├── .editorconfig ├── .github └── ISSUE_TEMPLATE.md ├── .gitignore ├── .travis.yml ├── AUTHORS.rst ├── CONTRIBUTING.rst ├── Dockerfile ├── HISTORY.rst ├── LICENSE ├── MANIFEST.in ├── Makefile ├── NeuralPLexer-requirements.txt ├── NeuralPLexer.yml ├── README.rst ├── baselines ├── calc_site_recovery_ref_stats.py └── rosettaligand │ ├── PDBBind2019+bychain_AF2selected_test.csv │ ├── PDBBind2019+bychain_AF2selected_test033023 │ ├── dock_protocol.xml │ ├── options.short │ └── summary.batch │ ├── benchmark.batch │ ├── benchmarking_summary_033023.csv │ ├── dock_protocol.xml │ ├── export_results_to_csv.py │ ├── options.short │ └── summary.batch ├── benchmark_tiny.sh ├── docs ├── Makefile ├── authors.rst ├── conf.py ├── contributing.rst ├── demo2_122023.gif ├── history.rst ├── index.rst ├── installation.rst ├── make.bat ├── readme.rst └── usage.rst ├── environment_dev.yaml ├── neuralplexer ├── __init__.py ├── af_common │ ├── __init__.py │ ├── protein.py │ └── residue_constants.py ├── cli.py ├── data │ ├── __init__.py │ ├── chemical │ │ ├── 20AA_template_peptide.pdb │ │ ├── ALA.pdb │ │ ├── ARG.pdb │ │ ├── ASN.pdb │ │ ├── ASP.pdb │ │ ├── CYS.pdb │ │ ├── GLN.pdb │ │ ├── GLU.pdb │ │ ├── GLY.pdb │ │ ├── HIS.pdb │ │ ├── ILE.pdb │ │ ├── LEU.pdb │ │ ├── LYS.pdb │ │ ├── MET.pdb │ │ ├── PHE.pdb │ │ ├── PRO.pdb │ │ ├── SER.pdb │ │ ├── Standard_aa_featurization_test.ipynb │ │ ├── THR.pdb │ │ ├── TRP.pdb │ │ ├── TYR.pdb │ │ └── VAL.pdb │ ├── dataloading.py │ ├── indexers.py │ ├── molops.py │ ├── pdb_ligand_parsing.py │ ├── physical.py │ ├── pipeline.py │ └── uff_parameters.csv ├── inference.py ├── model │ ├── __init__.py │ ├── common.py │ ├── config.py │ ├── cpm.py │ ├── embedding.py │ ├── esdm.py │ ├── mht_encoder.py │ ├── modules.py │ ├── training.py │ └── wrappers.py └── util │ ├── __init__.py │ ├── distributions.py │ ├── ema.py │ ├── frame.py │ ├── pdb3d.py │ ├── sde_transform.py │ └── tensorgraph.py ├── notebooks ├── Figure3a-d_Table1.ipynb ├── Figure3e-g.ipynb ├── Figure4-5_Figure1b.ipynb ├── TableS1-S2.ipynb ├── extended_fig_1.ipynb ├── psp_summary_pocketminer.csv └── psp_summary_recent.csv ├── requirements.txt ├── setup.cfg ├── setup.py ├── tests ├── __init__.py ├── test_featurize.py └── test_template_stack.py ├── tox.ini └── training_index ├── 013023_general_pretraining_set_timesplit-pocketminer_reviewed.csv └── 021723_motionfinetuning_pocketminerval_reviewed_3A_plddt70_noNUC_balanced4.csv /.editorconfig: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zrqiao/NeuralPLexer/HEAD/.editorconfig -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zrqiao/NeuralPLexer/HEAD/.github/ISSUE_TEMPLATE.md -------------------------------------------------------------------------------- /.gitignore: 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