diff --git a/CHANGELOG.md b/CHANGELOG.md index 29d4d3e4..7edd9e9d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,8 @@ **Changes**: - Added dot plots on top of bar plots for improved clarity in CASP15 results. +- Enhanced figures by converting PNGs to PDFs. +- Updated Zenodo links. ### 0.7.1 - 08/11/2025 diff --git a/README.md b/README.md index dafabf7e..1b304864 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ # PoseBench [![Paper](http://img.shields.io/badge/arXiv-2405.14108-B31B1B.svg)](https://arxiv.org/abs/2405.14108) -[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.16791095.svg)](https://doi.org/10.5281/zenodo.16791095) +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17536252.svg)](https://doi.org/10.5281/zenodo.17536252) [![PyPI version](https://badge.fury.io/py/posebench.svg)](https://badge.fury.io/py/posebench) [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![Docs](https://assets.readthedocs.org/static/projects/badges/passing-flat.svg)](https://bioinfomachinelearning.github.io/PoseBench/) @@ -209,10 +209,10 @@ of how to extend `PoseBench`, as outlined below. ```bash # fetch, extract, and clean-up preprocessed Astex Diverse, PoseBusters Benchmark, DockGen, and CASP15 data (~3 GB) # -wget https://zenodo.org/records/16791095/files/astex_diverse_set.tar.gz -wget https://zenodo.org/records/16791095/files/posebusters_benchmark_set.tar.gz -wget https://zenodo.org/records/16791095/files/dockgen_set.tar.gz -wget https://zenodo.org/records/16791095/files/casp15_set.tar.gz +wget https://zenodo.org/records/17536252/files/astex_diverse_set.tar.gz +wget https://zenodo.org/records/17536252/files/posebusters_benchmark_set.tar.gz +wget https://zenodo.org/records/17536252/files/dockgen_set.tar.gz +wget https://zenodo.org/records/17536252/files/casp15_set.tar.gz tar -xzf astex_diverse_set.tar.gz tar -xzf posebusters_benchmark_set.tar.gz tar -xzf dockgen_set.tar.gz @@ -228,39 +228,39 @@ rm casp15_set.tar.gz ```bash # fetch, extract, and clean-up benchmark method predictions to reproduce paper results (~19 GB) # # AutoDock Vina predictions and results -wget https://zenodo.org/records/16791095/files/vina_benchmark_method_predictions.tar.gz +wget https://zenodo.org/records/17536252/files/vina_benchmark_method_predictions.tar.gz tar -xzf vina_benchmark_method_predictions.tar.gz rm vina_benchmark_method_predictions.tar.gz # DiffDock predictions and results -wget https://zenodo.org/records/16791095/files/diffdock_benchmark_method_predictions.tar.gz +wget https://zenodo.org/records/17536252/files/diffdock_benchmark_method_predictions.tar.gz tar -xzf diffdock_benchmark_method_predictions.tar.gz rm diffdock_benchmark_method_predictions.tar.gz # DynamicBind predictions and results -wget https://zenodo.org/records/16791095/files/dynamicbind_benchmark_method_predictions.tar.gz +wget https://zenodo.org/records/17536252/files/dynamicbind_benchmark_method_predictions.tar.gz tar -xzf dynamicbind_benchmark_method_predictions.tar.gz rm dynamicbind_benchmark_method_predictions.tar.gz # NeuralPLexer predictions and results -wget https://zenodo.org/records/16791095/files/neuralplexer_benchmark_method_predictions.tar.gz +wget https://zenodo.org/records/17536252/files/neuralplexer_benchmark_method_predictions.tar.gz tar -xzf neuralplexer_benchmark_method_predictions.tar.gz rm neuralplexer_benchmark_method_predictions.tar.gz # RoseTTAFold-All-Atom predictions and results -wget https://zenodo.org/records/16791095/files/rfaa_benchmark_method_predictions.tar.gz +wget https://zenodo.org/records/17536252/files/rfaa_benchmark_method_predictions.tar.gz tar -xzf rfaa_benchmark_method_predictions.tar.gz rm rfaa_benchmark_method_predictions.tar.gz # Chai-1 predictions and results -wget https://zenodo.org/records/16791095/files/chai_benchmark_method_predictions.tar.gz +wget https://zenodo.org/records/17536252/files/chai_benchmark_method_predictions.tar.gz tar -xzf chai_benchmark_method_predictions.tar.gz rm chai_benchmark_method_predictions.tar.gz # Boltz-1 predictions and results -wget https://zenodo.org/records/16791095/files/boltz_benchmark_method_predictions.tar.gz +wget https://zenodo.org/records/17536252/files/boltz_benchmark_method_predictions.tar.gz tar -xzf boltz_benchmark_method_predictions.tar.gz rm boltz_benchmark_method_predictions.tar.gz # AlphaFold 3 predictions and results -wget https://zenodo.org/records/16791095/files/af3_benchmark_method_predictions.tar.gz +wget https://zenodo.org/records/17536252/files/af3_benchmark_method_predictions.tar.gz tar -xzf af3_benchmark_method_predictions.tar.gz rm af3_benchmark_method_predictions.tar.gz # CASP15 predictions and results for all methods -wget https://zenodo.org/records/16791095/files/casp15_benchmark_method_predictions.tar.gz +wget https://zenodo.org/records/17536252/files/casp15_benchmark_method_predictions.tar.gz tar -xzf casp15_benchmark_method_predictions.tar.gz rm casp15_benchmark_method_predictions.tar.gz ``` @@ -270,7 +270,7 @@ rm casp15_benchmark_method_predictions.tar.gz ```bash # fetch, extract, and clean-up benchmark method interactions to reproduce paper results (~12 GB) # # cached ProLIF interactions for notebook plots -wget https://zenodo.org/records/16791095/files/posebench_notebooks.tar.gz +wget https://zenodo.org/records/17536252/files/posebench_notebooks.tar.gz tar -xzf posebench_notebooks.tar.gz rm posebench_notebooks.tar.gz ``` @@ -357,7 +357,7 @@ python3 posebench/data/components/protein_apo_to_holo_alignment.py dataset=casp1 conda deactivate ``` -**NOTE:** The preprocessed Astex Diverse, PoseBusters Benchmark, DockGen, and CASP15 data available