├── .bumpversion.toml ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md ├── actions │ └── install-python-and-package │ │ └── action.yml └── workflows │ ├── _ghcr.yml │ ├── build-latest-release.yml │ ├── build-repo-frozen-env.yml │ ├── build-repo.yml │ ├── cffconvert.yml │ ├── coveralls.yml │ ├── draft-pdf.yml │ ├── fair-software.yml │ ├── linting.yml │ ├── markdown-link-check.yml │ ├── notebooks.yml │ ├── release_github.yml │ ├── release_pypi.yml │ ├── stale_issue_pr.yml │ └── test-docker-image.yml ├── .gitignore ├── .readthedocs.yaml ├── .ruff.toml ├── .vscode └── settings.json ├── .zenodo.json ├── CHANGELOG.md ├── CITATION.cff ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── Dockerfile ├── LICENSE ├── MANIFEST.in ├── NOTICE ├── README.dev.md ├── README.md ├── deeprank2.png ├── deeprank2 ├── __init__.py ├── dataset.py ├── domain │ ├── __init__.py │ ├── aminoacid_summary.xlsx │ ├── aminoacidlist.py │ ├── edgestorage.py │ ├── forcefield │ │ ├── __init__.py │ │ ├── patch.top │ │ ├── protein-allhdg5-4_new.param │ │ ├── protein-allhdg5-5_new.top │ │ └── residue-classes │ ├── gridstorage.py │ ├── losstypes.py │ ├── nodestorage.py │ └── targetstorage.py ├── features │ ├── __init__.py │ ├── components.py │ ├── conservation.py │ ├── contact.py │ ├── exposure.py │ ├── irc.py │ ├── secondary_structure.py │ └── surfacearea.py ├── molstruct │ ├── __init__.py │ ├── aminoacid.py │ ├── atom.py │ ├── pair.py │ ├── residue.py │ └── structure.py ├── neuralnets │ ├── __init__.py │ ├── cnn │ │ ├── __init__.py │ │ └── model3d.py │ └── gnn │ │ ├── __init__.py │ │ ├── alignmentnet.py │ │ ├── foutnet.py │ │ ├── ginet.py │ │ ├── ginet_nocluster.py │ │ ├── sgat.py │ │ └── vanilla_gnn.py ├── query.py ├── tools │ ├── __init__.py │ └── target.py ├── trainer.py └── utils │ ├── __init__.py │ ├── buildgraph.py │ ├── community_pooling.py │ ├── earlystopping.py │ ├── exporters.py │ ├── graph.py │ ├── grid.py │ ├── parsing │ ├── __init__.py │ ├── patch.py │ ├── pssm.py │ ├── residue.py │ ├── top.py │ └── vdwparam.py │ └── pssmdata.py ├── docs ├── .gitignore ├── Makefile ├── make.bat ├── requirements.txt └── source │ ├── conf.py │ ├── contributing_link.md │ ├── deeprank2.molstruct.rst │ ├── deeprank2.neuralnets.rst │ ├── deeprank2.rst │ ├── deeprank2.tools.rst │ ├── docking.md │ ├── features.md │ ├── getstarted.md │ ├── index.rst │ └── installation.md ├── env ├── deeprank2.yml └── deeprank2_frozen.yml ├── joss ├── deeprank2.png ├── paper.bib ├── paper.md └── paper.pdf ├── pyproject.toml ├── tests ├── __init__.py ├── data │ ├── dssp │ │ ├── 1ak4.dssp.txt │ │ └── 9api.dssp.txt │ ├── hdf5 │ │ ├── .gitignore │ │ ├── 1ATN_ppi.hdf5 │ │ ├── _generate_testdata.ipynb │ │ ├── original-deeprank-1ak4.hdf5 │ │ ├── test.hdf5 │ │ ├── test_no_target.hdf5 │ │ ├── train.hdf5 │ │ ├── valid.hdf5 │ │ └── variants.hdf5 │ ├── pdb │ │ ├── 101M │ │ │ └── 101M.pdb │ │ ├── 1A0Z │ │ │ └── 1A0Z.pdb │ │ ├── 1A6B │ │ │ └── 1A6B.pdb │ │ ├── 1ATN │ │ │ ├── 1ATN_1w.pdb │ │ │ ├── 1ATN_2w.pdb │ │ │ ├── 1ATN_3w.pdb │ │ │ └── 1ATN_4w.pdb │ │ ├── 1CRN │ │ │ └── 1CRN.pdb │ │ ├── 1ak4 │ │ │ └── 1ak4.pdb │ │ ├── 2g98 │ │ │ └── pdb2g98.pdb │ │ ├── 3C8P │ │ │ └── 3C8P.pdb │ │ ├── 3MRC │ │ │ └── 3MRC.pdb │ │ └── 9api │ │ │ └── 9api.pdb │ ├── pretrained │ │ ├── testing_graph_model.pth.tar │ │ └── testing_grid_model.pth.tar │ ├── pssm │ │ ├── 101M │ │ │ └── 101M.A.pdb.pssm │ │ ├── 1A0Z │ │ │ ├── 1A0Z.A.pdb.pssm │ │ │ └── 1A0Z.B.pdb.pssm │ │ ├── 1AK4 │ │ │ ├── 1AK4.C.pssm │ │ │ ├── 1AK4.D.pssm │ │ │ └── 1AK4.old.pssm │ │ ├── 1ATN │ │ │ ├── 1ATN.A.pdb.pssm │ │ │ └── 1ATN.B.pdb.pssm │ │ ├── 2g98 │ │ │ └── 2g98.A.pdb.pssm │ │ ├── 3C8P │ │ │ ├── 3C8P.A.pdb.pssm │ │ │ └── 3C8P.B.pdb.pssm │ │ ├── 3C8P_incorrect │ │ │ ├── 3C8P.A.wrong_order.pdb.pssm │ │ │ └── 3C8P.B.missing_res.pdb.pssm │ │ └── 9api │ │ │ ├── 9api.A.pdb.pssm │ │ │ └── 9api.B.pdb.pssm │ ├── ref │ │ ├── 1ATN │ │ │ ├── 1ATN.pdb │ │ │ └── 1ATN.pdb.save │ │ └── 3C8P │ │ │ └── 3C8P.pdb │ └── train_ref │ │ ├── train_data.csv │ │ └── train_data.hdf5 ├── domain │ ├── __init__.py │ ├── test_aminoacidlist.py │ └── test_forcefield.py ├── features │ ├── __init__.py │ ├── test_components.py │ ├── test_conservation.py │ ├── test_contact.py │ ├── test_exposure.py │ ├── test_irc.py │ ├── test_secondary_structure.py │ └── test_surfacearea.py ├── molstruct │ ├── __init__.py │ ├── test_pair.py │ └── test_structure.py ├── perf │ ├── __init__.py │ ├── ppi_perf.py │ └── srv_perf.py ├── test_dataset.py ├── test_integration.py ├── test_query.py ├── test_querycollection.py ├── test_set_lossfunction.py ├── test_trainer.py ├── tools │ ├── __init__.py │ └── test_target.py └── utils │ ├── __init__.py │ ├── test_buildgraph.py │ ├── test_community_pooling.py │ ├── test_earlystopping.py │ ├── test_exporters.py │ ├── test_graph.py │ ├── test_grid.py │ ├── test_pssmdata.py │ ├── uml_data_processing.svg │ └── uml_training.svg └── tutorials ├── .gitignore ├── TUTORIAL.md ├── data_generation_ppi.ipynb ├── data_generation_srv.ipynb ├── images 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