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Update Zenodo link
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‎README.md‎

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# PoseBench
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[![Paper](http://img.shields.io/badge/arXiv-2405.14108-B31B1B.svg)](https://arxiv.org/abs/2405.14108)
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[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.16791095.svg)](https://doi.org/10.5281/zenodo.16791095)
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[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17536252.svg)](https://doi.org/10.5281/zenodo.17536252)
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[![PyPI version](https://badge.fury.io/py/posebench.svg)](https://badge.fury.io/py/posebench)
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[![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)
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[![Docs](https://assets.readthedocs.org/static/projects/badges/passing-flat.svg)](https://bioinfomachinelearning.github.io/PoseBench/)
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```bash
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# fetch, extract, and clean-up preprocessed Astex Diverse, PoseBusters Benchmark, DockGen, and CASP15 data (~3 GB) #
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wget https://zenodo.org/records/16791095/files/astex_diverse_set.tar.gz
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wget https://zenodo.org/records/16791095/files/posebusters_benchmark_set.tar.gz
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wget https://zenodo.org/records/16791095/files/dockgen_set.tar.gz
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wget https://zenodo.org/records/16791095/files/casp15_set.tar.gz
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wget https://zenodo.org/records/17536252/files/astex_diverse_set.tar.gz
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wget https://zenodo.org/records/17536252/files/posebusters_benchmark_set.tar.gz
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wget https://zenodo.org/records/17536252/files/dockgen_set.tar.gz
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wget https://zenodo.org/records/17536252/files/casp15_set.tar.gz
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tar -xzf astex_diverse_set.tar.gz
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tar -xzf posebusters_benchmark_set.tar.gz
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tar -xzf dockgen_set.tar.gz
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```bash
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# fetch, extract, and clean-up benchmark method predictions to reproduce paper results (~19 GB) #
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# AutoDock Vina predictions and results
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wget https://zenodo.org/records/16791095/files/vina_benchmark_method_predictions.tar.gz
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wget https://zenodo.org/records/17536252/files/vina_benchmark_method_predictions.tar.gz
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tar -xzf vina_benchmark_method_predictions.tar.gz
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rm vina_benchmark_method_predictions.tar.gz
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# DiffDock predictions and results
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wget https://zenodo.org/records/16791095/files/diffdock_benchmark_method_predictions.tar.gz
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wget https://zenodo.org/records/17536252/files/diffdock_benchmark_method_predictions.tar.gz
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tar -xzf diffdock_benchmark_method_predictions.tar.gz
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rm diffdock_benchmark_method_predictions.tar.gz
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# DynamicBind predictions and results
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wget https://zenodo.org/records/16791095/files/dynamicbind_benchmark_method_predictions.tar.gz
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wget https://zenodo.org/records/17536252/files/dynamicbind_benchmark_method_predictions.tar.gz
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tar -xzf dynamicbind_benchmark_method_predictions.tar.gz
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rm dynamicbind_benchmark_method_predictions.tar.gz
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# NeuralPLexer predictions and results
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wget https://zenodo.org/records/16791095/files/neuralplexer_benchmark_method_predictions.tar.gz
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wget https://zenodo.org/records/17536252/files/neuralplexer_benchmark_method_predictions.tar.gz
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tar -xzf neuralplexer_benchmark_method_predictions.tar.gz
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rm neuralplexer_benchmark_method_predictions.tar.gz
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# RoseTTAFold-All-Atom predictions and results
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wget https://zenodo.org/records/16791095/files/rfaa_benchmark_method_predictions.tar.gz
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wget https://zenodo.org/records/17536252/files/rfaa_benchmark_method_predictions.tar.gz
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tar -xzf rfaa_benchmark_method_predictions.tar.gz
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rm rfaa_benchmark_method_predictions.tar.gz
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# Chai-1 predictions and results
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wget https://zenodo.org/records/16791095/files/chai_benchmark_method_predictions.tar.gz
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wget https://zenodo.org/records/17536252/files/chai_benchmark_method_predictions.tar.gz
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tar -xzf chai_benchmark_method_predictions.tar.gz
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rm chai_benchmark_method_predictions.tar.gz
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# Boltz-1 predictions and results
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wget https://zenodo.org/records/16791095/files/boltz_benchmark_method_predictions.tar.gz
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wget https://zenodo.org/records/17536252/files/boltz_benchmark_method_predictions.tar.gz
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tar -xzf boltz_benchmark_method_predictions.tar.gz
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rm boltz_benchmark_method_predictions.tar.gz
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# AlphaFold 3 predictions and results
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wget https://zenodo.org/records/16791095/files/af3_benchmark_method_predictions.tar.gz
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wget https://zenodo.org/records/17536252/files/af3_benchmark_method_predictions.tar.gz
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tar -xzf af3_benchmark_method_predictions.tar.gz
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rm af3_benchmark_method_predictions.tar.gz
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# CASP15 predictions and results for all methods
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wget https://zenodo.org/records/16791095/files/casp15_benchmark_method_predictions.tar.gz
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wget https://zenodo.org/records/17536252/files/casp15_benchmark_method_predictions.tar.gz
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tar -xzf casp15_benchmark_method_predictions.tar.gz
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rm casp15_benchmark_method_predictions.tar.gz
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```
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```bash
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# fetch, extract, and clean-up benchmark method interactions to reproduce paper results (~12 GB) #
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# cached ProLIF interactions for notebook plots
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wget https://zenodo.org/records/16791095/files/posebench_notebooks.tar.gz
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wget https://zenodo.org/records/17536252/files/posebench_notebooks.tar.gz
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tar -xzf posebench_notebooks.tar.gz
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rm posebench_notebooks.tar.gz
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```
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conda deactivate
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```
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**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).
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**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).
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</details>
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‎docs/source/data_preparation.rst‎

