Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Z _ __getitem__() (OCDocker.OCScore.Dimensionality.AutoencoderOptimizer.AutoencoderDataset method) (OCDocker.OCScore.Dimensionality.future.datasets.AutoencoderDataset method) (OCDocker.OCScore.DNN.DNNOptimizer.CustomDataset method) (OCDocker.OCScore.DNN.DNNOptimizer.MultiBranchCustomDataset method) (OCDocker.OCScore.DNN.future.datasets.EnergyDataset method) (OCDocker.OCScore.DNN.future.datasets.TargetRankingDataset method) (OCDocker.OCScore.Transformer.TransOptimizer.CustomDataset method) __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.Dimensionality.AutoencoderOptimizer.Autoencoder method) (OCDocker.OCScore.Dimensionality.AutoencoderOptimizer.AutoencoderDataset method) (OCDocker.OCScore.Dimensionality.AutoencoderOptimizer.AutoencoderOptimizer method) (OCDocker.OCScore.Dimensionality.future.AETrainer.AETrainer method) (OCDocker.OCScore.Dimensionality.future.AETrainer.EarlyStopping method) (OCDocker.OCScore.Dimensionality.future.Autoencoder.Autoencoder method) (OCDocker.OCScore.Dimensionality.future.Autoencoder.EncoderModule method) (OCDocker.OCScore.Dimensionality.future.Autoencoder.MLP method) (OCDocker.OCScore.Dimensionality.future.AutoencoderOptimizer.AutoencoderOptimizer method) (OCDocker.OCScore.Dimensionality.future.datasets.AutoencoderDataset method) (OCDocker.OCScore.Dimensionality.GeneticAlgorithm.GeneticAlgorithm method) (OCDocker.OCScore.DNN.DNNOptimizer.CustomDataset method) (OCDocker.OCScore.DNN.DNNOptimizer.DNNOptimizer method) (OCDocker.OCScore.DNN.DNNOptimizer.DynamicNN method) (OCDocker.OCScore.DNN.DNNOptimizer.MultiBranchCustomDataset method) (OCDocker.OCScore.DNN.DNNOptimizer.MultiBranchDynamicNN method) (OCDocker.OCScore.DNN.DNNOptimizer.NeuralNet method) (OCDocker.OCScore.DNN.future.datasets.EnergyDataset method) (OCDocker.OCScore.DNN.future.datasets.TargetBatchSampler method) (OCDocker.OCScore.DNN.future.datasets.TargetRankingDataset method) (OCDocker.OCScore.DNN.future.DNNOptimizer.DNNOptimizer method) (OCDocker.OCScore.DNN.future.losses.UncertaintyWeighting method) (OCDocker.OCScore.DNN.future.models.MLP method) (OCDocker.OCScore.DNN.future.models.MultiTaskModel method) (OCDocker.OCScore.Transformer.TransOptimizer.CustomDataset method) (OCDocker.OCScore.Transformer.TransOptimizer.Transformer method) (OCDocker.OCScore.Transformer.TransOptimizer.TransformerModel method) (OCDocker.OCScore.Transformer.TransOptimizer.TransOptimizer method) (OCDocker.OCScore.XGBoost.XGBoostOptimizer.XGBoostOptimizer method) (OCDocker.Receptor.Receptor method) __iter__() (OCDocker.OCScore.DNN.future.datasets.TargetBatchSampler method) __len__() (OCDocker.OCScore.Dimensionality.AutoencoderOptimizer.AutoencoderDataset method) (OCDocker.OCScore.Dimensionality.future.datasets.AutoencoderDataset method) (OCDocker.OCScore.DNN.DNNOptimizer.CustomDataset method) (OCDocker.OCScore.DNN.DNNOptimizer.MultiBranchCustomDataset method) (OCDocker.OCScore.DNN.future.datasets.EnergyDataset method) (OCDocker.OCScore.DNN.future.datasets.TargetBatchSampler method) (OCDocker.OCScore.DNN.future.datasets.TargetRankingDataset method) (OCDocker.OCScore.Transformer.TransOptimizer.CustomDataset method) __repr__() (OCDocker.DB.Models.Base.Base class method) (OCDocker.Ligand.Ligand method) A ablate() (OCDocker.OCScore.DNN.DNNOptimizer.DNNOptimizer method) accurate_line (OCDocker.Config.GninaConfig attribute) (OCDocker.Config.SminaConfig attribute) add_dynamic_columns() (OCDocker.DB.Models.Base.Base class method) addH (OCDocker.Config.GninaConfig attribute) AETrainer (class in OCDocker.OCScore.Dimensionality.future.AETrainer) AEworker() (in module OCDocker.OCScore.Utils.Workers) allDescriptors (OCDocker.DB.Models.Complexes.Complexes attribute), [1] (OCDocker.DB.Models.Ligands.Ligands attribute) (OCDocker.DB.Models.Receptors.Receptors attribute), [1] (OCDocker.Ligand.Ligand attribute) (OCDocker.Receptor.Receptor attribute) allow_unsafe_runtime() (in module OCDocker.Toolbox.Security) analyze_studies() (in module OCDocker.OCScore.Utils.StudyParser) analyze_studies_old() (in module OCDocker.OCScore.Utils.StudyParser) apply_basic_style() (in module OCDocker.OCScore.Analysis.Plotting.Core) apply_noise() (in module OCDocker.OCScore.Dimensionality.future.utils) apply_pca() (in module OCDocker.OCScore.Utils.Data) approximation (OCDocker.Config.GninaConfig attribute) (OCDocker.Config.SminaConfig attribute) Aromaticity (OCDocker.DB.Models.Receptors.Receptors attribute) (OCDocker.Receptor.Receptor attribute) Asphericity (OCDocker.DB.Models.Ligands.Ligands attribute) atom_term_data (OCDocker.Config.GninaConfig attribute) atom_terms (OCDocker.Config.GninaConfig attribute) 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) Autoencoder (class in OCDocker.OCScore.Dimensionality.AutoencoderOptimizer) (class in OCDocker.OCScore.Dimensionality.future.Autoencoder) AutoencoderDataset (class in OCDocker.OCScore.Dimensionality.AutoencoderOptimizer) (class