LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.py
example/atlas.py
example/ligands.txt
example/protein_files.txt
example/proteins/1fbl.pdb
example/proteins/2W83.pdb
notebooks/atlas_colab.ipynb
notebooks/colab_setup.py
notebooks/quickstart_colab.ipynb
pocketvina/Makefile
pocketvina/PocketVina-GPU
pocketvina/__init__.py
pocketvina/__main__.py
pocketvina/atlas.py
pocketvina/bust.py
pocketvina/cli.py
pocketvina/convert.py
pocketvina/engine.py
pocketvina/gpu.py
pocketvina/ligands.py
pocketvina/main.py
pocketvina/p2rank.py
pocketvina/pdbqt.py
pocketvina/pipeline.py
pocketvina/selection.py
pocketvina/viz.py
pocketvina/workspace.py
pocketvina.egg-info/PKG-INFO
pocketvina.egg-info/SOURCES.txt
pocketvina.egg-info/dependency_links.txt
pocketvina.egg-info/entry_points.txt
pocketvina.egg-info/requires.txt
pocketvina.egg-info/top_level.txt
pocketvina/OpenCL/inc/commonMacros.h
pocketvina/OpenCL/inc/kernel2.h
pocketvina/OpenCL/inc/wrapcl.h
pocketvina/OpenCL/src/wrapcl.cpp
pocketvina/OpenCL/src/kernels/code_head.cl
pocketvina/OpenCL/src/kernels/kernel1.cl
pocketvina/OpenCL/src/kernels/kernel2.cl
pocketvina/OpenCL/src/kernels/matrix.cl
pocketvina/OpenCL/src/kernels/mutate_conf.cl
pocketvina/OpenCL/src/kernels/quasi_newton.cl
pocketvina/OpenCL/src/kernels/visited.cl
pocketvina/io/__init__.py
pocketvina/io/atlas_source.py
pocketvina/io/importer.py
pocketvina/io/posefile.py
pocketvina/io/results.py
pocketvina/io/tables.py
pocketvina/io/writer.py
pocketvina/lib/1getname.bat
pocketvina/lib/LIST.TXT
pocketvina/lib/array3d.h
pocketvina/lib/atom.h
pocketvina/lib/atom_base.h
pocketvina/lib/atom_constants.h
pocketvina/lib/atom_type.h
pocketvina/lib/bfgs.h
pocketvina/lib/brick.h
pocketvina/lib/cache.cpp
pocketvina/lib/cache.h
pocketvina/lib/common.h
pocketvina/lib/conf.h
pocketvina/lib/convert_substring.h
pocketvina/lib/coords.cpp
pocketvina/lib/coords.h
pocketvina/lib/curl.h
pocketvina/lib/current_weights.cpp
pocketvina/lib/current_weights.h
pocketvina/lib/everything.cpp
pocketvina/lib/everything.h
pocketvina/lib/file.h
pocketvina/lib/grid.cpp
pocketvina/lib/grid.h
pocketvina/lib/grid_dim.h
pocketvina/lib/igrid.h
pocketvina/lib/incrementable.h
pocketvina/lib/int_pow.h
pocketvina/lib/json.hpp
pocketvina/lib/macros.h
pocketvina/lib/main_procedure_cl.cpp
pocketvina/lib/main_procedure_cl.h
pocketvina/lib/manifold.cpp
pocketvina/lib/manifold.h
pocketvina/lib/matrix.h
pocketvina/lib/model.cpp
pocketvina/lib/model.h
pocketvina/lib/monte_carlo.cpp
pocketvina/lib/monte_carlo.h
pocketvina/lib/mutate.cpp
pocketvina/lib/mutate.h
pocketvina/lib/my_pid.cpp
pocketvina/lib/my_pid.h
pocketvina/lib/naive_non_cache.cpp
pocketvina/lib/naive_non_cache.h
pocketvina/lib/non_cache.cpp
pocketvina/lib/non_cache.h
pocketvina/lib/parallel.h
pocketvina/lib/parallel_mc.cpp
pocketvina/lib/parallel_mc.h
pocketvina/lib/parallel_progress.cpp
pocketvina/lib/parallel_progress.h
pocketvina/lib/parse_error.h
pocketvina/lib/parse_pdbqt.cpp
pocketvina/lib/parse_pdbqt.h
pocketvina/lib/pdb.cpp
pocketvina/lib/pdb.h
pocketvina/lib/precalculate.h
pocketvina/lib/quasi_newton.cpp
pocketvina/lib/quasi_newton.h
pocketvina/lib/quaternion.cpp
pocketvina/lib/quaternion.h
pocketvina/lib/random.cpp
pocketvina/lib/random.h
pocketvina/lib/recent_history.h
pocketvina/lib/scoring_function.h
pocketvina/lib/ssd.cpp
pocketvina/lib/ssd.h
pocketvina/lib/statistics.h