via [Zenodo](https://doi.org/10.5281/zenodo.16791095) provide pre-holo-aligned protein structures predicted by AlphaFold 3 (and alternatively MIT-licensed ESMFold) for these respective datasets. Accordingly, users must ensure their usage of such predicted protein structures from AlphaFold 3 aligns with AlphaFold 3's [Terms of Use](https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md). +**NOTE:** The preprocessed Astex Diverse, PoseBusters Benchmark, DockGen, and CASP15 data available via [Zenodo](https://doi.org/10.5281/zenodo.17536252) provide pre-holo-aligned protein structures predicted by AlphaFold 3 (and alternatively MIT-licensed ESMFold) for these respective datasets. Accordingly, users must ensure their usage of such predicted protein structures from AlphaFold 3 aligns with AlphaFold 3's [Terms of Use](https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md). diff --git a/docs/source/_static/PoseBench.png b/docs/source/_static/PoseBench.png index c16a6bf9..7dc21d02 100644 Binary files a/docs/source/_static/PoseBench.png and b/docs/source/_static/PoseBench.png differ diff --git a/docs/source/data_preparation.rst b/docs/source/data_preparation.rst index 234c185a..cf0e21e8 100644 --- a/docs/source/data_preparation.rst +++ b/docs/source/data_preparation.rst @@ -6,4 +6,4 @@ How to prepare `PoseBench` data :end-line: 359 .. note:: - The preprocessed Astex Diverse, PoseBusters Benchmark, DockGen, and CASP15 data (available via Zenodo at https://doi.org/10.5281/zenodo.16791095) provide pre-holo-aligned protein structures predicted by AlphaFold 3 (and alternatively MIT-licensed ESMFold) for these respective datasets. Accordingly, users must ensure their usage of such predicted protein structures from AlphaFold 3 aligns with AlphaFold 3's Terms of Use at https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md. + The preprocessed Astex Diverse, PoseBusters Benchmark, DockGen, and CASP15 data (available via Zenodo at https://doi.org/10.5281/zenodo.17536252) provide pre-holo-aligned protein structures predicted by AlphaFold 3 (and alternatively MIT-licensed ESMFold) for these respective datasets. Accordingly, users must ensure their usage of such predicted protein structures from AlphaFold 3 aligns with AlphaFold 3's Terms of Use at https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md. diff --git a/img/PoseBench.png b/img/PoseBench.png index c16a6bf9..7dc21d02 100644 Binary files a/img/PoseBench.png and b/img/PoseBench.png differ diff --git a/img/PoseBench_Datasets.png b/img/PoseBench_Datasets.png index cc7d7179..4a3dfccb 100644 Binary files a/img/PoseBench_Datasets.png and b/img/PoseBench_Datasets.png differ diff --git a/notebooks/astex_diverse_inference_results_plotting.ipynb b/notebooks/astex_diverse_inference_results_plotting.ipynb index 4e296a83..d3869059 100644 --- a/notebooks/astex_diverse_inference_results_plotting.ipynb +++ b/notebooks/astex_diverse_inference_results_plotting.ipynb @@ -520,7 +520,7 @@ "\n", "# display the plots\n", "plt.tight_layout()\n", - "plt.savefig(\"astex_diverse_primary_ligand_relaxed_rmsd_violin_plot.png\", dpi=300)\n", + "plt.savefig(\"astex_diverse_primary_ligand_relaxed_rmsd_violin_plot.pdf\")\n", "plt.show()" ] }, @@ -1113,7 +1113,7 @@ "\n", "# display the plots\n", "plt.tight_layout()\n", - "plt.savefig(\"astex_diverse_primary_ligand_relaxed_bar_chart.png\", dpi=300)\n", + "plt.savefig(\"astex_diverse_primary_ligand_relaxed_bar_chart.pdf\")\n", "plt.show()" ] } diff --git a/notebooks/astex_diverse_method_interaction_analysis.pdf b/notebooks/astex_diverse_method_interaction_analysis.pdf new file mode 100644 index 00000000..3f28b961 Binary files /dev/null and b/notebooks/astex_diverse_method_interaction_analysis.pdf differ diff --git a/notebooks/astex_diverse_method_interaction_analysis.png b/notebooks/astex_diverse_method_interaction_analysis.png deleted file mode 100644 index 56b4fdb1..00000000 Binary files a/notebooks/astex_diverse_method_interaction_analysis.png and /dev/null differ diff --git a/notebooks/astex_diverse_plif_emd_values.pdf 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a/notebooks/astex_diverse_primary_ligand_relaxed_rmsd_violin_plot.png and /dev/null differ diff --git a/notebooks/astex_diverse_structured_vs_unstructured_emd_values.pdf b/notebooks/astex_diverse_structured_vs_unstructured_emd_values.pdf new file mode 100644 index 00000000..aa30d36e Binary files /dev/null and b/notebooks/astex_diverse_structured_vs_unstructured_emd_values.pdf differ diff --git a/notebooks/astex_diverse_structured_vs_unstructured_emd_values.png b/notebooks/astex_diverse_structured_vs_unstructured_emd_values.png deleted file mode 100644 index 54dcb747..00000000 Binary files a/notebooks/astex_diverse_structured_vs_unstructured_emd_values.png and /dev/null differ diff --git a/notebooks/astex_method_interaction_analysis_plotting.ipynb b/notebooks/astex_method_interaction_analysis_plotting.ipynb index 8b9c1fd5..3fc28d08 100644 --- a/notebooks/astex_method_interaction_analysis_plotting.ipynb +++ b/notebooks/astex_method_interaction_analysis_plotting.ipynb @@ -104,7 +104,7 @@ ")\n", "assert os.path.exists(\n", " ad_set_dir\n", - "), \"Please download the Astex Diverse set from `https://zenodo.org/records/16791095` before proceeding.\"\n", + "), \"Please download the Astex Diverse set from `https://zenodo.org/records/17536252` before proceeding.