in OCDocker.OCScore.Dimensionality.future.datasets) AutoencoderOptimizer (class in OCDocker.OCScore.Dimensionality.AutoencoderOptimizer) (class in OCDocker.OCScore.Dimensionality.future.AutoencoderOptimizer) available_cores (OCDocker.Config.OCDockerConfig attribute) AvgAALength (OCDocker.DB.Models.Receptors.Receptors attribute) (OCDocker.Receptor.Receptor attribute) B backend (OCDocker.Config.DatabaseConfig attribute) backup_log() (in module OCDocker.Toolbox.Logging) BalabanJ (OCDocker.DB.Models.Ligands.Ligands attribute) Base (class in OCDocker.DB.Models.Base) base (in module OCDocker.DB.Models.Base) 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) beeswarm() (in module OCDocker.OCScore.Analysis.SHAP.Plots) BertzCT (OCDocker.DB.Models.Ligands.Ligands 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) build_argparser() (in module OCDocker.OCScore.Analysis.SHAP.Cli) build_charmm_to_canonical_map() (in module OCDocker.Toolbox.MoleculeProcessing) build_impact_overview() (in module OCDocker.OCScore.Analysis.Impact) build_neural_net() (in module OCDocker.OCScore.Analysis.SHAP.Model) build_stratified_background() (in module OCDocker.OCScore.Analysis.FeatureImportance) 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) calculate_metrics() (in module OCDocker.OCScore.Utils.Data) 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) chunkenize_dataset() (in module OCDocker.OCScore.Utils.Data) class_func() (in module OCDocker.Ligand) 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 OCDockerConsole) cleanup_engine() (in module OCDocker.DB.DBMinimal) cleanup_session() (in module OCDocker.DB.DBMinimal) clear_past_logs() (in module OCDocker.Toolbox.Logging) cluster_rmsd (OCDocker.Config.PLANTSConfig attribute) cluster_rmsd() (in module OCDocker.Processing.Preprocessing.RmsdClustering) cluster_structures (OCDocker.Config.PLANTSConfig attribute) 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) collect_periodically() (in module OCDocker.Processing.GarbageCollection) Complexes (class in OCDocker.DB.Models.Complexes) complexes (OCDocker.DB.Models.Ligands.Ligands attribute), [1] (OCDocker.DB.Models.Receptors.Receptors attribute), [1] compute_aromaticity() (in module OCDocker.Receptor) compute_auc() (in module OCDocker.OCScore.Utils.Evaluation) compute_classification_metrics() (in module OCDocker.OCScore.DNN.future.metrics) compute_dipole_moment() (in module OCDocker.Receptor) compute_gravy() (in module OCDocker.Receptor) compute_group_metrics() (in module OCDocker.OCScore.DNN.future.metrics) compute_instability_index() (in module OCDocker.Receptor) compute_isoelectric_point() (in module OCDocker.Receptor) compute_metrics() (in module OCDocker.OCScore.Utils.Evaluation) compute_rmse() (in module OCDocker.OCScore.Utils.Evaluation) compute_sasa() (in module OCDocker.Receptor) compute_shap_values() (in module OCDocker.OCScore.Analysis.FeatureImportance) (in module OCDocker.OCScore.Analysis.SHAP.Explain) compute_zscore() (in module OCDocker.OCScore.Utils.Data) configure() (in module OCDocker.Toolbox.Logging) contractive_penalty() (in module OCDocker.OCScore.Dimensionality.future.losses) 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) correlation_analysis() (in module OCDocker.OCScore.Analysis.Correlation) 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_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) crossover() (OCDocker.OCScore.Dimensionality.GeneticAlgorithm.GeneticAlgorithm method) custom_atoms (OCDocker.Config.GninaConfig attribute) (OCDocker.Config.SminaConfig attribute) custom_scoring (OCDocker.Config.GninaConfig attribute) (OCDocker.Config.SminaConfig attribute) CustomDataset (class in OCDocker.OCScore.DNN.DNNOptimizer) (class in OCDocker.OCScore.Transformer.TransOptimizer) D database (OCDocker.Config.DatabaseConfig attribute) (OCDocker.Config.OCDockerConfig attribute) DatabaseConfig (class in OCDocker.Config) DEBUG (OCDocker.Error.ReportLevel attribute) delete() (OCDocker.DB.Models.Base.Base class method) descriptors_names (OCDocker.DB.Models.Complexes.Complexes attribute) (OCDocker.DB.Models.Receptors.Receptors attribute) (OCDocker.Ligand.Ligand attribute) (OCDocker.Receptor.Receptor attribute) detect_extreme_outliers_iqr_columns_positive() (in module OCDocker.OCScore.Utils.Data) determine_column_type() (OCDocker.DB.Models.Base.Base class method) device (OCDocker.Config.GninaConfig attribute) (OCDocker.OCScore.Dimensionality.AutoencoderOptimizer.AutoencoderOptimizer attribute) df_to_dict() (in module OCDocker.Rescoring.ODDT) DipoleMoment (OCDocker.DB.Models.Receptors.Receptors attribute) (OCDocker.Receptor.Receptor attribute) DNNOptimizer (class in OCDocker.OCScore.DNN.DNNOptimizer) (class in OCDocker.OCScore.DNN.future.DNNOptimizer) 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) download_url() (in module OCDocker.Toolbox.Downloading) DownloadProgressBar (class in OCDocker.Toolbox.Downloading) dssp (OCDocker.Config.ToolsConfig attribute) dudez_archive (OCDocker.Config.OCDockerConfig attribute) dudez_download (OCDocker.Config.ToolsConfig attribute) DynamicNN (class in OCDocker.OCScore.DNN.DNNOptimizer) E EarlyStopping (class in OCDocker.OCScore.Dimensionality.future.AETrainer) Eccentricity (OCDocker.DB.Models.Ligands.Ligands attribute) embedding_stats() (in module OCDocker.OCScore.Dimensionality.future.utils) empty_docking_digest() (in module OCDocker.Toolbox.FilesFolders) encode() (OCDocker.OCScore.Dimensionality.future.Autoencoder.Autoencoder method) EncoderModule (class in OCDocker.OCScore.Dimensionality.future.Autoencoder) energy (OCDocker.OCScore.Dimensionality.future.Autoencoder.ForwardOutput attribute) energy_loss() (in module OCDocker.OCScore.Dimensionality.future.losses) energy_range (OCDocker.Config.SminaConfig attribute) (OCDocker.Config.VinaConfig attribute) EnergyDataset (class in OCDocker.OCScore.DNN.future.datasets) enrichment_factor() (in module OCDocker.OCScore.Analysis.Metrics.Ranking) enrichment_plot() (in module OCDocker.OCScore.Analysis.Plotting.MetricsPlots) ensure_parent_dir() (in module OCDocker.Toolbox.FilesFolders) env_flag_enabled() (in module OCDocker.Toolbox.Security) ERROR (OCDocker.Error.ReportLevel 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() (OCDocker.OCScore.Dimensionality.future.AETrainer.AETrainer method) evaluate_autoencoder() (OCDocker.OCScore.Dimensionality.AutoencoderOptimizer.AutoencoderOptimizer method) ExactMolWt (OCDocker.DB.Models.Ligands.Ligands 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) export_db_to_csv() (in module OCDocker.DB.DB) export_table_to_csv() (in module OCDocker.DB.DB) F factor (OCDocker.Config.GninaConfig attribute) (OCDocker.Config.SminaConfig attribute) feature_importance_barh() (in module OCDocker.OCScore.Analysis.SHAP.Plots) feature_report_2xk() (in module OCDocker.OCScore.Analysis.Plotting.ImpactPlots) 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_first() (OCDocker.DB.Models.Base.Base class method) find_iter() (OCDocker.DB.Models.Base.Base class method) 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) 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) fit() (OCDocker.OCScore.Dimensionality.future.AETrainer.AETrainer method) fitness() (OCDocker.OCScore.Dimensionality.GeneticAlgorithm.GeneticAlgorithm method) 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) focal_binary_loss() (in module OCDocker.OCScore.DNN.future.losses) force_cap (OCDocker.Config.GninaConfig attribute) (OCDocker.Config.SminaConfig attribute) forward() (OCDocker.OCScore.Dimensionality.AutoencoderOptimizer.Autoencoder method) (OCDocker.OCScore.Dimensionality.future.Autoencoder.Autoencoder method) (OCDocker.OCScore.Dimensionality.future.Autoencoder.EncoderModule method) (OCDocker.OCScore.Dimensionality.future.Autoencoder.MLP method) (OCDocker.OCScore.DNN.DNNOptimizer.DynamicNN method) (OCDocker.OCScore.DNN.DNNOptimizer.MultiBranchDynamicNN method) (OCDocker.OCScore.DNN.future.losses.UncertaintyWeighting method) (OCDocker.OCScore.DNN.future.models.MLP method) (OCDocker.OCScore.DNN.future.models.MultiTaskModel method) (OCDocker.OCScore.Transformer.TransOptimizer.TransformerModel method) ForwardOutput (class in OCDocker.OCScore.Dimensionality.future.Autoencoder) 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) from_embeddings() (OCDocker.OCScore.DNN.future.DNNOptimizer.DNNOptimizer 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 GAWorker() (in module OCDocker.OCScore.Utils.Workers) 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_mask() (in module OCDocker.OCScore.Utils.Data) generate_plants_files_database() (in module OCDocker.Docking.PLANTS) generate_reproducibility_manifest() (in module OCDocker.CLI) (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) genetic_algorithm() (OCDocker.OCScore.Dimensionality.GeneticAlgorithm.GeneticAlgorithm method) GeneticAlgorithm (class in OCDocker.OCScore.Dimensionality.GeneticAlgorithm) 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) (in module OCDockerConsole) get_decoder() (OCDocker.OCScore.Dimensionality.AutoencoderOptimizer.Autoencoder method) (OCDocker.OCScore.Dimensionality.future.Autoencoder.Autoencoder method) get_decoder_topology() (OCDocker.OCScore.Dimensionality.AutoencoderOptimizer.Autoencoder method) (OCDocker.OCScore.Dimensionality.future.Autoencoder.Autoencoder method) 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_encoder() (OCDocker.OCScore.Dimensionality.AutoencoderOptimizer.Autoencoder method) (OCDocker.OCScore.Dimensionality.future.Autoencoder.Autoencoder method) get_encoder_topology() (OCDocker.OCScore.Dimensionality.AutoencoderOptimizer.Autoencoder method) (OCDocker.OCScore.Dimensionality.future.Autoencoder.Autoencoder 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_model() (OCDocker.OCScore.DNN.DNNOptimizer.NeuralNet method) (OCDocker.OCScore.Transformer.TransOptimizer.Transformer