LICENSE
MANIFEST.in
README.md
pyproject.toml
requirements.txt
setup.py
demos/demo_f1_recovery.py
demos/demo_lddt.py
demos/demo_rhodesign.py
demos/demo_rhofold.py
demos/demo_ribodiffusion.py
demos/demo_rmsd.py
demos/demo_rna_fm.py
demos/demo_rna_msm.py
demos/demo_similarity.py
demos/demo_tm_score.py
demos/configs/default.yaml
demos/configs/ribodiffusion.yaml
demos/configs/rna_fm.yaml
demos/dataset/demo_download_datasets.py
demos/input/2zh6_B.npy
demos/input/2zh6_B.pdb
demos/input/R1107.pdb
demos/input/rmsd_tests/conftest.py
demos/input/rmsd_tests/test_args.py
demos/input/rmsd_tests/test_centroid.py
demos/input/rmsd_tests/test_file_reading.py
demos/input/rmsd_tests/test_kabsch.py
demos/input/rmsd_tests/test_kabsch_weighted.py
demos/input/rmsd_tests/test_main.py
demos/input/rmsd_tests/test_pdb.py
demos/input/rmsd_tests/test_quaternion.py
demos/input/rmsd_tests/test_reflections.py
demos/input/rmsd_tests/test_reorder.py
demos/input/rmsd_tests/test_reorder_inertia.py
demos/input/rmsd_tests/test_reorder_print.py
demos/input/rmsd_tests/test_reorder_qml.py
demos/input/rmsd_tests/resources/CHEMBL3039407.xyz
demos/input/rmsd_tests/resources/CHEMBL3039407_order.xyz
demos/input/rmsd_tests/resources/SF2HClBrI-a.xyz
demos/input/rmsd_tests/resources/SF2HClBrI-b-nxnz.xyz
demos/input/rmsd_tests/resources/SF2HClBrI-nxnz.xyz
demos/input/rmsd_tests/resources/SF2HClBrI-nyz.xyz
demos/input/rmsd_tests/resources/SF2HClBrI-xnz.xyz
demos/input/rmsd_tests/resources/SF2HClBrI-xy.xyz
demos/input/rmsd_tests/resources/SF2HClBrI-xz.xyz
demos/input/rmsd_tests/resources/SF2HClBrI-yz.xyz
demos/input/rmsd_tests/resources/bad_format.xyz
demos/input/rmsd_tests/resources/butane.xyz
demos/input/rmsd_tests/resources/butane_prime.xyz
demos/input/rmsd_tests/resources/c6h7-int1-a.xyz
demos/input/rmsd_tests/resources/c6h7-int1-b.xyz
demos/input/rmsd_tests/resources/c6h7-int1-c.xyz
demos/input/rmsd_tests/resources/c6h7-int1-xz.xyz
demos/input/rmsd_tests/resources/c6h7-int2-t-b.xyz
demos/input/rmsd_tests/resources/c6h7-int2-t.xyz
demos/input/rmsd_tests/resources/ci2_1.pdb
demos/input/rmsd_tests/resources/ci2_12.pdb
demos/input/rmsd_tests/resources/ci2_1r+t.pdb
demos/input/rmsd_tests/resources/ci2_2.pdb
demos/input/rmsd_tests/resources/ethane-1-2-diolate_a.xyz
demos/input/rmsd_tests/resources/ethane-1-2-diolate_b.xyz
demos/input/rmsd_tests/resources/ethane.xyz
demos/input/rmsd_tests/resources/ethane_bond.xyz
demos/input/rmsd_tests/resources/ethane_mini.xyz
demos/input/rmsd_tests/resources/ethane_translate.xyz
demos/input/rmsd_tests/resources/water.xyz
demos/input/rmsd_tests/resources/water_16.xyz
demos/input/rmsd_tests/resources/water_16_idx.xyz
demos/input/rmsd_tests/resources/water_swapped.xyz
demos/input/rmsd_tests/resources/examples/CHEMBL135626.xyz
demos/input/rmsd_tests/resources/examples/NS00006345.xyz
demos/input/rmsd_tests/resources/issue78/a.xyz
demos/input/rmsd_tests/resources/issue78/b.xyz
demos/input/rmsd_tests/resources/issue88/native.pdb