\"\n", "\n", "# Mappings\n", "method_mapping = {\n", @@ -525,7 +525,7 @@ " ax.grid(True)\n", "\n", "plt.tight_layout()\n", - "plt.savefig(\"astex_diverse_method_interaction_analysis.png\", dpi=300)\n", + "plt.savefig(\"astex_diverse_method_interaction_analysis.pdf\")\n", "plt.show()" ] }, @@ -694,7 +694,7 @@ "sns.boxplot(data=emd_values_df, x=\"Category\", y=\"EMD\")\n", "plt.xlabel(\"\")\n", "plt.ylabel(\"PLIF-EMD\")\n", - "plt.savefig(\"astex_diverse_plif_emd_values.png\")\n", + "plt.savefig(\"astex_diverse_plif_emd_values.pdf\")\n", "plt.show()\n", "\n", "plt.close(\"all\")\n", @@ -703,7 +703,7 @@ "sns.boxplot(data=emd_values_df, x=\"Category\", y=\"WM\")\n", "plt.xlabel(\"\")\n", "plt.ylabel(\"PLIF-WM\")\n", - "plt.savefig(\"astex_diverse_plif_wm_values.png\")\n", + "plt.savefig(\"astex_diverse_plif_wm_values.pdf\")\n", "plt.show()\n", "\n", "plt.close(\"all\")" @@ -853,7 +853,7 @@ "plt.ylabel(\"EMD Value\")\n", "plt.title(\"Comparison of Structured_EMD and Unstructured_EMD by Method\")\n", "plt.legend()\n", - "plt.savefig(\"astex_diverse_structured_vs_unstructured_emd_values.png\")\n", + "plt.savefig(\"astex_diverse_structured_vs_unstructured_emd_values.pdf\")\n", "plt.show()\n", "\n", "plt.close(\"all\")" diff --git a/notebooks/astex_method_interaction_analysis_plotting.py b/notebooks/astex_method_interaction_analysis_plotting.py index 842b876d..e40dfe51 100644 --- a/notebooks/astex_method_interaction_analysis_plotting.py +++ b/notebooks/astex_method_interaction_analysis_plotting.py @@ -69,7 +69,7 @@ ) assert os.path.exists( ad_set_dir -), "Please download the Astex Diverse set from `https://zenodo.org/records/16791095` before proceeding." +), "Please download the Astex Diverse set from `https://zenodo.org/records/17536252` before proceeding." # Mappings method_mapping = { @@ -448,7 +448,7 @@ def process_method(file_path, category): ax.grid(True) plt.tight_layout() -plt.savefig("astex_diverse_method_interaction_analysis.png", dpi=300) +plt.savefig("astex_diverse_method_interaction_analysis.pdf") plt.show() # %% [markdown] @@ -607,7 +607,7 @@ def histogram_to_vector(histogram, bins): sns.boxplot(data=emd_values_df, x="Category", y="EMD") plt.xlabel("") plt.ylabel("PLIF-EMD") -plt.savefig("astex_diverse_plif_emd_values.png") +plt.savefig("astex_diverse_plif_emd_values.pdf") plt.show() plt.close("all") @@ -616,7 +616,7 @@ def histogram_to_vector(histogram, bins): sns.boxplot(data=emd_values_df, x="Category", y="WM") plt.xlabel("") plt.ylabel("PLIF-WM") -plt.savefig("astex_diverse_plif_wm_values.png") +plt.savefig("astex_diverse_plif_wm_values.pdf") plt.show() plt.close("all") @@ -756,7 +756,7 @@ def histogram_to_vector(histogram, bins): plt.ylabel("EMD Value") 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b/notebooks/casp15_all_single_ligand_relaxed_rmsd_violin_plot.png deleted file mode 100644 index 3e55984a..00000000 Binary files a/notebooks/casp15_all_single_ligand_relaxed_rmsd_violin_plot.png and /dev/null differ diff --git a/notebooks/casp15_inference_results_plotting.ipynb b/notebooks/casp15_inference_results_plotting.ipynb index 67f3a28c..2bac916d 100644 --- a/notebooks/casp15_inference_results_plotting.ipynb +++ b/notebooks/casp15_inference_results_plotting.ipynb @@ -462,8 +462,7 @@ " # display the plots\n", " plt.tight_layout()\n", " plt.savefig(\n", - " f\"casp15_{complex_license}_{complex_type}_ligand_relaxed_lddt_pli_violin_plot.png\",\n", - " dpi=300,\n", + " f\"casp15_{complex_license}_{complex_type}_ligand_relaxed_lddt_pli_violin_plot.pdf\"\n", " )\n", " plt.show()" ] @@ -549,9 +548,7 @@ "\n", " # display the plots\n", " plt.tight_layout()\n", - " plt.savefig(\n", - " f\"casp15_{complex_license}_{complex_type}_ligand_relaxed_rmsd_violin_plot.png\", dpi=300\n", - " )\n", + " plt.savefig(f\"casp15_{complex_license}_{complex_type}_ligand_relaxed_rmsd_violin_plot.pdf\")\n", " plt.show()" ] }, @@ -980,8 +977,7 @@ " # display the plots\n", " plt.tight_layout()\n", " plt.savefig(\n", - " f\"casp15_{complex_license}_{complex_type}_ligand_relaxed_rmsd_lt2_bar_chart.png\",\n", - " dpi=300,\n", + " f\"casp15_{complex_license}_{complex_type}_ligand_relaxed_rmsd_lt2_bar_chart.pdf\"\n", " )\n", " plt.show()" ] @@ -1299,8 +1295,7 @@ " # display the plots\n", " plt.tight_layout()\n", " plt.savefig(\n", - " f\"casp15_{complex_license}_{complex_type}_ligand_relaxed_pb_valid_bar_chart.png\",\n", - " dpi=300,\n", + " f\"casp15_{complex_license}_{complex_type}_ligand_relaxed_pb_valid_bar_chart.pdf\"\n", " )\n", " plt.show()" ] diff --git a/notebooks/casp15_method_interaction_analysis.pdf b/notebooks/casp15_method_interaction_analysis.pdf new file mode 100644 index 00000000..41221982 Binary files /dev/null and b/notebooks/casp15_method_interaction_analysis.pdf differ diff --git a/notebooks/casp15_method_interaction_analysis.png b/notebooks/casp15_method_interaction_analysis.png deleted file mode 100644 index 36a58f7f..00000000 Binary files a/notebooks/casp15_method_interaction_analysis.png and /dev/null differ diff --git a/notebooks/casp15_method_interaction_analysis_plotting.ipynb b/notebooks/casp15_method_interaction_analysis_plotting.ipynb index cc6e5664..05394f1f 100644 --- a/notebooks/casp15_method_interaction_analysis_plotting.ipynb +++ b/notebooks/casp15_method_interaction_analysis_plotting.ipynb @@ -101,7 +101,7 @@ ")\n", "assert os.path.exists(\n", " casp15_set_dir\n", - "), \"Please download the (public) CASP15 set from `https://zenodo.org/records/16791095` before proceeding.\"\n", + "), \"Please download the (public) CASP15 set from `https://zenodo.org/records/17536252` before proceeding.