method) get_models() (in module OCDocker.Rescoring.ODDT) get_models_dir() (in module OCDocker.OCScore.Utils.IO) get_neutral_features() (in module OCDocker.OCScore.Analysis.Impact) 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_study_data() (in module OCDocker.OCScore.Analysis.StudyProcessing) 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) groupwise() (in module OCDocker.OCScore.Analysis.Metrics.Ranking) H HallKierAlpha (OCDocker.DB.Models.Ligands.Ligands attribute) HeavyAtomCount (OCDocker.DB.Models.Ligands.Ligands attribute) HeavyAtomMolWt (OCDocker.DB.Models.Ligands.Ligands attribute) host (OCDocker.Config.DatabaseConfig 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] InertialShapeFactor (OCDocker.DB.Models.Ligands.Ligands attribute) INFO (OCDocker.Error.ReportLevel attribute) initialize_population() (OCDocker.OCScore.Dimensionality.GeneticAlgorithm.GeneticAlgorithm method) initialize_weights() (OCDocker.OCScore.Transformer.TransOptimizer.TransformerModel method) insert() (OCDocker.DB.Models.Base.Base class method) insert_or_update() (OCDocker.DB.Models.Base.Base class method) 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_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) IsoelectricPoint (OCDocker.DB.Models.Receptors.Receptors attribute) (OCDocker.Receptor.Receptor attribute) J J_to_cal() (in module OCDocker.Toolbox.Constants) 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) kikd_to_deltag() (in module OCDocker.Toolbox.Conversion) kl_divergence() (in module OCDocker.OCScore.Dimensionality.future.losses) L LabuteASA (OCDocker.DB.Models.Ligands.Ligands attribute) lambda_rank_ndcg_loss() (in module OCDocker.OCScore.DNN.future.losses) latent (OCDocker.OCScore.Dimensionality.future.Autoencoder.ForwardOutput attribute) 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) 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) load_data() (in module OCDocker.OCScore.Utils.Data) (in module OCDocker.OCScore.Utils.IO) load_encoder() (OCDocker.OCScore.Dimensionality.future.Autoencoder.Autoencoder method) load_mask() (in module OCDocker.OCScore.Utils.IO) load_mol() (in module OCDocker.Ligand) (in module OCDocker.Receptor) load_object() (in module OCDocker.OCScore.Utils.IO) local_only (OCDocker.Config.GninaConfig attribute) (OCDocker.Config.SminaConfig attribute) logdir (OCDocker.Config.OCDockerConfig attribute) logvar (OCDocker.OCScore.Dimensionality.future.Autoencoder.ForwardOutput attribute) M main() (in module OCDocker.CLI) (in module OCDocker.OCScore.Analysis.SHAP.Cli) make_explainer() (in module OCDocker.OCScore.Analysis.FeatureImportance) mask (OCDocker.OCScore.DNN.future.DNNOptimizer.DNNOptimizer 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) metadata (OCDocker.DB.Models.Base.Base attribute) MGLToolsPreparationStrategy (class in OCDocker.Toolbox.Preparation) 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) MLP (class in OCDocker.OCScore.Dimensionality.future.Autoencoder) (class in OCDocker.OCScore.DNN.future.models) 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.CLI OCDocker.Config OCDocker.DB OCDocker.DB.baseDB OCDocker.DB.DB OCDocker.DB.DBMinimal OCDocker.DB.DUDEz 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.OCScore OCDocker.OCScore.Analysis.Correlation OCDocker.OCScore.Analysis.FeatureImportance OCDocker.OCScore.Analysis.Impact OCDocker.OCScore.Analysis.Metrics OCDocker.OCScore.Analysis.Metrics.Bootstrap OCDocker.OCScore.Analysis.Metrics.Ranking OCDocker.OCScore.Analysis.NNUtils OCDocker.OCScore.Analysis.Plotting OCDocker.OCScore.Analysis.Plotting.Colouring OCDocker.OCScore.Analysis.Plotting.Core OCDocker.OCScore.Analysis.Plotting.ImpactPlots OCDocker.OCScore.Analysis.Plotting.MetricsPlots OCDocker.OCScore.Analysis.Plotting.Stats OCDocker.OCScore.Analysis.SHAP.Cli OCDocker.OCScore.Analysis.SHAP.Explain OCDocker.OCScore.Analysis.SHAP.Model OCDocker.OCScore.Analysis.SHAP.Plots OCDocker.OCScore.Analysis.StudyProcessing OCDocker.OCScore.Dimensionality OCDocker.OCScore.Dimensionality.AutoencoderOptimizer OCDocker.OCScore.Dimensionality.future OCDocker.OCScore.Dimensionality.future.AETrainer OCDocker.OCScore.Dimensionality.future.Autoencoder OCDocker.OCScore.Dimensionality.future.AutoencoderOptimizer OCDocker.OCScore.Dimensionality.future.datasets OCDocker.OCScore.Dimensionality.future.losses OCDocker.OCScore.Dimensionality.future.utils OCDocker.OCScore.Dimensionality.GeneticAlgorithm OCDocker.OCScore.Dimensionality.PCA OCDocker.OCScore.DNN OCDocker.OCScore.DNN.DNNOptimizer OCDocker.OCScore.DNN.future OCDocker.OCScore.DNN.future.datasets OCDocker.OCScore.DNN.future.DNNOptimizer OCDocker.OCScore.DNN.future.losses OCDocker.OCScore.DNN.future.metrics OCDocker.OCScore.DNN.future.models OCDocker.OCScore.Optimization OCDocker.OCScore.Optimization.DNN OCDocker.OCScore.Optimization.future OCDocker.OCScore.Optimization.future.DNN OCDocker.OCScore.Optimization.Transformer