.gitattributes
.gitignore
AMDock Backend Refactoring.md
LICENSE
MANIFEST.in
README.md
pyproject.toml
zensical.toml
.github/workflows/docs.yml
.github/workflows/publish.yml
data/README.md
data/ligs.sdf
data/docking/1iep_ligand.sdf
data/docking/1iep_receptor.box.pdb
data/docking/1iep_receptor.box.txt
data/docking/1iep_receptor.pdbqt
data/docking/1iep_receptorH.pdb
data/docking/ligs.sdf
data/qsar/tox21.csv
examples/README.md
examples/pipeline_demo.py
examples/runtime_quickstart.py
src/AMDockVS.egg-info/PKG-INFO
src/AMDockVS.egg-info/SOURCES.txt
src/AMDockVS.egg-info/dependency_links.txt
src/AMDockVS.egg-info/entry_points.txt
src/AMDockVS.egg-info/requires.txt
src/AMDockVS.egg-info/scm_file_list.json
src/AMDockVS.egg-info/scm_version.json
src/AMDockVS.egg-info/top_level.txt
src/amdockvs/__init__.py
src/amdockvs/__main__.py
src/amdockvs/app.py
src/amdockvs/manifest.py
src/amdockvs/runtime.py
src/amdockvs/shards.py
src/amdockvs/binding_sites/__init__.py
src/amdockvs/binding_sites/api.py
src/amdockvs/binding_sites/boxes.py
src/amdockvs/binding_sites/cavity.py
src/amdockvs/binding_sites/from_structure.py
src/amdockvs/binding_sites/jobs.py
src/amdockvs/binding_sites/p2rank.py
src/amdockvs/binding_sites/repository.py
src/amdockvs/binding_sites/scopes.py
src/amdockvs/binding_sites/tasks.py
src/amdockvs/chemistry/__init__.py
src/amdockvs/chemistry/alignment.py
src/amdockvs/chemistry/api.py
src/amdockvs/chemistry/conformers.py
src/amdockvs/chemistry/descriptors.py
src/amdockvs/chemistry/filtering.py
src/amdockvs/chemistry/fingerprints.py
src/amdockvs/chemistry/jobs.py
src/amdockvs/chemistry/pipeline.py
src/amdockvs/chemistry/protonation.py
src/amdockvs/chemistry/repository.py
src/amdockvs/chemistry/rmsd.py
src/amdockvs/chemistry/service.py
src/amdockvs/chemistry/shards.py
src/amdockvs/chemistry/standardization.py
src/amdockvs/chemistry/state.py
src/amdockvs/chemistry/structures.py
src/amdockvs/chemistry/tasks.py
src/amdockvs/chemistry/tools/__init__.py
src/amdockvs/chemistry/tools/esmfold.py
src/amdockvs/chemistry/tools/ligands.py
src/amdockvs/chemistry/tools/receptors.py
src/amdockvs/complexes/__init__.py
src/amdockvs/complexes/api.py
src/amdockvs/core/__init__.py
src/amdockvs/core/config.toml
src/amdockvs/core/configuration.py
src/amdockvs/core/constants.py
src/amdockvs/core/home.py
src/amdockvs/core/jobs.py
src/amdockvs/core/normalize.py
src/amdockvs/core/paths.py
src/amdockvs/core/payloads.py
src/amdockvs/core/rows.py
src/amdockvs/core/user_env.py
src/amdockvs/core/vocab.py
src/amdockvs/core/worker_io.py
src/amdockvs/data/hetero_codes.json
src/amdockvs/data/tutorials/simple_docking/README.md
src/amdockvs/data/tutorials/simple_docking/SAR405.sdf
src/amdockvs/data/tutorials/simple_docking/Vps34_receptor.pdb
src/amdockvs/data/tutorials/simple_docking/example.json
src/amdockvs/diversity/__init__.py
src/amdockvs/diversity/api.py
src/amdockvs/diversity/clustering.py
src/amdockvs/diversity/jobs.py
src/amdockvs/diversity/tasks.py
src/amdockvs/docking/__init__.py
src/amdockvs/docking/api.py
src/amdockvs/docking/jobs.py
src/amdockvs/docking/methods.py
