From 9b9665045c53cc8800f4d5b1d737ce3143875060 Mon Sep 17 00:00:00 2001 From: Anthony Gitter Date: Sun, 13 Oct 2024 07:32:08 -0500 Subject: [PATCH] Rename docking results dir --- docking/README.md | 3 +++ .../docking_results_llm_high_medium_low_smi.pkl | Bin .../all_targets_ecr_score_pdfs.png | Bin .../all_targets_ecr_score_pdfs_logscale.png | Bin .../docking_all_ecr_qt_qtmean_scores_high.png | Bin .../docking_all_ecr_qt_qtmean_scores_low.png | Bin .../docking_all_ecr_qt_qtmean_scores_medium.png | Bin .../plot_qt_docking_score_dists_all.py | 0 .../docking_all_ecr_qt_qtmean_scores_high_layer.png | Bin .../docking_all_ecr_qt_qtmean_scores_low_layer.png | Bin ...ocking_all_ecr_qt_qtmean_scores_medium_layer.png | Bin .../plot_qt_docking_score_dists_all_layer_v1.1.py | 0 .../sns_histplot_ecr_score_PDFs.py | 0 .../sns_histplot_ecr_score_PDFs_logscale.py | 0 .../raw_docking_data/scores_high_ranking_ECR.pkl | Bin .../raw_docking_data/scores_low_ranking_ECR.pkl | Bin 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new file mode 100644 index 0000000..b34a3f9 --- /dev/null +++ b/docking/README.md @@ -0,0 +1,3 @@ +# Docking case study results + +Update in progress diff --git a/docking_result/docking_results_llm_high_medium_low_smi.pkl b/docking/docking_results_llm_high_medium_low_smi.pkl similarity index 100% rename from docking_result/docking_results_llm_high_medium_low_smi.pkl rename to docking/docking_results_llm_high_medium_low_smi.pkl diff --git a/docking_result/plots_docking_score_distributions/all_targets_ecr_score_pdfs.png b/docking/plots_docking_score_distributions/all_targets_ecr_score_pdfs.png similarity index 100% rename from docking_result/plots_docking_score_distributions/all_targets_ecr_score_pdfs.png rename to docking/plots_docking_score_distributions/all_targets_ecr_score_pdfs.png diff --git a/docking_result/plots_docking_score_distributions/all_targets_ecr_score_pdfs_logscale.png b/docking/plots_docking_score_distributions/all_targets_ecr_score_pdfs_logscale.png similarity index 100% rename from docking_result/plots_docking_score_distributions/all_targets_ecr_score_pdfs_logscale.png rename to docking/plots_docking_score_distributions/all_targets_ecr_score_pdfs_logscale.png diff --git a/docking_result/plots_docking_score_distributions/quantile_normalized/docking_all_ecr_qt_qtmean_scores_high.png b/docking/plots_docking_score_distributions/quantile_normalized/docking_all_ecr_qt_qtmean_scores_high.png similarity index 100% rename from docking_result/plots_docking_score_distributions/quantile_normalized/docking_all_ecr_qt_qtmean_scores_high.png rename to docking/plots_docking_score_distributions/quantile_normalized/docking_all_ecr_qt_qtmean_scores_high.png diff --git a/docking_result/plots_docking_score_distributions/quantile_normalized/docking_all_ecr_qt_qtmean_scores_low.png b/docking/plots_docking_score_distributions/quantile_normalized/docking_all_ecr_qt_qtmean_scores_low.png similarity index 100% rename from docking_result/plots_docking_score_distributions/quantile_normalized/docking_all_ecr_qt_qtmean_scores_low.png rename to docking/plots_docking_score_distributions/quantile_normalized/docking_all_ecr_qt_qtmean_scores_low.png diff --git a/docking_result/plots_docking_score_distributions/quantile_normalized/docking_all_ecr_qt_qtmean_scores_medium.png b/docking/plots_docking_score_distributions/quantile_normalized/docking_all_ecr_qt_qtmean_scores_medium.png similarity index 100% rename from docking_result/plots_docking_score_distributions/quantile_normalized/docking_all_ecr_qt_qtmean_scores_medium.png rename to docking/plots_docking_score_distributions/quantile_normalized/docking_all_ecr_qt_qtmean_scores_medium.png diff --git a/docking_result/plots_docking_score_distributions/quantile_normalized/plot_qt_docking_score_dists_all.py