pocketvina/lib/szv_grid.cpp
pocketvina/lib/szv_grid.h
pocketvina/lib/tee.h
pocketvina/lib/terms.cpp
pocketvina/lib/terms.h
pocketvina/lib/tree.h
pocketvina/lib/triangular_matrix_index.h
pocketvina/lib/weighted_terms.cpp
pocketvina/lib/weighted_terms.h
pocketvina/main/main.cpp
pocketvina/viewer/README.md
pocketvina/viewer/bridge.js
pocketvina/viewer/viewer.css
pocketvina/viewer/viewer.js
pocketvina/viewer/workspace.css
pocketvina/viewer/workspace.js
pocketvina/viewer/molstar-pv-5.13.1/LICENSE
pocketvina/viewer/molstar-pv-5.13.1/SOURCES.txt
pocketvina/viewer/molstar-pv-5.13.1/THIRD-PARTY-LICENSES.txt
pocketvina/viewer/molstar-pv-5.13.1/molstar-pv.css
pocketvina/viewer/molstar-pv-5.13.1/molstar-pv.js
pocketvina/viewer/upstream/viewer.js
tests/conftest.py
tests/fake_engine.py
tests/test_atlas.py
tests/test_atlas_view.py
tests/test_bust.py
tests/test_cli.py
tests/test_convert.py
tests/test_docs.py
tests/test_engine.py
tests/test_fake_engine.py
tests/test_gpu.py
tests/test_io_importer.py
tests/test_io_posefile.py
tests/test_io_results.py
tests/test_io_writer.py
tests/test_ligands.py
tests/test_notebook.py
tests/test_p2rank.py
tests/test_packaging.py
tests/test_pdbqt.py
tests/test_pipeline.py
tests/test_readme.py
tests/test_recipe.py
tests/test_selection.py
tests/test_viz.py
tests/test_workspace.py
tests/data/smiles.csv
tests/data/atlas/make_fixture.py
tests/data/atlas/v1.1/MANIFEST.json
tests/data/atlas/v1.1/cidx.json
tests/data/atlas/v1.1/ligand_ids.json
tests/data/atlas/v1.1/meta.json
tests/data/atlas/v1.1/compounds/PVL00129.all.json.gz
tests/data/atlas/v1.1/compounds/PVL00129.json.gz
tests/data/atlas/v1.1/compounds/PVL00133.all.json.gz
tests/data/atlas/v1.1/compounds/PVL00133.json.gz
tests/data/atlas/v1.1/compounds/PVL00250.all.json.gz
tests/data/atlas/v1.1/compounds/PVL00250.json.gz
tests/data/atlas/v1.1/compounds/PVL00257.all.json.gz
tests/data/atlas/v1.1/compounds/PVL00257.json.gz
tests/data/atlas/v1.1/compounds/PVL00327.all.json.gz
tests/data/atlas/v1.1/compounds/PVL00327.json.gz
tests/data/atlas/v1.1/compounds/PVL00609.all.json.gz
tests/data/atlas/v1.1/compounds/PVL00609.json.gz
tests/data/atlas/v1.1/compounds/PVL00669.all.json.gz
tests/data/atlas/v1.1/compounds/PVL00669.json.gz
tests/data/atlas/v1.1/compounds/PVL00839.all.json.gz
tests/data/atlas/v1.1/compounds/PVL00839.json.gz
tests/data/atlas/v1.1/compounds/PVL00898.all.json.gz
tests/data/atlas/v1.1/compounds/PVL00898.json.gz
tests/data/atlas/v1.1/compounds/PVL00958.all.json.gz
tests/data/atlas/v1.1/compounds/PVL00958.json.gz
tests/data/atlas/v1.1/compounds/PVL01579.all.json.gz
tests/data/atlas/v1.1/compounds/PVL01579.json.gz
tests/data/atlas/v1.1/compounds/PVL01982.all.json.gz
tests/data/atlas/v1.1/compounds/PVL01982.json.gz
tests/data/atlas/v1.1/compounds/PVL02131.all.json.gz
tests/data/atlas/v1.1/compounds/PVL02131.json.gz
tests/data/atlas/v1.1/compounds/PVL02156.all.json.gz
tests/data/atlas/v1.1/compounds/PVL02156.json.gz
tests/data/atlas/v1.1/compounds/PVL02203.all.json.gz
tests/data/atlas/v1.1/compounds/PVL02203.json.gz
tests/data/atlas/v1.1/poses/P00519.poses
tests/data/atlas/v1.1/poses/P00533.poses
tests/data/atlas/v1.1/poses/P35354.poses
tests/data/atlas/v1.1/poses_redock/P00519.poses
tests/data/atlas/v1.1/poses_redock/P00533.poses
tests/data/atlas/v1.1/poses_redock/P35354.poses
tests/data/atlas/v1.1/proteins/P00519.json.gz
