├── DRfold.sh ├── DeepE2EPotential ├── EvoMSA.py ├── EvoMSA2XYZ.py ├── EvoPair.py ├── Evoformer.py ├── IPA.py ├── Structure.py ├── __init__.py ├── base.npy ├── basic.py └── predict.py ├── DeepGeoPotential ├── Feature.py ├── combine.py ├── config1 │ ├── DPRmodel.py │ ├── Embedder.py │ ├── EvoMSA.py │ ├── EvoPair.py │ ├── Evoformer.py │ ├── __init__.py │ ├── base.npy │ ├── basic.py │ └── predict.py ├── config2 │ ├── DPRmodel.py │ ├── Embedder.py │ ├── EvoMSA.py │ ├── EvoPair.py │ ├── Evoformer.py │ ├── __init__.py │ ├── __pycache__ │ │ ├── DPRmodel.cpython-38.pyc │ │ ├── DPRmodel.cpython-39.pyc │ │ ├── Embedder.cpython-38.pyc │ │ ├── Embedder.cpython-39.pyc │ │ ├── EvoMSA.cpython-38.pyc │ │ ├── EvoMSA.cpython-39.pyc │ │ ├── EvoPair.cpython-38.pyc │ │ ├── EvoPair.cpython-39.pyc │ │ ├── Evoformer.cpython-38.pyc │ │ ├── Evoformer.cpython-39.pyc │ │ ├── Feature.cpython-39.pyc │ │ ├── IPAModule.cpython-39.pyc │ │ ├── Loss.cpython-39.pyc │ │ ├── StructureModule.cpython-39.pyc │ │ ├── basic.cpython-38.pyc │ │ ├── basic.cpython-39.pyc │ │ └── geo.cpython-39.pyc │ ├── base.npy │ ├── basic.py │ └── predict.py ├── config3 │ ├── EvoMSA.py │ ├── EvoMSA2XYZ.py │ ├── EvoPair.py │ ├── Evoformer.py │ ├── __init__.py │ ├── __pycache__ │ │ ├── EvoMSA.cpython-38.pyc │ │ ├── EvoMSA.cpython-39.pyc │ │ ├── EvoMSA2XYZ.cpython-38.pyc │ │ ├── EvoMSA2XYZ.cpython-39.pyc │ │ ├── EvoPair.cpython-38.pyc │ │ ├── EvoPair.cpython-39.pyc │ │ ├── Evoformer.cpython-38.pyc │ │ ├── Evoformer.cpython-39.pyc │ │ ├── IPA.cpython-39.pyc │ │ ├── Structure.cpython-39.pyc │ │ ├── basic.cpython-38.pyc │ │ ├── basic.cpython-39.pyc │ │ ├── geo.cpython-39.pyc │ │ ├── loss.cpython-39.pyc │ │ ├── metrics.cpython-39.pyc │ │ └── precision.cpython-39.pyc │ ├── base.npy │ ├── basic.py │ └── predict.py ├── fold.py └── rDP.sh ├── PotentialFold ├── Cubic.py ├── Fold.py ├── Potential.py ├── __init__.py ├── __pycache__ │ ├── Cubic.cpython-38.pyc │ ├── Cubic.cpython-39.pyc │ ├── Potential.cpython-38.pyc │ ├── Potential.cpython-39.pyc │ ├── a2b.cpython-38.pyc │ ├── a2b.cpython-39.pyc │ ├── lbfgs_rosetta.cpython-38.pyc │ ├── lbfgs_rosetta.cpython-39.pyc │ ├── operations.cpython-38.pyc │ ├── operations.cpython-39.pyc │ ├── rigid.cpython-38.pyc │ └── rigid.cpython-39.pyc ├── a2b.py ├── geo.py ├── lbfgs_rosetta.py ├── lib │ ├── base.npy │ ├── ddf.json │ ├── other2.npy │ ├── others.npy │ ├── side.npy │ └── vdw.json ├── operations.py └── rigid.py ├── bin └── Arena ├── readme.txt ├── scripts ├── Feature.py ├── combine.py ├── fold.py ├── rDP.sh └── refine.py └── test └── seq.fasta /DRfold.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/leeyang/DRfold/HEAD/DRfold.sh -------------------------------------------------------------------------------- /DeepE2EPotential/EvoMSA.py: -------------------------------------------------------------------------------- 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