src/amdockvs/docking/pairs.py
src/amdockvs/docking/planning.py
src/amdockvs/docking/protocols.py
src/amdockvs/docking/readiness.py
src/amdockvs/docking/repository.py
src/amdockvs/docking/rerun.py
src/amdockvs/docking/residues.py
src/amdockvs/docking/shard_jobs.py
src/amdockvs/docking/shard_tasks.py
src/amdockvs/docking/submission.py
src/amdockvs/docking/tasks.py
src/amdockvs/docking/engines/__init__.py
src/amdockvs/docking/engines/adgpu.py
src/amdockvs/docking/engines/autogrid.py
src/amdockvs/docking/engines/gnina.py
src/amdockvs/docking/engines/programs.py
src/amdockvs/docking/engines/qvina.py
src/amdockvs/docking/engines/registry.py
src/amdockvs/docking/engines/unidock.py
src/amdockvs/docking/engines/vina.py
src/amdockvs/docking/engines/zinc/AD4Zn.dat
src/amdockvs/docking/engines/zinc/LICENSE
src/amdockvs/docking/engines/zinc/NOTICE
src/amdockvs/docking/engines/zinc/zinc_pseudo.py
src/amdockvs/docking/preparation/__init__.py
src/amdockvs/docking/preparation/entities.py
src/amdockvs/docking/preparation/jobs.py
src/amdockvs/docking/preparation/meeko.py
src/amdockvs/docking/preparation/profiles.py
src/amdockvs/docking/preparation/shards.py
src/amdockvs/docking/preparation/state.py
src/amdockvs/docking/preparation/tasks.py
src/amdockvs/docking/results/__init__.py
src/amdockvs/docking/results/dataset.py
src/amdockvs/docking/results/diagram.py
src/amdockvs/docking/results/interactions.py
src/amdockvs/docking/results/jobs.py
src/amdockvs/docking/results/metrics.py
src/amdockvs/docking/results/redocking.py
src/amdockvs/docking/results/repository.py
src/amdockvs/docking/results/rmsd.py
src/amdockvs/docking/results/tables.py
src/amdockvs/docking/results/tasks.py
src/amdockvs/integrations/__init__.py
src/amdockvs/integrations/api.py
src/amdockvs/integrations/contracts.py
src/amdockvs/integrations/envs.py
src/amdockvs/integrations/hosts.py
src/amdockvs/integrations/pkasso.py
src/amdockvs/integrations/registry.py
src/amdockvs/integrations/tools/adgpu.toml
src/amdockvs/integrations/tools/autogrid.toml
src/amdockvs/integrations/tools/gnina.toml
src/amdockvs/integrations/tools/ketcher.toml
src/amdockvs/integrations/tools/openbabel.toml
src/amdockvs/integrations/tools/pkasso.toml
src/amdockvs/integrations/tools/qvina.toml
src/amdockvs/integrations/tools/unidock.toml
src/amdockvs/integrations/tools/vina.toml
src/amdockvs/io/__init__.py
src/amdockvs/io/_common.py
src/amdockvs/io/api.py
src/amdockvs/io/batches.py
src/amdockvs/io/ccd_bonds.py
src/amdockvs/io/downloads.py
src/amdockvs/io/export.py
src/amdockvs/io/formats.py
src/amdockvs/io/import_stats.py
src/amdockvs/io/jobs.py
src/amdockvs/io/loaders.py
src/amdockvs/io/payloads.py
src/amdockvs/io/properties.py
src/amdockvs/io/receptor_preview.py
src/amdockvs/io/rows.py
src/amdockvs/io/shards.py
src/amdockvs/io/tasks.py
src/amdockvs/io/parsers/__init__.py
src/amdockvs/io/parsers/readers.py
src/amdockvs/io/transformers/__init__.py
src/amdockvs/io/transformers/materializers.py
src/amdockvs/io/transformers/rows.py
src/amdockvs/io/transformers/sdf.py
src/amdockvs/io/transformers/sequences.py
