├── DRfold_infer.py ├── PotentialFold ├── Clust.py ├── Cubic.py ├── Optimization.py ├── Potential.py ├── Selection.py ├── __init__.py ├── a2b.py ├── geo.py ├── lbfgs_rosetta.py ├── lib │ ├── base.npy │ ├── ddf.json │ ├── other2.npy │ ├── others.npy │ ├── side.npy │ └── vdw.json ├── operations.py └── rigid.py ├── README.md ├── cfg_95 ├── EvoMSA.py ├── EvoMSA2XYZ.py ├── EvoPair.py ├── Evoformer.py ├── IPA.py ├── RNALM2 │ ├── EvoMSA.py │ ├── EvoPair.py │ ├── Evoformer.py │ ├── Model.py │ └── basic.py ├── Structure.py ├── __init__.py ├── base.npy ├── basic.py ├── data.py ├── newconfig ├── test_modeldir.py └── util.py ├── cfg_96 ├── EvoMSA.py ├── EvoMSA2XYZ.py ├── EvoPair.py ├── Evoformer.py ├── IPA.py ├── RNALM2 │ ├── EvoMSA.py │ ├── EvoPair.py │ ├── Evoformer.py │ ├── Model.py │ └── basic.py ├── Structure.py ├── __init__.py ├── base.npy ├── basic.py ├── data.py ├── newconfig ├── test_modeldir.py └── util.py ├── cfg_97 ├── EvoMSA.py ├── EvoMSA2XYZ.py ├── EvoPair.py ├── Evoformer.py ├── IPA.py ├── RNALM2 │ ├── EvoMSA.py │ ├── EvoPair.py │ ├── Evoformer.py │ ├── Model.py │ └── basic.py ├── Structure.py ├── base.npy ├── basic.py ├── data.py ├── newconfig ├── test_modeldir.py └── util.py ├── cfg_99 ├── EvoMSA.py ├── EvoMSA2XYZ.py ├── EvoPair.py ├── Evoformer.py ├── IPA.py ├── RNALM2 │ ├── EvoMSA.py │ ├── EvoPair.py │ ├── Evoformer.py │ ├── Model.py │ └── basic.py ├── Structure.py ├── __init__.py ├── base.npy ├── basic.py ├── data.py ├── newconfig ├── test_modeldir.py └── util.py ├── cfg_for_folding.json ├── cfg_for_selection.json ├── install.sh ├── script ├── RNArefine.sh └── refine.py └── test └── seq.fasta /DRfold_infer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/leeyang/DRfold2/HEAD/DRfold_infer.py -------------------------------------------------------------------------------- /PotentialFold/Clust.py: -------------------------------------------------------------------------------- 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