OCDocker.OCScore package

Subpackages

• OCDocker.OCScore.Analysis package
  • Subpackages
    • OCDocker.OCScore.Analysis.Metrics package
      • Submodules
      • Module contents
    • OCDocker.OCScore.Analysis.Plotting package
      • Modules
      • plot_combined_metric_scatter()
      • plot_boxplots()
      • plot_barplots()
      • plot_scatterplot()
      • plot_bar_with_significance()
      • plot_heatmap()
      • plot_normality_and_variance_diagnostics()
      • plot_pca_importance_barplot()
      • plot_pca_importance_histogram()
      • save_pca_importance_groups()
      • save_pca_importance_bins()
      • set_color_mapping()
      • Submodules
    • OCDocker.OCScore.Analysis.SHAP package
      • Submodules
      • Module contents
  • Submodules
    • OCDocker.OCScore.Analysis.ProductionBaselines module
      • PRODUCTION_BASELINE_RANK_METRICS
      • ProductionBaselineConfig
      • TrainOnlyFitError
      • aggregate_baseline_rows()
      • build_baseline_rank_table()
      • evaluate_individual_sf_baselines()
      • evaluate_sf_consensus_baselines()
      • evaluate_descriptor_aggregate_baselines()
      • evaluate_learned_sf_baselines()
      • run_and_write_production_baselines()
      • run_production_baselines_for_replica()
      • validate_fit_uses_train_only()
      • write_production_baseline_reports()
  • Module contents
    • Modules (current / staged pipeline)
• OCDocker.OCScore.CLI package
  • Submodules
    • OCDocker.OCScore.CLI.reduce module
      • prepare_dudez_dataframe()
      • add_arguments()
      • build_argparser()
      • register_subparser()
      • cmd_reduce()
      • main()
      • main_from_args()
    • OCDocker.OCScore.CLI.train module
      • ReductionArtifacts
      • StagedTrainingRun
      • add_arguments()
      • build_argparser()
      • register_subparser()
      • cmd_train()
      • resolve_reduction_source()
      • load_selected_features()
      • load_reduced_datasets()
      • load_reduction_artifacts()
      • load_merged_input_dataset()
      • apply_train_only_feature_reduction()
      • validate_selected_features()
      • prepare_pdbbind_for_optuna()
      • prepare_dudez_for_optuna()
      • copy_feature_reduction_artifacts()
      • build_protocol_context()
      • write_example_outputs()
      • main()
      • main_from_args()
    • OCDocker.OCScore.CLI.export_tools module
      • DUDEZ_DATASET_VALUES
      • register_subparsers()
      • main()
  • Module contents
    • register_subparsers()
• OCDocker.OCScore.Optimization package
  • Module contents
    • Modules
  • Submodules
    • OCDocker.OCScore.Optimization.ModelCrossValidation module
      • CrossValidationConfig
      • CrossValidationFoldResult
      • CrossValidationResult
      • build_scorer_comparison_summary()
      • diagnose_entity_overlap()
      • evaluate_scoring_function_baselines_on_fold()
      • identify_scoring_function_columns()
      • infer_higher_is_better()
      • iter_receptor_group_kfold_indices()
      • iter_row_kfold_indices()
      • run_cross_validation_from_export()
      • save_cross_validation_result()
      • validate_fold_indices()
      • validate_fold_split()
      • validate_receptor_group_split()
    • OCDocker.OCScore.Optimization.ModelExport module
      • export_best_model_bundle()
      • load_exported_model()
      • predict_from_export()
      • retrain_from_export()
      • transform_export_features()
      • validate_export_bundle()
      • validate_export_features()
    • OCDocker.OCScore.Optimization.OptunaSearchSpace module
      • OptimizerSearchSpace
      • EncoderSearchSpace
