Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | Z _ __init__() (OCDocker.Docking.Future.Dock3.Dock3 method) (OCDocker.Docking.Future.Dock6.Dock6 method) (OCDocker.Docking.Future.GEMDOCK.GEMDOCK method) (OCDocker.Docking.Future.Ledock.Ledock method) (OCDocker.Docking.Future.RDock.Dock3 method) (OCDocker.Docking.Gnina.Gnina method) (OCDocker.Docking.PLANTS.PLANTS method) (OCDocker.Docking.Smina.Smina method) (OCDocker.Docking.Vina.Vina method) (OCDocker.Ligand.Ligand method) (OCDocker.OCScore.Optimization.Protocol.ReplicatedStagedProtocol method) (OCDocker.OCScore.Optimization.StagedOptuna.DUDEzOptunaStage method) (OCDocker.OCScore.Optimization.StagedOptuna.PDBbindOptunaStage method) (OCDocker.Receptor.Receptor method) (OCDocker.Workbench.Jobs.JobError method) (OCDocker.Workbench.Jobs.JobManager method) (OCDocker.Workbench.Server.WorkbenchAPIError method) __repr__() (OCDocker.DB.Models.Base.Base class method) (OCDocker.Ligand.Ligand method) A ablation (OCDocker.OCScore.Optimization.StagedTrainProtocol.StagedTrainProtocol attribute) ablation_container_paths() (in module OCDocker.Workbench.OCScoreLayout) AblationProtocolSection (class in OCDocker.OCScore.Optimization.StagedTrainProtocol) accurate_line (OCDocker.Config.GninaConfig attribute) (OCDocker.Config.SminaConfig attribute) activation_is_available() (in module OCDocker.OCScore.Optimization.OptunaSearchSpace) activation_options (OCDocker.OCScore.Optimization.OptunaSearchSpace.SharedNeuralSearchSpace attribute) add_arguments() (in module OCDocker.OCScore.CLI.reduce) (in module OCDocker.OCScore.CLI.train) add_dynamic_columns() (OCDocker.DB.Models.Base.Base class method) addH (OCDocker.Config.GninaConfig attribute) aggregate_baseline_rows() (in module OCDocker.OCScore.Analysis.ProductionBaselines) aggregate_cv_per_target_metrics() (in module OCDocker.OCScore.Analysis.Plotting.CrossValidationPlots) aggregate_group_classification_metrics() (in module OCDocker.OCScore.Analysis.Metrics.Ranking) aggregate_group_metric() (in module OCDocker.OCScore.Analysis.Metrics.Ranking) aggregate_scoring_function_metrics (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationResult attribute) aggregate_summary (OCDocker.OCScore.Optimization.Protocol.ReplicatedProtocolResult attribute) aggregate_validation_metrics (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationResult attribute) align_and_concatenate_inputs() (in module OCDocker.OCScore.Utils.RawModelingInput) allDescriptors (OCDocker.DB.Models.Complexes.Complexes attribute), [1] (OCDocker.DB.Models.Ligands.Ligands attribute), [1] (OCDocker.DB.Models.Receptors.Receptors attribute), [1] (OCDocker.Ligand.Ligand attribute) (OCDocker.Receptor.Receptor attribute) allow_empty_policy (OCDocker.OCScore.Utils.FeaturePolicy.FeaturePolicy attribute) allow_missing_exclude_features (OCDocker.OCScore.Utils.FeaturePolicy.FeaturePolicy attribute) allow_scratch (OCDocker.OCScore.Optimization.StagedOptuna.DUDEzOptunaConfig attribute) allow_unsafe_runtime() (in module OCDocker.Toolbox.Security) allowed_roots() (OCDocker.Workbench.OptunaDashboard.OptunaDashboardManager method) apply_basic_style() (in module OCDocker.OCScore.Analysis.Plotting.Core) apply_calibration_report_mode_to_metrics() (in module OCDocker.OCScore.Analysis.Metrics.Calibration) apply_feature_drops() (in module OCDocker.OCScore.Utils.FeatureReduction) apply_feature_policy() (in module OCDocker.OCScore.Utils.FeaturePolicy) apply_fine_tuning_mode() (in module OCDocker.OCScore.Optimization.StagedOptuna) apply_frozen_feature_selection() (in module OCDocker.OCScore.Utils.TrainOnlyFeatureReduction) apply_pca() (in module OCDocker.OCScore.Utils.Data) apply_train_only_feature_reduction() (in module OCDocker.OCScore.CLI.train) approximation (OCDocker.Config.GninaConfig attribute) (OCDocker.Config.SminaConfig attribute) ArchitectureBlock (class in OCDocker.OCScore.Analysis.Plotting.ArchitecturePlots) ArchitectureDiagram (class in OCDocker.OCScore.Analysis.Plotting.ArchitecturePlots) Aromaticity (OCDocker.DB.Models.Receptors.Receptors attribute) (OCDocker.Receptor.Receptor attribute) artifact_paths (OCDocker.OCScore.CLI.train.ReductionArtifacts attribute) (OCDocker.OCScore.Utils.RawModelingInput.RawModelingInput attribute) artifacts (OCDocker.OCScore.Analysis.SHAP.Paths.OutputPaths attribute) (OCDocker.OCScore.CLI.train.StagedTrainingRun attribute) (OCDocker.OCScore.Optimization.Protocol.ProtocolContext attribute) Asphericity (OCDocker.DB.Models.Ligands.Ligands attribute) assign_feature_families() (in module OCDocker.OCScore.Analysis.SHAP.Plots) atom_term_data (OCDocker.Config.GninaConfig attribute) atom_terms (OCDocker.Config.GninaConfig attribute) attach_feature_hashes() (in module OCDocker.OCScore.Utils.FeatureSelectionMetadata) autobox_add (OCDocker.Config.GninaConfig attribute) autobox_extend (OCDocker.Config.GninaConfig attribute) autobox_ligand (OCDocker.Config.GninaConfig attribute) AUTOCORR2D_1 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_10 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_100 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_101 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_102 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_103 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_104 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_105 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_106 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_107 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_108 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_109 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_11 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_110 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_111 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_112 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_113 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_114 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_115 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_116 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_117 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_118 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_119 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_12 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_120 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_121 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_122 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_123 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_124 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_125 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_126 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_127 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_128 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_129 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_13 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_130 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_131 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_132 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_133 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_134 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_135 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_136 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_137 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_138 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_139 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_14 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_140 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_141 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_142 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_143 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_144 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_145 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_146 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_147 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_148 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_149 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_15 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_150 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_151 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_152 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_153 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_154 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_155 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_156 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_157 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_158 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_159 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_16 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_160 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_161 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_162 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_163 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_164 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_165 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_166 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_167 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_168 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_169 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_17 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_170 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_171 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_172 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_173 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_174 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_175 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_176 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_177 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_178 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_179 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_18 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_180 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_181 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_182 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_183 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_184 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_185 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_186 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_187 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_188 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_189 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_19 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_190 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_191 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_192 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_2 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_20 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_21 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_22 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_23 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_24 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_25 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_26 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_27 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_28 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_29 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_3 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_30 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_31 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_32 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_33 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_34 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_35 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_36 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_37 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_38 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_39 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_4 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_40 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_41 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_42 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_43 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_44 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_45 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_46 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_47 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_48 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_49 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_5 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_50 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_51 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_52 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_53 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_54 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_55 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_56 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_57 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_58 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_59 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_6 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_60 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_61 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_62 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_63 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_64 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_65 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_66 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_67 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_68 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_69 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_7 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_70 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_71 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_72 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_73 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_74 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_75 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_76 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_77 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_78 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_79 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_8 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_80 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_81 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_82 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_83 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_84 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_85 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_86 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_87 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_88 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_89 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_9 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_90 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_91 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_92 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_93 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_94 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_95 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_96 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_97 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_98 (OCDocker.DB.Models.Ligands.Ligands attribute) AUTOCORR2D_99 (OCDocker.DB.Models.Ligands.Ligands attribute) auxiliary (OCDocker.OCScore.Analysis.Plotting.ArchitecturePlots.ArchitectureDiagram attribute) available_activation_options() (in module OCDocker.OCScore.Optimization.OptunaSearchSpace) available_cores (OCDocker.Config.OCDockerConfig attribute) available_names (OCDocker.OCScore.Utils.FeaturePolicy.FeaturePolicyDiscovery property) available_schema_names() (in module OCDocker.Workbench.Schema) available_template_names() (in module OCDocker.Workbench.Templates) AvgAALength (OCDocker.DB.Models.Receptors.Receptors attribute) (OCDocker.Receptor.Receptor attribute) B backend (OCDocker.Config.DatabaseConfig attribute) (OCDocker.DB.DBMinimal.DatabaseSettings attribute) backup_log() (in module OCDocker.Toolbox.Logging) BalabanJ (OCDocker.DB.Models.Ligands.Ligands attribute) balance_by (OCDocker.OCScore.Utils.DUDEzSplit.DUDEzSplitConfig attribute) Base (class in OCDocker.DB.Models.Base) base (in module OCDocker.DB.Models.Base) base_seed (OCDocker.OCScore.Optimization.Protocol.ReplicatedProtocolConfig attribute) batch_size_options (OCDocker.OCScore.Optimization.OptunaSearchSpace.OptimizerSearchSpace attribute) BCUT2D_CHGHI (OCDocker.DB.Models.Ligands.Ligands attribute) BCUT2D_CHGLO (OCDocker.DB.Models.Ligands.Ligands attribute) BCUT2D_LOGPHI (OCDocker.DB.Models.Ligands.Ligands attribute) BCUT2D_LOGPLOW (OCDocker.DB.Models.Ligands.Ligands attribute) BCUT2D_MRHI (OCDocker.DB.Models.Ligands.Ligands attribute) BCUT2D_MRLOW (OCDocker.DB.Models.Ligands.Ligands attribute) BCUT2D_MWHI (OCDocker.DB.Models.Ligands.Ligands attribute) BCUT2D_MWLOW (OCDocker.DB.Models.Ligands.Ligands attribute) bedroc() (in module OCDocker.OCScore.Analysis.Metrics.Ranking) bedroc_alpha (OCDocker.OCScore.Analysis.ProductionBaselines.ProductionBaselineConfig attribute) (OCDocker.OCScore.Optimization.StagedOptuna.DUDEzOptunaConfig attribute) beeswarm() (in module OCDocker.OCScore.Analysis.SHAP.Plots) beeswarm_png (OCDocker.OCScore.Analysis.SHAP.Paths.OutputPaths attribute) BertzCT (OCDocker.DB.Models.Ligands.Ligands attribute) binary_threshold_youden() (in module OCDocker.OCScore.Analysis.Metrics.Ranking) blind_csv (OCDocker.OCScore.Utils.ExternalBlindEvaluation.ExternalBlindConfig attribute) blocks (OCDocker.OCScore.Utils.FeaturePolicy.CandidateFeatureDiscovery attribute) bootstrap_ci() (in module OCDocker.OCScore.Analysis.Metrics.Bootstrap) box_path (OCDocker.Ligand.Ligand attribute) box_to_plants() (in module OCDocker.Docking.PLANTS) box_to_vina() (in module OCDocker.Docking.Vina) budget_dict() (OCDocker.OCScore.Optimization.StagedTrainProtocol.StagedTrainProtocol method) build_ablation_analysis() (in module OCDocker.Workbench.Ablation) build_ablation_design_context() (in module OCDocker.Workbench.AblationDesign) build_ablation_protocol_similarity_analysis() (in module OCDocker.Workbench.AblationProtocolSimilarity) build_activation_module() (in module OCDocker.OCScore.Optimization.OptunaSearchSpace) build_adoption_plan() (in module OCDocker.Workbench.Adoption) build_analysis_report() (in module OCDocker.Workbench.Report) build_argparser() (in module OCDocker.OCScore.CLI.reduce) (in module OCDocker.OCScore.CLI.train) build_artifact_index() (in module OCDocker.Workbench.Artifacts) build_baseline_rank_table() (in module OCDocker.OCScore.Analysis.ProductionBaselines) build_calibration_report_section() (in module OCDocker.OCScore.Analysis.Metrics.Calibration) build_campaign_script() (in module OCDocker.Workbench.Jobs) build_campaign_snakemake_command() (in module OCDocker.Workbench.Jobs) build_charmm_to_canonical_map() (in module OCDocker.Toolbox.MoleculeProcessing) build_database_urls() (in module OCDocker.DB.DBMinimal) build_dudez_model() (in module OCDocker.OCScore.Optimization.StagedOptuna) build_evidence_index() (in module OCDocker.Workbench.Evidence) build_feature_reduction_protocol() (in module OCDocker.OCScore.Utils.FeatureReduction) build_fixed_outer_split_assignment() (in module OCDocker.OCScore.Utils.FixedOuterSplit) build_json_schema() (in module OCDocker.Workbench.Schema) build_launch_script() (in module OCDocker.Workbench.Launch) build_leaderboard_plot() (in module OCDocker.Workbench.Plots) build_log_file_preview() (in module OCDocker.Workbench.Logs) build_metric_leaderboard() (in module OCDocker.Workbench.Leaderboard) build_metric_matrix() (in module OCDocker.Workbench.MetricsMatrix) build_metric_scatter_plot() (in module