demos/input/rmsd_tests/resources/issue88/redocked.pdb
demos/input/rmsd_tests/resources/issue93/a.xyz
demos/input/rmsd_tests/resources/issue93/b.xyz
demos/input/rmsd_tests/resources/issue93/c.xyz
demos/input/rmsd_tests/resources/issue93/d.xyz
demos/input/rmsd_tests/resources/issue98/test1.pdb
demos/input/rmsd_tests/resources/issue98/test2.pdb
docs/RNAToolkit_Usage_Guide.md
rnapy/__init__.py
rnapy/__main__.py
rnapy/cli.py
rnapy/toolkit.py
rnapy/core/__init__.py
rnapy/core/base.py
rnapy/core/config.py
rnapy/core/config_loader.py
rnapy/core/exceptions.py
rnapy/core/factory.py
rnapy/data/__init__.py
rnapy/data/dataset_downloader.py
rnapy/interfaces/__init__.py
rnapy/interfaces/inverse_folding.py
rnapy/interfaces/msa_analysis.py
rnapy/interfaces/sequence_analysis.py
rnapy/interfaces/structure_prediction.py
rnapy/providers/__init__.py
rnapy/providers/RiboDiffusion/__init__.py
rnapy/providers/RiboDiffusion/adapter.py
rnapy/providers/RiboDiffusion/config.py
rnapy/providers/RiboDiffusion/run_lib.py
rnapy/providers/RiboDiffusion/sampling.py
rnapy/providers/RiboDiffusion/utils.py
rnapy/providers/RiboDiffusion/diffusion/__init__.py
rnapy/providers/RiboDiffusion/diffusion/noise_schedule.py
rnapy/providers/RiboDiffusion/models/GVP_diff.py
rnapy/providers/RiboDiffusion/models/__init__.py
rnapy/providers/RiboDiffusion/models/ema.py
rnapy/providers/RiboDiffusion/models/esm_block.py
rnapy/providers/RiboDiffusion/models/esm_utils.py
rnapy/providers/RiboDiffusion/models/transformer_layer.py
rnapy/providers/RiboDiffusion/models/utils.py
rnapy/providers/lddt/__init__.py
rnapy/providers/lddt/lddt.py
rnapy/providers/lddt/ms.py
rnapy/providers/rhodesign/RhoDesign.py
rnapy/providers/rhodesign/RhoDesign_without2d.py
rnapy/providers/rhodesign/__init__.py
rnapy/providers/rhodesign/adapter.py
rnapy/providers/rhodesign/alphabet.py
rnapy/providers/rhodesign/config.py
rnapy/providers/rhodesign/gvp_transformer_encoder.py
rnapy/providers/rhodesign/gvp_transformer_encoder_without2d.py
rnapy/providers/rhodesign/util.py
rnapy/providers/rhodesign/gvp_src/__init__.py
rnapy/providers/rhodesign/gvp_src/features.py
rnapy/providers/rhodesign/gvp_src/gvp_encoder.py
rnapy/providers/rhodesign/gvp_src/gvp_modules.py
rnapy/providers/rhodesign/transformer_src/__init__.py
rnapy/providers/rhodesign/transformer_src/multihead_attention.py
rnapy/providers/rhodesign/transformer_src/transformer_decoder.py
rnapy/providers/rhodesign/transformer_src/transformer_layer.py
rnapy/providers/rhofold/__init__.py
rnapy/providers/rhofold/adapter.py
rnapy/providers/rhofold/config.py
rnapy/providers/rhofold/predictor.py
rnapy/providers/rhofold/rhofold.py
rnapy/providers/rhofold/data/balstn.py
rnapy/providers/rhofold/data/bin/blastn
rnapy/providers/rhofold/data/bin/parse_blastn_local.pl
rnapy/providers/rhofold/data/bin/reformat.pl
rnapy/providers/rhofold/model/__init__.py
rnapy/providers/rhofold/model/e2eformer.py
rnapy/providers/rhofold/model/embedders.py
rnapy/providers/rhofold/model/heads.py
