├── .gitignore ├── LICENSE ├── LinearFold-E.patch ├── LinearPartition-E.patch ├── README.md ├── README_LinearFold-E_patch.md ├── datalists ├── README.md ├── generate_datalist.sh └── write_all_datalists.sh ├── datasets_in_fasta_form ├── EternaBench_datasets │ ├── EB_ChemMapping_Filtered.fasta │ ├── EB_ChemMapping_unfiltered.fasta │ ├── EB_Riboswitch_Filtered.fasta │ └── EB_Riboswitch_unfiltered.fasta ├── README.md ├── holdout_datasets │ ├── ChemMappingData_holdout.fasta │ ├── RiboswitchData_holdout.fasta │ └── S-Processed-VAL.fasta ├── test_datasets │ ├── .DS_Store │ ├── ExternalData.fasta │ ├── ExternalData_window1200_uniq.fasta │ ├── ExternalData_window300_uniq.fasta │ ├── ExternalData_window600_uniq.fasta │ ├── ExternalData_window900_uniq.fasta │ ├── S-Processed-TES.fasta │ ├── archiveII_filt_80_NR.fasta │ └── archiveII_original.fasta └── train_datasets │ ├── All_EternaFold_training_data.fasta │ ├── ChemMappingData_train.fasta │ ├── RiboswitchData_train.fasta │ └── S-Processed-TRA.fasta ├── input_data.zip ├── parameters ├── EternaFoldParams.v1 ├── EternaFoldParams_PLUS_POTENTIALS.v1 ├── LICENSE └── README.md ├── scripts ├── ConvertRFAM ├── ConvertRFAM.cc ├── README.md ├── score_riboswitch_foldchange.sh └── score_single_structure_prediction.sh ├── src ├── .nfs0000000272a7723b000013b6 ├── BundleMethod.hpp ├── BundleMethod.ipp ├── CGLinear.hpp ├── CGLinear.ipp ├── CGOptimizationWrapper.hpp ├── CGOptimizationWrapper.ipp ├── ComputationEngine.hpp ├── ComputationEngine.ipp ├── ComputationWrapper.hpp ├── ComputationWrapper.ipp ├── Config.hpp ├── Contrafold.cpp ├── Defaults.ipp ├── DistributedComputation.hpp ├── DistributedComputation.ipp ├── EM.hpp ├── EM.ipp ├── EncapsulatedPostScript.cpp ├── EncapsulatedPostScript.hpp ├── FileDescription.cpp ├── FileDescription.hpp ├── GammaMLE.hpp ├── GammaMLE.ipp ├── InferenceEngine.hpp ├── InferenceEngine.ipp ├── InnerOptimizationWrapper.hpp ├── InnerOptimizationWrapper.ipp ├── 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