OCDocker.Workbench.Plots) build_metrics_catalog() (in module OCDocker.Workbench.Decision) build_namespace() (in module OCDocker.Console.session) build_ocdocker_mcp_server() (in module OCDocker.MCP) (in module OCDocker.MCP.Server) build_ocscore_workspace() (in module OCDocker.Workbench.OCScoreLayout) build_parallel_coordinates_plot() (in module OCDocker.Workbench.Plots) build_pareto_front() (in module OCDocker.Workbench.Decision) build_pareto_scatter_plot() (in module OCDocker.Workbench.Plots) build_parser() (in module OCDocker.CLI) build_pdbbind_model() (in module OCDocker.OCScore.Optimization.StagedOptuna) build_pose_engine_map() (in module OCDocker.Processing.Preprocessing.RMSDClustering) build_protocol_context() (in module OCDocker.OCScore.CLI.train) build_publication_export() (in module OCDocker.Workbench.Export) build_reduced_dataframe() (in module OCDocker.OCScore.Utils.FeatureReduction) build_replica_split_alignment_metadata() (in module OCDocker.OCScore.Utils.FixedOuterSplit) build_run_bundle() (in module OCDocker.Workbench.Bundle) build_run_comparison() (in module OCDocker.Workbench.Comparison) build_run_detail() (in module OCDocker.Workbench.RunDetail) build_run_launch_plan() (in module OCDocker.Workbench.Launch) build_run_manifest() (in module OCDocker.Workbench.Planner) build_schema_catalog() (in module OCDocker.Workbench.Schema) build_scorer_comparison_summary() (in module OCDocker.OCScore.Optimization.ModelCrossValidation) build_split_assignments_payload() (in module OCDocker.OCScore.Utils.ProtocolProvenance) build_template_payload() (in module OCDocker.Workbench.Templates) build_template_spec() (in module OCDocker.Workbench.Templates) build_workbench_api_app() (in module OCDocker.Workbench.Server) build_workbench_api_payload() (in module OCDocker.Workbench.Server) build_workbench_web_asset() (in module OCDocker.Workbench.Web) build_workspace_overview() (in module OCDocker.Workbench.Overview) bundled_protocol_names() (in module OCDocker.OCScore.Optimization.StagedTrainProtocol) C C_to_K() (in module OCDocker.Toolbox.Constants) CAL_TO_J (in module OCDocker.Toolbox.Constants) cal_to_J() (in module OCDocker.Toolbox.Constants) calibration_method (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationConfig attribute) calibration_metric_names() (in module OCDocker.OCScore.Analysis.Metrics.Calibration) calibration_report_mode (OCDocker.OCScore.Optimization.StagedOptuna.DUDEzOptunaConfig attribute) cancel() (OCDocker.Workbench.Jobs.JobManager method) candidate_features (OCDocker.OCScore.Utils.FeaturePolicy.CandidateFeatureDiscovery attribute) candidate_features_before_policy (OCDocker.OCScore.Utils.FeaturePolicy.FeaturePolicyApplication attribute) CandidateFeatureDiscovery (class in OCDocker.OCScore.Utils.FeaturePolicy) Chi0 (OCDocker.DB.Models.Ligands.Ligands attribute) Chi0n (OCDocker.DB.Models.Ligands.Ligands attribute) Chi0v (OCDocker.DB.Models.Ligands.Ligands attribute) Chi1 (OCDocker.DB.Models.Ligands.Ligands attribute) Chi1n (OCDocker.DB.Models.Ligands.Ligands attribute) Chi1v (OCDocker.DB.Models.Ligands.Ligands attribute) Chi2n (OCDocker.DB.Models.Ligands.Ligands attribute) Chi2v (OCDocker.DB.Models.Ligands.Ligands attribute) Chi3n (OCDocker.DB.Models.Ligands.Ligands attribute) Chi3v (OCDocker.DB.Models.Ligands.Ligands attribute) Chi4n (OCDocker.DB.Models.Ligands.Ligands attribute) Chi4v (OCDocker.DB.Models.Ligands.Ligands attribute) chimera (OCDocker.Config.ToolsConfig attribute) chunk_size (OCDocker.Config.ODDTConfig attribute) class_func() (in module OCDocker.Ligand) classification_metrics_at_threshold() (in module OCDocker.OCScore.Analysis.Metrics.Ranking) classifier_dropout_max (OCDocker.OCScore.Optimization.OptunaSearchSpace.DUDEzHeadSearchSpace attribute) classifier_dropout_min (OCDocker.OCScore.Optimization.OptunaSearchSpace.DUDEzHeadSearchSpace attribute) classifier_hidden_size_options (OCDocker.OCScore.Optimization.OptunaSearchSpace.DUDEzHeadSearchSpace attribute) classify_policies_by_eligibility_and_shortcut_risk() (in module OCDocker.OCScore.Analysis.Plotting.Stats) classify_policies_by_shortcut_rule() (in module OCDocker.OCScore.Analysis.Plotting.Stats) clean (OCDocker.Ligand.Ligand attribute) clean_for_dssp() (in module OCDocker.Toolbox.MoleculeProcessing) clean_pdb_file() (in module OCDocker.Toolbox.MoleculeProcessing) clean_source_path (OCDocker.Receptor.Receptor attribute) clean_test_files() (in module OCDocker.Console.session) cleaned_df (OCDocker.OCScore.Utils.TrainOnlyFeatureReduction.SelectedFeatureRowCleanupResult attribute) cleanup_dead() (OCDocker.Workbench.OptunaDashboard.OptunaDashboardManager method) cleanup_engine() (in module OCDocker.DB.DBMinimal) cleanup_session() (in module OCDocker.DB.DBMinimal) clear_past_logs() (in module OCDocker.Toolbox.Logging) clip_probabilities() (in module OCDocker.OCScore.Analysis.Metrics.Calibration) cluster_rmsd (OCDocker.Config.PLANTSConfig attribute) cluster_rmsd() (in module OCDocker.Processing.Preprocessing.RMSDClustering) cluster_structures (OCDocker.Config.PLANTSConfig attribute) cmd_ablations() (in module OCDocker.CLI.workbench) cmd_adopt() (in module OCDocker.CLI.workbench) cmd_adopt_plan() (in module OCDocker.CLI.workbench) cmd_artifacts() (in module OCDocker.CLI.workbench) cmd_build() (in module OCDocker.CLI.workbench) cmd_check() (in module OCDocker.CLI.workbench) cmd_compare() (in module OCDocker.CLI.workbench) cmd_evidence() (in module OCDocker.CLI.workbench) cmd_export() (in module OCDocker.CLI.workbench) cmd_inventory() (in module OCDocker.CLI.workbench) cmd_launch_plan() (in module OCDocker.CLI.workbench) cmd_leaderboard() (in module OCDocker.CLI.workbench) cmd_logs() (in module OCDocker.CLI.workbench) cmd_metrics_catalog() (in module OCDocker.CLI.workbench) cmd_metrics_matrix() (in module OCDocker.CLI.workbench) cmd_overview() (in module OCDocker.CLI.workbench) cmd_pareto() (in module OCDocker.CLI.workbench) cmd_plan() (in module OCDocker.CLI.workbench) cmd_plot() (in module OCDocker.CLI.workbench) cmd_reduce() (in module OCDocker.OCScore.CLI.reduce) cmd_report() (in module OCDocker.CLI.workbench) cmd_results() (in module OCDocker.CLI.workbench) cmd_schema() (in module OCDocker.CLI.workbench) cmd_serve() (in module OCDocker.CLI.workbench) cmd_status() (in module OCDocker.CLI.workbench) cmd_template() (in module OCDocker.CLI.workbench) cmd_train() (in module OCDocker.OCScore.CLI.train) cmd_validate() (in module OCDocker.CLI.workbench) cmd_workbench() (in module OCDocker.CLI.workbench) cnn (OCDocker.Config.GninaConfig attribute) cnn_center_x (OCDocker.Config.GninaConfig attribute) cnn_center_y (OCDocker.Config.GninaConfig attribute) cnn_center_z (OCDocker.Config.GninaConfig attribute) cnn_empirical_weight (OCDocker.Config.GninaConfig attribute) cnn_mix_emp_energy (OCDocker.Config.GninaConfig attribute) cnn_mix_emp_force (OCDocker.Config.GninaConfig attribute) cnn_model (OCDocker.Config.GninaConfig attribute) cnn_models (OCDocker.Config.GninaConfig attribute) cnn_rotation (OCDocker.Config.GninaConfig attribute) cnn_scoring (OCDocker.Config.GninaConfig attribute) cnn_verbose (OCDocker.Config.GninaConfig attribute) code (OCDocker.OCScore.Utils.LeakageAudit.LeakageFinding attribute) collect_calibration_report_issues() (in module OCDocker.OCScore.Analysis.Metrics.Calibration) collect_periodically() (in module OCDocker.Processing.GarbageCollection) command (OCDocker.OCScore.Utils.ExternalBlindEvaluation.ExternalBlindConfig attribute) Complexes (class in OCDocker.DB.Models.Complexes) complexes (OCDocker.DB.Models.Ligands.Ligands attribute), [1] (OCDocker.DB.Models.Receptors.Receptors attribute), [1] compose_selected_features() (in module OCDocker.OCScore.Utils.FeatureReduction) compute_aromaticity() (in module OCDocker.Receptor) compute_cross_block_correlations() (in module OCDocker.OCScore.Utils.FeatureReduction) compute_cross_block_predictability() (in module OCDocker.OCScore.Utils.FeatureReduction) compute_dipole_moment() (in module OCDocker.Receptor) compute_family_importance_table() (in module OCDocker.OCScore.Analysis.SHAP.Plots) compute_feature_importance_table() (in module OCDocker.OCScore.Analysis.SHAP.Plots) compute_gravy() (in module OCDocker.Receptor) compute_instability_index() (in module OCDocker.Receptor) compute_intra_block_correlations() (in module OCDocker.OCScore.Utils.FeatureReduction) compute_isoelectric_point() (in module OCDocker.Receptor) compute_label_family_distribution_table() (in module OCDocker.OCScore.Analysis.SHAP.Plots) compute_regression_reconstruction_loss() (in module OCDocker.OCScore.Optimization.StagedOptuna) compute_sasa() (in module OCDocker.Receptor) compute_shap_values() (in module OCDocker.OCScore.Analysis.SHAP.Explain) compute_target_family_shap_table() (in module OCDocker.OCScore.Analysis.SHAP.Plots) config (OCDocker.OCScore.Optimization.Protocol.ReplicatedStagedProtocol attribute) configure() (in module OCDocker.Toolbox.Logging) configure_sqlite_wal() (in module OCDocker.OCScore.Optimization.OptunaStorage) confusion_counts() (in module OCDocker.OCScore.Analysis.Metrics.Ranking) context (OCDocker.OCScore.CLI.train.StagedTrainingRun attribute) (OCDocker.OCScore.Optimization.Protocol.ReplicaResult attribute) continue_on_replica_failure (OCDocker.OCScore.Optimization.Protocol.ReplicatedProtocolConfig attribute) convert_dG_to_Ki_Kd() (in module OCDocker.Toolbox.Constants) convert_Ki_Kd_to_dG() (in module OCDocker.Toolbox.Constants) convert_mols() (in module OCDocker.Toolbox.Conversion) convert_mols_from_string() (in module OCDocker.Toolbox.Conversion) convert_pdb_charmm_to_canonical() (in module OCDocker.Toolbox.MoleculeProcessing) copy_feature_reduction_artifacts() (in module OCDocker.OCScore.CLI.train) count_AAs_and_chains() (in module OCDocker.Receptor) count_surface_AA() (in module OCDocker.Receptor) countA (OCDocker.DB.Models.Receptors.Receptors attribute) countC (OCDocker.DB.Models.Receptors.Receptors attribute) countChain (OCDocker.DB.Models.Receptors.Receptors attribute) (OCDocker.Receptor.Receptor attribute) countD (OCDocker.DB.Models.Receptors.Receptors attribute) countE (OCDocker.DB.Models.Receptors.Receptors attribute) countF (OCDocker.DB.Models.Receptors.Receptors attribute) countG (OCDocker.DB.Models.Receptors.Receptors attribute) countH (OCDocker.DB.Models.Receptors.Receptors attribute) countI (OCDocker.DB.Models.Receptors.Receptors attribute) countK (OCDocker.DB.Models.Receptors.Receptors attribute) countL (OCDocker.DB.Models.Receptors.Receptors attribute) countM (OCDocker.DB.Models.Receptors.Receptors attribute) countN (OCDocker.DB.Models.Receptors.Receptors attribute) countP (OCDocker.DB.Models.Receptors.Receptors attribute) countQ (OCDocker.DB.Models.Receptors.Receptors attribute) countR (OCDocker.DB.Models.Receptors.Receptors attribute) countS (OCDocker.DB.Models.Receptors.Receptors attribute) countT (OCDocker.DB.Models.Receptors.Receptors attribute) countV (OCDocker.DB.Models.Receptors.Receptors attribute) countW (OCDocker.DB.Models.Receptors.Receptors attribute) countY (OCDocker.DB.Models.Receptors.Receptors attribute) covalent_bond_order (OCDocker.Config.GninaConfig attribute) covalent_fix_lig_atom_position (OCDocker.Config.GninaConfig attribute) covalent_lig_atom_pattern (OCDocker.Config.GninaConfig attribute) covalent_lig_atom_position (OCDocker.Config.GninaConfig attribute) covalent_optimize_lig (OCDocker.Config.GninaConfig attribute) covalent_rec_atom (OCDocker.Config.GninaConfig attribute) cpu (OCDocker.Config.GninaConfig attribute) create_box() (OCDocker.Ligand.Ligand method) create_database() (in module OCDocker.DB.DBMinimal) create_database_if_not_exists() (in module OCDocker.DB.DBMinimal) create_engine() (in module OCDocker.DB.DBMinimal) create_session() (in module OCDocker.DB.DBMinimal) create_tables() (in module OCDocker.DB.DB) created_at (OCDocker.DB.Models.Base.Base attribute) (OCDocker.DB.Models.Complexes.Complexes attribute) (OCDocker.DB.Models.Ligands.Ligands attribute) (OCDocker.DB.Models.Receptors.Receptors attribute) CrossValidationConfig (class in OCDocker.OCScore.Optimization.ModelCrossValidation) CrossValidationFoldResult (class in OCDocker.OCScore.Optimization.ModelCrossValidation) CrossValidationResult (class in OCDocker.OCScore.Optimization.ModelCrossValidation) custom_atoms (OCDocker.Config.GninaConfig attribute) (OCDocker.Config.SminaConfig attribute) custom_scoring (OCDocker.Config.GninaConfig attribute) (OCDocker.Config.SminaConfig attribute) D database (OCDocker.Config.DatabaseConfig attribute) (OCDocker.Config.OCDockerConfig attribute) (OCDocker.DB.DBMinimal.DatabaseSettings attribute) database_exists() (in module OCDocker.DB.DBMinimal) DatabaseConfig (class in OCDocker.Config) DatabaseConfigurationError DatabaseConnectionError DatabaseCreationError DatabaseCreationNotAllowedError DatabaseError DatabaseSettings (class in OCDocker.DB.DBMinimal) DEBUG (OCDocker.Error.ReportLevel attribute) decoder (OCDocker.OCScore.Optimization.OptunaSearchSpace.PDBbindSearchSpaceConfig attribute) (OCDocker.OCScore.Optimization.StagedOptuna.PDBbindRegressionModel attribute) DecoderSearchSpace (class in OCDocker.OCScore.Optimization.OptunaSearchSpace) DEFAULT_SCREENING_COMPARISON_METRICS (in module OCDocker.OCScore.Analysis.Metrics.Ranking) delete() (OCDocker.DB.Models.Base.Base class method) depth_options (OCDocker.OCScore.Optimization.OptunaSearchSpace.DecoderSearchSpace attribute) (OCDocker.OCScore.Optimization.OptunaSearchSpace.EncoderSearchSpace attribute) derive_dudez_labels() (in module OCDocker.OCScore.Optimization.StagedOptuna) description (OCDocker.OCScore.Optimization.StagedTrainProtocol.StagedTrainProtocol attribute) (OCDocker.OCScore.Utils.FeaturePolicy.FeaturePolicy attribute) descriptors_names (OCDocker.DB.Models.Complexes.Complexes attribute) (OCDocker.DB.Models.Receptors.Receptors attribute) (OCDocker.Ligand.Ligand attribute) (OCDocker.Receptor.Receptor attribute) detail (OCDocker.OCScore.Analysis.Plotting.ArchitecturePlots.ArchitectureBlock attribute) details (OCDocker.OCScore.Utils.LeakageAudit.LeakageFinding attribute) determine_column_type() (OCDocker.DB.Models.Base.Base class method) device (OCDocker.Config.GninaConfig attribute) (OCDocker.OCScore.Utils.ExternalBlindEvaluation.ExternalBlindConfig attribute) df_to_dict() (in module OCDocker.Rescoring.ODDT) diagnose_entity_overlap() (in module OCDocker.OCScore.Optimization.ModelCrossValidation) diagnostics (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationFoldResult attribute) (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationResult attribute) (OCDocker.OCScore.Utils.DUDEzSplit.DUDEzSplitResult attribute) (OCDocker.OCScore.Utils.PDBbindSplit.PDBbindSplitResult attribute) dim (OCDocker.OCScore.Analysis.Plotting.ArchitecturePlots.ArchitectureBlock attribute) DipoleMoment (OCDocker.DB.Models.Receptors.Receptors attribute) (OCDocker.Receptor.Receptor attribute) direction (OCDocker.OCScore.Optimization.StagedOptuna.DUDEzOptunaConfig attribute) (OCDocker.OCScore.Optimization.StagedOptuna.PDBbindOptunaConfig attribute) discover_ablation_input_features() (in module OCDocker.Workbench.AblationDesign) discover_candidate_model_features() (in module OCDocker.OCScore.Utils.FeaturePolicy) discover_feature_policies() (in module OCDocker.OCScore.Utils.FeaturePolicy) discover_free_ports() (in module OCDocker.Workbench.OptunaDashboard) discover_raw_modeling_input_columns() (in module OCDocker.OCScore.Utils.RawModelingInput) discover_result_manifest_paths() (in module OCDocker.Workbench.Registry) discover_run_manifest_paths() (in module OCDocker.Workbench.Registry) discover_vs_campaign_candidates() (in module OCDocker.Workbench.VSDesign) discover_vs_design_candidates() (in module OCDocker.Workbench.VSDesign) Dock3 (class in OCDocker.Docking.Future.Dock3) (class in OCDocker.Docking.Future.RDock) Dock6 (class in OCDocker.Docking.Future.Dock6) dock6 (OCDocker.Config.OCDockerConfig attribute) Dock6Config (class in OCDocker.Config) done_marker (OCDocker.API.Pipeline.PipelineRunResult attribute) (OCDocker.API.PipelineRunResult attribute) download_url() (in module OCDocker.Toolbox.Downloading) DownloadProgressBar (class in OCDocker.Toolbox.Downloading) drop_empty_input_rows() (in module OCDocker.OCScore.Utils.IO) drop_nonfinite_selected_feature_rows() (in module OCDocker.OCScore.Utils.TrainOnlyFeatureReduction) drop_rows_with_missing_values() (in module OCDocker.OCScore.Utils.FeatureReduction) dropout_max (OCDocker.OCScore.Optimization.OptunaSearchSpace.EncoderSearchSpace attribute) dropout_min (OCDocker.OCScore.Optimization.OptunaSearchSpace.EncoderSearchSpace attribute) dropped_rows (OCDocker.OCScore.Utils.TrainOnlyFeatureReduction.SelectedFeatureRowCleanupResult attribute) dssp (OCDocker.Config.ToolsConfig attribute) dudez (OCDocker.OCScore.Optimization.StagedTrainProtocol.StagedTrainProtocol attribute) dudez_archive (OCDocker.Config.OCDockerConfig attribute) dudez_columns_from_header() (in module OCDocker.OCScore.Utils.IO) DUDEZ_DATASET_VALUES (in module OCDocker.OCScore.CLI.export_tools) dudez_df (OCDocker.OCScore.CLI.train.ReductionArtifacts attribute) (OCDocker.OCScore.CLI.train.StagedTrainingRun attribute) (OCDocker.OCScore.Optimization.Protocol.ProtocolContext attribute) dudez_download (OCDocker.Config.ToolsConfig attribute) dudez_hash (OCDocker.OCScore.Utils.RawModelingInput.RawModelingInput attribute) dudez_head (OCDocker.OCScore.Optimization.OptunaSearchSpace.DUDEzSearchSpaceConfig attribute) dudez_receptor_heldout_complete_config() (in module OCDocker.OCScore.Utils.DUDEzSplit) dudez_scaling_config (OCDocker.OCScore.Optimization.StagedOptuna.DUDEzOptunaConfig attribute) dudez_search_space_summary() (in module OCDocker.OCScore.Optimization.StagedOptuna) dudez_source (OCDocker.OCScore.Utils.RawModelingInput.RawModelingInput attribute) dudez_test_indices (OCDocker.OCScore.Utils.FixedOuterSplit.FixedOuterSplitAssignment attribute) dudez_test_indices_hash (OCDocker.OCScore.Utils.FixedOuterSplit.FixedOuterSplitAssignment attribute) dudez_train_indices (OCDocker.OCScore.Utils.FixedOuterSplit.FixedOuterSplitAssignment attribute) dudez_train_indices_hash (OCDocker.OCScore.Utils.FixedOuterSplit.FixedOuterSplitAssignment attribute) dudez_validation_indices (OCDocker.OCScore.Utils.FixedOuterSplit.FixedOuterSplitAssignment attribute) dudez_validation_indices_hash (OCDocker.OCScore.Utils.FixedOuterSplit.FixedOuterSplitAssignment attribute) DUDEzHeadSearchSpace (class in OCDocker.OCScore.Optimization.OptunaSearchSpace) DUDEzOptunaConfig (class in OCDocker.OCScore.Optimization.StagedOptuna) DUDEzOptunaStage (class in OCDocker.OCScore.Optimization.StagedOptuna) DUDEzScalingConfig (class in OCDocker.OCScore.Utils.DUDEzScaling) DUDEzScreeningModel (class in OCDocker.OCScore.Optimization.StagedOptuna) DUDEzSearchSpaceConfig (class in OCDocker.OCScore.Optimization.OptunaSearchSpace) DUDEzSplitConfig (class in OCDocker.OCScore.Utils.DUDEzSplit) DUDEzSplitResult (class in OCDocker.OCScore.Utils.DUDEzSplit) duplicate_assignments (OCDocker.OCScore.Utils.FeaturePolicy.CandidateFeatureDiscovery attribute) E Eccentricity (OCDocker.DB.Models.Ligands.Ligands attribute) effective_folds (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationResult attribute) empty_docking_digest() (in module OCDocker.Toolbox.FilesFolders) enable_pruning (OCDocker.OCScore.Optimization.StagedOptuna.PDBbindOptunaConfig attribute) enabled (OCDocker.OCScore.Optimization.StagedTrainProtocol.AblationProtocolSection attribute) encoder (OCDocker.OCScore.Optimization.OptunaSearchSpace.SharedNeuralSearchSpace attribute) EncoderSearchSpace (class in OCDocker.OCScore.Optimization.OptunaSearchSpace) energy_range (OCDocker.Config.SminaConfig attribute) (OCDocker.Config.VinaConfig attribute) enrich_dudez_export_metrics() (in module OCDocker.OCScore.Analysis.Metrics.Calibration) enrichment_factor() (in module OCDocker.OCScore.Analysis.Metrics.Ranking) enrichment_plot() (in module OCDocker.OCScore.Analysis.Plotting.MetricsPlots) ensure_output_dir() (OCDocker.OCScore.Optimization.Protocol.ProtocolContext method) ensure_parent_dir() (in module OCDocker.Toolbox.FilesFolders) entity_columns (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationConfig attribute) env_flag_enabled() (in module OCDocker.Toolbox.Security) epochs (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationConfig attribute) (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationResult attribute) (OCDocker.OCScore.Optimization.StagedOptuna.DUDEzOptunaConfig attribute) (OCDocker.OCScore.Optimization.StagedOptuna.PDBbindOptunaConfig attribute) ERROR (OCDocker.Error.ReportLevel attribute) error (OCDocker.OCScore.Optimization.Protocol.ReplicaResult attribute) EState_VSA1 (OCDocker.DB.Models.Ligands.Ligands attribute) EState_VSA10 (OCDocker.DB.Models.Ligands.Ligands attribute) EState_VSA11 (OCDocker.DB.Models.Ligands.Ligands attribute) EState_VSA2 (OCDocker.DB.Models.Ligands.Ligands attribute) EState_VSA3 (OCDocker.DB.Models.Ligands.Ligands attribute) EState_VSA4 (OCDocker.DB.Models.Ligands.Ligands attribute) EState_VSA5 (OCDocker.DB.Models.Ligands.Ligands attribute) EState_VSA6 (OCDocker.DB.Models.Ligands.Ligands attribute) EState_VSA7 (OCDocker.DB.Models.Ligands.Ligands attribute) EState_VSA8 (OCDocker.DB.Models.Ligands.Ligands attribute) EState_VSA9 (OCDocker.DB.Models.Ligands.Ligands attribute) evaluate_calibration_metrics() (in module OCDocker.OCScore.Analysis.Metrics.Calibration) evaluate_descriptor_aggregate_baselines() (in module OCDocker.OCScore.Analysis.ProductionBaselines) evaluate_descriptor_aggregate_baselines_on_fold() (in module OCDocker.OCScore.Utils.DescriptorAggregateBaselines) evaluate_descriptor_aggregates_by_group() (in module OCDocker.OCScore.Utils.DescriptorAggregateBaselines) evaluate_individual_sf_baselines() (in module OCDocker.OCScore.Analysis.ProductionBaselines) evaluate_learned_sf_baselines() (in module OCDocker.OCScore.Analysis.ProductionBaselines) evaluate_regression_metrics() (in module OCDocker.OCScore.Optimization.StagedOptuna) evaluate_scoring_function_baselines_on_fold() (in module OCDocker.OCScore.Optimization.ModelCrossValidation) evaluate_scoring_functions_by_group() (in module OCDocker.OCScore.Analysis.Metrics.Ranking) evaluate_screening_metrics() (in module OCDocker.OCScore.Analysis.Metrics.Ranking) evaluate_screening_metrics_by_group() (in module OCDocker.OCScore.Analysis.Metrics.Ranking) evaluate_sf_consensus_baselines() (in module OCDocker.OCScore.Analysis.ProductionBaselines) evaluate_sf_consensus_baselines_on_fold() (in module OCDocker.OCScore.Utils.DescriptorAggregateBaselines) evaluate_sf_consensus_by_group() (in module OCDocker.OCScore.Utils.DescriptorAggregateBaselines) ExactMolWt (OCDocker.DB.Models.Ligands.Ligands attribute) exclude_features (OCDocker.OCScore.Utils.FeaturePolicy.FeaturePolicy attribute) exclude_patterns (OCDocker.OCScore.Utils.FeaturePolicy.FeaturePolicy attribute) excluded_features_found (OCDocker.OCScore.Utils.FeaturePolicy.FeaturePolicyApplication attribute) executable (OCDocker.Config.Dock6Config attribute) (OCDocker.Config.GninaConfig attribute) (OCDocker.Config.LeDockConfig attribute) (OCDocker.Config.PLANTSConfig attribute) (OCDocker.Config.SminaConfig attribute) (OCDocker.Config.VinaConfig attribute) exhaustiveness (OCDocker.Config.GninaConfig attribute) (OCDocker.Config.SminaConfig attribute) (OCDocker.Config.VinaConfig attribute) expected_calibration_error() (in module OCDocker.OCScore.Analysis.Metrics.Calibration) explicit_ymls (OCDocker.OCScore.Utils.FeaturePolicy.FeaturePolicyDiscovery attribute) export_best_model_bundle() (in module OCDocker.OCScore.Optimization.ModelExport) export_db_to_csv() (in module OCDocker.DB.DB) export_dir (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationResult attribute) (OCDocker.OCScore.Utils.ExternalBlindEvaluation.ExternalBlindConfig attribute) export_table_to_csv() (in module OCDocker.DB.DB) ExternalBlindConfig (class in OCDocker.OCScore.Utils.ExternalBlindEvaluation) extract_calibration_metrics() (in module OCDocker.OCScore.Analysis.Metrics.Calibration) extracted_dir (OCDocker.OCScore.CLI.train.ReductionArtifacts attribute) F factor (OCDocker.Config.GninaConfig attribute) (OCDocker.Config.SminaConfig attribute) failed_replicas (OCDocker.OCScore.Optimization.Protocol.ReplicatedProtocolResult attribute) failed_stage (OCDocker.OCScore.Optimization.Protocol.ReplicaResult attribute) feature_importance_barh() (in module OCDocker.OCScore.Analysis.SHAP.Plots) feature_importance_png (OCDocker.OCScore.Analysis.SHAP.Paths.OutputPaths attribute) feature_policy_from_mapping() (in module OCDocker.OCScore.Utils.FeaturePolicy) feature_policy_metadata (OCDocker.OCScore.CLI.train.ReductionArtifacts attribute) feature_policy_to_yaml_text() (in module OCDocker.OCScore.Utils.FeaturePolicy) feature_reduction_artifact_path (OCDocker.OCScore.Utils.FixedOuterSplit.FixedOuterSplitAssignment attribute) feature_reduction_config_for_feature_blocks() (in module OCDocker.OCScore.Utils.TrainOnlyFeatureReduction) feature_selection (OCDocker.OCScore.CLI.train.ReductionArtifacts attribute) (OCDocker.OCScore.Utils.TrainOnlyFeatureReduction.TrainOnlyReductionArtifact attribute) feature_selection_fit_row_count (OCDocker.OCScore.Utils.FixedOuterSplit.FixedOuterSplitAssignment attribute) feature_selection_fit_split (OCDocker.OCScore.Utils.FixedOuterSplit.FixedOuterSplitAssignment attribute) feature_selection_mode (OCDocker.OCScore.Utils.FeatureSelectionMetadata.FeatureSelectionScope attribute) feature_selection_scope (OCDocker.OCScore.Utils.FixedOuterSplit.FixedOuterSplitAssignment attribute) feature_selection_split_hash (OCDocker.OCScore.Utils.FixedOuterSplit.FixedOuterSplitAssignment attribute) FeatureExtractor (class in OCDocker.OCScore.Optimization.StagedOptuna) FeaturePolicy (class in OCDocker.OCScore.Utils.FeaturePolicy) FeaturePolicyApplication (class in OCDocker.OCScore.Utils.FeaturePolicy) FeaturePolicyDiscovery (class in OCDocker.OCScore.Utils.FeaturePolicy) FeatureSelectionScope (class in OCDocker.OCScore.Utils.FeatureSelectionMetadata) filter_correlated_features() (in module OCDocker.OCScore.Utils.FeatureReduction) filter_cross_block_redundant_features() (in module OCDocker.OCScore.Utils.FeatureReduction) final_candidate_features_before_reduction (OCDocker.OCScore.Utils.FeaturePolicy.FeaturePolicyApplication attribute) find() (OCDocker.DB.Models.Base.Base class method) find_all() (OCDocker.DB.Models.Base.Base class method) find_all_iter() (OCDocker.DB.Models.Base.Base class method) find_all_names() (OCDocker.DB.Models.Base.Base class method) find_all_names_iter() (OCDocker.DB.Models.Base.Base class method) find_attribute() (OCDocker.DB.Models.Base.Base class method) find_attribute_iter() (OCDocker.DB.Models.Base.Base class method) find_constant_features() (in module OCDocker.OCScore.Utils.FeatureReduction) find_duplicate_features() (in module OCDocker.OCScore.Utils.FeatureReduction) find_first() (OCDocker.DB.Models.Base.Base class method) find_iter() (OCDocker.DB.Models.Base.Base class method) find_near_constant_features() (in module OCDocker.OCScore.Utils.FeatureReduction) findAsphericity() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_1() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_10() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_100() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_101() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_102() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_103() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_104() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_105() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_106() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_107() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_108() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_109() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_11() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_110() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_111() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_112() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_113() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_114() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_115() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_116() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_117() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_118() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_119() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_12() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_120() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_121() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_122() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_123() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_124() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_125() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_126() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_127() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_128() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_129() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_13() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_130() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_131() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_132() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_133() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_134() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_135() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_136() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_137() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_138() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_139() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_14() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_140() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_141() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_142() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_143() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_144() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_145() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_146() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_147() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_148() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_149() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_15() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_150() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_151() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_152() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_153() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_154() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_155() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_156() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_157() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_158() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_159() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_16() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_160() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_161() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_162() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_163() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_164() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_165() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_166() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_167() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_168() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_169() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_17() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_170() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_171() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_172() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_173() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_174() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_175() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_176() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_177() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_178() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_179() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_18() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_180() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_181() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_182() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_183() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_184() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_185() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_186() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_187() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_188() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_189() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_19() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_190() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_191() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_192() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_2() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_20() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_21() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_22() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_23() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_24() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_25() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_26() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_27() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_28() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_29() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_3() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_30() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_31() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_32() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_33() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_34() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_35() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_36() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_37() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_38() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_39() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_4() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_40() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_41() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_42() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_43() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_44() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_45() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_46() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_47() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_48() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_49() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_5() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_50() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_51() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_52() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_53() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_54() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_55() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_56() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_57() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_58() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_59() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_6() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_60() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_61() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_62() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_63() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_64() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_65() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_66() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_67() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_68() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_69() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_7() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_70() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_71() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_72() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_73() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_74() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_75() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_76() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_77() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_78() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_79() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_8() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_80() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_81() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_82() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_83() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_84() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_85() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_86() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_87() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_88() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_89() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_9() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_90() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_91() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_92() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_93() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_94() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_95() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_96() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_97() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_98() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findAUTOCORR2D_99() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findBalabanJ() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findBCUT2D_CHGHI() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findBCUT2D_CHGLO() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findBCUT2D_LOGPHI() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findBCUT2D_LOGPLOW() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findBCUT2D_MRHI() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findBCUT2D_MRLOW() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findBCUT2D_MWHI() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findBCUT2D_MWLOW() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findBertzCT() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findChi0() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findChi0n() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findChi0v() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findChi1() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findChi1n() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findChi1v() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findChi2n() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findChi2v() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findChi3n() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findChi3v() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findChi4n() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findChi4v() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findEccentricity() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findEState_VSA1() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findEState_VSA10() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findEState_VSA11() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findEState_VSA2() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findEState_VSA3() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findEState_VSA4() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findEState_VSA5() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findEState_VSA6() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findEState_VSA7() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findEState_VSA8() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