rnapy/providers/rhofold/model/msa.py
rnapy/providers/rhofold/model/outer_product_mean.py
rnapy/providers/rhofold/model/pair.py
rnapy/providers/rhofold/model/primitives.py
rnapy/providers/rhofold/model/structure_module.py
rnapy/providers/rhofold/model/triangular_attention.py
rnapy/providers/rhofold/model/triangular_update.py
rnapy/providers/rhofold/relax/__init__.py
rnapy/providers/rhofold/relax/relax.py
rnapy/providers/rhofold/tools/seqsim.py
rnapy/providers/rhofold/utils/__init__.py
rnapy/providers/rhofold/utils/alphabet.py
rnapy/providers/rhofold/utils/chunk_utils.py
rnapy/providers/rhofold/utils/constants.py
rnapy/providers/rhofold/utils/converter.py
rnapy/providers/rhofold/utils/rigid_utils.py
rnapy/providers/rhofold/utils/ss_utils.py
rnapy/providers/rhofold/utils/tensor_utils.py
rnapy/providers/rmsd/__init__.py
rnapy/providers/rmsd/calculate_rmsd.py
rnapy/providers/rna_fm/__init__.py
rnapy/providers/rna_fm/adapter.py
rnapy/providers/rna_fm/axial_attention.py
rnapy/providers/rna_fm/config.py
rnapy/providers/rna_fm/constants.py
rnapy/providers/rna_fm/data.py
rnapy/providers/rna_fm/model.py
rnapy/providers/rna_fm/modules.py
rnapy/providers/rna_fm/multihead_attention.py
rnapy/providers/rna_fm/predictor.py
rnapy/providers/rna_fm/pretrained.py
rnapy/providers/rna_fm/version.py
rnapy/providers/rna_fm/model/__init__.py
rnapy/providers/rna_fm/model/esm1.py
rnapy/providers/rna_msm/__init__.py
rnapy/providers/rna_msm/adapter.py
rnapy/providers/rna_msm/config.py
rnapy/providers/rna_msm/dataset.py
rnapy/providers/rna_msm/lr_schedulers.py
rnapy/providers/rna_msm/model.py
rnapy/providers/rna_msm/modules.py
rnapy/providers/rna_msm/predictor.py
rnapy/providers/rna_msm/product_key_memory.py
rnapy/providers/rna_msm/msm/__init__.py
rnapy/providers/rna_msm/msm/axial_attention.py
rnapy/providers/rna_msm/msm/constants.py
rnapy/providers/rna_msm/msm/data.py
rnapy/providers/rna_msm/msm/model.py
rnapy/providers/rna_msm/msm/modules.py
rnapy/providers/rna_msm/msm/multihead_attention.py
rnapy/providers/rna_msm/utils/__init__.py
rnapy/providers/rna_msm/utils/align.py
rnapy/providers/rna_msm/utils/dataset.py
rnapy/providers/rna_msm/utils/distribute.py
rnapy/providers/rna_msm/utils/ffindex.py
rnapy/providers/rna_msm/utils/likelihood.py
rnapy/providers/rna_msm/utils/metrics.py
rnapy/providers/rna_msm/utils/parsing.py
rnapy/providers/rna_msm/utils/sequence.py
rnapy/providers/rna_msm/utils/structure.py
rnapy/providers/rna_msm/utils/tensor.py
rnapy/providers/rna_msm/utils/tokenization.py
rnapy/providers/rna_msm/utils/typed.py
rnapy/providers/tm_score/__init__.py
rnapy/providers/tm_score/tm_score.py
rnapy/providers/tm_score/bin/TMscoreC-linux-x86
rnapy/providers/tm_score/bin/TMscoreC-win-x86.exe
rnapy/providers/tm_score/bin/TMscoreCmt-linux-x86
rnapy/providers/tm_score/bin/TMscoreCmt-win-x86.exe
rnapy/utils/__init__.py
rnapy/utils/config_utils.py
rnapy/utils/data_utils.py
rnapy/utils/download_model_utils.py
rnapy/utils/file_utils.py
scripts/process_rfam_dataset.py