b/docking/plots_docking_score_distributions/quantile_normalized/plot_qt_docking_score_dists_all.py similarity index 100% rename from docking_result/plots_docking_score_distributions/quantile_normalized/plot_qt_docking_score_dists_all.py rename to docking/plots_docking_score_distributions/quantile_normalized/plot_qt_docking_score_dists_all.py diff --git a/docking_result/plots_docking_score_distributions/quantile_normalized_overlay/docking_all_ecr_qt_qtmean_scores_high_layer.png b/docking/plots_docking_score_distributions/quantile_normalized_overlay/docking_all_ecr_qt_qtmean_scores_high_layer.png similarity index 100% rename from docking_result/plots_docking_score_distributions/quantile_normalized_overlay/docking_all_ecr_qt_qtmean_scores_high_layer.png rename to docking/plots_docking_score_distributions/quantile_normalized_overlay/docking_all_ecr_qt_qtmean_scores_high_layer.png diff --git a/docking_result/plots_docking_score_distributions/quantile_normalized_overlay/docking_all_ecr_qt_qtmean_scores_low_layer.png b/docking/plots_docking_score_distributions/quantile_normalized_overlay/docking_all_ecr_qt_qtmean_scores_low_layer.png similarity index 100% rename from docking_result/plots_docking_score_distributions/quantile_normalized_overlay/docking_all_ecr_qt_qtmean_scores_low_layer.png rename to docking/plots_docking_score_distributions/quantile_normalized_overlay/docking_all_ecr_qt_qtmean_scores_low_layer.png diff --git a/docking_result/plots_docking_score_distributions/quantile_normalized_overlay/docking_all_ecr_qt_qtmean_scores_medium_layer.png b/docking/plots_docking_score_distributions/quantile_normalized_overlay/docking_all_ecr_qt_qtmean_scores_medium_layer.png similarity index 100% rename from docking_result/plots_docking_score_distributions/quantile_normalized_overlay/docking_all_ecr_qt_qtmean_scores_medium_layer.png rename to docking/plots_docking_score_distributions/quantile_normalized_overlay/docking_all_ecr_qt_qtmean_scores_medium_layer.png diff --git a/docking_result/plots_docking_score_distributions/quantile_normalized_overlay/plot_qt_docking_score_dists_all_layer_v1.1.py b/docking/plots_docking_score_distributions/quantile_normalized_overlay/plot_qt_docking_score_dists_all_layer_v1.1.py similarity index 100% rename from docking_result/plots_docking_score_distributions/quantile_normalized_overlay/plot_qt_docking_score_dists_all_layer_v1.1.py rename to docking/plots_docking_score_distributions/quantile_normalized_overlay/plot_qt_docking_score_dists_all_layer_v1.1.py diff --git a/docking_result/plots_docking_score_distributions/sns_histplot_ecr_score_PDFs.py b/docking/plots_docking_score_distributions/sns_histplot_ecr_score_PDFs.py similarity index 100% rename from docking_result/plots_docking_score_distributions/sns_histplot_ecr_score_PDFs.py rename to docking/plots_docking_score_distributions/sns_histplot_ecr_score_PDFs.py diff --git a/docking_result/plots_docking_score_distributions/sns_histplot_ecr_score_PDFs_logscale.py b/docking/plots_docking_score_distributions/sns_histplot_ecr_score_PDFs_logscale.py similarity index 100% rename from docking_result/plots_docking_score_distributions/sns_histplot_ecr_score_PDFs_logscale.py rename to docking/plots_docking_score_distributions/sns_histplot_ecr_score_PDFs_logscale.py diff --git a/docking_result/raw_docking_data/scores_high_ranking_ECR.pkl b/docking/raw_docking_data/scores_high_ranking_ECR.pkl similarity index 100% rename from docking_result/raw_docking_data/scores_high_ranking_ECR.pkl rename to docking/raw_docking_data/scores_high_ranking_ECR.pkl diff --git a/docking_result/raw_docking_data/scores_low_ranking_ECR.pkl b/docking/raw_docking_data/scores_low_ranking_ECR.pkl similarity index 100% rename from docking_result/raw_docking_data/scores_low_ranking_ECR.pkl