\"\n", "\n", "# Mappings\n", "method_mapping = {\n", @@ -506,7 +506,7 @@ " ax.grid(True)\n", "\n", "plt.tight_layout()\n", - "plt.savefig(\"casp15_method_interaction_analysis.png\", dpi=300)\n", + "plt.savefig(\"casp15_method_interaction_analysis.pdf\")\n", "plt.show()" ] }, @@ -675,7 +675,7 @@ "sns.boxplot(data=emd_values_df, x=\"Category\", y=\"EMD\")\n", "plt.xlabel(\"\")\n", "plt.ylabel(\"PLIF-EMD\")\n", - "plt.savefig(\"casp15_plif_emd_values.png\")\n", + "plt.savefig(\"casp15_plif_emd_values.pdf\")\n", "plt.show()\n", "\n", "plt.close(\"all\")\n", @@ -684,7 +684,7 @@ "sns.boxplot(data=emd_values_df, x=\"Category\", y=\"WM\")\n", "plt.xlabel(\"\")\n", "plt.ylabel(\"PLIF-WM\")\n", - "plt.savefig(\"casp15_plif_wm_values.png\")\n", + "plt.savefig(\"casp15_plif_wm_values.pdf\")\n", "plt.show()\n", "\n", "plt.close(\"all\")" @@ -835,7 +835,7 @@ "plt.title(\"Comparison of Structured_EMD and Unstructured_EMD by Method\")\n", "plt.legend()\n", "plt.ylim(0, 50)\n", - "plt.savefig(\"casp15_structured_vs_unstructured_emd_values.png\")\n", + "plt.savefig(\"casp15_structured_vs_unstructured_emd_values.pdf\")\n", "plt.show()\n", "\n", "plt.close(\"all\")" diff --git a/notebooks/casp15_method_interaction_analysis_plotting.py b/notebooks/casp15_method_interaction_analysis_plotting.py index 787fc5fd..e5c23a84 100644 --- a/notebooks/casp15_method_interaction_analysis_plotting.py +++ b/notebooks/casp15_method_interaction_analysis_plotting.py @@ -66,7 +66,7 @@ ) assert os.path.exists( casp15_set_dir -), "Please download the (public) CASP15 set from `https://zenodo.org/records/16791095` before proceeding." +), "Please download the (public) CASP15 set from `https://zenodo.org/records/17536252` before proceeding." # Mappings method_mapping = { @@ -429,7 +429,7 @@ def process_method(file_path, category): ax.grid(True) plt.tight_layout() -plt.savefig("casp15_method_interaction_analysis.png", dpi=300) +plt.savefig("casp15_method_interaction_analysis.pdf") plt.show() # %% [markdown] @@ -588,7 +588,7 @@ def histogram_to_vector(histogram, bins): sns.boxplot(data=emd_values_df, x="Category", y="EMD") plt.xlabel("") plt.ylabel("PLIF-EMD") -plt.savefig("casp15_plif_emd_values.png") +plt.savefig("casp15_plif_emd_values.pdf") plt.show() plt.close("all") @@ -597,7 +597,7 @@ def histogram_to_vector(histogram, bins): sns.boxplot(data=emd_values_df, x="Category", y="WM") plt.xlabel("") plt.ylabel("PLIF-WM") -plt.savefig("casp15_plif_wm_values.png") +plt.savefig("casp15_plif_wm_values.pdf") plt.show() plt.close("all") @@ -738,7 +738,7 @@ def histogram_to_vector(histogram, bins): plt.title("Comparison of Structured_EMD and Unstructured_EMD by Method") plt.legend() plt.ylim(0, 50) -plt.savefig("casp15_structured_vs_unstructured_emd_values.png") +plt.savefig("casp15_structured_vs_unstructured_emd_values.pdf") plt.show() plt.close("all") diff --git a/notebooks/casp15_plif_emd_values.pdf b/notebooks/casp15_plif_emd_values.pdf new file mode 100644 index 00000000..a1c3209e Binary files /dev/null and b/notebooks/casp15_plif_emd_values.pdf differ diff --git a/notebooks/casp15_plif_emd_values.png 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b/notebooks/dataset_interaction_analysis.png deleted file mode 100644 index b6784b11..00000000 Binary files a/notebooks/dataset_interaction_analysis.png and /dev/null differ diff --git a/notebooks/dataset_interaction_analysis_plotting.ipynb b/notebooks/dataset_interaction_analysis_plotting.ipynb index 43582cee..1cbfebae 100644 --- a/notebooks/dataset_interaction_analysis_plotting.ipynb +++ b/notebooks/dataset_interaction_analysis_plotting.ipynb @@ -76,16 +76,16 @@ ")\n", "assert os.path.exists(\n", " ad_set_dir\n", - "), \"Please download the Astex Diverse set from `https://zenodo.org/records/16791095` before proceeding.\"\n", + "), \"Please download the Astex Diverse set from `https://zenodo.org/records/17536252` before proceeding.\"\n", "assert os.path.exists(\n", " pb_set_dir\n", - "), \"Please download the PoseBusters Benchmark set from `https://zenodo.org/records/16791095` before proceeding.\"\n", + "), \"Please download the PoseBusters Benchmark set from `https://zenodo.org/records/17536252` before proceeding.\"\n", "assert os.path.exists(\n", " dg_set_dir\n", - "), \"Please download the DockGen set from `https://zenodo.org/records/16791095` before proceeding.\"\n", + "), \"Please download the DockGen set from `https://zenodo.org/records/17536252` before proceeding.\"\n", "assert os.path.exists(\n", " casp15_set_dir\n", - "), \"Please download the (public) CASP15 set from `https://zenodo.org/records/16791095` before proceeding.\"\n", + "), \"Please download the (public) CASP15 set from `https://zenodo.org/records/17536252` before proceeding.\"\n", "\n", "CASP15_ANALYSIS_TARGETS_TO_SKIP = [\n", " \"T1170\"\n", @@ -651,7 +651,7 @@ " ax.grid(True)\n", "\n", "plt.tight_layout()\n", - "plt.savefig(\"dataset_interaction_analysis.png\", dpi=300)\n", + "plt.savefig(\"dataset_interaction_analysis.pdf\")\n", "plt.show()" ] } diff --git a/notebooks/dataset_interaction_analysis_plotting.py b/notebooks/dataset_interaction_analysis_plotting.py index 34d60932..802e4c08 100644 --- a/notebooks/dataset_interaction_analysis_plotting.py +++ b/notebooks/dataset_interaction_analysis_plotting.py @@ -41,16 +41,16 @@ ) assert os.path.exists( ad_set_dir -), "Please download the Astex Diverse set from `https://zenodo.org/records/16791095` before proceeding." +), "Please download the Astex Diverse set from `https://zenodo.org/records/17536252` before proceeding." assert os.path.exists( pb_set_dir -), "Please download the PoseBusters Benchmark set from `https://zenodo.org/records/16791095` before proceeding." +), "Please download the PoseBusters Benchmark set from `https://zenodo.org/records/17536252` before proceeding." assert os.path.exists( dg_set_dir -), "Please download the DockGen set from `https://zenodo.org/records/16791095` before proceeding." +), "Please download the DockGen set from `https://zenodo.org/records/17536252` before proceeding." assert os.path.exists( casp15_set_dir -), "Please download the (public) CASP15 set from `https://zenodo.org/records/16791095` before proceeding." +), "Please download the (public) CASP15 set from `https://zenodo.org/records/17536252` before proceeding." CASP15_ANALYSIS_TARGETS_TO_SKIP = [ "T1170" @@ -546,5 +546,5 @@ def process_dataset(file_path, category): ax.grid(True) plt.tight_layout() -plt.savefig("dataset_interaction_analysis.png", dpi=300) +plt.savefig("dataset_interaction_analysis.pdf") plt.show() diff --git a/notebooks/dockgen_inference_results_plotting.ipynb b/notebooks/dockgen_inference_results_plotting.ipynb index a3962381..5462275d 100644 --- a/notebooks/dockgen_inference_results_plotting.ipynb +++ b/notebooks/dockgen_inference_results_plotting.ipynb @@ -524,7 +524,7 @@ "\n", "# display the plots\n", "plt.tight_layout()\n", - "plt.savefig(\"dockgen_primary_ligand_relaxed_rmsd_violin_plot.png\", dpi=300)\n", + "plt.savefig(\"dockgen_primary_ligand_relaxed_rmsd_violin_plot.pdf\")\n", "plt.show()" ] }, @@ -1128,7 +1128,7 @@ "\n", "# display the plots\n", "plt.tight_layout()\n", - "plt.savefig(\"dockgen_primary_ligand_relaxed_bar_chart.png\", dpi=300)\n", + "plt.savefig(\"dockgen_primary_ligand_relaxed_bar_chart.pdf\")\n", "plt.show()" ] } diff --git a/notebooks/dockgen_method_interaction_analysis.pdf b/notebooks/dockgen_method_interaction_analysis.pdf new file mode 100644 index 00000000..0626ab42 Binary files /dev/null and b/notebooks/dockgen_method_interaction_analysis.pdf differ diff --git a/notebooks/dockgen_method_interaction_analysis.png b/notebooks/dockgen_method_interaction_analysis.png deleted file mode 100644 index bd36c4a2..00000000 Binary files a/notebooks/dockgen_method_interaction_analysis.png and /dev/null differ diff --git a/notebooks/dockgen_method_interaction_analysis_plotting.ipynb b/notebooks/dockgen_method_interaction_analysis_plotting.ipynb index f0d14fad..cadd38ec 100644 --- a/notebooks/dockgen_method_interaction_analysis_plotting.ipynb +++ b/notebooks/dockgen_method_interaction_analysis_plotting.ipynb @@ -104,7 +104,7 @@ ")\n", "assert os.path.exists(\n", " dg_set_dir\n", - "), \"Please download the DockGen set from `https://zenodo.org/records/16791095` before proceeding.\"\n", + "), \"Please download the DockGen set from `https://zenodo.org/records/17536252` before proceeding.\"\n", "\n", "# Mappings\n", "method_mapping = {\n", @@ -538,7 +538,7 @@ " ax.grid(True)\n", "\n", "plt.tight_layout()\n", - "plt.savefig(\"dockgen_method_interaction_analysis.png\", dpi=300)\n", + "plt.savefig(\"dockgen_method_interaction_analysis.pdf\")\n", "plt.show()" ] }, @@ -707,7 +707,7 @@ "sns.boxplot(data=emd_values_df, x=\"Category\", y=\"EMD\")\n", "plt.xlabel(\"\")\n", "plt.ylabel(\"PLIF-EMD\")\n", - "plt.savefig(\"dockgen_plif_emd_values.png\")\n", + "plt.savefig(\"dockgen_plif_emd_values.pdf\")\n", "plt.show()\n", "\n", "plt.close(\"all\")\n", @@ -716,7 +716,7 @@ "sns.boxplot(data=emd_values_df, x=\"Category\", y=\"WM\")\n", "plt.xlabel(\"\")\n", "plt.ylabel(\"PLIF-WM\")\n", - "plt.savefig(\"dockgen_plif_wm_values.png\")\n", + "plt.savefig(\"dockgen_plif_wm_values.pdf\")\n", "plt.show()\n", "\n", "plt.close(\"all\")" @@ -866,7 +866,7 @@ "plt.ylabel(\"EMD Value\")\n", "plt.title(\"Comparison of Structured_EMD and Unstructured_EMD by Method\")\n", "plt.legend()\n", - "plt.savefig(\"dockgen_structured_vs_unstructured_emd_values.png\")\n", + "plt.savefig(\"dockgen_structured_vs_unstructured_emd_values.pdf\")\n", "plt.show()\n", "\n", "plt.close(\"all\")" diff --git a/notebooks/dockgen_method_interaction_analysis_plotting.py b/notebooks/dockgen_method_interaction_analysis_plotting.py index 68e77449..d27c258a 100644 --- a/notebooks/dockgen_method_interaction_analysis_plotting.py +++ b/notebooks/dockgen_method_interaction_analysis_plotting.py @@ -69,7 +69,7 @@ ) assert os.path.exists( dg_set_dir -), "Please download the DockGen set from `https://zenodo.org/records/16791095` before proceeding." +), "Please download the DockGen set from `https://zenodo.org/records/17536252` before proceeding." # Mappings method_mapping = { @@ -461,7 +461,7 @@ def process_method(file_path, category): ax.grid(True) plt.tight_layout() -plt.savefig("dockgen_method_interaction_analysis.png", dpi=300) +plt.savefig("dockgen_method_interaction_analysis.pdf") plt.show() # %% [markdown] @@ -620,7 +620,7 @@ def histogram_to_vector(histogram, bins): sns.boxplot(data=emd_values_df, x="Category", y="EMD") plt.xlabel("") plt.ylabel("PLIF-EMD") -plt.savefig("dockgen_plif_emd_values.png") +plt.savefig("dockgen_plif_emd_values.pdf") plt.show() plt.close("all") @@ -629,7 +629,7 @@ def histogram_to_vector(histogram, bins): sns.boxplot(data=emd_values_df, x="Category", y="WM") plt.xlabel("") plt.ylabel("PLIF-WM") -plt.savefig("dockgen_plif_wm_values.png") +plt.savefig("dockgen_plif_wm_values.pdf") plt.show() plt.close("all") @@ -769,7 +769,7 @@ def histogram_to_vector(histogram, bins): plt.ylabel("EMD Value") plt.title("Comparison of Structured_EMD and Unstructured_EMD by Method") plt.legend() -plt.savefig("dockgen_structured_vs_unstructured_emd_values.png") +plt.savefig("dockgen_structured_vs_unstructured_emd_values.pdf") plt.show() plt.close("all") diff --git a/notebooks/dockgen_plif_emd_values.pdf b/notebooks/dockgen_plif_emd_values.pdf new file mode 100644 index 00000000..4d00eece Binary files /dev/null and b/notebooks/dockgen_plif_emd_values.pdf