├── .codespell-whitelist.txt ├── .github ├── merge_rules.yaml └── workflows │ └── push.yaml ├── .gitignore ├── .gitmodules ├── .pre-commit-config.yaml ├── README.md ├── README.zh.md ├── conftest.py ├── docs ├── docs │ ├── CNAME │ ├── about │ │ ├── index.md │ │ ├── index.zh.md │ │ ├── license-faq.md │ │ ├── license-faq.zh.md │ │ ├── license.md │ │ ├── license.zh.md │ │ ├── privacy.md │ │ └── privacy.zh.md │ ├── data │ │ ├── dataset.md │ │ ├── index.md │ │ └── index.zh.md │ ├── datasets │ │ ├── archiveii.md │ │ ├── bprna_1m.md │ │ ├── bprna_new.md │ │ ├── bprna_spot.md │ │ ├── casp_rna.md │ │ ├── eternabench_cm.md │ │ ├── eternabench_external.md │ │ ├── eternabench_switch.md │ │ ├── gencode.md │ │ ├── index.md │ │ ├── index.zh.md │ │ ├── rfam.md │ │ ├── rivas.md │ │ ├── rnacentral.md │ │ ├── rnastralign.md │ │ └── ryos.md │ ├── index.md │ ├── index.zh.md │ ├── license-faq.md │ ├── license-faq.zh.md │ ├── license.md │ ├── license.zh.md │ ├── models │ │ ├── aido_rna.md │ │ ├── calm.md │ │ ├── configuration_utils.md │ │ ├── ernierna.md │ │ ├── index.md │ │ ├── index.zh.md │ │ ├── modeling_outputs.md │ │ ├── ribonanzanet.md │ │ ├── rinalmo.md │ │ ├── rnabert.md │ │ ├── rnaernie.md │ │ ├── rnafm.md │ │ ├── rnamsm.md │ │ ├── spliceai.md │ │ ├── splicebert.md │ │ ├── unirna.md │ │ ├── utrbert.md │ │ └── utrlm.md │ ├── modules │ │ ├── embeddings.md │ │ ├── embeddings.zh.md │ │ ├── heads.md │ │ ├── heads.zh.md │ │ ├── index.md │ │ └── index.zh.md │ ├── pipelines │ │ ├── index.md │ │ ├── index.zh.md │ │ └── rna_secondary_structure.md │ ├── tokenisers │ │ ├── dna.md │ │ ├── dot_bracket.md │ │ ├── index.md │ │ ├── index.zh.md │ │ ├── protein.md │ │ └── rna.md │ └── utils │ │ └── rna_secondary_structure.md ├── mkdocs.yml ├── overrides │ ├── assets │ │ ├── css │ │ │ ├── extra.css │ │ │ └── fonts.css │ │ ├── fonts │ │ │ ├── CascadiaCodePL.woff2 │ │ │ ├── HYQiHei.ttf │ │ │ ├── HelveticaNowDisplay.otf │ │ │ └── HelveticaWorld.ttf │ │ └── images │ │ │ ├── favicon.ico │ │ │ └── logo.png │ ├── javascripts │ │ ├── mathjax.js │ │ └── shortcuts.js │ └── main.html └── requirements.txt ├── examples ├── data │ ├── huggingface-datasets.py │ ├── local-file.py │ └── python-dict.py ├── models │ ├── direct-access.py │ ├── multimolecule-automodel.py │ ├── transformers-automodel.py │ └── vanilla.py └── pipelines │ └── rna-secondary-structure.py ├── license-faq.md ├── license-faq.zh.md ├── license.header ├── license.md ├── license.zh.md ├── licensing.sh ├── multimolecule ├── __init__.py ├── data │ ├── README.md │ ├── README.zh.md │ ├── __init__.py │ ├── dataset.py │ ├── registry.py │ └── utils.py ├── datasets │ ├── README.md │ ├── README.zh.md │ ├── archiveii │ │ ├── README.md │ │ └── archiveii.py │ ├── bprna_1m │ │ ├── README.md │ │ └── bprna_1m.py │ ├── bprna_new │ │ ├── README.md │ │ └── bprna_new.py │ ├── bprna_spot │ │ ├── README.md │ │ └── bprna_spot.py │ ├── casp_rna │ │ ├── README.md │ │ └── casp_rna.py │ ├── chanrg │ │ ├── README.md │ │ ├── RNArchitecture.csv │ │ ├── chanrg.py │ │ ├── database.yaml │ │ └── utils.py │ ├── conversion_utils.py │ ├── database_utils.py │ ├── eternabench_cm │ │ ├── README.md │ │ └── eternabench_cm.py │ ├── eternabench_external │ │ ├── README.md │ │ └── eternabench_external.py │ ├── eternabench_switch │ │ ├── README.md │ │ └── eternabench_switch.py │ ├── gencode │ │ ├── README.md │ │ └── gencode.py │ ├── rfam │ │ ├── README.md │ │ └── rfam.py │ ├── rivas │ │ ├── README.md │ │ └── rivas.py │ ├── rnacentral │ │ ├── README.md │ │ ├── database.yaml │ │ ├── modifications.py │ │ ├── rnacentral.py │ │ ├── secondary_structure.py │ │ └── utils.py │ ├── rnastralign │ │ ├── README.md │ │ └── rnastralign.py │ └── ryos │ │ ├── README.md │ │ └── ryos.py ├── defaults.py ├── models │ ├── README.md │ ├── README.zh.md │ ├── __init__.py │ ├── aido_rna │ │ ├── README.aido.rna-1.6b-cds.md │ │ ├── README.aido.rna-1.6b-ss.md │ │ ├── README.aido.rna-650m-cds.md │ │ ├── README.aido.rna-650m.md │ │ ├── README.md │ │ ├── __init__.py │ │ ├── configuration_aido_rna.py │ │ ├── convert_checkpoint.py │ │ └── modeling_aido_rna.py │ ├── calm │ │ ├── README.md │ │ ├── __init__.py │ │ ├── configuration_calm.py │ │ ├── convert_checkpoint.py │ │ └── modeling_calm.py │ ├── configuration_utils.py │ ├── conversion_utils.py │ ├── ernierna │ │ ├── README.ernierna-ss.md │ │ ├── README.md │ │ ├── __init__.py │ │ ├── configuration_ernierna.py │ │ ├── convert_checkpoint.py │ │ └── modeling_ernierna.py │ ├── modeling_auto.py │ ├── modeling_outputs.py │ ├── ribonanzanet │ │ ├── README.md │ │ ├── README.ribonanzanet-deg.md │ │ ├── README.ribonanzanet-drop.md │ │ ├── README.ribonanzanet-ss.md │ │ ├── __init__.py │ │ ├── configuration_ribonanzanet.py │ │ ├── convert_checkpoint.py │ │ └── modeling_ribonanzanet.py │ ├── rinalmo │ │ ├── README.md │ │ ├── README.rinalmo-mega.md │ │ ├── README.rinalmo-micro.md │ │ ├── __init__.py │ │ ├── configuration_rinalmo.py │ │ ├── convert_checkpoint.py │ │ └── modeling_rinalmo.py │ ├── rnabert │ │ ├── README.md │ │ ├── __init__.py │ │ ├── configuration_rnabert.py │ │ ├── convert_checkpoint.py │ │ └── modeling_rnabert.py │ ├── rnaernie │ │ ├── README.md │ │ ├── __init__.py │ │ ├── configuration_rnaernie.py │ │ ├── convert_checkpoint.py │ │ └── modeling_rnaernie.py │ ├── rnafm │ │ ├── README.md │ │ ├── README.mrnafm.md │ │ ├── README.rnafm-ss.md │ │ ├── __init__.py │ │ ├── configuration_rnafm.py │ │ ├── convert_checkpoint.py │ │ └── modeling_rnafm.py │ ├── rnamsm │ │ ├── README.md │ │ ├── __init__.py │ │ ├── configuration_rnamsm.py │ │ ├── convert_checkpoint.py │ │ └── modeling_rnamsm.py │ ├── spliceai │ │ ├── README.md │ │ ├── __init__.py │ │ ├── configuration_spliceai.py │ │ ├── convert_checkpoint.py │ │ └── modeling_spliceai.py │ ├── splicebert │ │ ├── README.md │ │ ├── __init__.py │ │ ├── configuration_splicebert.py │ │ ├── convert_checkpoint.py │ │ └── modeling_splicebert.py │ ├── unirna │ │ ├── README.md │ │ ├── README.unirna.l12.md │ │ ├── README.unirna.l24.md │ │ ├── README.unirna.l8.md │ │ ├── __init__.py │ │ ├── configuration_unirna.py │ │ ├── convert_checkpoint.py │ │ └── modeling_unirna.py │ ├── utrbert │ │ ├── README.md │ │ ├── __init__.py │ │ ├── configuration_utrbert.py │ │ ├── convert_checkpoint.py │ │ └── modeling_utrbert.py │ └── utrlm │ │ ├── README.md │ │ ├── __init__.py │ │ ├── configuration_utrlm.py │ │ ├── convert_checkpoint.py │ │ └── modeling_utrlm.py ├── modules │ ├── README.md │ ├── README.zh.md │ ├── __init__.py │ ├── backbones │ │ ├── __init__.py │ │ ├── registry.py │ │ ├── sequence.py │ │ └── sequences │ │ │ ├── __init__.py │ │ │ ├── onehot.py │ │ │ └── registry.py │ ├── criterions │ │ ├── __init__.py │ │ ├── binary.py │ │ ├── generic.py │ │ ├── multiclass.py │ │ ├── multilabel.py │ │ ├── registry.py │ │ └── regression.py │ ├── embeddings │ │ ├── README.md │ │ ├── README.zh.md │ │ ├── __init__.py │ │ ├── registry.py │ │ ├── rotary.py │ │ └── sinusoidal.py │ ├── heads │ │ ├── README.md │ │ ├── README.zh.md │ │ ├── __init__.py │ │ ├── config.py │ │ ├── contact.py │ │ ├── generic.py │ │ ├── output.py │ │ ├── pretrain.py │ │ ├── registry.py │ │ ├── sequence.py │ │ ├── token.py │ │ └── transform.py │ ├── model.py │ ├── necks │ │ ├── __init__.py │ │ ├── bert.py │ │ ├── cat.py │ │ └── registry.py │ ├── networks │ │ ├── __init__.py │ │ ├── registry.py │ │ ├── resnet.py │ │ └── unet.py │ ├── normlizations.py │ └── registry.py ├── pipelines │ ├── README.md │ ├── README.zh.md │ ├── __init__.py │ └── rna_secondary_structure.py ├── tasks │ ├── __init__.py │ └── task.py ├── tokenisers │ ├── README.md │ ├── README.zh.md │ ├── __init__.py │ ├── alphabet.py │ ├── dna │ │ ├── ALPHABET.md │ │ ├── README.md │ │ ├── __init__.py │ │ ├── tokenization_dna.py │ │ └── utils.py │ ├── dot_bracket │ │ ├── ALPHABET.md │ │ ├── README.md │ │ ├── __init__.py │ │ ├── tokenization_db.py │ │ └── utils.py │ ├── protein │ │ ├── ALPHABET.md │ │ ├── README.md │ │ ├── __init__.py │ │ ├── tokenization_protein.py │ │ └── utils.py │ ├── rna │ │ ├── ALPHABET.md │ │ ├── README.md │ │ ├── __init__.py │ │ ├── tokenization_rna.py │ │ └── utils.py │ ├── tokenization_utils.py │ └── utils.py └── utils │ ├── __init__.py │ ├── parameters.py │ └── rna_secondary_structure.py ├── pyproject.toml ├── requirements.txt ├── setup.py ├── tests ├── data │ └── test_dataset.py ├── datasets │ └── test_database_utils.py ├── modules │ ├── criterions │ │ ├── test_binary.py │ │ ├── test_criterion.py │ │ ├── test_multiclass.py │ │ ├── test_multilabel.py │ │ └── test_regression.py │ ├── embeddings │ │ ├── test_rotary.py │ │ └── test_sinusoidal.py │ └── heads │ │ └── test_generic.py └── utils │ └── test_rna_secondary_structure.py └── tox.ini /.codespell-whitelist.txt: -------------------------------------------------------------------------------- 1 | datas 2 | ser 3 | marz 4 | manuel 5 | wass 6 | gir 7 | cna 8 | ine 9 | SorY 10 | -------------------------------------------------------------------------------- /.github/merge_rules.yaml: 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