findEState_VSA9() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findExactMolWt() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findFpDensityMorgan1() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findFpDensityMorgan2() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findFpDensityMorgan3() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_Al_COO() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_Al_OH() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_Al_OH_noTert() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_aldehyde() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_alkyl_carbamate() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_alkyl_halide() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_allylic_oxid() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_amide() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_amidine() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_aniline() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_Ar_COO() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_Ar_N() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_Ar_NH() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_Ar_OH() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_ArN() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_aryl_methyl() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_azide() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_azo() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_barbitur() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_benzene() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_benzodiazepine() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_bicyclic() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_C_O() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_C_O_noCOO() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_C_S() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_COO() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_COO2() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_diazo() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_dihydropyridine() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_epoxide() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_ester() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_ether() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_furan() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_guanido() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_halogen() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_hdrzine() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_hdrzone() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_HOCCN() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_imidazole() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_imide() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_Imine() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_isocyan() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_isothiocyan() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_ketone() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_ketone_Topliss() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_lactam() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_lactone() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_methoxy() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_morpholine() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_N_O() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_Ndealkylation1() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_Ndealkylation2() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_NH0() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_NH1() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_NH2() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_Nhpyrrole() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_nitrile() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_nitro() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_nitro_arom() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_nitro_arom_nonortho() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_nitroso() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_oxazole() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_oxime() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_para_hydroxylation() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_phenol() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_phenol_noOrthoHbond() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_phos_acid() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_phos_ester() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_piperdine() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_piperzine() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_priamide() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_prisulfonamd() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_pyridine() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_quatN() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_SH() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_sulfide() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_sulfonamd() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_sulfone() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_term_acetylene() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_tetrazole() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_thiazole() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_thiocyan() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_thiophene() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_unbrch_alkane() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findfr_urea() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findFractionCSP3() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findHallKierAlpha() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findHeavyAtomCount() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findHeavyAtomMolWt() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findInertialShapeFactor() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findings (OCDocker.OCScore.Utils.LeakageAudit.LeakageAuditResult attribute) findKappa1() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findKappa2() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findKappa3() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findLabuteASA() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findMaxAbsEStateIndex() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findMaxAbsPartialCharge() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findMaxEStateIndex() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findMaxPartialCharge() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findMinAbsEStateIndex() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findMinAbsPartialCharge() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findMinEStateIndex() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findMinPartialCharge() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findMolLogP() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findMolMR() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findMolWt() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findNHOHCount() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findNOCount() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findNPR1() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findNPR2() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findNumAliphaticCarbocycles() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findNumAliphaticHeterocycles() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findNumAliphaticRings() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findNumAromaticCarbocycles() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findNumAromaticHeterocycles() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findNumAromaticRings() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findNumHAcceptors() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findNumHDonors() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findNumHeteroatoms() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findNumRadicalElectrons() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findNumRotatableBonds() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findNumSaturatedCarbocycles() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findNumSaturatedHeterocycles() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findNumSaturatedRings() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findNumValenceElectrons() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findPEOE_VSA1() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findPEOE_VSA10() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findPEOE_VSA11() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findPEOE_VSA12() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findPEOE_VSA13() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findPEOE_VSA14() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findPEOE_VSA2() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findPEOE_VSA3() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findPEOE_VSA4() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findPEOE_VSA5() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findPEOE_VSA6() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findPEOE_VSA7() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findPEOE_VSA8() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findPEOE_VSA9() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findPMI1() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findPMI2() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findPMI3() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findqed() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findRadiusOfGyration() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findRingCount() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findSlogP_VSA1() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findSlogP_VSA10() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findSlogP_VSA11() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findSlogP_VSA12() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findSlogP_VSA2() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findSlogP_VSA3() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findSlogP_VSA4() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findSlogP_VSA5() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findSlogP_VSA6() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findSlogP_VSA7() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findSlogP_VSA8() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findSlogP_VSA9() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findSMR_VSA1() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findSMR_VSA10() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findSMR_VSA2() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findSMR_VSA3() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findSMR_VSA4() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findSMR_VSA5() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findSMR_VSA6() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findSMR_VSA7() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findSMR_VSA8() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findSMR_VSA9() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findSpherocityIndex() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findTPSA() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findVSA_EState1() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findVSA_EState10() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findVSA_EState2() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findVSA_EState3() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findVSA_EState4() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findVSA_EState5() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findVSA_EState6() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findVSA_EState7() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findVSA_EState8() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) findVSA_EState9() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) fine_tuning_mode_options (OCDocker.OCScore.Optimization.OptunaSearchSpace.DUDEzHeadSearchSpace attribute) fit() (OCDocker.OCScore.Analysis.Metrics.Calibration.ProbabilityCalibrator class method) fit_dataset (OCDocker.OCScore.Utils.FeatureSelectionMetadata.FeatureSelectionScope attribute) fit_row_content_hash (OCDocker.OCScore.Utils.FeatureSelectionMetadata.FeatureSelectionScope attribute) fit_row_count (OCDocker.OCScore.Utils.FeatureSelectionMetadata.FeatureSelectionScope attribute) fit_row_indices (OCDocker.OCScore.Utils.FeatureSelectionMetadata.FeatureSelectionScope attribute) fit_row_indices_artifact (OCDocker.OCScore.Utils.FeatureSelectionMetadata.FeatureSelectionScope attribute) fit_row_indices_hash (OCDocker.OCScore.Utils.FeatureSelectionMetadata.FeatureSelectionScope attribute) fit_split (OCDocker.OCScore.Utils.FeatureSelectionMetadata.FeatureSelectionScope attribute) fit_train_only_feature_reduction() (in module OCDocker.OCScore.Utils.TrainOnlyFeatureReduction) fixed_outer_split (OCDocker.OCScore.CLI.train.ReductionArtifacts attribute) FixedOuterSplitAssignment (class in OCDocker.OCScore.Utils.FixedOuterSplit) flex (OCDocker.Config.GninaConfig attribute) flex_defn_file (OCDocker.Config.Dock6Config attribute) flex_drive_file (OCDocker.Config.Dock6Config attribute) flex_limit (OCDocker.Config.GninaConfig attribute) flex_max (OCDocker.Config.GninaConfig attribute) flexdist (OCDocker.Config.GninaConfig attribute) flexdist_ligand (OCDocker.Config.GninaConfig attribute) flexres (OCDocker.Config.GninaConfig attribute) fold_index (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationFoldResult attribute) fold_results (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationResult attribute) forbidden_dataset_hashes (OCDocker.OCScore.Utils.ExternalBlindEvaluation.ExternalBlindConfig attribute) force_cap (OCDocker.Config.GninaConfig attribute) (OCDocker.Config.SminaConfig attribute) format_descriptor_aggregate_scorer() (in module OCDocker.OCScore.Utils.DescriptorAggregateBaselines) format_sf_consensus_scorer() (in module OCDocker.OCScore.Utils.DescriptorAggregateBaselines) forward() (OCDocker.OCScore.Optimization.StagedOptuna.DUDEzScreeningModel method) (OCDocker.OCScore.Optimization.StagedOptuna.FeatureExtractor method) (OCDocker.OCScore.Optimization.StagedOptuna.PDBbindRegressionModel method) FpDensityMorgan1 (OCDocker.DB.Models.Ligands.Ligands attribute) (OCDocker.Ligand.Ligand attribute) FpDensityMorgan2 (OCDocker.DB.Models.Ligands.Ligands attribute) (OCDocker.Ligand.Ligand attribute) FpDensityMorgan3 (OCDocker.DB.Models.Ligands.Ligands attribute) (OCDocker.Ligand.Ligand attribute) fr_Al_COO (OCDocker.DB.Models.Ligands.Ligands attribute) fr_Al_OH (OCDocker.DB.Models.Ligands.Ligands attribute) fr_Al_OH_noTert (OCDocker.DB.Models.Ligands.Ligands attribute) fr_aldehyde (OCDocker.DB.Models.Ligands.Ligands attribute) fr_alkyl_carbamate (OCDocker.DB.Models.Ligands.Ligands attribute) fr_alkyl_halide (OCDocker.DB.Models.Ligands.Ligands attribute) fr_allylic_oxid (OCDocker.DB.Models.Ligands.Ligands attribute) fr_amide (OCDocker.DB.Models.Ligands.Ligands attribute) fr_amidine (OCDocker.DB.Models.Ligands.Ligands attribute) fr_aniline (OCDocker.DB.Models.Ligands.Ligands attribute) fr_Ar_COO (OCDocker.DB.Models.Ligands.Ligands attribute) fr_Ar_N (OCDocker.DB.Models.Ligands.Ligands attribute) fr_Ar_NH (OCDocker.DB.Models.Ligands.Ligands attribute) fr_Ar_OH (OCDocker.DB.Models.Ligands.Ligands attribute) fr_ArN (OCDocker.DB.Models.Ligands.Ligands attribute) fr_aryl_methyl (OCDocker.DB.Models.Ligands.Ligands attribute) fr_azide (OCDocker.DB.Models.Ligands.Ligands attribute) fr_azo (OCDocker.DB.Models.Ligands.Ligands attribute) fr_barbitur (OCDocker.DB.Models.Ligands.Ligands attribute) fr_benzene (OCDocker.DB.Models.Ligands.Ligands attribute) fr_benzodiazepine (OCDocker.DB.Models.Ligands.Ligands attribute) fr_bicyclic (OCDocker.DB.Models.Ligands.Ligands attribute) fr_C_O (OCDocker.DB.Models.Ligands.Ligands attribute) fr_C_O_noCOO (OCDocker.DB.Models.Ligands.Ligands attribute) fr_C_S (OCDocker.DB.Models.Ligands.Ligands attribute) fr_COO (OCDocker.DB.Models.Ligands.Ligands attribute) fr_COO2 (OCDocker.DB.Models.Ligands.Ligands attribute) fr_diazo (OCDocker.DB.Models.Ligands.Ligands attribute) fr_dihydropyridine (OCDocker.DB.Models.Ligands.Ligands attribute) fr_epoxide (OCDocker.DB.Models.Ligands.Ligands attribute) fr_ester (OCDocker.DB.Models.Ligands.Ligands attribute) fr_ether (OCDocker.DB.Models.Ligands.Ligands attribute) fr_furan (OCDocker.DB.Models.Ligands.Ligands attribute) fr_guanido (OCDocker.DB.Models.Ligands.Ligands attribute) fr_halogen (OCDocker.DB.Models.Ligands.Ligands attribute) fr_hdrzine (OCDocker.DB.Models.Ligands.Ligands attribute) fr_hdrzone (OCDocker.DB.Models.Ligands.Ligands attribute) fr_HOCCN (OCDocker.DB.Models.Ligands.Ligands attribute) fr_imidazole (OCDocker.DB.Models.Ligands.Ligands attribute) fr_imide (OCDocker.DB.Models.Ligands.Ligands attribute) fr_Imine (OCDocker.DB.Models.Ligands.Ligands attribute) fr_isocyan (OCDocker.DB.Models.Ligands.Ligands attribute) fr_isothiocyan (OCDocker.DB.Models.Ligands.Ligands attribute) fr_ketone (OCDocker.DB.Models.Ligands.Ligands attribute) fr_ketone_Topliss (OCDocker.DB.Models.Ligands.Ligands attribute) fr_lactam (OCDocker.DB.Models.Ligands.Ligands attribute) fr_lactone (OCDocker.DB.Models.Ligands.Ligands attribute) fr_methoxy (OCDocker.DB.Models.Ligands.Ligands attribute) fr_morpholine (OCDocker.DB.Models.Ligands.Ligands attribute) fr_N_O (OCDocker.DB.Models.Ligands.Ligands attribute) fr_Ndealkylation1 (OCDocker.DB.Models.Ligands.Ligands attribute) fr_Ndealkylation2 (OCDocker.DB.Models.Ligands.Ligands attribute) fr_NH0 (OCDocker.DB.Models.Ligands.Ligands attribute) fr_NH1 (OCDocker.DB.Models.Ligands.Ligands attribute) fr_NH2 (OCDocker.DB.Models.Ligands.Ligands attribute) fr_Nhpyrrole (OCDocker.DB.Models.Ligands.Ligands attribute) fr_nitrile (OCDocker.DB.Models.Ligands.Ligands attribute) fr_nitro (OCDocker.DB.Models.Ligands.Ligands attribute) fr_nitro_arom (OCDocker.DB.Models.Ligands.Ligands attribute) fr_nitro_arom_nonortho (OCDocker.DB.Models.Ligands.Ligands attribute) fr_nitroso (OCDocker.DB.Models.Ligands.Ligands attribute) fr_oxazole (OCDocker.DB.Models.Ligands.Ligands attribute) fr_oxime (OCDocker.DB.Models.Ligands.Ligands attribute) fr_para_hydroxylation (OCDocker.DB.Models.Ligands.Ligands attribute) fr_phenol (OCDocker.DB.Models.Ligands.Ligands attribute) fr_phenol_noOrthoHbond (OCDocker.DB.Models.Ligands.Ligands attribute) fr_phos_acid (OCDocker.DB.Models.Ligands.Ligands attribute) fr_phos_ester (OCDocker.DB.Models.Ligands.Ligands attribute) fr_piperdine (OCDocker.DB.Models.Ligands.Ligands attribute) fr_piperzine (OCDocker.DB.Models.Ligands.Ligands attribute) fr_priamide (OCDocker.DB.Models.Ligands.Ligands attribute) fr_prisulfonamd (OCDocker.DB.Models.Ligands.Ligands attribute) fr_pyridine (OCDocker.DB.Models.Ligands.Ligands attribute) fr_quatN (OCDocker.DB.Models.Ligands.Ligands attribute) fr_SH (OCDocker.DB.Models.Ligands.Ligands attribute) fr_sulfide (OCDocker.DB.Models.Ligands.Ligands attribute) fr_sulfonamd (OCDocker.DB.Models.Ligands.Ligands attribute) fr_sulfone (OCDocker.DB.Models.Ligands.Ligands attribute) fr_term_acetylene (OCDocker.DB.Models.Ligands.Ligands attribute) fr_tetrazole (OCDocker.DB.Models.Ligands.Ligands attribute) fr_thiazole (OCDocker.DB.Models.Ligands.Ligands attribute) fr_thiocyan (OCDocker.DB.Models.Ligands.Ligands attribute) fr_thiophene (OCDocker.DB.Models.Ligands.Ligands attribute) fr_unbrch_alkane (OCDocker.DB.Models.Ligands.Ligands attribute) fr_urea (OCDocker.DB.Models.Ligands.Ligands attribute) FractionCSP3 (OCDocker.DB.Models.Ligands.Ligands attribute) from_config_file() (OCDocker.Config.OCDockerConfig class method) from_dict() (OCDocker.Config.OCDockerConfig class method) (OCDocker.OCScore.Utils.FeatureSelectionMetadata.FeatureSelectionScope