OCDocker.OCScore.Optimization.XGBoost OCDocker.OCScore.Scoring OCDocker.OCScore.Transformer OCDocker.OCScore.Transformer.TransOptimizer OCDocker.OCScore.Utils OCDocker.OCScore.Utils.Data OCDocker.OCScore.Utils.Evaluation OCDocker.OCScore.Utils.IO OCDocker.OCScore.Utils.Plotting OCDocker.OCScore.Utils.SimpleConsensus OCDocker.OCScore.Utils.StudyParser OCDocker.OCScore.Utils.Workers OCDocker.OCScore.XGBoost OCDocker.OCScore.XGBoost.OCxgboost OCDocker.OCScore.XGBoost.XGBoostOptimizer 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 OCDockerConsole 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) mu (OCDocker.OCScore.Dimensionality.future.Autoencoder.ForwardOutput attribute) MultiBranchCustomDataset (class in OCDocker.OCScore.DNN.DNNOptimizer) MultiBranchDynamicNN (class in OCDocker.OCScore.DNN.DNNOptimizer) multiple_molecules_sdf() (in module OCDocker.Ligand) multiprocess (OCDocker.Config.OCDockerConfig attribute) MultiTaskModel (class in OCDocker.OCScore.DNN.future.models) mutation() (OCDocker.OCScore.Dimensionality.GeneticAlgorithm.GeneticAlgorithm method) N 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.Receptor.Receptor attribute) ndcg_at_k() (in module OCDocker.OCScore.DNN.future.metrics) needs_canonical_pdb_fix() (in module OCDocker.Toolbox.MoleculeProcessing) NeuralNet (class in OCDocker.OCScore.DNN.DNNOptimizer) new_fig() (in module OCDocker.OCScore.Analysis.Plotting.Core) NHOHCount (OCDocker.DB.Models.Ligands.Ligands attribute) NNAblationworker() (in module OCDocker.OCScore.Utils.Workers) NNSeedAblationworker() (in module OCDocker.OCScore.Utils.Workers) NNworker() (in module OCDocker.OCScore.Utils.Workers) 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_path() (in module OCDocker.Toolbox.FilesFolders) normalize_smiles_with_openbabel (OCDocker.Ligand.Ligand 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) 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() (OCDocker.OCScore.Dimensionality.AutoencoderOptimizer.AutoencoderOptimizer method) (OCDocker.OCScore.Dimensionality.future.AutoencoderOptimizer.AutoencoderOptimizer method) (OCDocker.OCScore.Dimensionality.GeneticAlgorithm.GeneticAlgorithm method) (OCDocker.OCScore.DNN.DNNOptimizer.DNNOptimizer method) (OCDocker.OCScore.DNN.future.DNNOptimizer.DNNOptimizer method) (OCDocker.OCScore.Transformer.TransOptimizer.TransOptimizer method) (OCDocker.OCScore.XGBoost.XGBoostOptimizer.XGBoostOptimizer method) objective_ablation() (OCDocker.OCScore.DNN.DNNOptimizer.DNNOptimizer method) ocdb_path (OCDocker.Config.PathsConfig attribute) OCDocker module OCDocker.CLI module OCDocker.Config module OCDocker.DB module OCDocker.DB.baseDB module OCDocker.DB.DB module OCDocker.DB.DBMinimal module OCDocker.DB.DUDEz 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.OCScore module OCDocker.OCScore.Analysis.Correlation module OCDocker.OCScore.Analysis.FeatureImportance module OCDocker.OCScore.Analysis.Impact module OCDocker.OCScore.Analysis.Metrics module OCDocker.OCScore.Analysis.Metrics.Bootstrap module OCDocker.OCScore.Analysis.Metrics.Ranking module OCDocker.OCScore.Analysis.NNUtils module OCDocker.OCScore.Analysis.Plotting module OCDocker.OCScore.Analysis.Plotting.Colouring module OCDocker.OCScore.Analysis.Plotting.Core module OCDocker.OCScore.Analysis.Plotting.ImpactPlots module OCDocker.OCScore.Analysis.Plotting.MetricsPlots module OCDocker.OCScore.Analysis.Plotting.Stats module OCDocker.OCScore.Analysis.SHAP.Cli module OCDocker.OCScore.Analysis.SHAP.Explain module OCDocker.OCScore.Analysis.SHAP.Model module OCDocker.OCScore.Analysis.SHAP.Plots module OCDocker.OCScore.Analysis.StudyProcessing module OCDocker.OCScore.Dimensionality module OCDocker.OCScore.Dimensionality.AutoencoderOptimizer module OCDocker.OCScore.Dimensionality.future module OCDocker.OCScore.Dimensionality.future.AETrainer module OCDocker.OCScore.Dimensionality.future.Autoencoder module OCDocker.OCScore.Dimensionality.future.AutoencoderOptimizer module OCDocker.OCScore.Dimensionality.future.datasets module OCDocker.OCScore.Dimensionality.future.losses module OCDocker.OCScore.Dimensionality.future.utils module OCDocker.OCScore.Dimensionality.GeneticAlgorithm module OCDocker.OCScore.Dimensionality.PCA module OCDocker.OCScore.DNN module OCDocker.OCScore.DNN.DNNOptimizer module OCDocker.OCScore.DNN.future module OCDocker.OCScore.DNN.future.datasets module OCDocker.OCScore.DNN.future.DNNOptimizer module OCDocker.OCScore.DNN.future.losses module OCDocker.OCScore.DNN.future.metrics module OCDocker.OCScore.DNN.future.models module OCDocker.OCScore.Optimization module OCDocker.OCScore.Optimization.DNN module OCDocker.OCScore.Optimization.future module OCDocker.OCScore.Optimization.future.DNN module OCDocker.OCScore.Optimization.Transformer module OCDocker.OCScore.Optimization.XGBoost module OCDocker.OCScore.Scoring module OCDocker.OCScore.Transformer module OCDocker.OCScore.Transformer.TransOptimizer module OCDocker.OCScore.Utils