differ diff --git a/notebooks/dockgen_plif_emd_values.png b/notebooks/dockgen_plif_emd_values.png deleted file mode 100644 index 1ce2a8ee..00000000 Binary files a/notebooks/dockgen_plif_emd_values.png and /dev/null differ diff --git a/notebooks/dockgen_plif_wm_values.pdf b/notebooks/dockgen_plif_wm_values.pdf new file mode 100644 index 00000000..6d5a3ab1 Binary files /dev/null and b/notebooks/dockgen_plif_wm_values.pdf differ diff --git a/notebooks/dockgen_plif_wm_values.png b/notebooks/dockgen_plif_wm_values.png deleted file mode 100644 index a3648f3a..00000000 Binary files a/notebooks/dockgen_plif_wm_values.png and /dev/null differ diff --git a/notebooks/dockgen_primary_ligand_relaxed_bar_chart.pdf b/notebooks/dockgen_primary_ligand_relaxed_bar_chart.pdf new file 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a/notebooks/dockgen_structured_vs_unstructured_emd_values.pdf b/notebooks/dockgen_structured_vs_unstructured_emd_values.pdf new file mode 100644 index 00000000..151cd18a Binary files /dev/null and b/notebooks/dockgen_structured_vs_unstructured_emd_values.pdf differ diff --git a/notebooks/dockgen_structured_vs_unstructured_emd_values.png b/notebooks/dockgen_structured_vs_unstructured_emd_values.png deleted file mode 100644 index fd4dd55f..00000000 Binary files a/notebooks/dockgen_structured_vs_unstructured_emd_values.png and /dev/null differ diff --git a/notebooks/failed_af3_complexes_functional_keywords.pdf b/notebooks/failed_af3_complexes_functional_keywords.pdf new file mode 100644 index 00000000..3e33694f Binary files /dev/null and b/notebooks/failed_af3_complexes_functional_keywords.pdf differ diff --git a/notebooks/failed_af3_complexes_functional_keywords.png b/notebooks/failed_af3_complexes_functional_keywords.png deleted file mode 100644 index a44af721..00000000 Binary files a/notebooks/failed_af3_complexes_functional_keywords.png and /dev/null differ diff --git a/notebooks/failed_complexes_functional_keywords_1.pdf b/notebooks/failed_complexes_functional_keywords_1.pdf new file mode 100644 index 00000000..117d3444 Binary files /dev/null and b/notebooks/failed_complexes_functional_keywords_1.pdf differ diff --git a/notebooks/failed_complexes_functional_keywords_1.png b/notebooks/failed_complexes_functional_keywords_1.png deleted file mode 100644 index 3013a84a..00000000 Binary files a/notebooks/failed_complexes_functional_keywords_1.png and /dev/null differ diff --git a/notebooks/failure_modes_analysis_plotting.ipynb b/notebooks/failure_modes_analysis_plotting.ipynb index 9d9ada39..b86ac800 100644 --- a/notebooks/failure_modes_analysis_plotting.ipynb +++ b/notebooks/failure_modes_analysis_plotting.ipynb @@ -752,7 +752,7 @@ " plt.ylabel(\"Complex Annotation\")\n", "\n", " plt.tight_layout()\n", - " plt.savefig(f\"complexes_functional_keywords_{repeat_index}.png\", bbox_inches=\"tight\")\n", + " plt.savefig(f\"complexes_functional_keywords_{repeat_index}.pdf\", bbox_inches=\"tight\")\n", " plt.show()\n", "\n", " plt.close(\"all\")\n", @@ -825,7 +825,7 @@ "# plt.xlabel(\"Deposition Date\")\n", "# plt.xticks(rotation=45)\n", "# plt.tight_layout()\n", - "# plt.savefig(\"posebusters_benchmark_complex_pdb_deposition_dates.png\")\n", + "# plt.savefig(\"posebusters_benchmark_complex_pdb_deposition_dates.pdf\")\n", "# plt.show()\n", "# plt.close(\"all\")" ] @@ -954,7 +954,7 @@ " )\n", "\n", " plt.tight_layout()\n", - " plt.savefig(f\"failed_complexes_functional_keywords_{repeat_index}.png\")\n", + " plt.savefig(f\"failed_complexes_functional_keywords_{repeat_index}.pdf\")\n", " plt.show()\n", "\n", " plt.close(\"all\")\n", @@ -1084,7 +1084,7 @@ " )\n", "\n", "plt.tight_layout()\n", - "plt.savefig(\"failed_af3_complexes_functional_keywords.png\")\n", + "plt.savefig(\"failed_af3_complexes_functional_keywords.pdf\")\n", "plt.show()\n", "\n", "plt.close(\"all\")\n", @@ -1137,7 +1137,7 @@ " plt.xlim(0, 10)\n", " plt.xlabel(\"Refinement Resolution (Å)\")\n", " plt.tight_layout()\n", - " plt.savefig(f\"{report_type}_pdb_report_resolution.png\")\n", + " plt.savefig(f\"{report_type}_pdb_report_resolution.pdf\")\n", " plt.show()\n", "\n", " plt.close(\"all\")\n", @@ -1145,7 +1145,7 @@ " sns.histplot(pdb_report_df[\"Deposition Date\"].values)\n", " plt.xlabel(\"Deposition Date\")\n", " plt.tight_layout()\n", - " plt.savefig(f\"{report_type}_pdb_report_deposition_date.png\")\n", + " plt.savefig(f\"{report_type}_pdb_report_deposition_date.pdf\")\n", " plt.show()\n", "\n", " plt.close(\"all\")" @@ -1357,7 +1357,7 @@ "plt.xlabel(\"Deposition Date\")\n", "plt.xticks(rotation=45)\n", "plt.tight_layout()\n", - "plt.savefig(\"af3_failed_complex_pdb_deposition_dates.png\")\n", + "plt.savefig(\"af3_failed_complex_pdb_deposition_dates.pdf\")\n", "plt.show()\n", "plt.close(\"all\")\n", "\n", @@ -1380,7 +1380,7 @@ "plt.xlabel(\"Deposition Date\")\n", "plt.xticks(rotation=45)\n", "plt.tight_layout()\n", - "plt.savefig(\"af3_failed_complex_top_match_pdb_deposition_dates.png\")\n", + "plt.savefig(\"af3_failed_complex_top_match_pdb_deposition_dates.pdf\")\n", "plt.show()\n", "plt.close(\"all\")\n", "\n", diff --git a/notebooks/failure_modes_analysis_plotting_plinder.ipynb b/notebooks/failure_modes_analysis_plotting_plinder.ipynb index 1f47f7aa..8a70ede7 100644 --- a/notebooks/failure_modes_analysis_plotting_plinder.ipynb +++ b/notebooks/failure_modes_analysis_plotting_plinder.ipynb @@ -21,9 +21,8 @@ "outputs": [], "source": [ "import copy\n", - "import glob\n", "import os\n", - "from collections import Counter, defaultdict\n", + "from collections import Counter\n", "\n", "import matplotlib.pyplot as plt\n", "import