      • ProjectionSearchSpace
      • DecoderSearchSpace
      • PDBbindHeadSearchSpace
      • DUDEzHeadSearchSpace
      • SharedNeuralSearchSpace
      • PDBbindSearchSpaceConfig
      • DUDEzSearchSpaceConfig
      • validate_pdbbind_search_phase()
      • pdbbind_search_space_for_phase()
      • available_activation_options()
      • activation_is_available()
      • build_activation_module()
      • search_space_to_summary()
    • OCDocker.OCScore.Optimization.OptunaStorage module
      • configure_sqlite_wal()
      • resolve_optuna_storage()
    • OCDocker.OCScore.Optimization.Protocol module
      • ProtocolContext
      • ProtocolStage
      • ReplicaResult
      • ReplicatedProtocolConfig
      • ReplicatedProtocolResult
      • ReplicatedStagedProtocol
      • StagedProtocol
    • OCDocker.OCScore.Optimization.StagedOptuna module
      • DUDEzOptunaConfig
      • DUDEzOptunaStage
      • DUDEzScreeningModel
      • FeatureExtractor
      • PDBbindOptunaConfig
      • PDBbindOptunaStage
      • PDBbindRegressionModel
      • TransferFeatureExtractorStage
      • apply_fine_tuning_mode()
      • build_dudez_model()
      • build_pdbbind_model()
      • compute_regression_reconstruction_loss()
      • derive_dudez_labels()
      • dudez_search_space_summary()
      • evaluate_regression_metrics()
      • pdbbind_phase1_experiment_config()
      • pdbbind_search_space_summary()
      • prepare_dudez_screening_data()
      • summarize_dudez_split_diagnostics()
      • prepare_pdbbind_regression_data()
      • resolve_dudez_primary_metric()
      • run_staged_ocscore_optuna_protocol()
      • suggest_decoder_hidden_sizes()
      • suggest_dudez_trial_params()
      • suggest_encoder_architecture()
      • suggest_pdbbind_trial_params()
    • OCDocker.OCScore.Optimization.StagedTrainProtocol module
      • AblationProtocolSection
      • StagedTrainProtocol
      • bundled_protocol_names()
      • load_staged_train_protocol()
      • normalize_ablation_variant_name()
      • resolve_protocol_path()
• OCDocker.OCScore.Utils package
  • Submodules
    • OCDocker.OCScore.Utils.ContentHash module
      • hash_bytes()
      • hash_dataframe_partition()
      • hash_feature_list()
      • hash_file()
      • hash_json_dict()
      • hash_split_indices()
      • hash_text()
    • OCDocker.OCScore.Utils.Data module
      • apply_pca()
      • get_column_order()
      • invert_values_conditionally()
      • norm_data()
      • remove_other_columns()
      • reorder_columns_to_match_data_order()
    • OCDocker.OCScore.Utils.DescriptorAggregateBaselines module
      • evaluate_descriptor_aggregate_baselines_on_fold()
      • evaluate_descriptor_aggregates_by_group()
      • evaluate_sf_consensus_baselines_on_fold()
      • evaluate_sf_consensus_by_group()
      • format_descriptor_aggregate_scorer()
      • format_sf_consensus_scorer()
      • row_aggregate_feature_scores()
      • row_aggregate_sf_scores()
      • scorer_type_for_baseline_name()
    • OCDocker.OCScore.Utils.DUDEzScaling module
      • DUDEzScalingConfig
      • scale_dudez_features()
      • scaling_config_to_dict()
    • OCDocker.OCScore.Utils.DUDEzSplit module
      • DUDEzSplitConfig
      • DUDEzSplitResult
      • dudez_receptor_heldout_complete_config()
      • split_dudez_by_receptor_and_kind()
    • OCDocker.OCScore.Utils.ExternalBlindEvaluation module
      • ExternalBlindConfig
      • run_external_blind_evaluation()
    • OCDocker.OCScore.Utils.FeaturePolicy module
      • CandidateFeatureDiscovery
      • FeaturePolicy
      • FeaturePolicyApplication
      • FeaturePolicyDiscovery