module OCDocker.OCScore.Utils.Data module OCDocker.OCScore.Utils.Evaluation module OCDocker.OCScore.Utils.IO module OCDocker.OCScore.Utils.Plotting module OCDocker.OCScore.Utils.SimpleConsensus module OCDocker.OCScore.Utils.StudyParser module OCDocker.OCScore.Utils.Workers module OCDocker.OCScore.XGBoost module OCDocker.OCScore.XGBoost.OCxgboost module OCDocker.OCScore.XGBoost.XGBoostOptimizer 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_path (OCDocker.Config.OCDockerConfig attribute) OCDockerConfig (class in OCDocker.Config) OCDockerConsole module 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) OpenBabelPreparationStrategy (class in OCDocker.Toolbox.Preparation) optimize() (in module OCDocker.OCScore.Optimization.DNN) (in module OCDocker.OCScore.Optimization.future.DNN) (in module OCDocker.OCScore.Optimization.Transformer) (in module OCDocker.OCScore.Optimization.XGBoost) (OCDocker.OCScore.Dimensionality.AutoencoderOptimizer.AutoencoderOptimizer method) (OCDocker.OCScore.Dimensionality.future.AutoencoderOptimizer.AutoencoderOptimizer method) (OCDocker.OCScore.Dimensionality.GeneticAlgorithm.GeneticAlgorithm method) (OCDocker.OCScore.DNN.DNNOptimizer.DNNOptimizer method) (OCDocker.OCScore.DNN.future.DNNOptimizer.DNNOptimizer method) (OCDocker.OCScore.Transformer.TransOptimizer.TransOptimizer method) (OCDocker.OCScore.XGBoost.XGBoostOptimizer.XGBoostOptimizer method) optimize_NN() (in module OCDocker.OCScore.Optimization.DNN) optimize_NN_future() (in module OCDocker.OCScore.Optimization.future.DNN) optimize_Transformer() (in module OCDocker.OCScore.Optimization.Transformer) optimize_XGB() (in module OCDocker.OCScore.Optimization.XGBoost) optimizedb (OCDocker.Config.DatabaseConfig attribute) order (in module OCDocker.Toolbox.Constants) original_path (OCDocker.Receptor.Receptor attribute) out_flex (OCDocker.Config.GninaConfig attribute) output_level (OCDocker.Config.OCDockerConfig attribute) overwrite (OCDocker.Config.OCDockerConfig attribute) P parse_encoder_params() (in module OCDocker.OCScore.DNN.future.models) parse_study_type() (in module OCDocker.OCScore.Utils.StudyParser) parsed_archive (OCDocker.Config.OCDockerConfig attribute) partial_auc() (in module OCDocker.OCScore.DNN.future.metrics) password (OCDocker.Config.DatabaseConfig attribute) path (OCDocker.Ligand.Ligand attribute) (OCDocker.Receptor.Receptor attribute) paths (OCDocker.Config.OCDockerConfig attribute) PathsConfig (class in OCDocker.Config) pca_path (OCDocker.Config.PathsConfig attribute) pdbbind_archive (OCDocker.Config.OCDockerConfig attribute) pdbbind_kdki_order (OCDocker.Config.PathsConfig attribute) 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) perform_ablation_study_NN() (in module OCDocker.OCScore.Optimization.DNN) perform_seed_ablation_study_NN() (in module OCDocker.OCScore.Optimization.DNN) perform_simple_consensus() (in module OCDocker.OCScore.Utils.SimpleConsensus) 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_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_boxplots() (in module OCDocker.OCScore.Analysis.Plotting) (in module OCDocker.OCScore.Analysis.Plotting.Stats) plot_chi2_contrib() (in module OCDocker.OCScore.Analysis.Plotting.ImpactPlots) plot_combined_metric_scatter() (in module OCDocker.OCScore.Analysis.Plotting) (in module OCDocker.OCScore.Analysis.Plotting.Stats) plot_correlation_similarity() (in module OCDocker.OCScore.Utils.Plotting) plot_heatmap() (in module OCDocker.OCScore.Analysis.Plotting) (in module OCDocker.OCScore.Analysis.Plotting.Stats) plot_impact_arrows_inline_labels() (in module OCDocker.OCScore.Analysis.Impact) plot_normality_and_variance_diagnostics() (in module OCDocker.OCScore.Analysis.Plotting) (in module OCDocker.OCScore.Analysis.Plotting.Stats) 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_prop_delta() (in module OCDocker.OCScore.Analysis.Plotting.ImpactPlots) plot_residuals_lollipop() (in module OCDocker.OCScore.Analysis.Plotting.ImpactPlots) plot_residuals_matrix() (in module OCDocker.OCScore.Analysis.Plotting.ImpactPlots) plot_roc_curves() (in module OCDocker.OCScore.Utils.Plotting) 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) pool_chunksize() (in module OCDocker.Processing.GarbageCollection) port (OCDocker.Config.DatabaseConfig attribute) pose_sort_order (OCDocker.Config.GninaConfig attribute) pr_auc() (in module OCDocker.OCScore.Analysis.Metrics.Ranking) pr_plot() (in module OCDocker.OCScore.Analysis.Plotting.MetricsPlots) PreparationStrategy (class in OCDocker.Toolbox.Preparation) prepare() (in module OCDocker.DB.baseDB) (in module OCDocker.DB.DUDEz) (in module OCDocker.DB.PDBbind) (in module OCDocker.Processing.Preprocessing.Prepare) 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_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) preprocess_df() (in module OCDocker.OCScore.Utils.Data) print_args() (in module OCDockerConsole) 