Index A | B | C | D | E | F | G | H | I | K | L | M | N | P | R | S | T | V | W | Y A artifacts_dir (psma.PsmaResult attribute) (psma.results.PsmaResult attribute) auc (psma.PsmaMetrics attribute) (psma.results.PsmaMetrics attribute) auc_defined (psma.PsmaMetrics attribute) (psma.results.PsmaMetrics attribute) B build_similarity_embedding_cosine() (in module psma.similarity) build_similarity_from_triples() (in module psma.similarity) build_similarity_rdkit_morgan() (in module psma.similarity) butina_distance_cutoff (psma.PsmaParams attribute) (psma.results.PsmaParams attribute) C c_test (psma.results.PsmaCoordinates attribute) c_train (psma.results.PsmaCoordinates attribute) c_train_scaled (psma.kde.KDEResult attribute) compute_metrics() (in module psma.metrics) compute_posterior() (in module psma.psma) compute_psma_surface() (in module psma) (in module psma.main) confusion (psma.PsmaMetrics attribute) (psma.results.PsmaMetrics attribute) coords (psma.PsmaResult attribute) (psma.results.PsmaResult attribute) D d_test_train (psma.results.PsmaDistance attribute) d_train (psma.results.PsmaDistance attribute) DensityGrid (class in psma.kde) diagnostics (psma.results.ProjectionDiagnostics attribute) distance (psma.PsmaResult attribute) (psma.results.PsmaResult attribute) distance_k (psma.PsmaParams attribute) (psma.results.PsmaParams attribute) E embed_method (psma.PsmaParams attribute) (psma.results.PsmaParams attribute) embed_train() (in module psma.embed) ensure_output_dir() (in module psma.io) eps (psma.PsmaParams attribute) (psma.results.PsmaParams attribute) evaluate_density_grid() (in module psma.kde) extract_core_arrays() (in module psma.io) F fit_class_kdes() (in module psma.kde) frames (psma.PsmaResult attribute) (psma.results.PsmaResult attribute) G grid (psma.PsmaResult attribute) (psma.results.PsmaResult attribute) grid_lims_scale (psma.PsmaParams attribute) (psma.results.PsmaParams attribute) grid_n (psma.PsmaParams attribute) (psma.results.PsmaParams attribute) grid_x (psma.kde.DensityGrid attribute) (psma.results.PsmaGrid attribute) grid_y (psma.kde.DensityGrid attribute) (psma.results.PsmaGrid attribute) H hx (psma.kde.KDEResult attribute) hy (psma.kde.KDEResult attribute) I indices (psma.PsmaResult attribute) (psma.results.PsmaResult attribute) is_ill_conditioned (psma.results.ProjectionDiagnostics attribute) K kde_neg (psma.kde.KDEResult attribute) kde_pos (psma.kde.KDEResult attribute) KDEResult (class in psma.kde) L label_direction (psma.PsmaParams attribute) (psma.results.PsmaParams attribute) label_threshold (psma.PsmaParams attribute) (psma.results.PsmaParams attribute) LabelResult (class in psma.labels) labels (psma.PsmaResult attribute) (psma.results.PsmaResult attribute) M main() (in module psma.cli) make_train_test_split() (in module psma.split) mcc (psma.PsmaMetrics attribute) (psma.results.PsmaMetrics attribute) mcc_prob_threshold (psma.PsmaParams attribute) (psma.results.PsmaParams attribute) metric_notes (psma.PsmaMetrics attribute) (psma.results.PsmaMetrics attribute) metrics (psma.PsmaResult attribute) (psma.results.PsmaResult attribute) module psma psma.cli psma.distance psma.embed psma.io psma.kde psma.labels psma.main psma.metrics psma.plot psma.project psma.psma psma.results psma.score psma.similarity psma.split morgan_n_bits (psma.PsmaParams attribute) (psma.results.PsmaParams attribute) morgan_radius (psma.PsmaParams attribute) (psma.results.PsmaParams attribute) N neg_density_z (psma.kde.DensityGrid attribute) (psma.results.PsmaGrid attribute) P params (psma.PsmaResult attribute) (psma.results.PsmaResult attribute) pcoa_embed() (in module psma.embed) plot_posterior_2d() (in module psma.plot) plot_posterior_2d_interactive() (in module psma.plot) plot_posterior_3d() (in module psma.plot) pos_density_z (psma.kde.DensityGrid attribute) (psma.results.PsmaGrid attribute) posterior_z (psma.results.PsmaGrid attribute) prior_neg (psma.labels.LabelResult attribute) (psma.results.PsmaLabels attribute) prior_pos (psma.labels.LabelResult attribute) (psma.results.PsmaLabels attribute) prob_test (psma.PsmaResult attribute) (psma.results.PsmaResult attribute) project_test_coordinates() (in module psma.project) projection (psma.PsmaResult attribute) (psma.results.PsmaResult attribute) ProjectionDiagnostics (class in psma.results) psma module psma.cli module psma.distance module psma.embed module psma.io module psma.kde module psma.labels module psma.main module psma.metrics module psma.plot module psma.project module psma.psma module psma.results module psma.score module psma.similarity module psma.split module PsmaCoordinates (class in psma.results) PsmaDistance (class in psma.results) PsmaFrames (class in psma.results) PsmaGrid (class in psma.results) PsmaIndices (class in psma.results) PsmaLabels (class in psma.results) PsmaMetrics (class in psma) (class in psma.results) PsmaParams (class in psma) (class in psma.results) PsmaResult (class in psma) (class in psma.results) PsmaSimilarity (class in psma.results) R random_state (psma.PsmaParams attribute) (psma.results.PsmaParams attribute) run_psma_surface() (in module psma) (in module psma.main) S s_full (psma.results.PsmaSimilarity attribute) s_test_train (psma.results.PsmaSimilarity attribute) s_train (psma.results.PsmaSimilarity attribute) save_csv() (in module psma.io) save_json() (in module psma.io) score_test_points() (in module psma.score) similarity (psma.PsmaResult attribute) (psma.results.PsmaResult attribute) similarity_method (psma.PsmaParams attribute) (psma.results.PsmaParams attribute) similarity_to_distance() (in module psma.distance) split_method (psma.PsmaParams attribute) (psma.results.PsmaParams attribute) T test (psma.results.PsmaFrames attribute) (psma.results.PsmaIndices attribute) test_fraction (psma.PsmaParams attribute) (psma.results.PsmaParams attribute) threshold (psma.PsmaMetrics attribute) (psma.results.PsmaMetrics attribute) threshold_labels() (in module psma.labels) train (psma.results.PsmaFrames attribute) (psma.results.PsmaIndices attribute) train_condition_number (psma.results.ProjectionDiagnostics attribute) train_rank (psma.results.ProjectionDiagnostics attribute) tsne_embed() (in module psma.embed) tsne_max_iter (psma.PsmaParams attribute) (psma.results.PsmaParams attribute) tsne_perplexity (psma.PsmaParams attribute) (psma.results.PsmaParams attribute) V validate_input_dataframe() (in module psma.io) validate_thresholded_training_labels() (in module psma.labels) W write_psma_artifacts() (in module psma.io) Y y_col (psma.PsmaParams attribute) (psma.results.PsmaParams attribute) y_test_bin (psma.labels.LabelResult attribute) (psma.results.PsmaLabels attribute) y_train_bin (psma.labels.LabelResult attribute) (psma.results.PsmaLabels attribute)