tests/data/atlas/v1.1/proteins/P00533.json.gz
tests/data/atlas/v1.1/proteins/P35354.json.gz
tests/data/atlas/v1.1/salt_forms/P00519.json.gz
tests/data/atlas/v1.1/salt_forms/P00533.json.gz
tests/data/atlas/v1.1/salt_forms/P35354.json.gz
tests/data/atlas/v1.1/search/1.json.gz
tests/data/atlas/v1.1/search/2.json.gz
tests/data/atlas/v1.1/search/3.json.gz
tests/data/atlas/v1.1/search/4.json.gz
tests/data/atlas/v1.1/search/5.json.gz
tests/data/atlas/v1.1/search/a.json.gz
tests/data/atlas/v1.1/search/acc_p0.json.gz
tests/data/atlas/v1.1/search/acc_p1.json.gz
tests/data/atlas/v1.1/search/acc_p3.json.gz
tests/data/atlas/v1.1/search/acc_p5.json.gz
tests/data/atlas/v1.1/search/acc_q1.json.gz
tests/data/atlas/v1.1/search/acc_q9.json.gz
tests/data/atlas/v1.1/search/c.json.gz
tests/data/atlas/v1.1/search/d.json.gz
tests/data/atlas/v1.1/search/e.json.gz
tests/data/atlas/v1.1/search/ensg07.json.gz
tests/data/atlas/v1.1/search/ensg09.json.gz
tests/data/atlas/v1.1/search/ensg13.json.gz
tests/data/atlas/v1.1/search/ensg14.json.gz
tests/data/atlas/v1.1/search/ensg16.json.gz
tests/data/atlas/v1.1/search/ensg19.json.gz
tests/data/atlas/v1.1/search/f.json.gz
tests/data/atlas/v1.1/search/g.json.gz
tests/data/atlas/v1.1/search/h.json.gz
tests/data/atlas/v1.1/search/i.json.gz
tests/data/atlas/v1.1/search/index.json.gz
tests/data/atlas/v1.1/search/j.json.gz
tests/data/atlas/v1.1/search/k.json.gz
tests/data/atlas/v1.1/search/l.json.gz
tests/data/atlas/v1.1/search/m.json.gz
tests/data/atlas/v1.1/search/n.json.gz
tests/data/atlas/v1.1/search/o.json.gz
tests/data/atlas/v1.1/search/p.json.gz
tests/data/atlas/v1.1/search/r.json.gz
tests/data/atlas/v1.1/search/s.json.gz
tests/data/atlas/v1.1/search/t.json.gz
tests/data/atlas/v1.1/search/v.json.gz
tests/data/atlas/v1.1/search/y.json.gz
tests/data/atlas/v1.1/search/z.json.gz
tests/data/atlas/v1.1/structures/AF-P00519-F1-model_v6.pdb.gz
tests/data/atlas/v1.1/structures/AF-P00533-F1-model_v6.pdb.gz
tests/data/atlas/v1.1/structures/AF-P35354-F1-model_v6.pdb.gz
tests/data/atlas/v1.1/tables/compound_entries.parquet
tests/data/atlas/v1.1/tables/compound_entries_annotated.parquet
tests/data/atlas/v1.1/tables/compounds.parquet
tests/data/atlas/v1.1/tables/proteins.parquet
tests/data/legacy_run/combined_results.csv
tests/data/legacy_run/combined_results.json
tests/data/legacy_run/batch_1/molecule10_cleaned.pdbqt
tests/data/legacy_run/batch_1/molecule2_cleaned.pdbqt
tests/data/legacy_run/batch_1/molecule5_cleaned.pdbqt
tests/data/legacy_run/batch_1_out/AF-Q96LA5-F1-model_v4-pocket1-molecule2_cleaned_out.json
tests/data/legacy_run/batch_1_out/AF-Q96LA5-F1-model_v4-pocket1-molecule2_cleaned_out.pdbqt
tests/data/legacy_run/batch_1_out/AF-Q96LA5-F1-model_v4-pocket1-molecule5_cleaned_out.json
tests/data/legacy_run/batch_1_out/AF-Q96LA5-F1-model_v4-pocket1-molecule5_cleaned_out.pdbqt
tests/data/legacy_run/batch_1_out/AF-Q96LA5-F1-model_v4-pocket2-molecule2_cleaned_out.json
tests/data/legacy_run/batch_1_out/AF-Q96LA5-F1-model_v4-pocket2-molecule2_cleaned_out.pdbqt
tests/data/legacy_run/batch_1_out/AF-Q96LA5-F1-model_v4-pocket2-molecule5_cleaned_out.json
tests/data/legacy_run/batch_1_out/AF-Q96LA5-F1-model_v4-pocket2-molecule5_cleaned_out.pdbqt
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tests/data/legacy_run/proteins/structures/AF-Q96LA5-F1-model_v4.pdbqt