class method) (OCDocker.OCScore.Utils.FixedOuterSplit.FixedOuterSplitAssignment class method) from_hdf5() (in module OCDocker.Toolbox.FilesFolders) from_json_descriptors (OCDocker.Ligand.Ligand attribute) from_pickle() (in module OCDocker.Toolbox.FilesFolders) full_flex_output (OCDocker.Config.GninaConfig attribute) func() (in module OCDocker.Ligand) G gc_collect_interval() (in module OCDocker.Processing.GarbageCollection) GEMDOCK (class in OCDocker.Docking.Future.GEMDOCK) gen_gnina_conf() (in module OCDocker.Docking.Gnina) gen_smina_conf() (in module OCDocker.Docking.Smina) generate_digest() (in module OCDocker.Docking.PLANTS) (in module OCDocker.Processing.Postprocessing.Digest) generate_gnina_digest() (in module OCDocker.Docking.BaseVinaLike) generate_manifest() (in module OCDocker.Toolbox.Reproducibility) generate_plants_files_database() (in module OCDocker.Docking.PLANTS) generate_reproducibility_manifest() (in module OCDocker.Toolbox.Reproducibility) generate_smina_digest() (in module OCDocker.Docking.BaseVinaLike) generate_vina_digest() (in module OCDocker.Docking.BaseVinaLike) generate_vina_files_database() (in module OCDocker.Docking.Vina) get() (OCDocker.Workbench.Jobs.JobManager method) get_binding_site() (in module OCDocker.Docking.PLANTS) get_centroid() (in module OCDocker.Ligand) (OCDocker.Ligand.Ligand method) get_column_order() (in module OCDocker.OCScore.Utils.Data) get_config() (in module OCDocker.Config) get_db_url() (in module OCDocker.Initialise) get_default_engine() (in module OCDocker.DB.DBMinimal) get_default_session() (in module OCDocker.DB.DBMinimal) get_descriptors() (OCDocker.Ligand.Ligand method) (OCDocker.Receptor.Receptor method) get_docked_poses() (in module OCDocker.Docking.PLANTS) (OCDocker.Docking.Gnina.Gnina method) (OCDocker.Docking.PLANTS.PLANTS method) (OCDocker.Docking.Smina.Smina method) (OCDocker.Docking.Vina.Vina method) get_gnina_docked_poses() (in module OCDocker.Docking.BaseVinaLike) get_input_ligand_path() (OCDocker.Docking.Gnina.Gnina method) (OCDocker.Docking.PLANTS.PLANTS method) (OCDocker.Docking.Smina.Smina method) (OCDocker.Docking.Vina.Vina method) get_input_receptor_path() (OCDocker.Docking.Gnina.Gnina method) (OCDocker.Docking.PLANTS.PLANTS method) (OCDocker.Docking.Smina.Smina method) (OCDocker.Docking.Vina.Vina method) get_ligand_command() (OCDocker.Toolbox.Preparation.MGLToolsPreparationStrategy method) (OCDocker.Toolbox.Preparation.OpenBabelPreparationStrategy method) (OCDocker.Toolbox.Preparation.PreparationStrategy method) (OCDocker.Toolbox.Preparation.SPORESPreparationStrategy method) get_logger() (in module OCDocker.Toolbox.Logging) get_medoids() (in module OCDocker.Processing.Preprocessing.RMSDClustering) get_models() (in module OCDocker.Rescoring.ODDT) get_models_dir() (in module OCDocker.OCScore.Utils.IO) get_pose_index_from_file_path() (in module OCDocker.Docking.Gnina) (in module OCDocker.Docking.PLANTS) (in module OCDocker.Docking.Smina) (in module OCDocker.Docking.Vina) get_receptor_command() (OCDocker.Toolbox.Preparation.MGLToolsPreparationStrategy method) (OCDocker.Toolbox.Preparation.OpenBabelPreparationStrategy method) (OCDocker.Toolbox.Preparation.PreparationStrategy method) (OCDocker.Toolbox.Preparation.SPORESPreparationStrategy method) get_res() (in module OCDocker.Receptor) get_rescore_log_paths() (in module OCDocker.Docking.Gnina) (in module OCDocker.Docking.Smina) (in module OCDocker.Docking.Vina) (OCDocker.Docking.PLANTS.PLANTS method) get_rmsd() (in module OCDocker.Toolbox.MoleculeProcessing) get_rmsd_matrix() (in module OCDocker.Toolbox.MoleculeProcessing) get_score() (in module OCDocker.OCScore.Scoring) get_smiles() (in module OCDocker.Ligand) get_smina_docked_poses() (in module OCDocker.Docking.BaseVinaLike) get_vina_docked_poses() (in module OCDocker.Docking.BaseVinaLike) Gnina (class in OCDocker.Docking.Gnina) gnina (OCDocker.Config.OCDockerConfig attribute) GNINA_AD4_SCORING (OCDocker.DB.Models.Complexes.Complexes attribute) GNINA_DEFAULT (OCDocker.DB.Models.Complexes.Complexes attribute) GNINA_DKOES_FAST (OCDocker.DB.Models.Complexes.Complexes attribute) GNINA_DKOES_SCORING (OCDocker.DB.Models.Complexes.Complexes attribute) GNINA_DKOES_SCORING_OLD (OCDocker.DB.Models.Complexes.Complexes attribute) GNINA_VINA (OCDocker.DB.Models.Complexes.Complexes attribute) GNINA_VINARDO (OCDocker.DB.Models.Complexes.Complexes attribute) GninaConfig (class in OCDocker.Config) GRAVY (OCDocker.DB.Models.Receptors.Receptors attribute) (OCDocker.Receptor.Receptor attribute) group_column (OCDocker.OCScore.Analysis.ProductionBaselines.ProductionBaselineConfig attribute) (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationConfig attribute) (OCDocker.OCScore.Utils.ExternalBlindEvaluation.ExternalBlindConfig attribute) groupwise() (in module OCDocker.OCScore.Analysis.Metrics.Ranking) H HallKierAlpha (OCDocker.DB.Models.Ligands.Ligands attribute) handle_ablation_design_post() (in module OCDocker.Workbench.AblationDesign) handle_command() (in module OCDocker.Console.commands) hash_bytes() (in module OCDocker.OCScore.Utils.ContentHash) hash_dataframe_partition() (in module OCDocker.OCScore.Utils.ContentHash) hash_feature_list() (in module OCDocker.OCScore.Utils.ContentHash) hash_file() (in module OCDocker.OCScore.Utils.ContentHash) hash_json_dict() (in module OCDocker.OCScore.Utils.ContentHash) hash_split_indices() (in module OCDocker.OCScore.Utils.ContentHash) hash_text() (in module OCDocker.OCScore.Utils.ContentHash) HeavyAtomCount (OCDocker.DB.Models.Ligands.Ligands attribute) HeavyAtomMolWt (OCDocker.DB.Models.Ligands.Ligands attribute) hidden_size_options (OCDocker.OCScore.Optimization.OptunaSearchSpace.DecoderSearchSpace attribute) (OCDocker.OCScore.Optimization.OptunaSearchSpace.EncoderSearchSpace attribute) host (OCDocker.Config.DatabaseConfig attribute) (OCDocker.DB.DBMinimal.DatabaseSettings attribute) (OCDocker.Workbench.OptunaDashboard.OptunaDashboardSession attribute) huber_delta_max (OCDocker.OCScore.Optimization.OptunaSearchSpace.PDBbindHeadSearchSpace attribute) huber_delta_min (OCDocker.OCScore.Optimization.OptunaSearchSpace.PDBbindHeadSearchSpace attribute) I id (OCDocker.DB.Models.Base.Base attribute) (OCDocker.DB.Models.Complexes.Complexes attribute), [1] (OCDocker.DB.Models.Ligands.Ligands attribute), [1] (OCDocker.DB.Models.Receptors.Receptors attribute), [1] identify_scoring_function_columns() (in module OCDocker.OCScore.Optimization.ModelCrossValidation) include_calibration_metrics (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationConfig attribute) include_descriptor_aggregate_baselines (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationConfig attribute) include_descriptor_aggregates (OCDocker.OCScore.Analysis.ProductionBaselines.ProductionBaselineConfig attribute) include_features (OCDocker.OCScore.Utils.FeaturePolicy.FeaturePolicy attribute) include_lgbm (OCDocker.OCScore.Analysis.ProductionBaselines.ProductionBaselineConfig attribute) include_patterns (OCDocker.OCScore.Utils.FeaturePolicy.FeaturePolicy attribute) include_scoring_function_baselines (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationConfig attribute) include_sf_consensus (OCDocker.OCScore.Analysis.ProductionBaselines.ProductionBaselineConfig attribute) include_sf_consensus_baselines (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationConfig attribute) include_shuffle_control (OCDocker.OCScore.Analysis.ProductionBaselines.ProductionBaselineConfig attribute) include_xgb (OCDocker.OCScore.Analysis.ProductionBaselines.ProductionBaselineConfig attribute) included_features_found (OCDocker.OCScore.Utils.FeaturePolicy.FeaturePolicyApplication attribute) InertialShapeFactor (OCDocker.DB.Models.Ligands.Ligands attribute) infer_higher_is_better() (in module OCDocker.OCScore.Optimization.ModelCrossValidation) INFO (OCDocker.Error.ReportLevel attribute) insert() (OCDocker.DB.Models.Base.Base class method) insert_or_update() (OCDocker.DB.Models.Base.Base class method) inspect_run_status() (in module OCDocker.Workbench.Status) InstabilityIndex (OCDocker.DB.Models.Receptors.Receptors attribute) (OCDocker.Receptor.Receptor attribute) invert_values_conditionally() (in module OCDocker.OCScore.Utils.Data) is_algorithm_allowed() (in module OCDocker.Toolbox.Validation) is_available() (OCDocker.Workbench.OptunaDashboard.OptunaDashboardManager static method) is_calibration_metric_key() (in module OCDocker.OCScore.Analysis.Metrics.Calibration) is_molecule_valid() (in module OCDocker.Toolbox.Validation) is_molecule_valid_with_retry() (in module OCDocker.Toolbox.Validation) is_rich_enabled() (in module OCDocker.Toolbox.Logging) is_same_molecule() (OCDocker.Ligand.Ligand method) is_same_molecule_SMILES() (OCDocker.Ligand.Ligand method) is_tool_available() (in module OCDocker.Toolbox.Running) is_valid() (OCDocker.Ligand.Ligand method) (OCDocker.Receptor.Receptor method) is_valid_ranking_scores() (in module OCDocker.OCScore.Analysis.Metrics.Ranking) is_workbench_web_asset_path() (in module OCDocker.Workbench.Web) IsoelectricPoint (OCDocker.DB.Models.Receptors.Receptors attribute) (OCDocker.Receptor.Receptor attribute) iter_receptor_group_kfold_indices() (in module OCDocker.OCScore.Optimization.ModelCrossValidation) iter_row_kfold_indices() (in module OCDocker.OCScore.Optimization.ModelCrossValidation) J J_to_cal() (in module OCDocker.Toolbox.Constants) JobError JobManager (class in OCDocker.Workbench.Jobs) K K_to_C() (in module OCDocker.Toolbox.Constants) Kappa1 (OCDocker.DB.Models.Ligands.Ligands attribute) Kappa2 (OCDocker.DB.Models.Ligands.Ligands attribute) Kappa3 (OCDocker.DB.Models.Ligands.Ligands attribute) kept_mask (OCDocker.OCScore.Utils.TrainOnlyFeatureReduction.SelectedFeatureRowCleanupResult attribute) kikd_to_deltag() (in module OCDocker.Toolbox.Conversion) kind (OCDocker.OCScore.Analysis.Plotting.ArchitecturePlots.ArchitectureBlock attribute) kind_column (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationConfig attribute) (OCDocker.OCScore.Optimization.StagedOptuna.DUDEzOptunaConfig attribute) (OCDocker.OCScore.Utils.DUDEzSplit.DUDEzSplitConfig attribute) (OCDocker.OCScore.Utils.ExternalBlindEvaluation.ExternalBlindConfig attribute) L label (OCDocker.OCScore.Analysis.Plotting.ArchitecturePlots.ArchitectureBlock attribute) label_column (OCDocker.OCScore.Analysis.ProductionBaselines.ProductionBaselineConfig attribute) (OCDocker.OCScore.Utils.ExternalBlindEvaluation.ExternalBlindConfig attribute) LabuteASA (OCDocker.DB.Models.Ligands.Ligands attribute) lambda_rec_options (OCDocker.OCScore.Optimization.OptunaSearchSpace.DecoderSearchSpace attribute) latent_dim_options (OCDocker.OCScore.Optimization.OptunaSearchSpace.EncoderSearchSpace attribute) launch() (OCDocker.Workbench.Jobs.JobManager method) lazyread() (in module OCDocker.Toolbox.IO) lazyread_mmap() (in module OCDocker.Toolbox.IO) lazyread_reverse_order() (in module OCDocker.Toolbox.IO) lazyread_reverse_order_mmap() (in module OCDocker.Toolbox.IO) LeakageAuditResult (class in OCDocker.OCScore.Utils.LeakageAudit) LeakageFinding (class in OCDocker.OCScore.Utils.LeakageAudit) learning_rate_max (OCDocker.OCScore.Optimization.OptunaSearchSpace.OptimizerSearchSpace attribute) learning_rate_min (OCDocker.OCScore.Optimization.OptunaSearchSpace.OptimizerSearchSpace attribute) Ledock (class in OCDocker.Docking.Future.Ledock) ledock (OCDocker.Config.OCDockerConfig attribute) LeDockConfig (class in OCDocker.Config) lepro (OCDocker.Config.LeDockConfig attribute) Ligand (class in OCDocker.Ligand) ligand (OCDocker.DB.Models.Complexes.Complexes attribute), [1] ligand_id (OCDocker.DB.Models.Complexes.Complexes attribute), [1] Ligands (class in OCDocker.DB.Models.Ligands) list() (OCDocker.Workbench.Jobs.JobManager method) litpcba_archive (OCDocker.Config.OCDockerConfig attribute) load_architecture_document() (in module OCDocker.OCScore.Analysis.Plotting.ArchitecturePlots) load_cross_validation_artifacts() (in module OCDocker.OCScore.Analysis.Plotting.CrossValidationPlots) load_data() (in module OCDocker.OCScore.Utils.IO) load_exported_model() (in module OCDocker.OCScore.Optimization.ModelExport) load_family_spec() (in module OCDocker.OCScore.Analysis.SHAP.Plots) load_feature_policy() (in module OCDocker.OCScore.Utils.FeaturePolicy) load_feature_selection_json() (in module OCDocker.OCScore.Utils.FeatureSelectionMetadata) load_fixed_outer_split() (in module OCDocker.OCScore.Utils.FixedOuterSplit) load_if_exists (OCDocker.OCScore.Optimization.StagedOptuna.DUDEzOptunaConfig attribute) (OCDocker.OCScore.Optimization.StagedOptuna.PDBbindOptunaConfig attribute) load_mask() (in module OCDocker.OCScore.Utils.IO) load_merged_input_dataset() (in module OCDocker.OCScore.CLI.train) load_mol() (in module OCDocker.Ligand) (in module OCDocker.Receptor) load_object() (in module OCDocker.OCScore.Utils.IO) load_pipeline_results() (in module OCDocker.OCScore.Utils.IO) load_pipeline_results_from_archive() (in module OCDocker.OCScore.Utils.IO) load_raw_modeling_input() (in module OCDocker.OCScore.Utils.RawModelingInput) load_reduced_datasets() (in module OCDocker.OCScore.CLI.train) load_reduction_artifacts() (in module OCDocker.OCScore.CLI.train) load_selected_features() (in module OCDocker.OCScore.CLI.train) load_staged_train_protocol() (in module OCDocker.OCScore.Optimization.StagedTrainProtocol) load_train_only_reduction_artifact() (in module OCDocker.OCScore.Utils.TrainOnlyFeatureReduction) local_only (OCDocker.Config.GninaConfig attribute) (OCDocker.Config.SminaConfig attribute) logdir (OCDocker.Config.OCDockerConfig attribute) LOGGER (in module OCDocker.OCScore.Analysis.Plotting.Colouring) (in module OCDocker.OCScore.Utils.IO) LOGIT_CLIP (in module OCDocker.OCScore.Analysis.Metrics.Calibration) logits_to_probabilities() (in module OCDocker.OCScore.Analysis.Metrics.Calibration) logs() (OCDocker.Workbench.Jobs.JobManager method) lookup_dirs (OCDocker.OCScore.Utils.FeaturePolicy.FeaturePolicyApplication attribute) (OCDocker.OCScore.Utils.FeaturePolicy.FeaturePolicyDiscovery attribute) M main (OCDocker.OCScore.Analysis.Plotting.ArchitecturePlots.ArchitectureDiagram attribute) main() (in module OCDocker.CLI) (in module OCDocker.Console.app) (in module OCDocker.OCScore.CLI.export_tools) (in module OCDocker.OCScore.CLI.reduce) (in module OCDocker.OCScore.CLI.train) main_from_args() (in module OCDocker.OCScore.CLI.reduce) (in module OCDocker.OCScore.CLI.train) max_hidden_layers (OCDocker.OCScore.Optimization.OptunaSearchSpace.EncoderSearchSpace attribute) max_mc_steps (OCDocker.Config.GninaConfig attribute) MaxAbsEStateIndex (OCDocker.DB.Models.Ligands.Ligands attribute) MaxAbsPartialCharge (OCDocker.DB.Models.Ligands.Ligands attribute) MaxEStateIndex (OCDocker.DB.Models.Ligands.Ligands attribute) MaxPartialCharge (OCDocker.DB.Models.Ligands.Ligands attribute) merge_calibration_metrics() (in module OCDocker.OCScore.Analysis.Metrics.Calibration) merged (OCDocker.OCScore.Utils.RawModelingInput.RawModelingInput attribute) merged_hash (OCDocker.OCScore.Utils.RawModelingInput.RawModelingInput attribute) merged_source (OCDocker.OCScore.Utils.RawModelingInput.RawModelingInput attribute) message (OCDocker.OCScore.Utils.LeakageAudit.LeakageFinding attribute) metadata (OCDocker.DB.Models.Base.Base attribute) (OCDocker.OCScore.CLI.train.StagedTrainingRun attribute) (OCDocker.OCScore.Optimization.Protocol.ProtocolContext attribute) metadata_columns (OCDocker.OCScore.Utils.FeaturePolicy.CandidateFeatureDiscovery attribute) (OCDocker.OCScore.Utils.TrainOnlyFeatureReduction.TrainOnlyReductionArtifact attribute) method (OCDocker.OCScore.Analysis.Metrics.Calibration.ProbabilityCalibrator attribute) metric_names (OCDocker.OCScore.Analysis.ProductionBaselines.ProductionBaselineConfig attribute) MGLToolsPreparationStrategy (class in OCDocker.Toolbox.Preparation) min_kind_per_split (OCDocker.OCScore.Utils.DUDEzSplit.DUDEzSplitConfig attribute) min_rmsd_filter (OCDocker.Config.GninaConfig attribute) MinAbsEStateIndex (OCDocker.DB.Models.Ligands.Ligands attribute) MinAbsPartialCharge (OCDocker.DB.Models.Ligands.Ligands attribute) MinEStateIndex (OCDocker.DB.Models.Ligands.Ligands attribute) minimize (OCDocker.Config.GninaConfig attribute) (OCDocker.Config.SminaConfig attribute) minimize_early_term (OCDocker.Config.GninaConfig attribute) (OCDocker.Config.SminaConfig attribute) minimize_iters (OCDocker.Config.GninaConfig attribute) (OCDocker.Config.SminaConfig attribute) minimize_single_full (OCDocker.Config.GninaConfig attribute) MinPartialCharge (OCDocker.DB.Models.Ligands.Ligands attribute) missing_exclude_features (OCDocker.OCScore.Utils.FeaturePolicy.FeaturePolicyApplication attribute) missing_include_features (OCDocker.OCScore.Utils.FeaturePolicy.FeaturePolicyApplication attribute) MissingDatabaseDependencyError model_config (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationResult attribute) model_to_data() (in module OCDocker.Workbench.IO) modified_at (OCDocker.DB.Models.Base.Base attribute) (OCDocker.DB.Models.Complexes.Complexes attribute) (OCDocker.DB.Models.Ligands.Ligands attribute) (OCDocker.DB.Models.Receptors.Receptors attribute) module OCDocker OCDocker.API OCDocker.API.Pipeline OCDocker.CLI OCDocker.CLI.workbench OCDocker.Config OCDocker.Console OCDocker.Console.app OCDocker.Console.commands OCDocker.Console.render OCDocker.Console.session OCDocker.DB OCDocker.DB.baseDB OCDocker.DB.DB OCDocker.DB.DBMinimal OCDocker.DB.DUDEz OCDocker.DB.LITPCBA OCDocker.DB.Models OCDocker.DB.Models.Base OCDocker.DB.Models.Complexes OCDocker.DB.Models.Ligands OCDocker.DB.Models.Receptors OCDocker.DB.PDBbind OCDocker.Docking OCDocker.Docking.BaseVinaLike OCDocker.Docking.Future OCDocker.Docking.Future.Dock3 OCDocker.Docking.Future.Dock6 OCDocker.Docking.Future.GEMDOCK OCDocker.Docking.Future.Ledock OCDocker.Docking.Future.RDock OCDocker.Docking.Gnina OCDocker.Docking.PLANTS OCDocker.Docking.Smina OCDocker.Docking.Vina OCDocker.Error OCDocker.Initialise OCDocker.Ligand OCDocker.MCP OCDocker.MCP.Server OCDocker.OCScore OCDocker.OCScore.Analysis.Metrics OCDocker.OCScore.Analysis.Metrics.Bootstrap OCDocker.OCScore.Analysis.Metrics.Calibration OCDocker.OCScore.Analysis.Metrics.Ranking OCDocker.OCScore.Analysis.Plotting OCDocker.OCScore.Analysis.Plotting.ArchitecturePlots OCDocker.OCScore.Analysis.Plotting.Colouring OCDocker.OCScore.Analysis.Plotting.Core OCDocker.OCScore.Analysis.Plotting.CrossValidationPlots OCDocker.OCScore.Analysis.Plotting.MetricsPlots OCDocker.OCScore.Analysis.Plotting.Stats OCDocker.OCScore.Analysis.ProductionBaselines OCDocker.OCScore.Analysis.SHAP.Explain OCDocker.OCScore.Analysis.SHAP.ExportRunner OCDocker.OCScore.Analysis.SHAP.Paths OCDocker.OCScore.Analysis.SHAP.Plots OCDocker.OCScore.CLI OCDocker.OCScore.CLI.export_tools OCDocker.OCScore.CLI.reduce OCDocker.OCScore.CLI.train OCDocker.OCScore.Optimization OCDocker.OCScore.Optimization.ModelCrossValidation OCDocker.OCScore.Optimization.ModelExport OCDocker.OCScore.Optimization.OptunaSearchSpace OCDocker.OCScore.Optimization.OptunaStorage OCDocker.OCScore.Optimization.Protocol OCDocker.OCScore.Optimization.StagedOptuna OCDocker.OCScore.Optimization.StagedTrainProtocol OCDocker.OCScore.Scoring OCDocker.OCScore.Utils OCDocker.OCScore.Utils.ContentHash OCDocker.OCScore.Utils.Data OCDocker.OCScore.Utils.DescriptorAggregateBaselines OCDocker.OCScore.Utils.DUDEzScaling OCDocker.OCScore.Utils.DUDEzSplit OCDocker.OCScore.Utils.ExternalBlindEvaluation OCDocker.OCScore.Utils.FeaturePolicy OCDocker.OCScore.Utils.FeatureSelectionMetadata OCDocker.OCScore.Utils.FixedOuterSplit OCDocker.OCScore.Utils.IO OCDocker.OCScore.Utils.LeakageAudit OCDocker.OCScore.Utils.PDBbindSplit OCDocker.OCScore.Utils.ProtocolProvenance OCDocker.OCScore.Utils.RawModelingInput OCDocker.OCScore.Utils.TrainOnlyFeatureReduction OCDocker.Processing OCDocker.Processing.Dock OCDocker.Processing.GarbageCollection OCDocker.Processing.Postprocessing OCDocker.Processing.Postprocessing.Digest OCDocker.Processing.Preprocessing OCDocker.Processing.Preprocessing.Prepare OCDocker.Processing.Preprocessing.RMSDClustering OCDocker.Receptor OCDocker.Rescoring OCDocker.Rescoring.ODDT OCDocker.Toolbox OCDocker.Toolbox.Basetools OCDocker.Toolbox.Constants OCDocker.Toolbox.Conversion OCDocker.Toolbox.Downloading OCDocker.Toolbox.FilesFolders