.gitignore
LICENSE
README.md
pyproject.toml
zensical.toml
.github/workflows/docs.yml
.github/workflows/publish.yml
docs/api_reference.md
docs/examples.md
docs/index.md
docs/runtime_api.md
docs/images/favicon.svg
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/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/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/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/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/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/vina.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/openbabel.toml
src/amdockvs/integrations/tools/pkasso.toml
src/amdockvs/integrations/tools/qvina.toml
src/amdockvs/io/__init__.py
src/amdockvs/io/_common.py
src/amdockvs/io/api.py
src/amdockvs/io/ccd_bonds.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/base.py
src/amdockvs/models/clustering.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/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/summaries.py
src/amdockvs/qsar/__init__.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/main_window.py
src/amdockvs/ui/registry.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/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/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/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/favicon.svg
src/amdockvs/ui/resources/icons/file-plus.svg
src/amdockvs/ui/resources/icons/filter.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/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/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_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/view_coordinator.py
src/amdockvs/ui/tools/__init__.py
src/amdockvs/ui/tools/import_workspace.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/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/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/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_build_ui.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_deletion.py
test/test_distributed_file_contracts.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_phase4.py
test/test_docking_preconditions.py
test/test_docking_scope_filters.py
test/test_docking_skip_existing.py
test/test_domain_repositories.py
test/test_esmfold.py
test/test_external_tools.py
test/test_formats.py
test/test_fragment_split.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_binding_sites.py
test/test_import_record_spans.py
test/test_import_rows.py
test/test_import_stats.py
test/test_import_writes_last.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_ligand_store.py
test/test_light_workers.py
test/test_metric_columns.py
test/test_mode_badge.py
test/test_naive_datetime_columns.py
test/test_notifications.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_switch_shutdown.py
test/test_props_offload.py
test/test_protonation.py
test/test_pymol_ribbon.py
test/test_pymol_scene_memory.py
test/test_qsar_activities.py
test/test_qsar_e2e.py
test/test_qsar_modeling.py
test/test_qvina.py
test/test_receptor_hetero.py
test/test_receptor_import_variant.py
test/test_redock_keeps_results.py
test/test_redocking_rmsd.py
test/test_results_pivot.py
test/test_run_destinations.py
test/test_scope.py
test/test_scope_feed_agreement.py
test/test_settings_defaults.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_splash.py
test/test_standardization.py
test/test_tab_close_button.py
test/test_table_scope.py
test/test_ui_api_boundary.py
test/test_ui_job_feedback.py
test/test_unified_screening_backend.py
test/test_user_env.py
test/test_workflow_steps.py
test/data/README.md
test/data/ccd_ligand.cif
test/data/ccd_ligand.pdb
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