Enhance figures as PDFs

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
 

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).
 
 </details>
 

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.

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()"
    ]
   }

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\")"

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")
 plt.title("Comparison of Structured_EMD and Unstructured_EMD by Method")
 plt.legend()
-plt.savefig("astex_diverse_structured_vs_unstructured_emd_values.png")
+plt.savefig("astex_diverse_structured_vs_unstructured_emd_values.pdf")
 plt.show()
 
 plt.close("all")

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()"
    ]

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\")"

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")

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()"
    ]
   }