src/amdockvs/io/transformers/smiles.py
src/amdockvs/io/transformers/structures.py
src/amdockvs/models/__init__.py
src/amdockvs/models/clustering.py
src/amdockvs/models/codes.py
src/amdockvs/models/complexes.py
src/amdockvs/models/descriptors.py
src/amdockvs/models/docking.py
src/amdockvs/models/molecules.py
src/amdockvs/models/qsar.py
src/amdockvs/models/screening.py
src/amdockvs/models/sets.py
src/amdockvs/molecules/__init__.py
src/amdockvs/molecules/api.py
src/amdockvs/molecules/editing.py
src/amdockvs/molecules/filtering.py
src/amdockvs/molecules/fragments.py
src/amdockvs/molecules/repository.py
src/amdockvs/molecules/scopes.py
src/amdockvs/molecules/storage.py
src/amdockvs/project/__init__.py
src/amdockvs/project/deletion.py
src/amdockvs/project/sets.py
src/amdockvs/project/storage.py
src/amdockvs/project/summaries.py
src/amdockvs/qsar/__init__.py
src/amdockvs/qsar/activities.py
src/amdockvs/qsar/api.py
src/amdockvs/qsar/jobs.py
src/amdockvs/qsar/modeling.py
src/amdockvs/qsar/tasks.py
src/amdockvs/screening/__init__.py
src/amdockvs/screening/campaign.py
src/amdockvs/screening/filters.py
src/amdockvs/screening/materialize.py
src/amdockvs/ui/__init__.py
src/amdockvs/ui/docking_tutorial.py
src/amdockvs/ui/main_window.py
src/amdockvs/ui/registry.py
src/amdockvs/ui/tutorials.py
src/amdockvs/ui/view_ids.py
src/amdockvs/ui/app_widget/__init__.py
src/amdockvs/ui/app_widget/widget.py
src/amdockvs/ui/catalog/__init__.py
src/amdockvs/ui/catalog/activity.py
src/amdockvs/ui/catalog/binding_sites.py
src/amdockvs/ui/catalog/common.py
src/amdockvs/ui/catalog/complexes.py
src/amdockvs/ui/catalog/deletion.py
src/amdockvs/ui/catalog/details.py
src/amdockvs/ui/catalog/domain_views.py
src/amdockvs/ui/catalog/export.py
src/amdockvs/ui/catalog/ligands.py
src/amdockvs/ui/catalog/molecules.py
src/amdockvs/ui/catalog/receptors.py
src/amdockvs/ui/catalog/results.py
src/amdockvs/ui/catalog/shards.py
src/amdockvs/ui/common/__init__.py
src/amdockvs/ui/common/async_query.py
src/amdockvs/ui/common/drop_area.py
src/amdockvs/ui/common/failures.py
src/amdockvs/ui/common/job_follower.py
src/amdockvs/ui/common/theme.py
src/amdockvs/ui/common/widgets.py
src/amdockvs/ui/monitor/__init__.py
src/amdockvs/ui/monitor/monitor.py
src/amdockvs/ui/resources/__init__.py
src/amdockvs/ui/resources/icons/__init__.py
src/amdockvs/ui/resources/icons/activity.svg
src/amdockvs/ui/resources/icons/bell.svg
src/amdockvs/ui/resources/icons/binding_site.svg
src/amdockvs/ui/resources/icons/build.svg
src/amdockvs/ui/resources/icons/caffeine.svg
src/amdockvs/ui/resources/icons/catalog.svg
src/amdockvs/ui/resources/icons/cloud.svg
src/amdockvs/ui/resources/icons/columns.svg
src/amdockvs/ui/resources/icons/complexes.svg
src/amdockvs/ui/resources/icons/cpu.svg
src/amdockvs/ui/resources/icons/details.svg
src/amdockvs/ui/resources/icons/diversity.svg
src/amdockvs/ui/resources/icons/doc.svg
src/amdockvs/ui/resources/icons/docking.svg
src/amdockvs/ui/resources/icons/docking_results.svg
src/amdockvs/ui/resources/icons/error.svg
src/amdockvs/ui/resources/icons/favicon.svg