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) printv() (in module OCDocker.Toolbox.Printing) prop_delta_2xk() (in module OCDocker.OCScore.Analysis.Plotting.ImpactPlots) 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) ramp_weight() (in module OCDocker.OCScore.Dimensionality.future.utils) randomize_only (OCDocker.Config.GninaConfig attribute) (OCDocker.Config.SminaConfig attribute) rank_train (OCDocker.OCScore.DNN.future.DNNOptimizer.DNNOptimizer attribute) rank_val (OCDocker.OCScore.DNN.future.DNNOptimizer.DNNOptimizer attribute) 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_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_smina_log() (in module OCDocker.Docking.BaseVinaLike) read_smina_rescoring_log() (in module OCDocker.Docking.BaseVinaLike) 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_id (OCDocker.DB.Models.Complexes.Complexes attribute), [1] Receptors (class in OCDocker.DB.Models.Receptors) reconstruct() (OCDocker.OCScore.Dimensionality.future.Autoencoder.Autoencoder method) reconstruction (OCDocker.OCScore.Dimensionality.future.Autoencoder.ForwardOutput attribute) reconstruction_loss() (in module OCDocker.OCScore.Dimensionality.future.losses) redirect_to_tqdm() (in module OCDocker.Toolbox.Basetools) reference_column_order (OCDocker.Config.PathsConfig attribute) registry (OCDocker.DB.Models.Base.Base attribute) remove_extreme_outliers_iqr_columns_positive() (in module OCDocker.OCScore.Utils.Data) remove_other_columns() (in module OCDocker.OCScore.Utils.Data) renumber_pdb_residues() (in module OCDocker.Receptor) reorder_columns_to_match_data_order() (in module OCDocker.OCScore.Utils.Data) reparameterize() (OCDocker.OCScore.Dimensionality.future.Autoencoder.EncoderModule method) ReportLevel (class in OCDocker.Error) require_trusted_input() (in module OCDocker.Toolbox.Security) rescoring_mode (OCDocker.Config.PLANTSConfig attribute) reset_config() (in module OCDocker.Config) residuals_matrix_from_dict() (in module OCDocker.OCScore.Analysis.Plotting.ImpactPlots) 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) run() (in module OCDocker.Toolbox.Running) run_ae_feature_importance() (in module OCDocker.OCScore.Analysis.NNUtils) 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) (in module OCDocker.Processing.Dock) run_gnina() (in module OCDocker.DB.DUDEz) (in module OCDocker.DB.PDBbind) (in module OCDocker.Docking.Gnina) (OCDocker.Docking.Gnina.Gnina method) run_oddt() (in module OCDocker.Rescoring.ODDT) run_pca() (in module OCDocker.OCScore.Dimensionality.PCA) run_plants() (in module OCDocker.DB.DUDEz) (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_ligand_from_cmd() (in module OCDocker.Docking.Gnina) (in module OCDocker.Docking.Smina) (OCDocker.Docking.Gnina.Gnina method) (OCDocker.Docking.Smina.Smina 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_prepare_receptor_from_cmd() (in module OCDocker.Docking.Gnina) (in module OCDocker.Docking.Smina) (OCDocker.Docking.Gnina.Gnina method) (OCDocker.Docking.Smina.Smina method) 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.PDBbind) (in module OCDocker.Docking.Smina) (OCDocker.Docking.Smina.Smina method) run_vina() (in module OCDocker.DB.DUDEz) (in module OCDocker.DB.PDBbind) (in module OCDocker.Docking.Vina) (OCDocker.Docking.Vina.Vina method) run_xgboost() (in module OCDocker.OCScore.XGBoost.OCxgboost) S safe_auc() (in module OCDocker.OCScore.DNN.future.metrics) safe_create_dir() (in module OCDocker.Toolbox.FilesFolders) safe_log_loss() (in module OCDocker.OCScore.DNN.future.metrics) safe_pr_auc() (in module OCDocker.OCScore.DNN.future.metrics) safe_remove_dir() (in module OCDocker.Toolbox.FilesFolders) safe_remove_file() (in module OCDocker.Toolbox.FilesFolders) sanitize (OCDocker.Ligand.Ligand attribute) sanity_check() (OCDocker.OCScore.Dimensionality.future.Autoencoder.Autoencoder method) SASA (OCDocker.DB.Models.Receptors.Receptors attribute) (OCDocker.Receptor.Receptor attribute) save_encoder() (OCDocker.OCScore.Dimensionality.future.Autoencoder.Autoencoder method) 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) score_only (OCDocker.Config.GninaConfig attribute) scoring (OCDocker.Config.GninaConfig attribute) (OCDocker.Config.PLANTSConfig attribute) (OCDocker.Config.SminaConfig attribute) (OCDocker.Config.VinaConfig attribute) scoring_functions (OCDocker.Config.GninaConfig attribute) (OCDocker.Config.ODDTConfig attribute) (OCDocker.Config.PLANTSConfig attribute) (OCDocker.Config.SminaConfig attribute) (OCDocker.Config.VinaConfig attribute) search_speed (OCDocker.Config.PLANTSConfig attribute) section() (in module OCDocker.Toolbox.Printing) seed (OCDocker.Config.GninaConfig attribute) (OCDocker.Config.ODDTConfig attribute) 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) set_random_seed() (OCDocker.OCScore.Dimensionality.AutoencoderOptimizer.AutoencoderOptimizer method) (OCDocker.OCScore.Dimensionality.future.AutoencoderOptimizer.AutoencoderOptimizer