rename to docking/raw_docking_data/scores_low_ranking_ECR.pkl diff --git a/docking_result/raw_docking_data/scores_medium_ranking_ECR.pkl b/docking/raw_docking_data/scores_medium_ranking_ECR.pkl similarity index 100% rename from docking_result/raw_docking_data/scores_medium_ranking_ECR.pkl rename to docking/raw_docking_data/scores_medium_ranking_ECR.pkl diff --git a/docking_result/visual_cpds/07_rdkit_draw_cluster_reps_all_bytarg_landscape_v1.6.py b/docking/visual_cpds/07_rdkit_draw_cluster_reps_all_bytarg_landscape_v1.6.py similarity index 100% rename from docking_result/visual_cpds/07_rdkit_draw_cluster_reps_all_bytarg_landscape_v1.6.py rename to docking/visual_cpds/07_rdkit_draw_cluster_reps_all_bytarg_landscape_v1.6.py diff --git a/docking_result/visual_cpds/adapter_ref_gen_cpds_landscape.png b/docking/visual_cpds/adapter_ref_gen_cpds_landscape.png similarity index 100% rename from docking_result/visual_cpds/adapter_ref_gen_cpds_landscape.png rename to docking/visual_cpds/adapter_ref_gen_cpds_landscape.png diff --git a/docking_result/visual_cpds/cluster_medoids_high_0.750_landscape.png b/docking/visual_cpds/cluster_medoids_high_0.750_landscape.png similarity index 100% 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-{"version":1970,"schema_version":1,"doc":{"type":"doc","attrs":{"table_of_contents":{"enabled":true,"allowedLevels":[1,2,3]}},"content":[{"type":"paragraph","content":[{"type":"text","marks":[{"type":"strong"},{"type":"author_id","attrs":{"authorId":"222648505"}}],"text":"NOTE"},{"type":"text","marks":[{"type":"author_id","attrs":{"authorId":"222648505"}}],"text":": landscape grid images of compounds show single representatives from each cluster. The cluster sizes (population) is also appended to the compound labels in the figures. The compounds are ordered by size of cluster--cluster sizes decreasing from left-to-right and top-to-bottom. I think these images would be more meaningful if I could include the reference compound. I added an additional image that shows the reference cpds and the original generated compound."}]},{"type":"paragraph"},{"type":"paragraph","content":[{"type":"text","marks":[{"type":"author_id","attrs":{"authorId":"222648505"}}],"text":"Clustering (HAC, average linkage, ECFP6 2024 bit with Jaccard distance matrix) was performed simultaneously on all 300 compounds (100 contributed from each target). Therefore, in some cases compound generated from different targets belong to a common cluster (cid_0.750)."}]},{"type":"paragraph"},{"type":"paragraph","content":[{"type":"text","marks":[{"type":"strong"},{"type":"author_id","attrs":{"authorId":"222648505"}}],"text":"Upon inspection of the compound structures, I am surprised by the structural diversity in the generated ensembles. I assumed the generated compounds would closely resemble the reference since the scores are favorably shifted from the mean in the ‘low’ and ‘medium’ targets. It is exciting that the model can produce "},{"type":"text","marks":[{"type":"em"},{"type":"strong"},{"type":"author_id","attrs":{"authorId":"222648505"}}],"text":"favorable"},{"type":"text","marks":[{"type":"strong"},{"type":"author_id","attrs":{"authorId":"222648505"}}],"text":" variation in the molecules it generates--at least based on docking scores."}]},{"type":"paragraph"}]},"savepoint_metadata":{"savepointFileId":null,"savepointsInfo":{"1039":{"timestamp":1719416855158,"type":"session","authorsSinceLastSavepoint":["222648505"]},"1200":{"timestamp":1719417541355,"type":"periodic","authorsSinceLastSavepoint":["222648505"]}},"shouldCreateSavepointBeforeApplyingNextVersion":false,"authorsSinceLastSavepoint":{"222648505":true},"allAuthorNames":{"222648505":"SPENCER ERICKSEN"}},"last_edit_timestamp":1719417839344} \ No newline at end of file