OCDocker.Toolbox.IO OCDocker.Toolbox.Logging OCDocker.Toolbox.MoleculeProcessing OCDocker.Toolbox.Preparation OCDocker.Toolbox.Printing OCDocker.Toolbox.Reproducibility OCDocker.Toolbox.Running OCDocker.Toolbox.Security OCDocker.Toolbox.Validation OCDocker.Workbench.Ablation OCDocker.Workbench.AblationDesign OCDocker.Workbench.AblationProtocolSimilarity OCDocker.Workbench.Adoption OCDocker.Workbench.Artifacts OCDocker.Workbench.Auth OCDocker.Workbench.Bundle OCDocker.Workbench.CampaignProgress OCDocker.Workbench.Comparison OCDocker.Workbench.Decision OCDocker.Workbench.Evidence OCDocker.Workbench.Export OCDocker.Workbench.IO OCDocker.Workbench.Jobs OCDocker.Workbench.Launch OCDocker.Workbench.Leaderboard OCDocker.Workbench.Logs OCDocker.Workbench.MetricsMatrix OCDocker.Workbench.OCScoreLayout OCDocker.Workbench.OptunaDashboard OCDocker.Workbench.Overview OCDocker.Workbench.Planner OCDocker.Workbench.Plots OCDocker.Workbench.Preflight OCDocker.Workbench.Registry OCDocker.Workbench.Report OCDocker.Workbench.Results OCDocker.Workbench.RunDetail OCDocker.Workbench.Schema OCDocker.Workbench.Server OCDocker.Workbench.Status OCDocker.Workbench.Templates OCDocker.Workbench.VSDesign OCDocker.Workbench.Web molecule (OCDocker.Ligand.Ligand attribute) MolLogP (OCDocker.DB.Models.Ligands.Ligands attribute) MolMR (OCDocker.DB.Models.Ligands.Ligands attribute) MolWt (OCDocker.DB.Models.Ligands.Ligands attribute) multiple_molecules_sdf() (in module OCDocker.Ligand) multiprocess (OCDocker.Config.OCDockerConfig attribute) N n_affinity_bins (OCDocker.OCScore.Utils.PDBbindSplit.PDBbindSplitConfig attribute) n_folds (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationConfig attribute) (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationResult attribute) n_jobs (OCDocker.OCScore.Optimization.StagedOptuna.DUDEzOptunaConfig attribute) (OCDocker.OCScore.Optimization.StagedOptuna.PDBbindOptunaConfig attribute) n_replicas (OCDocker.OCScore.Optimization.Protocol.ReplicatedProtocolConfig attribute) n_selected_features (OCDocker.OCScore.Utils.FeatureSelectionMetadata.FeatureSelectionScope attribute) n_test_receptors (OCDocker.OCScore.Utils.DUDEzSplit.DUDEzSplitConfig attribute) n_train (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationFoldResult attribute) n_train_receptors (OCDocker.OCScore.Utils.DUDEzSplit.DUDEzSplitConfig attribute) n_trials (OCDocker.OCScore.Optimization.StagedOptuna.DUDEzOptunaConfig attribute) (OCDocker.OCScore.Optimization.StagedOptuna.PDBbindOptunaConfig attribute) n_validation (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationFoldResult attribute) n_validation_receptors (OCDocker.OCScore.Utils.DUDEzSplit.DUDEzSplitConfig attribute) name (OCDocker.DB.Models.Base.Base attribute) (OCDocker.DB.Models.Complexes.Complexes attribute) (OCDocker.DB.Models.Ligands.Ligands attribute) (OCDocker.DB.Models.Receptors.Receptors attribute) (OCDocker.Ligand.Ligand attribute) (OCDocker.OCScore.Optimization.Protocol.ProtocolStage attribute), [1] (OCDocker.OCScore.Optimization.StagedOptuna.DUDEzOptunaStage attribute) (OCDocker.OCScore.Optimization.StagedOptuna.PDBbindOptunaStage attribute) (OCDocker.OCScore.Optimization.StagedOptuna.TransferFeatureExtractorStage attribute) (OCDocker.OCScore.Optimization.StagedTrainProtocol.StagedTrainProtocol attribute) (OCDocker.OCScore.Utils.FeaturePolicy.FeaturePolicy attribute) (OCDocker.Receptor.Receptor attribute) ndcg_at_fraction() (in module OCDocker.OCScore.Analysis.Metrics.Ranking) needs_canonical_pdb_fix() (in module OCDocker.Toolbox.MoleculeProcessing) negative_kind (OCDocker.OCScore.Utils.DUDEzSplit.DUDEzSplitConfig attribute) new_fig() (in module OCDocker.OCScore.Analysis.Plotting.Core) NHOHCount (OCDocker.DB.Models.Ligands.Ligands attribute) no_gpu (OCDocker.Config.GninaConfig attribute) no_lig (OCDocker.Config.GninaConfig attribute) NOCount (OCDocker.DB.Models.Ligands.Ligands attribute) NONE (OCDocker.Error.ReportLevel attribute) norm_data() (in module OCDocker.OCScore.Utils.Data) normalize_ablation_variant_name() (in module OCDocker.OCScore.Optimization.StagedTrainProtocol) normalize_architecture() (in module OCDocker.OCScore.Analysis.Plotting.ArchitecturePlots) normalize_db_backend() (in module OCDocker.DB.DBMinimal) normalize_path() (in module OCDocker.Toolbox.FilesFolders) normalize_smiles_with_openbabel (OCDocker.Ligand.Ligand attribute) notes (OCDocker.OCScore.Analysis.Plotting.ArchitecturePlots.ArchitectureDiagram attribute) (OCDocker.OCScore.Utils.FeatureSelectionMetadata.FeatureSelectionScope attribute) (OCDocker.OCScore.Utils.FixedOuterSplit.FixedOuterSplitAssignment attribute) NPR1 (OCDocker.DB.Models.Ligands.Ligands attribute) NPR2 (OCDocker.DB.Models.Ligands.Ligands attribute) num_mc_saved (OCDocker.Config.GninaConfig attribute) num_mc_steps (OCDocker.Config.GninaConfig attribute) num_modes (OCDocker.Config.GninaConfig attribute) (OCDocker.Config.SminaConfig attribute) (OCDocker.Config.VinaConfig attribute) num_poses (OCDocker.Config.LeDockConfig attribute) num_unfrozen_layers_options (OCDocker.OCScore.Optimization.OptunaSearchSpace.DUDEzHeadSearchSpace attribute) NumAliphaticCarbocycles (OCDocker.DB.Models.Ligands.Ligands attribute) NumAliphaticHeterocycles (OCDocker.DB.Models.Ligands.Ligands attribute) NumAliphaticRings (OCDocker.DB.Models.Ligands.Ligands attribute) NumAromaticCarbocycles (OCDocker.DB.Models.Ligands.Ligands attribute) NumAromaticHeterocycles (OCDocker.DB.Models.Ligands.Ligands attribute) NumAromaticRings (OCDocker.DB.Models.Ligands.Ligands attribute) NumHAcceptors (OCDocker.DB.Models.Ligands.Ligands attribute) NumHDonors (OCDocker.DB.Models.Ligands.Ligands attribute) NumHeteroatoms (OCDocker.DB.Models.Ligands.Ligands attribute) NumRadicalElectrons (OCDocker.DB.Models.Ligands.Ligands attribute) NumRotatableBonds (OCDocker.DB.Models.Ligands.Ligands attribute) NumSaturatedCarbocycles (OCDocker.DB.Models.Ligands.Ligands attribute) NumSaturatedHeterocycles (OCDocker.DB.Models.Ligands.Ligands attribute) NumSaturatedRings (OCDocker.DB.Models.Ligands.Ligands attribute) NumValenceElectrons (OCDocker.DB.Models.Ligands.Ligands attribute) O obabel (OCDocker.Config.ToolsConfig attribute) objective_metric (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationResult attribute) (OCDocker.OCScore.Optimization.StagedOptuna.PDBbindOptunaConfig attribute) ocdb_path (OCDocker.Config.PathsConfig attribute) OCDocker module OCDocker.API module OCDocker.API.Pipeline module OCDocker.CLI module OCDocker.CLI.workbench module OCDocker.Config module OCDocker.Console module OCDocker.Console.app module OCDocker.Console.commands module OCDocker.Console.render module OCDocker.Console.session module OCDocker.DB module OCDocker.DB.baseDB module OCDocker.DB.DB module OCDocker.DB.DBMinimal module OCDocker.DB.DUDEz module OCDocker.DB.LITPCBA module OCDocker.DB.Models module OCDocker.DB.Models.Base module OCDocker.DB.Models.Complexes module OCDocker.DB.Models.Ligands module OCDocker.DB.Models.Receptors module OCDocker.DB.PDBbind module OCDocker.Docking module OCDocker.Docking.BaseVinaLike module OCDocker.Docking.Future module OCDocker.Docking.Future.Dock3 module OCDocker.Docking.Future.Dock6 module OCDocker.Docking.Future.GEMDOCK module OCDocker.Docking.Future.Ledock module OCDocker.Docking.Future.RDock module OCDocker.Docking.Gnina module OCDocker.Docking.PLANTS module OCDocker.Docking.Smina module OCDocker.Docking.Vina module OCDocker.Error module OCDocker.Initialise module OCDocker.Ligand module OCDocker.MCP module OCDocker.MCP.Server module OCDocker.OCScore module OCDocker.OCScore.Analysis.Metrics module OCDocker.OCScore.Analysis.Metrics.Bootstrap module OCDocker.OCScore.Analysis.Metrics.Calibration module OCDocker.OCScore.Analysis.Metrics.Ranking module OCDocker.OCScore.Analysis.Plotting module OCDocker.OCScore.Analysis.Plotting.ArchitecturePlots module OCDocker.OCScore.Analysis.Plotting.Colouring module OCDocker.OCScore.Analysis.Plotting.Core module OCDocker.OCScore.Analysis.Plotting.CrossValidationPlots module OCDocker.OCScore.Analysis.Plotting.MetricsPlots module OCDocker.OCScore.Analysis.Plotting.Stats module OCDocker.OCScore.Analysis.ProductionBaselines module OCDocker.OCScore.Analysis.SHAP.Explain module OCDocker.OCScore.Analysis.SHAP.ExportRunner module OCDocker.OCScore.Analysis.SHAP.Paths module OCDocker.OCScore.Analysis.SHAP.Plots module OCDocker.OCScore.CLI module OCDocker.OCScore.CLI.export_tools module OCDocker.OCScore.CLI.reduce module OCDocker.OCScore.CLI.train module OCDocker.OCScore.Optimization module OCDocker.OCScore.Optimization.ModelCrossValidation module OCDocker.OCScore.Optimization.ModelExport module OCDocker.OCScore.Optimization.OptunaSearchSpace module OCDocker.OCScore.Optimization.OptunaStorage module OCDocker.OCScore.Optimization.Protocol module OCDocker.OCScore.Optimization.StagedOptuna module OCDocker.OCScore.Optimization.StagedTrainProtocol module OCDocker.OCScore.Scoring module OCDocker.OCScore.Utils module OCDocker.OCScore.Utils.ContentHash module OCDocker.OCScore.Utils.Data module OCDocker.OCScore.Utils.DescriptorAggregateBaselines module OCDocker.OCScore.Utils.DUDEzScaling module OCDocker.OCScore.Utils.DUDEzSplit module OCDocker.OCScore.Utils.ExternalBlindEvaluation module OCDocker.OCScore.Utils.FeaturePolicy module OCDocker.OCScore.Utils.FeatureSelectionMetadata module OCDocker.OCScore.Utils.FixedOuterSplit module OCDocker.OCScore.Utils.IO module OCDocker.OCScore.Utils.LeakageAudit module OCDocker.OCScore.Utils.PDBbindSplit module OCDocker.OCScore.Utils.ProtocolProvenance module OCDocker.OCScore.Utils.RawModelingInput module OCDocker.OCScore.Utils.TrainOnlyFeatureReduction module OCDocker.Processing module OCDocker.Processing.Dock module OCDocker.Processing.GarbageCollection module OCDocker.Processing.Postprocessing module OCDocker.Processing.Postprocessing.Digest module OCDocker.Processing.Preprocessing module OCDocker.Processing.Preprocessing.Prepare module OCDocker.Processing.Preprocessing.RMSDClustering module OCDocker.Receptor module OCDocker.Rescoring module OCDocker.Rescoring.ODDT module OCDocker.Toolbox module OCDocker.Toolbox.Basetools module OCDocker.Toolbox.Constants module OCDocker.Toolbox.Conversion module OCDocker.Toolbox.Downloading module OCDocker.Toolbox.FilesFolders module OCDocker.Toolbox.IO module OCDocker.Toolbox.Logging module OCDocker.Toolbox.MoleculeProcessing module OCDocker.Toolbox.Preparation module OCDocker.Toolbox.Printing module OCDocker.Toolbox.Reproducibility module OCDocker.Toolbox.Running module OCDocker.Toolbox.Security module OCDocker.Toolbox.Validation module OCDocker.Workbench.Ablation module OCDocker.Workbench.AblationDesign module OCDocker.Workbench.AblationProtocolSimilarity module OCDocker.Workbench.Adoption module OCDocker.Workbench.Artifacts module OCDocker.Workbench.Auth module OCDocker.Workbench.Bundle module OCDocker.Workbench.CampaignProgress module OCDocker.Workbench.Comparison module OCDocker.Workbench.Decision module OCDocker.Workbench.Evidence module OCDocker.Workbench.Export module OCDocker.Workbench.IO module OCDocker.Workbench.Jobs module OCDocker.Workbench.Launch module OCDocker.Workbench.Leaderboard module OCDocker.Workbench.Logs module OCDocker.Workbench.MetricsMatrix module OCDocker.Workbench.OCScoreLayout module OCDocker.Workbench.OptunaDashboard module OCDocker.Workbench.Overview module OCDocker.Workbench.Planner module OCDocker.Workbench.Plots module OCDocker.Workbench.Preflight module OCDocker.Workbench.Registry module OCDocker.Workbench.Report module OCDocker.Workbench.Results module OCDocker.Workbench.RunDetail module OCDocker.Workbench.Schema module OCDocker.Workbench.Server module OCDocker.Workbench.Status module OCDocker.Workbench.Templates module OCDocker.Workbench.VSDesign module OCDocker.Workbench.Web module ocdocker_path (OCDocker.Config.OCDockerConfig attribute) OCDockerConfig (class in OCDocker.Config) OCDockerMCPError, [1] OCSCORE (OCDocker.DB.Models.Complexes.Complexes attribute) oddt (OCDocker.Config.OCDockerConfig attribute) oddt_models_dir (OCDocker.Config.OCDockerConfig attribute) ODDT_NNSCORE (OCDocker.DB.Models.Complexes.Complexes attribute) ODDT_PLECRF_P5_L1_S65536 (OCDocker.DB.Models.Complexes.Complexes attribute) ODDT_RFSCORE_V1 (OCDocker.DB.Models.Complexes.Complexes attribute) ODDT_RFSCORE_V2 (OCDocker.DB.Models.Complexes.Complexes attribute) ODDT_RFSCORE_V3 (OCDocker.DB.Models.Complexes.Complexes attribute) ODDTConfig (class in OCDocker.Config) ok (OCDocker.API.Pipeline.PipelineRunResult property) (OCDocker.API.PipelineRunResult property) OpenBabelPreparationStrategy (class in OCDocker.Toolbox.Preparation) optimizedb (OCDocker.Config.DatabaseConfig attribute) (OCDocker.DB.DBMinimal.DatabaseSettings attribute) optimizer (OCDocker.OCScore.Optimization.OptunaSearchSpace.SharedNeuralSearchSpace attribute) OptimizerSearchSpace (class in OCDocker.OCScore.Optimization.OptunaSearchSpace) OptunaDashboardError OptunaDashboardManager (class in OCDocker.Workbench.OptunaDashboard) OptunaDashboardSession (class in OCDocker.Workbench.OptunaDashboard) order (in module OCDocker.Toolbox.Constants) orient_scores() (in module OCDocker.OCScore.Analysis.Metrics.Ranking) original_path (OCDocker.Receptor.Receptor attribute) out_dir (OCDocker.OCScore.Analysis.SHAP.Paths.OutputPaths attribute) out_flex (OCDocker.Config.GninaConfig attribute) outdir (OCDocker.API.Pipeline.PipelineRunResult attribute) (OCDocker.API.PipelineRunResult attribute) outer_split_assignment_hash (OCDocker.OCScore.Utils.FixedOuterSplit.FixedOuterSplitAssignment attribute) outer_split_id (OCDocker.OCScore.Utils.FixedOuterSplit.FixedOuterSplitAssignment attribute) outer_split_seed (OCDocker.OCScore.Utils.FixedOuterSplit.FixedOuterSplitAssignment attribute) output_dir (OCDocker.OCScore.Optimization.Protocol.ProtocolContext attribute) (OCDocker.OCScore.Optimization.Protocol.ReplicaResult attribute) (OCDocker.OCScore.Utils.ExternalBlindEvaluation.ExternalBlindConfig attribute) output_level (OCDocker.Config.OCDockerConfig attribute) output_paths (OCDocker.OCScore.Optimization.Protocol.ReplicatedProtocolResult attribute) OutputPaths (class in OCDocker.OCScore.Analysis.SHAP.Paths) overwrite (OCDocker.Config.OCDockerConfig attribute) P parse_ablation_metric() (in module OCDocker.Workbench.Ablation) parse_campaign_progress() (in module OCDocker.Workbench.CampaignProgress) parse_comparison_metric() (in module OCDocker.Workbench.Comparison) parse_pareto_objective() (in module OCDocker.Workbench.Decision) parse_report_metric() (in module OCDocker.Workbench.Report) parsed_archive (OCDocker.Config.OCDockerConfig attribute) passed (OCDocker.OCScore.Utils.LeakageAudit.LeakageAuditResult attribute) password (OCDocker.Config.DatabaseConfig attribute) (OCDocker.DB.DBMinimal.DatabaseSettings attribute) path (OCDocker.Ligand.Ligand attribute) (OCDocker.Receptor.Receptor attribute) paths (OCDocker.Config.OCDockerConfig attribute) PathsConfig (class in OCDocker.Config) patterns_with_no_matches (OCDocker.OCScore.Utils.FeaturePolicy.FeaturePolicyApplication attribute) pca_path (OCDocker.Config.PathsConfig attribute) pdbbind (OCDocker.OCScore.Optimization.StagedTrainProtocol.StagedTrainProtocol attribute) pdbbind_archive (OCDocker.Config.OCDockerConfig attribute) pdbbind_columns_from_header() (in module OCDocker.OCScore.Utils.IO) pdbbind_df (OCDocker.OCScore.CLI.train.ReductionArtifacts attribute) (OCDocker.OCScore.CLI.train.StagedTrainingRun attribute) (OCDocker.OCScore.Optimization.Protocol.ProtocolContext attribute) pdbbind_export_dir (OCDocker.OCScore.Utils.ExternalBlindEvaluation.ExternalBlindConfig attribute) pdbbind_hash (OCDocker.OCScore.Utils.RawModelingInput.RawModelingInput attribute) pdbbind_head (OCDocker.OCScore.Optimization.OptunaSearchSpace.PDBbindSearchSpaceConfig attribute) pdbbind_kdki_order (OCDocker.Config.PathsConfig attribute) pdbbind_phase1_experiment_config() (in module OCDocker.OCScore.Optimization.StagedOptuna) pdbbind_search_space_for_phase() (in module OCDocker.OCScore.Optimization.OptunaSearchSpace) pdbbind_search_space_summary() (in module OCDocker.OCScore.Optimization.StagedOptuna) pdbbind_source (OCDocker.OCScore.Utils.RawModelingInput.RawModelingInput attribute) pdbbind_split_config() (OCDocker.OCScore.Optimization.StagedTrainProtocol.StagedTrainProtocol method) pdbbind_test_indices (OCDocker.OCScore.Utils.FixedOuterSplit.FixedOuterSplitAssignment attribute) pdbbind_test_indices_hash (OCDocker.OCScore.Utils.FixedOuterSplit.FixedOuterSplitAssignment attribute) pdbbind_train_indices (OCDocker.OCScore.Utils.FixedOuterSplit.FixedOuterSplitAssignment attribute) pdbbind_train_indices_hash (OCDocker.OCScore.Utils.FixedOuterSplit.FixedOuterSplitAssignment attribute) pdbbind_validation_indices (OCDocker.OCScore.Utils.FixedOuterSplit.FixedOuterSplitAssignment attribute) pdbbind_validation_indices_hash (OCDocker.OCScore.Utils.FixedOuterSplit.FixedOuterSplitAssignment attribute) PDBbindHeadSearchSpace (class in OCDocker.OCScore.Optimization.OptunaSearchSpace) PDBbindOptunaConfig (class in OCDocker.OCScore.Optimization.StagedOptuna) PDBbindOptunaStage (class in OCDocker.OCScore.Optimization.StagedOptuna) PDBbindRegressionModel (class in OCDocker.OCScore.Optimization.StagedOptuna) PDBbindSearchSpaceConfig (class in OCDocker.OCScore.Optimization.OptunaSearchSpace) PDBbindSplitConfig (class in OCDocker.OCScore.Utils.PDBbindSplit) PDBbindSplitResult (class in OCDocker.OCScore.Utils.PDBbindSplit) PEOE_VSA1 (OCDocker.DB.Models.Ligands.Ligands attribute) PEOE_VSA10 (OCDocker.DB.Models.Ligands.Ligands attribute) PEOE_VSA11 (OCDocker.DB.Models.Ligands.Ligands attribute) PEOE_VSA12 (OCDocker.DB.Models.Ligands.Ligands attribute) PEOE_VSA13 (OCDocker.DB.Models.Ligands.Ligands attribute) PEOE_VSA14 (OCDocker.DB.Models.Ligands.Ligands attribute) PEOE_VSA2 (OCDocker.DB.Models.Ligands.Ligands attribute) PEOE_VSA3 (OCDocker.DB.Models.Ligands.Ligands attribute) PEOE_VSA4 (OCDocker.DB.Models.Ligands.Ligands attribute) PEOE_VSA5 (OCDocker.DB.Models.Ligands.Ligands attribute) PEOE_VSA6 (OCDocker.DB.Models.Ligands.Ligands attribute) PEOE_VSA7 (OCDocker.DB.Models.Ligands.Ligands attribute) PEOE_VSA8 (OCDocker.DB.Models.Ligands.Ligands attribute) PEOE_VSA9 (OCDocker.DB.Models.Ligands.Ligands attribute) per_target_metrics (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationFoldResult attribute) pid (OCDocker.Workbench.OptunaDashboard.OptunaDashboardSession attribute) PipelineRunResult (class in OCDocker.API) (class in OCDocker.API.Pipeline) plan() (OCDocker.Workbench.Jobs.JobManager method) plan_ablation_design() (in module OCDocker.Workbench.AblationDesign) plan_command() (in module OCDocker.Workbench.Planner) plan_ocscore_train_command() (in module OCDocker.Workbench.Planner) plan_snakemake_command() (in module OCDocker.Workbench.Planner) plan_vs_campaign() (in module OCDocker.Workbench.VSDesign) plan_vs_campaign_command() (in module OCDocker.Workbench.Planner) plan_vs_design() (in module OCDocker.Workbench.VSDesign) PLANTS (class in OCDocker.Docking.PLANTS) plants (OCDocker.Config.OCDockerConfig attribute) PLANTS_CHEMPLP (OCDocker.DB.Models.Complexes.Complexes attribute) PLANTS_PLP (OCDocker.DB.Models.Complexes.Complexes attribute) PLANTS_PLP95 (OCDocker.DB.Models.Complexes.Complexes attribute) PLANTSConfig (class in OCDocker.Config) plot_ablation_bedroc_significance_bars() (in module OCDocker.OCScore.Analysis.Plotting.Stats) plot_architecture_diagram() (in module OCDocker.OCScore.Analysis.Plotting.ArchitecturePlots) plot_bar_with_significance() (in module OCDocker.OCScore.Analysis.Plotting) (in module OCDocker.OCScore.Analysis.Plotting.Stats) plot_barplots() (in module OCDocker.OCScore.Analysis.Plotting) (in module OCDocker.OCScore.Analysis.Plotting.Stats) plot_bedroc_vs_shortcut_risk_scatter() (in module OCDocker.OCScore.Analysis.Plotting.Stats) plot_boxplots() (in module OCDocker.OCScore.Analysis.Plotting) (in module OCDocker.OCScore.Analysis.Plotting.Stats) plot_combined_metric_scatter() (in module OCDocker.OCScore.Analysis.Plotting) (in module OCDocker.OCScore.Analysis.Plotting.Stats) plot_fold_metric_bars() (in module OCDocker.OCScore.Analysis.Plotting.CrossValidationPlots) plot_fold_metric_heatmap() (in module OCDocker.OCScore.Analysis.Plotting.CrossValidationPlots) plot_fold_metric_lines() (in module