method) (OCDocker.OCScore.DNN.DNNOptimizer.DNNOptimizer method) (OCDocker.OCScore.DNN.DNNOptimizer.NeuralNet method) (OCDocker.OCScore.DNN.future.DNNOptimizer.DNNOptimizer method) (OCDocker.OCScore.Transformer.TransOptimizer.Transformer method) (OCDocker.OCScore.Transformer.TransOptimizer.TransformerModel method) (OCDocker.OCScore.Transformer.TransOptimizer.TransOptimizer method) setup_database() (in module OCDocker.DB.DB) shap_correlation_heatmap() (in module OCDocker.OCScore.Analysis.SHAP.Plots) shap_importance_table() (in module OCDocker.OCScore.Analysis.FeatureImportance) simple_ascent (OCDocker.Config.GninaConfig attribute) simple_consensus() (in module OCDocker.OCScore.Utils.SimpleConsensus) 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) spearman_corr() (in module OCDocker.OCScore.Dimensionality.future.utils) SpherocityIndex (OCDocker.DB.Models.Ligands.Ligands attribute) split_and_convert() (in module OCDocker.Toolbox.Conversion) split_dataset() (in module OCDocker.OCScore.Utils.Data) split_executable (OCDocker.Config.VinaConfig attribute) split_molecules() (in module OCDocker.Ligand) split_poses() (in module OCDocker.Toolbox.MoleculeProcessing) (OCDocker.Docking.Gnina.Gnina method) (OCDocker.Docking.Smina.Smina method) (OCDocker.Docking.Vina.Vina method) spores (OCDocker.Config.ToolsConfig attribute) SPORESPreparationStrategy (class in OCDocker.Toolbox.Preparation) sqlite_path (OCDocker.Config.DatabaseConfig attribute) STANDARD_TEMPERATURE_K (in module OCDocker.Toolbox.Constants) step() (OCDocker.OCScore.Dimensionality.future.AETrainer.EarlyStopping method) stripH (OCDocker.Config.GninaConfig attribute) structure (OCDocker.Receptor.Receptor attribute) SubprocessError subsection() (in module OCDocker.Toolbox.Printing) SUCCESS (OCDocker.Error.ReportLevel attribute) supervised_contrastive_loss() (in module OCDocker.OCScore.DNN.future.losses) T TargetBatchSampler (class in OCDocker.OCScore.DNN.future.datasets) TargetRankingDataset (class in OCDocker.OCScore.DNN.future.datasets) temperature (OCDocker.Config.GninaConfig attribute) test_loader (OCDocker.OCScore.Dimensionality.AutoencoderOptimizer.AutoencoderOptimizer 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.Receptor.Receptor method) to_hdf5() (in module OCDocker.Toolbox.FilesFolders) to_json() (OCDocker.Ligand.Ligand method) (OCDocker.Receptor.Receptor 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) tournament_selection() (OCDocker.OCScore.Dimensionality.GeneticAlgorithm.GeneticAlgorithm method) TPSA (OCDocker.DB.Models.Ligands.Ligands attribute) train_autoencoder() (OCDocker.OCScore.Dimensionality.AutoencoderOptimizer.AutoencoderOptimizer method) train_loader (OCDocker.OCScore.Dimensionality.AutoencoderOptimizer.AutoencoderOptimizer attribute) train_model() (OCDocker.OCScore.DNN.DNNOptimizer.NeuralNet method) (OCDocker.OCScore.Transformer.TransOptimizer.Transformer method) train_test_model() (OCDocker.OCScore.DNN.DNNOptimizer.DNNOptimizer method) (OCDocker.OCScore.Transformer.TransOptimizer.TransOptimizer method) Transformer (class in OCDocker.OCScore.Transformer.TransOptimizer) TransformerModel (class in OCDocker.OCScore.Transformer.TransOptimizer) TransOptimizer (class in OCDocker.OCScore.Transformer.TransOptimizer) Transworker() (in module OCDocker.OCScore.Utils.Workers) U UncertaintyWeighting (class in OCDocker.OCScore.DNN.future.losses) untar() (in module OCDocker.Toolbox.FilesFolders) update() (OCDocker.DB.Models.Base.Base class method) update_to() (OCDocker.Toolbox.Downloading.DownloadProgressBar method) user (OCDocker.Config.DatabaseConfig attribute) user_grid (OCDocker.Config.GninaConfig attribute) (OCDocker.Config.SminaConfig attribute) user_grid_lambda (OCDocker.Config.GninaConfig attribute) (OCDocker.Config.SminaConfig attribute) V validate_digest_extension() (in module OCDocker.Toolbox.Validation) validate_obabel_extension() (in module OCDocker.Toolbox.Validation) validation_loader (OCDocker.OCScore.Dimensionality.AutoencoderOptimizer.AutoencoderOptimizer attribute) vdw_defn_file (OCDocker.Config.Dock6Config attribute) 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) write_config_file() (in module OCDocker.Docking.PLANTS) (OCDocker.Docking.PLANTS.PLANTS method) write_pose_list() (in module OCDocker.Docking.PLANTS) (OCDocker.Docking.PLANTS.PLANTS method) write_reproducibility_manifest() (in module OCDocker.Toolbox.Reproducibility) write_rescoring_config_file() (in module OCDocker.Docking.PLANTS) X X_test (OCDocker.OCScore.Dimensionality.AutoencoderOptimizer.AutoencoderOptimizer attribute) X_train (OCDocker.OCScore.Dimensionality.AutoencoderOptimizer.AutoencoderOptimizer attribute) X_validation (OCDocker.OCScore.Dimensionality.AutoencoderOptimizer.AutoencoderOptimizer attribute) XGBoostOptimizer (class in OCDocker.OCScore.XGBoost.XGBoostOptimizer) XGBworker() (in module OCDocker.OCScore.Utils.Workers) Z ZERO_C_IN_K (in module OCDocker.Toolbox.Constants)