src/amdockvs/ui/resources/icons/file-plus.svg
src/amdockvs/ui/resources/icons/filter.svg
src/amdockvs/ui/resources/icons/folder-plus.svg
src/amdockvs/ui/resources/icons/help.svg
src/amdockvs/ui/resources/icons/info.svg
src/amdockvs/ui/resources/icons/ligands.svg
src/amdockvs/ui/resources/icons/logo.png
src/amdockvs/ui/resources/icons/logo.svg
src/amdockvs/ui/resources/icons/menu.svg
src/amdockvs/ui/resources/icons/models.svg
src/amdockvs/ui/resources/icons/mol_tools.svg
src/amdockvs/ui/resources/icons/offtarget.svg
src/amdockvs/ui/resources/icons/predictions.svg
src/amdockvs/ui/resources/icons/protein.svg
src/amdockvs/ui/resources/icons/pymol.svg
src/amdockvs/ui/resources/icons/qsar.svg
src/amdockvs/ui/resources/icons/receptor.svg
src/amdockvs/ui/resources/icons/redocking.svg
src/amdockvs/ui/resources/icons/reset.svg
src/amdockvs/ui/resources/icons/search.svg
src/amdockvs/ui/resources/icons/settings.svg
src/amdockvs/ui/resources/icons/shredder.svg
src/amdockvs/ui/resources/icons/sort-asc.svg
src/amdockvs/ui/resources/icons/sort-desc.svg
src/amdockvs/ui/resources/icons/sort.svg
src/amdockvs/ui/resources/icons/style.svg
src/amdockvs/ui/resources/icons/target.svg
src/amdockvs/ui/resources/icons/text-input.svg
src/amdockvs/ui/resources/icons/theme.svg
src/amdockvs/ui/resources/icons/themed.py
src/amdockvs/ui/resources/icons/trash.svg
src/amdockvs/ui/resources/icons/warning.svg
src/amdockvs/ui/resources/icons/web.svg
src/amdockvs/ui/resources/icons/workflow.svg
src/amdockvs/ui/resources/icons/x.svg
src/amdockvs/ui/resources/images/__init__.py
src/amdockvs/ui/shell/__init__.py
src/amdockvs/ui/shell/auxiliary_panel.py
src/amdockvs/ui/shell/job_feedback.py
src/amdockvs/ui/shell/main_content.py
src/amdockvs/ui/shell/notifications.py
src/amdockvs/ui/shell/project_summary.py
src/amdockvs/ui/shell/projects.py
src/amdockvs/ui/shell/settings_downloads.py
src/amdockvs/ui/shell/settings_tools.py
src/amdockvs/ui/shell/splash.py
src/amdockvs/ui/shell/statusbar.py
src/amdockvs/ui/shell/tool_coordinator.py
src/amdockvs/ui/shell/tutorials_panel.py
src/amdockvs/ui/shell/view_coordinator.py
src/amdockvs/ui/tools/__init__.py
src/amdockvs/ui/tools/pymol_ribbon.py
src/amdockvs/ui/tools/workflow_panel.py
src/amdockvs/ui/tools/binding_sites/__init__.py
src/amdockvs/ui/tools/binding_sites/box.py
src/amdockvs/ui/tools/binding_sites/detection.py
src/amdockvs/ui/tools/binding_sites/flexible_residues.py
src/amdockvs/ui/tools/docking/__init__.py
src/amdockvs/ui/tools/docking/diagram_dock.py
src/amdockvs/ui/tools/docking/offtarget.py
src/amdockvs/ui/tools/docking/preparation_panel.py
src/amdockvs/ui/tools/docking/protocol_editor.py
src/amdockvs/ui/tools/docking/redocking.py
src/amdockvs/ui/tools/docking/redocking_charts.py
src/amdockvs/ui/tools/docking/results_pivot.py
src/amdockvs/ui/tools/docking/run_panel.py
src/amdockvs/ui/tools/docking/scope_panel.py
src/amdockvs/ui/tools/docking/studio.py
src/amdockvs/ui/tools/importing/__init__.py
src/amdockvs/ui/tools/importing/common.py
src/amdockvs/ui/tools/importing/download.py
src/amdockvs/ui/tools/importing/ligand_forms.py