OCDocker.OCScore.Analysis.Plotting.CrossValidationPlots) plot_heatmap() (in module OCDocker.OCScore.Analysis.Plotting) (in module OCDocker.OCScore.Analysis.Plotting.Stats) plot_mean_std_bars() (in module OCDocker.OCScore.Analysis.Plotting.CrossValidationPlots) plot_normality_and_variance_diagnostics() (in module OCDocker.OCScore.Analysis.Plotting) (in module OCDocker.OCScore.Analysis.Plotting.Stats) plot_ocscore_wins() (in module OCDocker.OCScore.Analysis.Plotting.CrossValidationPlots) plot_pca_importance_barplot() (in module OCDocker.OCScore.Analysis.Plotting) (in module OCDocker.OCScore.Analysis.Plotting.Stats) plot_pca_importance_histogram() (in module OCDocker.OCScore.Analysis.Plotting) (in module OCDocker.OCScore.Analysis.Plotting.Stats) plot_per_target_boxplot() (in module OCDocker.OCScore.Analysis.Plotting.CrossValidationPlots) plot_per_target_heatmap() (in module OCDocker.OCScore.Analysis.Plotting.CrossValidationPlots) plot_per_target_ocscore_wins() (in module OCDocker.OCScore.Analysis.Plotting.CrossValidationPlots) plot_scatterplot() (in module OCDocker.OCScore.Analysis.Plotting) (in module OCDocker.OCScore.Analysis.Plotting.Stats) PMI1 (OCDocker.DB.Models.Ligands.Ligands attribute) PMI2 (OCDocker.DB.Models.Ligands.Ligands attribute) PMI3 (OCDocker.DB.Models.Ligands.Ligands attribute) policies (OCDocker.OCScore.Utils.FeaturePolicy.FeaturePolicyDiscovery attribute) policy (OCDocker.OCScore.Utils.FeaturePolicy.FeaturePolicyApplication attribute) pool_chunksize() (in module OCDocker.Processing.GarbageCollection) port (OCDocker.Config.DatabaseConfig attribute) (OCDocker.DB.DBMinimal.DatabaseSettings attribute) (OCDocker.Workbench.OptunaDashboard.OptunaDashboardSession attribute) pose_sort_order (OCDocker.Config.GninaConfig attribute) positive_kind (OCDocker.OCScore.Utils.DUDEzSplit.DUDEzSplitConfig attribute) pr_auc() (in module OCDocker.OCScore.Analysis.Metrics.Ranking) pr_plot() (in module OCDocker.OCScore.Analysis.Plotting.MetricsPlots) precomputed_global() (OCDocker.OCScore.Utils.FeatureSelectionMetadata.FeatureSelectionScope class method) predict() (OCDocker.OCScore.Analysis.Metrics.Calibration.ProbabilityCalibrator method) predict_from_export() (in module OCDocker.OCScore.Optimization.ModelExport) preflight_spec() (in module OCDocker.Workbench.Preflight) preflight_spec_file() (in module OCDocker.Workbench.Preflight) PreparationStrategy (class in OCDocker.Toolbox.Preparation) prepare() (in module OCDocker.DB.baseDB) (in module OCDocker.DB.DUDEz) (in module OCDocker.DB.LITPCBA) (in module OCDocker.DB.PDBbind) (in module OCDocker.Processing.Preprocessing.Prepare) prepare_dudez_dataframe() (in module OCDocker.OCScore.CLI.reduce) (in module OCDocker.OCScore.Utils.IO) prepare_dudez_for_optuna() (in module OCDocker.OCScore.CLI.train) prepare_dudez_screening_data() (in module OCDocker.OCScore.Optimization.StagedOptuna) prepare_ligand (OCDocker.Config.ToolsConfig attribute) prepare_ligand() (OCDocker.Toolbox.Preparation.MGLToolsPreparationStrategy method) (OCDocker.Toolbox.Preparation.OpenBabelPreparationStrategy method) (OCDocker.Toolbox.Preparation.PreparationStrategy method) (OCDocker.Toolbox.Preparation.SPORESPreparationStrategy method) prepare_pdbbind_dataframe() (in module OCDocker.OCScore.Utils.IO) prepare_pdbbind_for_optuna() (in module OCDocker.OCScore.CLI.train) prepare_pdbbind_regression_data() (in module OCDocker.OCScore.Optimization.StagedOptuna) prepare_receptor (OCDocker.Config.ToolsConfig attribute) prepare_receptor() (OCDocker.Toolbox.Preparation.MGLToolsPreparationStrategy method) (OCDocker.Toolbox.Preparation.OpenBabelPreparationStrategy method) (OCDocker.Toolbox.Preparation.PreparationStrategy method) (OCDocker.Toolbox.Preparation.SPORESPreparationStrategy method) preview_ablation_design() (in module OCDocker.Workbench.AblationDesign) preview_run_logs() (in module OCDocker.Workbench.Logs) preview_vs_campaign() (in module OCDocker.Workbench.VSDesign) preview_vs_design() (in module OCDocker.Workbench.VSDesign) primary_metric (OCDocker.OCScore.Optimization.StagedOptuna.DUDEzOptunaConfig attribute) print_args() (in module OCDocker.Console.session) print_atom_types (OCDocker.Config.GninaConfig attribute) print_attributes() (OCDocker.Docking.Gnina.Gnina method) (OCDocker.Docking.PLANTS.PLANTS method) (OCDocker.Docking.Smina.Smina method) (OCDocker.Docking.Vina.Vina method) (OCDocker.Ligand.Ligand method) (OCDocker.Receptor.Receptor method) print_error() (in module OCDocker.Toolbox.Printing) print_error_log() (in module OCDocker.Toolbox.Printing) print_info() (in module OCDocker.Toolbox.Printing) print_info_log() (in module OCDocker.Toolbox.Printing) print_section() (in module OCDocker.Toolbox.Printing) print_sorry() (in module OCDocker.Toolbox.Printing) print_subsection() (in module OCDocker.Toolbox.Printing) print_success() (in module OCDocker.Toolbox.Printing) print_success_log() (in module OCDocker.Toolbox.Printing) print_terms (OCDocker.Config.GninaConfig attribute) print_warning() (in module OCDocker.Toolbox.Printing) print_warning_log() (in module OCDocker.Toolbox.Printing) print_welcome_banner() (in module OCDocker.Console.render) printv() (in module OCDocker.Toolbox.Printing) ProbabilityCalibrator (class in OCDocker.OCScore.Analysis.Metrics.Calibration) PRODUCTION_BASELINE_RANK_METRICS (in module OCDocker.OCScore.Analysis.ProductionBaselines) production_claim (OCDocker.OCScore.Optimization.StagedTrainProtocol.StagedTrainProtocol attribute) ProductionBaselineConfig (class in OCDocker.OCScore.Analysis.ProductionBaselines) projection (OCDocker.OCScore.Optimization.OptunaSearchSpace.SharedNeuralSearchSpace attribute) (OCDocker.OCScore.Optimization.StagedOptuna.FeatureExtractor attribute) projection_dim_options (OCDocker.OCScore.Optimization.OptunaSearchSpace.ProjectionSearchSpace attribute) ProjectionSearchSpace (class in OCDocker.OCScore.Optimization.OptunaSearchSpace) protocol (OCDocker.OCScore.Utils.TrainOnlyFeatureReduction.TrainOnlyReductionArtifact attribute) protocol_log (OCDocker.OCScore.Optimization.Protocol.ProtocolContext attribute) protocol_metadata (OCDocker.OCScore.CLI.train.StagedTrainingRun attribute) ProtocolContext (class in OCDocker.OCScore.Optimization.Protocol) ProtocolStage (class in OCDocker.OCScore.Optimization.Protocol) pruner_n_startup_trials (OCDocker.OCScore.Optimization.StagedOptuna.PDBbindOptunaConfig attribute) pruner_n_warmup_steps (OCDocker.OCScore.Optimization.StagedOptuna.PDBbindOptunaConfig attribute) pythonsh (OCDocker.Config.ToolsConfig attribute) Q qed (OCDocker.DB.Models.Ligands.Ligands attribute) quiet (OCDocker.Config.GninaConfig attribute) R R (in module OCDocker.Toolbox.Constants) RadiusOfGyration (OCDocker.DB.Models.Ligands.Ligands attribute) (OCDocker.Ligand.Ligand attribute) random_seed (OCDocker.OCScore.Analysis.ProductionBaselines.ProductionBaselineConfig attribute) (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationConfig attribute) (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationResult attribute) (OCDocker.OCScore.Optimization.Protocol.ProtocolContext attribute) (OCDocker.OCScore.Optimization.StagedOptuna.DUDEzOptunaConfig attribute) (OCDocker.OCScore.Optimization.StagedOptuna.PDBbindOptunaConfig attribute) (OCDocker.OCScore.Utils.DUDEzSplit.DUDEzSplitConfig attribute) (OCDocker.OCScore.Utils.PDBbindSplit.PDBbindSplitConfig attribute) randomize_only (OCDocker.Config.GninaConfig attribute) (OCDocker.Config.SminaConfig attribute) raw (OCDocker.OCScore.Optimization.StagedTrainProtocol.StagedTrainProtocol attribute) RawModelingInput (class in OCDocker.OCScore.Utils.RawModelingInput) read_csv_column_names() (in module OCDocker.OCScore.Utils.IO) read_data() (in module OCDocker.Workbench.IO) read_descriptors_from_json() (in module OCDocker.Ligand) (in module OCDocker.Receptor) read_gnina_log() (in module OCDocker.Docking.BaseVinaLike) read_gnina_rescoring_log() (in module OCDocker.Docking.BaseVinaLike) read_index() (in module OCDocker.DB.PDBbind) read_log() (in module OCDocker.Docking.PLANTS) (in module OCDocker.Rescoring.ODDT) (OCDocker.Docking.Gnina.Gnina method) (OCDocker.Docking.PLANTS.PLANTS method) (OCDocker.Docking.Smina.Smina method) (OCDocker.Docking.Vina.Vina method) read_pipeline_csv_columns() (in module OCDocker.OCScore.Utils.IO) read_rescore_logs() (in module OCDocker.Docking.Gnina) (in module OCDocker.Docking.PLANTS) (in module OCDocker.Docking.Smina) (in module OCDocker.Docking.Vina) (OCDocker.Docking.Gnina.Gnina method) (OCDocker.Docking.PLANTS.PLANTS method) (OCDocker.Docking.Smina.Smina method) (OCDocker.Docking.Vina.Vina method) read_result_manifest() (in module OCDocker.Workbench.IO) read_run_manifest() (in module OCDocker.Workbench.IO) read_smina_log() (in module OCDocker.Docking.BaseVinaLike) read_smina_rescoring_log() (in module OCDocker.Docking.BaseVinaLike) read_spec() (in module OCDocker.Workbench.IO) read_vina_log() (in module OCDocker.Docking.BaseVinaLike) read_vina_rescoring_log() (in module OCDocker.Docking.BaseVinaLike) Receptor (class in OCDocker.Receptor) receptor (OCDocker.DB.Models.Complexes.Complexes attribute), [1] receptor_column (OCDocker.OCScore.Utils.DUDEzSplit.DUDEzSplitConfig attribute) (OCDocker.OCScore.Utils.PDBbindSplit.PDBbindSplitConfig attribute) receptor_id (OCDocker.DB.Models.Complexes.Complexes attribute), [1] Receptors (class in OCDocker.DB.Models.Receptors) redirect_to_tqdm() (in module OCDocker.Toolbox.Basetools) reduction_archive (OCDocker.OCScore.Utils.FeatureSelectionMetadata.FeatureSelectionScope attribute) ReductionArtifacts (class in OCDocker.OCScore.CLI.train) reference_column_order (OCDocker.Config.PathsConfig attribute) register_subparser() (in module OCDocker.CLI.workbench) (in module OCDocker.OCScore.CLI.reduce) (in module OCDocker.OCScore.CLI.train) register_subparsers() (in module OCDocker.OCScore.CLI) (in module OCDocker.OCScore.CLI.export_tools) registry (OCDocker.DB.Models.Base.Base attribute) regression_loss_options (OCDocker.OCScore.Optimization.OptunaSearchSpace.PDBbindHeadSearchSpace attribute) reject_precomputed_training_artifacts() (in module OCDocker.OCScore.Utils.RawModelingInput) relaxed_split (OCDocker.OCScore.Utils.DUDEzSplit.DUDEzSplitConfig attribute) (OCDocker.OCScore.Utils.PDBbindSplit.PDBbindSplitConfig attribute) reliability_curve_points() (in module OCDocker.OCScore.Analysis.Metrics.Calibration) reliability_plot() (in module OCDocker.OCScore.Analysis.Plotting.MetricsPlots) remove_other_columns() (in module OCDocker.OCScore.Utils.Data) removed_features (OCDocker.OCScore.Utils.FeatureSelectionMetadata.FeatureSelectionScope attribute) (OCDocker.OCScore.Utils.TrainOnlyFeatureReduction.TrainOnlyReductionArtifact attribute) removed_features_hash (OCDocker.OCScore.Utils.FeatureSelectionMetadata.FeatureSelectionScope attribute) (OCDocker.OCScore.Utils.FixedOuterSplit.FixedOuterSplitAssignment attribute) render_analysis_report_markdown() (in module OCDocker.Workbench.Report) renumber_pdb_residues() (in module OCDocker.Receptor) reorder_columns_to_match_data_order() (in module OCDocker.OCScore.Utils.Data) replica_alignments (OCDocker.OCScore.CLI.train.StagedTrainingRun attribute) replica_index (OCDocker.OCScore.Optimization.Protocol.ReplicaResult attribute) replica_jobs (OCDocker.OCScore.Optimization.Protocol.ReplicatedProtocolConfig attribute) replica_name (OCDocker.OCScore.Optimization.Protocol.ReplicaResult attribute) replica_name_prefix (OCDocker.OCScore.Optimization.Protocol.ReplicatedProtocolConfig attribute) replica_path (OCDocker.Workbench.OptunaDashboard.OptunaDashboardSession attribute) replica_results (OCDocker.OCScore.Optimization.Protocol.ReplicatedProtocolResult attribute) replica_uses_fixed_outer_split (OCDocker.OCScore.Utils.FixedOuterSplit.FixedOuterSplitAssignment attribute) ReplicaResult (class in OCDocker.OCScore.Optimization.Protocol) replicas (OCDocker.OCScore.Optimization.StagedTrainProtocol.StagedTrainProtocol attribute) ReplicatedProtocolConfig (class in OCDocker.OCScore.Optimization.Protocol) ReplicatedProtocolResult (class in OCDocker.OCScore.Optimization.Protocol) ReplicatedStagedProtocol (class in OCDocker.OCScore.Optimization.Protocol) report_entity_overlap (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationConfig attribute) reporting (OCDocker.OCScore.Optimization.StagedTrainProtocol.StagedTrainProtocol attribute) ReportLevel (class in OCDocker.Error) request_payload() (OCDocker.OCScore.Utils.FeaturePolicy.FeaturePolicy method) require_trusted_input() (in module OCDocker.Toolbox.Security) rescoring_mode (OCDocker.Config.PLANTSConfig attribute) reset_config() (in module OCDocker.Config) resolve_cross_validation_dir() (in module OCDocker.OCScore.Analysis.Plotting.CrossValidationPlots) resolve_dudez_primary_metric() (in module OCDocker.OCScore.Optimization.StagedOptuna) resolve_evidence_asset() (in module OCDocker.Workbench.Evidence) resolve_ocscore_layout_root() (in module OCDocker.Workbench.OCScoreLayout) resolve_optuna_dashboard_slot_count() (in module OCDocker.Workbench.OCScoreLayout) resolve_optuna_storage() (in module OCDocker.OCScore.Optimization.OptunaStorage) resolve_protocol_path() (in module OCDocker.OCScore.Optimization.StagedTrainProtocol) resolve_reduction_source() (in module OCDocker.OCScore.CLI.train) resolve_replica_storage() (OCDocker.Workbench.OptunaDashboard.OptunaDashboardManager static method) resolve_requested_feature_policies() (in module OCDocker.OCScore.Utils.FeaturePolicy) resolve_workbench_job_token() (in module OCDocker.Workbench.Auth) result (OCDocker.OCScore.CLI.train.StagedTrainingRun attribute) resume_completed (OCDocker.OCScore.Optimization.Protocol.ReplicatedProtocolConfig attribute) retrain_from_export() (in module OCDocker.OCScore.Optimization.ModelExport) return_code (OCDocker.API.Pipeline.PipelineRunResult attribute) (OCDocker.API.PipelineRunResult attribute) rie() (in module OCDocker.OCScore.Analysis.Metrics.Ranking) riep() (in module OCDocker.OCScore.Analysis.Metrics.Ranking) RingCount (OCDocker.DB.Models.Ligands.Ligands attribute) RJ (in module OCDocker.Toolbox.Constants) RJK (in module OCDocker.Toolbox.Constants) Rk (in module OCDocker.Toolbox.Constants) rmsd (OCDocker.Config.LeDockConfig attribute) roc_auc() (in module OCDocker.OCScore.Analysis.Metrics.Ranking) roc_plot() (in module OCDocker.OCScore.Analysis.Plotting.MetricsPlots) row_aggregate_feature_scores() (in module OCDocker.OCScore.Utils.DescriptorAggregateBaselines) row_aggregate_sf_scores() (in module OCDocker.OCScore.Utils.DescriptorAggregateBaselines) row_cleanup_summary (OCDocker.OCScore.CLI.train.ReductionArtifacts attribute) run() (in module OCDocker.Toolbox.Running) (OCDocker.OCScore.Optimization.Protocol.ProtocolStage method) (OCDocker.OCScore.Optimization.Protocol.ReplicatedStagedProtocol method) (OCDocker.OCScore.Optimization.Protocol.StagedProtocol method) (OCDocker.OCScore.Optimization.StagedOptuna.DUDEzOptunaStage method) (OCDocker.OCScore.Optimization.StagedOptuna.PDBbindOptunaStage method) (OCDocker.OCScore.Optimization.StagedOptuna.TransferFeatureExtractorStage method) run_and_write_production_baselines() (in module OCDocker.OCScore.Analysis.ProductionBaselines) run_console() (in module OCDocker.Console.app) run_cross_validation_from_export() (in module OCDocker.OCScore.Optimization.ModelCrossValidation) run_dock() (in module OCDocker.Processing.Dock) run_docking() (in module OCDocker.DB.baseDB) (in module OCDocker.Docking.Gnina) (in module OCDocker.Docking.PLANTS) (in module OCDocker.Docking.Smina) run_export_shap_analysis() (in module OCDocker.OCScore.Analysis.SHAP.ExportRunner) run_external_blind_evaluation() (in module OCDocker.OCScore.Utils.ExternalBlindEvaluation) run_feature_reduction_protocol() (in module OCDocker.OCScore.Utils.FeatureReduction) run_gnina() (in module OCDocker.DB.DUDEz) (in module OCDocker.DB.LITPCBA) (in module OCDocker.DB.PDBbind) (in module OCDocker.Docking.Gnina) (OCDocker.Docking.Gnina.Gnina method) run_interactive() (in module OCDocker.Console.session) run_leakage_audit() (in module OCDocker.OCScore.Utils.LeakageAudit) run_oddt() (in module OCDocker.Rescoring.ODDT) run_pipeline() (in module OCDocker.API) (in module OCDocker.API.Pipeline) run_plants() (in module OCDocker.DB.DUDEz) (in module OCDocker.DB.LITPCBA) (in module OCDocker.DB.PDBbind) (in module OCDocker.Docking.PLANTS) (OCDocker.Docking.PLANTS.PLANTS method) run_prepare_ligand() (in module OCDocker.Docking.Gnina) (in module OCDocker.Docking.PLANTS) (in module OCDocker.Docking.Smina) (in module OCDocker.Docking.Vina) (OCDocker.Docking.Gnina.Gnina method) (OCDocker.Docking.PLANTS.PLANTS method) (OCDocker.Docking.Smina.Smina method) (OCDocker.Docking.Vina.Vina method) run_prepare_receptor() (in module OCDocker.Docking.Gnina) (in module OCDocker.Docking.PLANTS) (in module OCDocker.Docking.Smina) (in module OCDocker.Docking.Vina) (OCDocker.Docking.Gnina.Gnina method) (OCDocker.Docking.PLANTS.PLANTS method) (OCDocker.Docking.Smina.Smina method) (OCDocker.Docking.Vina.Vina method) run_production_baselines_for_replica() (in module OCDocker.OCScore.Analysis.ProductionBaselines) run_rescore() (in module OCDocker.Docking.Gnina) (in module OCDocker.Docking.PLANTS) (in module OCDocker.Docking.Smina) (in module OCDocker.Docking.Vina) (OCDocker.Docking.Gnina.Gnina method) (OCDocker.Docking.PLANTS.PLANTS method) (OCDocker.Docking.Smina.Smina method) (OCDocker.Docking.Vina.Vina method) run_smina() (in module OCDocker.DB.DUDEz) (in module OCDocker.DB.LITPCBA) (in module OCDocker.DB.PDBbind) (in module OCDocker.Docking.Smina) (OCDocker.Docking.Smina.Smina method) run_staged_ocscore_optuna_protocol() (in module OCDocker.OCScore.Optimization.StagedOptuna) run_vina() (in module OCDocker.DB.DUDEz) (in module OCDocker.DB.LITPCBA) (in module OCDocker.DB.PDBbind) (in module OCDocker.Docking.Vina) (OCDocker.Docking.Vina.Vina method) runtime (OCDocker.OCScore.Optimization.StagedTrainProtocol.StagedTrainProtocol attribute) S safe_create_dir() (in module OCDocker.Toolbox.FilesFolders) safe_remove_dir() (in module OCDocker.Toolbox.FilesFolders) safe_remove_file() (in module OCDocker.Toolbox.FilesFolders) sampler_seed (OCDocker.OCScore.Optimization.StagedOptuna.DUDEzOptunaConfig attribute) (OCDocker.OCScore.Optimization.StagedOptuna.PDBbindOptunaConfig attribute) sanitize (OCDocker.Ligand.Ligand attribute) SASA (OCDocker.DB.Models.Receptors.Receptors attribute) (OCDocker.Receptor.Receptor attribute) save_architecture_figures() (in module OCDocker.OCScore.Analysis.Plotting.ArchitecturePlots) save_baseline_comparison_figures() (in module OCDocker.OCScore.Analysis.Plotting.CrossValidationPlots) save_beeswarm_plot() (in module OCDocker.OCScore.Analysis.SHAP.Plots) save_calibration_reliability_figures() (in module OCDocker.OCScore.Analysis.Plotting.CrossValidationPlots) save_cross_validation_figures() (in module OCDocker.OCScore.Analysis.Plotting.CrossValidationPlots) save_cross_validation_result() (in module OCDocker.OCScore.Optimization.ModelCrossValidation) save_dependence_plots() (in module OCDocker.OCScore.Analysis.SHAP.Plots) save_family_importance_plot() (in module OCDocker.OCScore.Analysis.SHAP.Plots) save_global_feature_importance_plot() (in module OCDocker.OCScore.Analysis.SHAP.Plots) save_label_family_distribution_plot() (in module OCDocker.OCScore.Analysis.SHAP.Plots) save_mask() (in module OCDocker.OCScore.Utils.IO) save_object() (in module OCDocker.OCScore.Utils.IO) save_pca_importance_bins() (in module OCDocker.OCScore.Analysis.Plotting) (in module OCDocker.OCScore.Analysis.Plotting.Stats) save_pca_importance_groups() (in module OCDocker.OCScore.Analysis.Plotting) (in module OCDocker.OCScore.Analysis.Plotting.Stats) save_per_target_figures() (in module OCDocker.OCScore.Analysis.Plotting.CrossValidationPlots) save_shap_plot_suite() (in module OCDocker.OCScore.Analysis.SHAP.Plots) save_shap_plot_suite_from_paths() (in module OCDocker.OCScore.Analysis.SHAP.Plots) save_target_family_heatmap() (in module OCDocker.OCScore.Analysis.SHAP.Plots) scale_dudez_features() (in module OCDocker.OCScore.Utils.DUDEzScaling) scaling_config_to_dict() (in module OCDocker.OCScore.Utils.DUDEzScaling) scan_workspace() (in module OCDocker.Workbench.Registry) scope (OCDocker.OCScore.Utils.FeatureSelectionMetadata.FeatureSelectionScope attribute) score_only (OCDocker.Config.GninaConfig attribute) score_ranking_diagnostics() (in