psma

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