      • apply_feature_policy()
      • discover_candidate_model_features()
      • discover_feature_policies()
      • feature_policy_from_mapping()
      • feature_policy_to_yaml_text()
      • load_feature_policy()
      • resolve_requested_feature_policies()
      • write_feature_policy_metadata()
    • OCDocker.OCScore.Utils.FeatureReduction module
      • API Surface
      • Rewiring Notes
      • Versioning Notes
      • API Reference
    • OCDocker.OCScore.Utils.FeatureSelectionMetadata module
      • FeatureSelectionScope
      • attach_feature_hashes()
      • load_feature_selection_json()
      • validate_train_only_feature_selection()
      • verify_selected_features_against_scope()
      • write_feature_selection_fit_rows_json()
      • write_feature_selection_json()
    • OCDocker.OCScore.Utils.FixedOuterSplit module
      • FixedOuterSplitAssignment
      • build_fixed_outer_split_assignment()
      • build_replica_split_alignment_metadata()
      • validate_protocol_integrity()
      • load_fixed_outer_split()
      • validate_replica_split_alignment()
      • write_fixed_outer_split_json()
    • OCDocker.OCScore.Utils.IO module
      • LOGGER
      • get_models_dir()
      • load_data()
      • load_mask()
      • load_object()
      • save_mask()
      • save_object()
      • read_csv_column_names()
      • pdbbind_columns_from_header()
      • dudez_columns_from_header()
      • read_pipeline_csv_columns()
      • load_pipeline_results_from_archive()
      • load_pipeline_results()
      • drop_empty_input_rows()
      • prepare_pdbbind_dataframe()
      • prepare_dudez_dataframe()
    • OCDocker.OCScore.Utils.LeakageAudit module
      • LeakageAuditResult
      • LeakageFinding
      • run_leakage_audit()
      • write_leakage_audit_report()
    • OCDocker.OCScore.Utils.PDBbindSplit module
      • PDBbindSplitConfig
      • PDBbindSplitResult
      • split_pdbbind_regression()
    • OCDocker.OCScore.Utils.ProtocolProvenance module
      • build_split_assignments_payload()
      • write_production_provenance_bundle()
    • OCDocker.OCScore.Utils.RawModelingInput module
      • RawModelingInput
      • align_and_concatenate_inputs()
      • discover_raw_modeling_input_columns()
      • load_raw_modeling_input()
      • reject_precomputed_training_artifacts()
      • validate_raw_schema()
      • write_prepare_manifest()
    • OCDocker.OCScore.Utils.TrainOnlyFeatureReduction module
      • SelectedFeatureRowCleanupResult
      • TrainOnlyReductionArtifact
      • apply_frozen_feature_selection()
      • drop_nonfinite_selected_feature_rows()
      • feature_reduction_config_for_feature_blocks()
      • fit_train_only_feature_reduction()
      • load_train_only_reduction_artifact()
      • split_wide_dataset_by_column()
      • write_train_only_reduction_artifact()
  • Module contents
    • Modules (current / staged pipeline)
• Bundled OCScore protocol data
  • Training protocols
  • Feature-policy ablations

Submodules

• OCDocker.OCScore.Scoring module
  • get_score()

Module contents

OCScore package for scoring and ranking docking poses.

Usage:

import OCDocker.OCScore as ocscore

Packages

• Analysis: Analysis workflows and plotting.

• DNN: Deep neural network utilities.

• Dimensionality: Dimensionality reduction utilities.

• Optimization: Model training and optimization pipelines.

• Transformer: Transformer training utilities.

• Utils: Shared OCScore utilities.

• XGBoost: XGBoost utilities.

Modules

• Scoring: Model loading and scoring pipelines.

Current OCScore pipeline: feature reduction, staged Optuna, export, analysis, and scoring.