src/amdockvs/ui/tools/importing/ligands.py
src/amdockvs/ui/tools/importing/receptors.py
src/amdockvs/ui/tools/molecules/__init__.py
src/amdockvs/ui/tools/molecules/build.py
src/amdockvs/ui/tools/molecules/clusters.py
src/amdockvs/ui/tools/molecules/diversity.py
src/amdockvs/ui/tools/molecules/filter.py
src/amdockvs/ui/tools/qsar/__init__.py
src/amdockvs/ui/tools/qsar/activities.py
src/amdockvs/ui/tools/qsar/chart.py
src/amdockvs/ui/tools/qsar/panels.py
src/amdockvs/ui/viewers/__init__.py
src/amdockvs/ui/viewers/interactions_3d.py
src/amdockvs/ui/viewers/ketcher_editor.py
src/amdockvs/ui/viewers/molecular_viewer.py
src/amdockvs/ui/visualization/__init__.py
src/amdockvs/ui/visualization/chart_controller.py
src/amdockvs/workflows/__init__.py
src/amdockvs/workflows/orchestrator.py
src/amdockvs/workflows/rules.py
src/amdockvs/workflows/steps.py
test/payload_seed.py
test/test_2d_preview_settings.py
test/test_adgpu.py
test/test_amdock_benchmark.py
test/test_amdock_runtime.py
test/test_amdock_ui.py
test/test_async_query.py
test/test_boron_docking.py
test/test_build_ui.py
test/test_catalog_toolbar.py
test/test_chemistry_payloads.py
test/test_chemistry_pipeline.py
test/test_chemistry_state.py
test/test_cif_assembly_chains.py
test/test_clusters_view.py
test/test_cocrystal_descriptors.py
test/test_codes.py
test/test_core_payloads.py
test/test_deletion.py
test/test_diagram_dock.py
test/test_diagram_follows_results.py
test/test_diversity_representatives.py
test/test_docking_extensibility.py
test/test_docking_ligand_efficiency.py
test/test_docking_ligand_scope.py
test/test_docking_methods.py
test/test_docking_phase4.py
test/test_docking_poses.py
test/test_docking_preconditions.py
test/test_docking_rerun.py
test/test_docking_scope_filters.py
test/test_docking_skip_existing.py
test/test_docking_studio_steps.py
test/test_docking_tutorial.py
test/test_domain_repositories.py
test/test_downloads.py
test/test_esmfold.py
test/test_export.py
test/test_export_ui.py
test/test_external_tools.py
test/test_formats.py
test/test_fragment_split.py
test/test_freeze_watchdog.py
test/test_gnina.py
test/test_grid_box_widget.py
test/test_hit_materialization.py
test/test_home.py
test/test_host_env.py
test/test_htp_screening.py
test/test_icons.py
test/test_import_batches.py
test/test_import_binding_sites.py
test/test_import_payload_sharing.py
test/test_import_record_spans.py
test/test_import_rows.py
test/test_import_stats.py
test/test_import_toolbar.py
test/test_import_writes_last.py
test/test_interactions_3d.py
test/test_io_parsers.py
test/test_io_payloads.py
test/test_job_adapter.py
test/test_job_dependencies.py
test/test_job_output_specs.py
test/test_ketcher_editor.py
test/test_ligand_columns.py
test/test_ligand_import_table.py
test/test_ligand_store.py
test/test_light_workers.py
test/test_metric_columns.py
test/test_molecule_editing.py
test/test_molecule_indexes.py
test/test_naive_datetime_columns.py
test/test_notifications.py
test/test_number_locale.py
test/test_offtarget_colors.py
test/test_offtarget_pymol.py
test/test_opengl_startup.py
test/test_orchestrator.py
