxnscribe/dataset.py -------------------------------------------------------------------------------- /rxnscribe/evaluate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/rxnscribe/evaluate.py -------------------------------------------------------------------------------- /rxnscribe/inference/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/rxnscribe/inference/__init__.py -------------------------------------------------------------------------------- /rxnscribe/inference/beam_search.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/rxnscribe/inference/beam_search.py -------------------------------------------------------------------------------- /rxnscribe/inference/decode_strategy.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/rxnscribe/inference/decode_strategy.py -------------------------------------------------------------------------------- /rxnscribe/inference/greedy_search.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/rxnscribe/inference/greedy_search.py -------------------------------------------------------------------------------- /rxnscribe/interface.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/rxnscribe/interface.py -------------------------------------------------------------------------------- /rxnscribe/loss.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/rxnscribe/loss.py -------------------------------------------------------------------------------- /rxnscribe/model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/rxnscribe/model.py -------------------------------------------------------------------------------- /rxnscribe/pix2seq/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/rxnscribe/pix2seq/__init__.py -------------------------------------------------------------------------------- /rxnscribe/pix2seq/attention_layer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/rxnscribe/pix2seq/attention_layer.py -------------------------------------------------------------------------------- /rxnscribe/pix2seq/backbone.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/rxnscribe/pix2seq/backbone.py -------------------------------------------------------------------------------- /rxnscribe/pix2seq/misc.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/rxnscribe/pix2seq/misc.py -------------------------------------------------------------------------------- /rxnscribe/pix2seq/pix2seq.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/rxnscribe/pix2seq/pix2seq.py -------------------------------------------------------------------------------- /rxnscribe/pix2seq/position_encoding.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/rxnscribe/pix2seq/position_encoding.py -------------------------------------------------------------------------------- /rxnscribe/pix2seq/transformer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/rxnscribe/pix2seq/transformer.py -------------------------------------------------------------------------------- /rxnscribe/tokenizer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/rxnscribe/tokenizer.py -------------------------------------------------------------------------------- /rxnscribe/transformer/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/rxnscribe/transformer/__init__.py -------------------------------------------------------------------------------- /rxnscribe/transformer/decoder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/rxnscribe/transformer/decoder.py -------------------------------------------------------------------------------- /rxnscribe/transformer/embedding.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/rxnscribe/transformer/embedding.py -------------------------------------------------------------------------------- /rxnscribe/transformer/swin_transformer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/rxnscribe/transformer/swin_transformer.py -------------------------------------------------------------------------------- /rxnscribe/transforms.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/rxnscribe/transforms.py -------------------------------------------------------------------------------- /rxnscribe/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/rxnscribe/utils.py -------------------------------------------------------------------------------- /scripts/train_pix2seq_cv.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/scripts/train_pix2seq_cv.sh -------------------------------------------------------------------------------- /scripts/train_pix2seq_full.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/scripts/train_pix2seq_full.sh -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thomas0809/RxnScribe/HEAD/setup.py --------------------------------------------------------------------------------