numpy as np\n", @@ -731,7 +730,7 @@ " plt.ylabel(\"Complex Annotation\")\n", "\n", " plt.tight_layout()\n", - " plt.savefig(f\"complexes_functional_keywords_{repeat_index}.png\", bbox_inches=\"tight\")\n", + " plt.savefig(f\"complexes_functional_keywords_{repeat_index}.pdf\", bbox_inches=\"tight\")\n", " plt.show()\n", "\n", " plt.close(\"all\")\n", @@ -804,7 +803,7 @@ "# plt.xlabel(\"Deposition Date\")\n", "# plt.xticks(rotation=45)\n", "# plt.tight_layout()\n", - "# plt.savefig(\"posebusters_benchmark_complex_pdb_deposition_dates.png\")\n", + "# plt.savefig(\"posebusters_benchmark_complex_pdb_deposition_dates.pdf\")\n", "# plt.show()\n", "# plt.close(\"all\")" ] @@ -933,7 +932,7 @@ " )\n", "\n", " plt.tight_layout()\n", - " plt.savefig(f\"failed_complexes_functional_keywords_{repeat_index}.png\")\n", + " plt.savefig(f\"failed_complexes_functional_keywords_{repeat_index}.pdf\")\n", " plt.show()\n", "\n", " plt.close(\"all\")\n", @@ -1063,7 +1062,7 @@ " )\n", "\n", "plt.tight_layout()\n", - "plt.savefig(\"failed_af3_complexes_functional_keywords.png\")\n", + "plt.savefig(\"failed_af3_complexes_functional_keywords.pdf\")\n", "plt.show()\n", "\n", "plt.close(\"all\")\n", @@ -1116,7 +1115,7 @@ " plt.xlim(0, 10)\n", " plt.xlabel(\"Refinement Resolution (Å)\")\n", " plt.tight_layout()\n", - " plt.savefig(f\"{report_type}_pdb_report_resolution.png\")\n", + " plt.savefig(f\"{report_type}_pdb_report_resolution.pdf\")\n", " plt.show()\n", "\n", " plt.close(\"all\")\n", @@ -1124,7 +1123,7 @@ " sns.histplot(pdb_report_df[\"Deposition Date\"].values)\n", " plt.xlabel(\"Deposition Date\")\n", " plt.tight_layout()\n", - " plt.savefig(f\"{report_type}_pdb_report_deposition_date.png\")\n", + " plt.savefig(f\"{report_type}_pdb_report_deposition_date.pdf\")\n", " plt.show()\n", "\n", " plt.close(\"all\")" @@ -1343,7 +1342,7 @@ "ax_neg.set_ylabel(\"RMSD\")\n", "\n", "plt.tight_layout()\n", - "plt.savefig(\"posebusters_benchmark_methods_generalization_analysis.png\", dpi=300)\n", + "plt.savefig(\"posebusters_benchmark_methods_generalization_analysis.pdf\")\n", "plt.show()\n", "\n", "# print sorted summary to console\n", diff --git a/notebooks/immune_system_pdb_report_deposition_date.pdf b/notebooks/immune_system_pdb_report_deposition_date.pdf new file mode 100644 index 00000000..0f639462 Binary files /dev/null and b/notebooks/immune_system_pdb_report_deposition_date.pdf differ diff --git a/notebooks/immune_system_pdb_report_deposition_date.png b/notebooks/immune_system_pdb_report_deposition_date.png deleted file mode 100644 index b695c2bb..00000000 Binary files a/notebooks/immune_system_pdb_report_deposition_date.png and /dev/null differ diff --git a/notebooks/immune_system_pdb_report_resolution.pdf b/notebooks/immune_system_pdb_report_resolution.pdf new file mode 100644 index 00000000..a82a66f8 Binary files /dev/null and b/notebooks/immune_system_pdb_report_resolution.pdf differ diff --git a/notebooks/immune_system_pdb_report_resolution.png b/notebooks/immune_system_pdb_report_resolution.png deleted file mode 100644 index 04d8d8d2..00000000 Binary files a/notebooks/immune_system_pdb_report_resolution.png and /dev/null differ diff --git a/notebooks/posebusters_benchmark_complex_pdb_deposition_dates.png b/notebooks/posebusters_benchmark_complex_pdb_deposition_dates.png deleted file mode 100644 index 01b5f84f..00000000 Binary files a/notebooks/posebusters_benchmark_complex_pdb_deposition_dates.png and /dev/null differ diff --git a/notebooks/posebusters_benchmark_inference_results_plotting.ipynb b/notebooks/posebusters_benchmark_inference_results_plotting.ipynb index b1cb48c4..61701fde 100644 --- a/notebooks/posebusters_benchmark_inference_results_plotting.ipynb +++ b/notebooks/posebusters_benchmark_inference_results_plotting.ipynb @@ -581,7 +581,7 @@ "\n", "# display the plots\n", "plt.tight_layout()\n", - "plt.savefig(\"posebusters_benchmark_primary_ligand_relaxed_rmsd_violin_plot.png\", dpi=300)\n", + "plt.savefig(\"posebusters_benchmark_primary_ligand_relaxed_rmsd_violin_plot.pdf\")\n", "plt.show()" ] }, @@ -1203,7 +1203,7 @@ "\n", "# display the plots\n", "plt.tight_layout()\n", - "plt.savefig(\"posebusters_benchmark_primary_ligand_relaxed_bar_chart.png\", dpi=300)\n", + "plt.savefig(\"posebusters_benchmark_primary_ligand_relaxed_bar_chart.pdf\")\n", "plt.show()" ] } diff --git a/notebooks/posebusters_benchmark_method_interaction_analysis.pdf b/notebooks/posebusters_benchmark_method_interaction_analysis.pdf new file mode 100644 index 00000000..70000bb9 Binary files /dev/null and b/notebooks/posebusters_benchmark_method_interaction_analysis.pdf differ diff --git a/notebooks/posebusters_benchmark_method_interaction_analysis.png b/notebooks/posebusters_benchmark_method_interaction_analysis.png deleted file mode 100644 index 6f53c673..00000000 Binary files a/notebooks/posebusters_benchmark_method_interaction_analysis.png and /dev/null differ diff --git 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b/notebooks/posebusters_benchmark_primary_ligand_relaxed_bar_chart.png deleted file mode 100644 index 55935f32..00000000 Binary files a/notebooks/posebusters_benchmark_primary_ligand_relaxed_bar_chart.png and /dev/null differ diff --git a/notebooks/posebusters_benchmark_primary_ligand_relaxed_rmsd_violin_plot.pdf b/notebooks/posebusters_benchmark_primary_ligand_relaxed_rmsd_violin_plot.pdf new file mode 100644 index 00000000..18701762 Binary files /dev/null and b/notebooks/posebusters_benchmark_primary_ligand_relaxed_rmsd_violin_plot.pdf differ diff --git a/notebooks/posebusters_benchmark_primary_ligand_relaxed_rmsd_violin_plot.png