test/test_p2rank.py
test/test_pdb_proximity_fallback.py
test/test_pose_diagram.py
test/test_preparation_stream.py
test/test_preview_tabs.py
test/test_project_mode.py
test/test_project_storage.py
test/test_project_switch_shutdown.py
test/test_props_offload.py
test/test_protonation.py
test/test_pymol_multiple_selection.py
test/test_pymol_ribbon.py
test/test_qsar_activities.py
test/test_qsar_e2e.py
test/test_qsar_modeling.py
test/test_qvina.py
test/test_readers_payloads.py
test/test_receptor_hetero.py
test/test_receptor_import_variant.py
test/test_receptor_metals.py
test/test_receptor_preview_contacts.py
test/test_redock_keeps_results.py
test/test_redocking_rmsd.py
test/test_results_pivot.py
test/test_rigid_rings.py
test/test_ro5_column.py
test/test_run_destinations.py
test/test_scope.py
test/test_scope_feed_agreement.py
test/test_settings_defaults.py
test/test_settings_tools_filter.py
test/test_shard_batching.py
test/test_shard_details.py
test/test_shard_docking.py
test/test_shard_generations.py
test/test_shard_identity.py
test/test_shard_preparation.py
test/test_shard_queue.py
test/test_shard_reductions.py
test/test_slim_library_row.py
test/test_splash.py
test/test_standardization.py
test/test_storage_panel.py
test/test_tab_close_button.py
test/test_table_first_row.py
test/test_table_scope.py
test/test_tool_stack.py
test/test_tutorial_help.py
test/test_tutorials_panel.py
test/test_ui_api_boundary.py
test/test_ui_job_feedback.py
test/test_unidock.py
test/test_unified_screening_backend.py
test/test_user_env.py
test/test_viewer_payloads.py
test/test_welcome_page.py
test/test_workflow_steps.py
test/benchmarks/bench_docking_steps.py
test/benchmarks/bench_import_scale.py
test/benchmarks/bench_project_files.py
test/benchmarks/bench_storage_formats.py
test/benchmarks/bench_table_backends.py
test/benchmarks/results/docking_steps_2026-10-17.html
test/benchmarks/results/docking_steps_2026-10-17.jsonl
test/benchmarks/results/docking_steps_2026-10-17.md
test/benchmarks/results/import_scale_2026-10-23.jsonl
test/benchmarks/results/import_scale_2026-10-24.jsonl
test/benchmarks/results/storage_formats_2026-10-22.jsonl
test/data/1s63_ligand.pdbqt
test/data/1s63_zn_site.pdbqt
test/data/README.md
test/data/ccd_ligand.cif
test/data/ccd_ligand.pdb
test/e2e/simple_docking_walkthrough.py
test/e2e/smoke_diversity.py
test/e2e/smoke_full_pipeline.py
test/e2e/smoke_qsar_simple.py
test/e2e/test_amdock_dual_sdf_import_concurrency.py
test/e2e/test_amdock_screening_load_profiles.py
test/e2e/test_htpvs_shard_pipeline.py
test/e2e/test_simple_docking_tutorial.py
test/e2e/screenshots/simple_docking/README.md
test/e2e/screenshots/simple_docking/create-project.png
test/e2e/screenshots/simple_docking/import-ligand.png
test/e2e/screenshots/simple_docking/import-receptor.png
test/e2e/screenshots/simple_docking/welcome.png
test/e2e/screenshots/simple_docking/native/README.md
test/e2e/screenshots/simple_docking/native/completed.png
test/e2e/screenshots/simple_docking/native/graphics.json
test/e2e/screenshots/simple_docking/native/pymol-native-window.png