module OCDocker.OCScore.Analysis.Metrics.Ranking) scorer_comparison_summary (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationResult attribute) scorer_type_for_baseline_name() (in module OCDocker.OCScore.Utils.DescriptorAggregateBaselines) scores_are_logits (OCDocker.OCScore.Analysis.Metrics.Calibration.ProbabilityCalibrator attribute) scoring (OCDocker.Config.GninaConfig attribute) (OCDocker.Config.PLANTSConfig attribute) (OCDocker.Config.SminaConfig attribute) (OCDocker.Config.VinaConfig attribute) scoring_function_columns (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationResult attribute) scoring_function_metrics (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationFoldResult attribute) scoring_functions (OCDocker.Config.GninaConfig attribute) (OCDocker.Config.ODDTConfig attribute) (OCDocker.Config.PLANTSConfig attribute) (OCDocker.Config.SminaConfig attribute) (OCDocker.Config.VinaConfig attribute) search_phase (OCDocker.OCScore.Optimization.StagedOptuna.PDBbindOptunaConfig attribute) search_space (OCDocker.OCScore.Optimization.StagedOptuna.DUDEzOptunaConfig attribute) (OCDocker.OCScore.Optimization.StagedOptuna.PDBbindOptunaConfig attribute) search_space_to_summary() (in module OCDocker.OCScore.Optimization.OptunaSearchSpace) search_speed (OCDocker.Config.PLANTSConfig attribute) section() (in module OCDocker.Toolbox.Printing) seed (OCDocker.Config.GninaConfig attribute) (OCDocker.Config.ODDTConfig attribute) (OCDocker.OCScore.Optimization.Protocol.ReplicaResult attribute) (OCDocker.OCScore.Optimization.StagedTrainProtocol.StagedTrainProtocol attribute) selected_features (OCDocker.OCScore.CLI.train.ReductionArtifacts attribute) (OCDocker.OCScore.Optimization.Protocol.ProtocolContext attribute) (OCDocker.OCScore.Utils.FeatureSelectionMetadata.FeatureSelectionScope attribute) (OCDocker.OCScore.Utils.TrainOnlyFeatureReduction.TrainOnlyReductionArtifact attribute) selected_features_hash (OCDocker.OCScore.Utils.FeatureSelectionMetadata.FeatureSelectionScope attribute) (OCDocker.OCScore.Utils.FixedOuterSplit.FixedOuterSplitAssignment attribute) selected_features_source (OCDocker.OCScore.Utils.FeatureSelectionMetadata.FeatureSelectionScope attribute) SelectedFeatureRowCleanupResult (class in OCDocker.OCScore.Utils.TrainOnlyFeatureReduction) serve_ocdocker_mcp() (in module OCDocker.MCP) (in module OCDocker.MCP.Server) serve_workbench_api() (in module OCDocker.Workbench.Server) set_color_mapping() (in module OCDocker.OCScore.Analysis.Plotting) (in module OCDocker.OCScore.Analysis.Plotting.Colouring) set_config() (in module OCDocker.Config) set_level_from_report() (in module OCDocker.Toolbox.Logging) setup_database() (in module OCDocker.DB.DB) severity (OCDocker.OCScore.Utils.LeakageAudit.LeakageFinding attribute) shap_correlation_heatmap() (in module OCDocker.OCScore.Analysis.SHAP.Plots) shap_values_csv (OCDocker.OCScore.Analysis.SHAP.Paths.OutputPaths attribute) shap_values_npy (OCDocker.OCScore.Analysis.SHAP.Paths.OutputPaths attribute) SharedNeuralSearchSpace (class in OCDocker.OCScore.Optimization.OptunaSearchSpace) shuffle (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationConfig attribute) shuffle_within_splits (OCDocker.OCScore.Utils.DUDEzSplit.DUDEzSplitConfig attribute) simple_ascent (OCDocker.Config.GninaConfig attribute) single_descriptors (OCDocker.DB.Models.Receptors.Receptors attribute) (OCDocker.Ligand.Ligand attribute) (OCDocker.Receptor.Receptor attribute) SlogP_VSA1 (OCDocker.DB.Models.Ligands.Ligands attribute) SlogP_VSA10 (OCDocker.DB.Models.Ligands.Ligands attribute) SlogP_VSA11 (OCDocker.DB.Models.Ligands.Ligands attribute) SlogP_VSA12 (OCDocker.DB.Models.Ligands.Ligands attribute) SlogP_VSA2 (OCDocker.DB.Models.Ligands.Ligands attribute) SlogP_VSA3 (OCDocker.DB.Models.Ligands.Ligands attribute) SlogP_VSA4 (OCDocker.DB.Models.Ligands.Ligands attribute) SlogP_VSA5 (OCDocker.DB.Models.Ligands.Ligands attribute) SlogP_VSA6 (OCDocker.DB.Models.Ligands.Ligands attribute) SlogP_VSA7 (OCDocker.DB.Models.Ligands.Ligands attribute) SlogP_VSA8 (OCDocker.DB.Models.Ligands.Ligands attribute) SlogP_VSA9 (OCDocker.DB.Models.Ligands.Ligands attribute) Smina (class in OCDocker.Docking.Smina) smina (OCDocker.Config.OCDockerConfig attribute) SMINA_FAST_DKOES (OCDocker.DB.Models.Complexes.Complexes attribute) SMINA_OLD_SCORING_DKOES (OCDocker.DB.Models.Complexes.Complexes attribute) SMINA_SCORING_AD4 (OCDocker.DB.Models.Complexes.Complexes attribute) SMINA_SCORING_DKOES (OCDocker.DB.Models.Complexes.Complexes attribute) SMINA_VINA (OCDocker.DB.Models.Complexes.Complexes attribute) SMINA_VINARDO (OCDocker.DB.Models.Complexes.Complexes attribute) SminaConfig (class in OCDocker.Config) SMR_VSA1 (OCDocker.DB.Models.Ligands.Ligands attribute) SMR_VSA10 (OCDocker.DB.Models.Ligands.Ligands attribute) SMR_VSA2 (OCDocker.DB.Models.Ligands.Ligands attribute) SMR_VSA3 (OCDocker.DB.Models.Ligands.Ligands attribute) SMR_VSA4 (OCDocker.DB.Models.Ligands.Ligands attribute) SMR_VSA5 (OCDocker.DB.Models.Ligands.Ligands attribute) SMR_VSA6 (OCDocker.DB.Models.Ligands.Ligands attribute) SMR_VSA7 (OCDocker.DB.Models.Ligands.Ligands attribute) SMR_VSA8 (OCDocker.DB.Models.Ligands.Ligands attribute) SMR_VSA9 (OCDocker.DB.Models.Ligands.Ligands attribute) source_hash (OCDocker.OCScore.Utils.FeaturePolicy.FeaturePolicy attribute) source_kind (OCDocker.OCScore.Utils.FeaturePolicy.FeaturePolicy attribute) source_path (OCDocker.OCScore.Optimization.StagedTrainProtocol.StagedTrainProtocol attribute) (OCDocker.OCScore.Utils.FeaturePolicy.FeaturePolicy attribute) SpherocityIndex (OCDocker.DB.Models.Ligands.Ligands attribute) split_and_convert() (in module OCDocker.Toolbox.Conversion) split_config (OCDocker.OCScore.Optimization.StagedOptuna.DUDEzOptunaConfig attribute) (OCDocker.OCScore.Optimization.StagedOptuna.PDBbindOptunaConfig attribute) split_descriptor_blocks() (in module OCDocker.OCScore.Utils.FeatureReduction) split_dudez_by_receptor_and_kind() (in module OCDocker.OCScore.Utils.DUDEzSplit) split_executable (OCDocker.Config.VinaConfig attribute) split_molecules() (in module OCDocker.Ligand) split_pdbbind_regression() (in module OCDocker.OCScore.Utils.PDBbindSplit) split_poses() (in module OCDocker.Toolbox.MoleculeProcessing) (OCDocker.Docking.Gnina.Gnina method) (OCDocker.Docking.Smina.Smina method) (OCDocker.Docking.Vina.Vina method) split_wide_dataset_by_column() (in module OCDocker.OCScore.Utils.TrainOnlyFeatureReduction) spores (OCDocker.Config.ToolsConfig attribute) SPORESPreparationStrategy (class in OCDocker.Toolbox.Preparation) sqlite_path (OCDocker.Config.DatabaseConfig attribute) (OCDocker.DB.DBMinimal.DatabaseSettings attribute) stage_results (OCDocker.OCScore.Optimization.Protocol.ProtocolContext attribute) StagedProtocol (class in OCDocker.OCScore.Optimization.Protocol) StagedTrainingRun (class in OCDocker.OCScore.CLI.train) StagedTrainProtocol (class in OCDocker.OCScore.Optimization.StagedTrainProtocol) stages (OCDocker.OCScore.Optimization.Protocol.ReplicatedStagedProtocol attribute) (OCDocker.OCScore.Optimization.Protocol.StagedProtocol attribute) STANDARD_TEMPERATURE_K (in module OCDocker.Toolbox.Constants) start() (OCDocker.Workbench.OptunaDashboard.OptunaDashboardManager method) status() (OCDocker.Workbench.OptunaDashboard.OptunaDashboardManager method) stop() (OCDocker.Workbench.OptunaDashboard.OptunaDashboardManager method) stop_all() (OCDocker.Workbench.OptunaDashboard.OptunaDashboardManager method) storage (OCDocker.OCScore.Optimization.StagedOptuna.DUDEzOptunaConfig attribute) (OCDocker.OCScore.Optimization.StagedOptuna.PDBbindOptunaConfig attribute) storage_path (OCDocker.Workbench.OptunaDashboard.OptunaDashboardSession attribute) strategy (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationConfig attribute) (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationResult attribute) (OCDocker.OCScore.Utils.DUDEzScaling.DUDEzScalingConfig attribute) (OCDocker.OCScore.Utils.DUDEzSplit.DUDEzSplitConfig attribute) (OCDocker.OCScore.Utils.PDBbindSplit.PDBbindSplitConfig attribute) strict (OCDocker.OCScore.Utils.DUDEzScaling.DUDEzScalingConfig attribute) stripH (OCDocker.Config.GninaConfig attribute) structure (OCDocker.Receptor.Receptor attribute) study_name (OCDocker.OCScore.Optimization.StagedOptuna.DUDEzOptunaConfig attribute) (OCDocker.OCScore.Optimization.StagedOptuna.PDBbindOptunaConfig attribute) SubprocessError subsection() (in module OCDocker.Toolbox.Printing) SUCCESS (OCDocker.Error.ReportLevel attribute) success (OCDocker.OCScore.Optimization.Protocol.ReplicaResult attribute) suggest_decoder_hidden_sizes() (in module OCDocker.OCScore.Optimization.StagedOptuna) suggest_dudez_trial_params() (in module OCDocker.OCScore.Optimization.StagedOptuna) suggest_encoder_architecture() (in module OCDocker.OCScore.Optimization.StagedOptuna) suggest_pdbbind_trial_params() (in module OCDocker.OCScore.Optimization.StagedOptuna) summarize_blocks() (in module OCDocker.OCScore.Utils.FeatureReduction) summarize_dudez_split_diagnostics() (in module OCDocker.OCScore.Optimization.StagedOptuna) summarize_results() (in module OCDocker.Workbench.Results) summarize_run_manifest() (in module OCDocker.Workbench.Registry) summary (OCDocker.API.Pipeline.PipelineRunResult attribute) (OCDocker.API.PipelineRunResult attribute) (OCDocker.OCScore.Optimization.Protocol.ReplicaResult attribute) (OCDocker.OCScore.Utils.TrainOnlyFeatureReduction.SelectedFeatureRowCleanupResult attribute) summary_df (OCDocker.OCScore.Optimization.Protocol.ReplicatedProtocolResult attribute) T target_column (OCDocker.OCScore.Optimization.StagedOptuna.PDBbindOptunaConfig attribute) (OCDocker.OCScore.Utils.PDBbindSplit.PDBbindSplitConfig attribute) target_columns (OCDocker.OCScore.Utils.FeaturePolicy.CandidateFeatureDiscovery attribute) (OCDocker.OCScore.Utils.TrainOnlyFeatureReduction.TrainOnlyReductionArtifact attribute) target_group_column (OCDocker.OCScore.Optimization.StagedOptuna.DUDEzOptunaConfig attribute) task (OCDocker.OCScore.Analysis.Plotting.ArchitecturePlots.ArchitectureDiagram attribute) (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationResult attribute) temperature (OCDocker.Config.GninaConfig attribute) test_idx (OCDocker.OCScore.Utils.DUDEzSplit.DUDEzSplitResult attribute) (OCDocker.OCScore.Utils.PDBbindSplit.PDBbindSplitResult attribute) test_receptors (OCDocker.OCScore.Utils.DUDEzSplit.DUDEzSplitConfig attribute) test_size (OCDocker.OCScore.Optimization.StagedOptuna.DUDEzOptunaConfig attribute) (OCDocker.OCScore.Optimization.StagedOptuna.PDBbindOptunaConfig attribute) (OCDocker.OCScore.Utils.DUDEzSplit.DUDEzSplitConfig attribute) (OCDocker.OCScore.Utils.PDBbindSplit.PDBbindSplitConfig attribute) threshold_at_precision() (in module OCDocker.OCScore.Analysis.Metrics.Ranking) tmp_dir (OCDocker.Config.OCDockerConfig attribute) to_dict() (OCDocker.DB.Models.Base.Base class method) (OCDocker.Ligand.Ligand method) (OCDocker.OCScore.Analysis.Metrics.Calibration.ProbabilityCalibrator method) (OCDocker.OCScore.Utils.FeatureSelectionMetadata.FeatureSelectionScope method) (OCDocker.OCScore.Utils.FixedOuterSplit.FixedOuterSplitAssignment method) (OCDocker.OCScore.Utils.LeakageAudit.LeakageAuditResult method) (OCDocker.OCScore.Utils.TrainOnlyFeatureReduction.TrainOnlyReductionArtifact method) (OCDocker.Receptor.Receptor method) to_hdf5() (in module OCDocker.Toolbox.FilesFolders) to_json() (OCDocker.Ligand.Ligand method) (OCDocker.Receptor.Receptor method) to_metadata() (OCDocker.OCScore.Utils.FeaturePolicy.FeaturePolicyApplication method) to_pickle() (in module OCDocker.Toolbox.FilesFolders) to_smiles() (OCDocker.Ligand.Ligand method) tools (OCDocker.Config.OCDockerConfig attribute) ToolsConfig (class in OCDocker.Config) top_fraction_precision() (in module OCDocker.OCScore.Analysis.Metrics.Ranking) top_k_precision() (in module OCDocker.OCScore.Analysis.Metrics.Ranking) TotalAALength (OCDocker.DB.Models.Receptors.Receptors attribute) (OCDocker.Receptor.Receptor attribute) TPSA (OCDocker.DB.Models.Ligands.Ligands attribute) traceback (OCDocker.OCScore.Optimization.Protocol.ReplicaResult attribute) train_idx (OCDocker.OCScore.Utils.DUDEzSplit.DUDEzSplitResult attribute) (OCDocker.OCScore.Utils.PDBbindSplit.PDBbindSplitResult attribute) train_indices (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationFoldResult attribute) train_only() (OCDocker.OCScore.Utils.FeatureSelectionMetadata.FeatureSelectionScope class method) train_receptors (OCDocker.OCScore.Utils.DUDEzSplit.DUDEzSplitConfig attribute) train_size (OCDocker.OCScore.Utils.DUDEzSplit.DUDEzSplitConfig attribute) (OCDocker.OCScore.Utils.PDBbindSplit.PDBbindSplitConfig attribute) TrainOnlyFitError TrainOnlyReductionArtifact (class in OCDocker.OCScore.Utils.TrainOnlyFeatureReduction) TransferFeatureExtractorStage (class in OCDocker.OCScore.Optimization.StagedOptuna) transform_artifact_hashes (OCDocker.OCScore.Utils.FeatureSelectionMetadata.FeatureSelectionScope attribute) (OCDocker.OCScore.Utils.TrainOnlyFeatureReduction.TrainOnlyReductionArtifact attribute) transform_artifacts (OCDocker.OCScore.Utils.FeatureSelectionMetadata.FeatureSelectionScope attribute) (OCDocker.OCScore.Utils.TrainOnlyFeatureReduction.TrainOnlyReductionArtifact attribute) transform_export_features() (in module OCDocker.OCScore.Optimization.ModelExport) U unmatched_columns (OCDocker.OCScore.Utils.FeaturePolicy.CandidateFeatureDiscovery attribute) untar() (in module OCDocker.Toolbox.FilesFolders) update() (OCDocker.DB.Models.Base.Base class method) update_to() (OCDocker.Toolbox.Downloading.DownloadProgressBar method) url (OCDocker.Workbench.OptunaDashboard.OptunaDashboardSession attribute) use_class_weighting (OCDocker.OCScore.Optimization.StagedOptuna.DUDEzOptunaConfig attribute) use_class_weighting_options (OCDocker.OCScore.Optimization.OptunaSearchSpace.DUDEzHeadSearchSpace attribute) use_gpu (OCDocker.OCScore.Optimization.StagedOptuna.DUDEzOptunaConfig attribute) (OCDocker.OCScore.Optimization.StagedOptuna.PDBbindOptunaConfig attribute) use_transfer_options (OCDocker.OCScore.Optimization.OptunaSearchSpace.DUDEzHeadSearchSpace attribute) user (OCDocker.Config.DatabaseConfig attribute) (OCDocker.DB.DBMinimal.DatabaseSettings attribute) user_grid (OCDocker.Config.GninaConfig attribute) (OCDocker.Config.SminaConfig attribute) user_grid_lambda (OCDocker.Config.GninaConfig attribute) (OCDocker.Config.SminaConfig attribute) uses_supervised_target (OCDocker.OCScore.Utils.FeatureSelectionMetadata.FeatureSelectionScope attribute) V val_idx (OCDocker.OCScore.Utils.DUDEzSplit.DUDEzSplitResult attribute) (OCDocker.OCScore.Utils.PDBbindSplit.PDBbindSplitResult attribute) validate_calibration_report_mode() (in module OCDocker.OCScore.Analysis.Metrics.Calibration) validate_database_config() (in module OCDocker.DB.DBMinimal) validate_descriptor_frame() (in module OCDocker.OCScore.Utils.FeatureReduction) validate_digest_extension() (in module OCDocker.Toolbox.Validation) validate_export_bundle() (in module OCDocker.OCScore.Optimization.ModelExport) validate_export_features() (in module OCDocker.OCScore.Optimization.ModelExport) validate_fit_uses_train_only() (in module OCDocker.OCScore.Analysis.ProductionBaselines) validate_fold_indices() (in module OCDocker.OCScore.Optimization.ModelCrossValidation) validate_fold_split() (in module OCDocker.OCScore.Optimization.ModelCrossValidation) validate_obabel_extension() (in module OCDocker.Toolbox.Validation) validate_pdbbind_search_phase() (in module OCDocker.OCScore.Optimization.OptunaSearchSpace) validate_production_claim_budget() (OCDocker.OCScore.Optimization.StagedTrainProtocol.StagedTrainProtocol method) validate_protocol_integrity() (in module OCDocker.OCScore.Utils.FixedOuterSplit) validate_raw_schema() (in module OCDocker.OCScore.Utils.RawModelingInput) validate_receptor_group_split() (in module OCDocker.OCScore.Optimization.ModelCrossValidation) validate_replica_path() (OCDocker.Workbench.OptunaDashboard.OptunaDashboardManager method) validate_replica_split_alignment() (in module OCDocker.OCScore.Utils.FixedOuterSplit) validate_selected_features() (in module OCDocker.OCScore.CLI.train) validate_train_only_feature_selection() (in module OCDocker.OCScore.Utils.FeatureSelectionMetadata) validation_indices (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationFoldResult attribute) validation_metrics (OCDocker.OCScore.Optimization.ModelCrossValidation.CrossValidationFoldResult attribute) validation_receptors (OCDocker.OCScore.Utils.DUDEzSplit.DUDEzSplitConfig attribute) validation_size (OCDocker.OCScore.Optimization.StagedOptuna.DUDEzOptunaConfig attribute) (OCDocker.OCScore.Optimization.StagedOptuna.PDBbindOptunaConfig attribute) (OCDocker.OCScore.Utils.DUDEzSplit.DUDEzSplitConfig attribute) (OCDocker.OCScore.Utils.PDBbindSplit.PDBbindSplitConfig attribute) variants (OCDocker.OCScore.Optimization.StagedTrainProtocol.AblationProtocolSection attribute) vdw_defn_file (OCDocker.Config.Dock6Config attribute) verbose (OCDocker.OCScore.Optimization.StagedOptuna.DUDEzOptunaConfig attribute) (OCDocker.OCScore.Optimization.StagedOptuna.PDBbindOptunaConfig attribute) verify_selected_features_against_scope() (in module OCDocker.OCScore.Utils.FeatureSelectionMetadata) Vina (class in OCDocker.Docking.Vina) vina (OCDocker.Config.OCDockerConfig attribute) VINA_VINA (OCDocker.DB.Models.Complexes.Complexes attribute) VINA_VINARDO (OCDocker.DB.Models.Complexes.Complexes attribute) VinaConfig (class in OCDocker.Config) VSA_EState1 (OCDocker.DB.Models.Ligands.Ligands attribute) VSA_EState10 (OCDocker.DB.Models.Ligands.Ligands attribute) VSA_EState2 (OCDocker.DB.Models.Ligands.Ligands attribute) VSA_EState3 (OCDocker.DB.Models.Ligands.Ligands attribute) VSA_EState4 (OCDocker.DB.Models.Ligands.Ligands attribute) VSA_EState5 (OCDocker.DB.Models.Ligands.Ligands attribute) VSA_EState6 (OCDocker.DB.Models.Ligands.Ligands attribute) VSA_EState7 (OCDocker.DB.Models.Ligands.Ligands attribute) VSA_EState8 (OCDocker.DB.Models.Ligands.Ligands attribute) VSA_EState9 (OCDocker.DB.Models.Ligands.Ligands attribute) W WARNING (OCDocker.Error.ReportLevel attribute) weight_decay_max (OCDocker.OCScore.Optimization.OptunaSearchSpace.OptimizerSearchSpace attribute) weight_decay_min (OCDocker.OCScore.Optimization.OptunaSearchSpace.OptimizerSearchSpace attribute) workbench_job_token_path() (in module OCDocker.Workbench.Auth) WorkbenchAPIError write_ablation_design_policy() (in module OCDocker.Workbench.AblationDesign) write_adoption_workspace() (in module OCDocker.Workbench.Adoption) write_config_file() (in module OCDocker.Docking.PLANTS) (OCDocker.Docking.PLANTS.PLANTS method) write_example_outputs() (in module OCDocker.OCScore.CLI.train) write_feature_policy_metadata() (in module OCDocker.OCScore.Utils.FeaturePolicy) write_feature_reduction_outputs() (in module OCDocker.OCScore.Utils.FeatureReduction) write_feature_selection_fit_rows_json() (in module OCDocker.OCScore.Utils.FeatureSelectionMetadata) write_feature_selection_json() (in module OCDocker.OCScore.Utils.FeatureSelectionMetadata) write_fixed_outer_split_json() (in module OCDocker.OCScore.Utils.FixedOuterSplit) write_launch_script() (in module OCDocker.Workbench.Launch) write_leakage_audit_report() (in module OCDocker.OCScore.Utils.LeakageAudit) write_model() (in module OCDocker.Workbench.IO) write_pose_list() (in module OCDocker.Docking.PLANTS) (OCDocker.Docking.PLANTS.PLANTS method) write_prepare_manifest() (in module OCDocker.OCScore.Utils.RawModelingInput) write_production_baseline_reports() (in module OCDocker.OCScore.Analysis.ProductionBaselines) write_production_provenance_bundle() (in module OCDocker.OCScore.Utils.ProtocolProvenance) write_protocol_log (OCDocker.OCScore.Optimization.Protocol.ReplicatedProtocolConfig attribute) (OCDocker.OCScore.Optimization.Protocol.StagedProtocol attribute) write_reports (OCDocker.OCScore.Optimization.Protocol.ReplicatedProtocolConfig attribute) write_reproducibility_manifest() (in module OCDocker.Toolbox.Reproducibility) write_rescoring_config_file() (in module OCDocker.Docking.PLANTS) write_train_only_reduction_artifact() (in module OCDocker.OCScore.Utils.TrainOnlyFeatureReduction) written (OCDocker.OCScore.CLI.train.StagedTrainingRun attribute) Z ZERO_C_IN_K (in module OCDocker.Toolbox.Constants)