b/notebooks/posebusters_benchmark_primary_ligand_relaxed_rmsd_violin_plot.png deleted file mode 100644 index 71d6c435..00000000 Binary files a/notebooks/posebusters_benchmark_primary_ligand_relaxed_rmsd_violin_plot.png and /dev/null differ diff --git a/notebooks/posebusters_benchmark_structured_vs_unstructured_plif_emd_values.pdf b/notebooks/posebusters_benchmark_structured_vs_unstructured_plif_emd_values.pdf new file mode 100644 index 00000000..209ef2cc Binary files /dev/null and b/notebooks/posebusters_benchmark_structured_vs_unstructured_plif_emd_values.pdf differ diff --git a/notebooks/posebusters_benchmark_structured_vs_unstructured_plif_emd_values.png b/notebooks/posebusters_benchmark_structured_vs_unstructured_plif_emd_values.png deleted file mode 100644 index b7aa002d..00000000 Binary files a/notebooks/posebusters_benchmark_structured_vs_unstructured_plif_emd_values.png and /dev/null differ diff --git a/notebooks/posebusters_method_interaction_analysis_plotting.ipynb b/notebooks/posebusters_method_interaction_analysis_plotting.ipynb index dde7ed9f..59e4c5ae 100644 --- a/notebooks/posebusters_method_interaction_analysis_plotting.ipynb +++ b/notebooks/posebusters_method_interaction_analysis_plotting.ipynb @@ -105,7 +105,7 @@ ")\n", "assert os.path.exists(\n", " pb_set_dir\n", - "), \"Please download the PoseBusters Benchmark set from `https://zenodo.org/records/16791095` before proceeding.\"\n", + "), \"Please download the PoseBusters Benchmark set from `https://zenodo.org/records/17536252` before proceeding.\"\n", "\n", "# PoseBusters Benchmark deposition dates\n", "pb_deposition_dates_filepath = \"posebusters_benchmark_complex_pdb_deposition_dates.csv\"\n", @@ -568,7 +568,7 @@ " ax.grid(True)\n", "\n", "plt.tight_layout()\n", - "plt.savefig(\"posebusters_benchmark_method_interaction_analysis.png\", dpi=300)\n", + "plt.savefig(\"posebusters_benchmark_method_interaction_analysis.pdf\")\n", "plt.show()" ] }, @@ -742,7 +742,7 @@ "sns.boxplot(data=emd_values_df, x=\"Category\", y=\"EMD\")\n", "plt.xlabel(\"\")\n", "plt.ylabel(\"PLIF-EMD\")\n", - "plt.savefig(\"posebusters_benchmark_plif_emd_values.png\")\n", + "plt.savefig(\"posebusters_benchmark_plif_emd_values.pdf\")\n", "plt.show()\n", "\n", "plt.close(\"all\")\n", @@ -751,7 +751,7 @@ "sns.boxplot(data=emd_values_df, x=\"Category\", y=\"WM\")\n", "plt.xlabel(\"\")\n", "plt.ylabel(\"PLIF-WM\")\n", - "plt.savefig(\"posebusters_benchmark_plif_wm_values.png\")\n", + "plt.savefig(\"posebusters_benchmark_plif_wm_values.pdf\")\n", "plt.show()\n", "\n", "plt.close(\"all\")" @@ -901,7 +901,7 @@ "plt.ylabel(\"EMD Value\")\n", "plt.title(\"Comparison of Structured_EMD and Unstructured_EMD by Method\")\n", "plt.legend()\n", - "plt.savefig(\"posebusters_benchmark_structured_vs_unstructured_plif_emd_values.png\")\n", + "plt.savefig(\"posebusters_benchmark_structured_vs_unstructured_plif_emd_values.pdf\")\n", "plt.show()\n", "\n", "plt.close(\"all\")" diff --git a/notebooks/posebusters_method_interaction_analysis_plotting.py b/notebooks/posebusters_method_interaction_analysis_plotting.py index 20707235..f59aa47e 100644 --- a/notebooks/posebusters_method_interaction_analysis_plotting.py +++ b/notebooks/posebusters_method_interaction_analysis_plotting.py @@ -70,7 +70,7 @@ ) assert os.path.exists( pb_set_dir -), "Please download the PoseBusters Benchmark set from `https://zenodo.org/records/16791095` before proceeding." +), "Please download the PoseBusters Benchmark set from `https://zenodo.org/records/17536252` before proceeding." # PoseBusters Benchmark deposition dates pb_deposition_dates_filepath = "posebusters_benchmark_complex_pdb_deposition_dates.csv" @@ -491,7 +491,7 @@ def process_method(file_path, category): ax.grid(True) plt.tight_layout() -plt.savefig("posebusters_benchmark_method_interaction_analysis.png", dpi=300) +plt.savefig("posebusters_benchmark_method_interaction_analysis.pdf") plt.show() # %% [markdown] @@ -655,7 +655,7 @@ def histogram_to_vector(histogram, bins): sns.boxplot(data=emd_values_df, x="Category", y="EMD") plt.xlabel("") plt.ylabel("PLIF-EMD") -plt.savefig("posebusters_benchmark_plif_emd_values.png") +plt.savefig("posebusters_benchmark_plif_emd_values.pdf") plt.show() plt.close("all") @@ -664,7 +664,7 @@ def histogram_to_vector(histogram, bins): sns.boxplot(data=emd_values_df, x="Category", y="WM") plt.xlabel("") plt.ylabel("PLIF-WM") -plt.savefig("posebusters_benchmark_plif_wm_values.png") +plt.savefig("posebusters_benchmark_plif_wm_values.pdf") plt.show() plt.close("all") @@ -804,7 +804,7 @@ def histogram_to_vector(histogram, bins): plt.ylabel("EMD Value") plt.title("Comparison of Structured_EMD and Unstructured_EMD by Method") plt.legend() -plt.savefig("posebusters_benchmark_structured_vs_unstructured_plif_emd_values.png") +plt.savefig("posebusters_benchmark_structured_vs_unstructured_plif_emd_values.pdf") plt.show() plt.close("all") diff --git a/posebench/data/components/plot_dataset_rmsd.py b/posebench/data/components/plot_dataset_rmsd.py index 9d78c8af..1e83302c 100644 --- a/posebench/data/components/plot_dataset_rmsd.py +++ b/posebench/data/components/plot_dataset_rmsd.py @@ -221,12 +221,12 @@ def plot_dataset_rmsd( plt.clf() sns.histplot(dataset_df["TM-score"]) plt.title("Apo-To-Holo Protein TM-score") - plt.savefig(plot_dir / f"{dataset}_a2h_TM-score_hist.png") + plt.savefig(plot_dir / f"{dataset}_a2h_TM-score_hist.pdf") plt.clf() sns.histplot(dataset_df["RMSD"]) plt.title("Apo-To-Holo Protein RMSD") - plt.savefig(plot_dir / f"{dataset}_a2h_RMSD_hist.png") + plt.savefig(plot_dir / f"{dataset}_a2h_RMSD_hist.pdf") @hydra.main(