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:end-line: 359
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.. note::
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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.
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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_method_interaction_analysis_plotting.ipynb‎

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")\n",
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"assert os.path.exists(\n",
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" ad_set_dir\n",
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"), \"Please download the Astex Diverse set from `https://zenodo.org/records/16791095` before proceeding.\"\n",
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"), \"Please download the Astex Diverse set from `https://zenodo.org/records/17536252` before proceeding.\"\n",
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"\n",
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"# Mappings\n",
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"method_mapping = {\n",

‎notebooks/astex_method_interaction_analysis_plotting.py‎

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)
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assert os.path.exists(
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ad_set_dir
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), "Please download the Astex Diverse set from `https://zenodo.org/records/16791095` before proceeding."
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), "Please download the Astex Diverse set from `https://zenodo.org/records/17536252` before proceeding."
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# Mappings
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method_mapping = {

‎notebooks/casp15_method_interaction_analysis_plotting.ipynb‎

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")\n",
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"assert os.path.exists(\n",
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" casp15_set_dir\n",
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"), \"Please download the (public) CASP15 set from `https://zenodo.org/records/16791095` before proceeding.\"\n",
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"), \"Please download the (public) CASP15 set from `https://zenodo.org/records/17536252` before proceeding.\"\n",
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"\n",
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"# Mappings\n",
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"method_mapping = {\n",

‎notebooks/casp15_method_interaction_analysis_plotting.py‎

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)
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), "Please download the (public) CASP15 set from `https://zenodo.org/records/16791095` before proceeding."
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), "Please download the (public) CASP15 set from `https://zenodo.org/records/17536252` before proceeding."
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# Mappings
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method_mapping = {

‎notebooks/dataset_interaction_analysis_plotting.ipynb‎

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")\n",
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"assert os.path.exists(\n",
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" ad_set_dir\n",
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"), \"Please download the Astex Diverse set from `https://zenodo.org/records/16791095` before proceeding.\"\n",
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"), \"Please download the Astex Diverse set from `https://zenodo.org/records/17536252` before proceeding.\"\n",
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"assert os.path.exists(\n",
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" pb_set_dir\n",
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"), \"Please download the PoseBusters Benchmark set from `https://zenodo.org/records/16791095` before proceeding.\"\n",
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"), \"Please download the PoseBusters Benchmark set from `https://zenodo.org/records/17536252` before proceeding.\"\n",
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"assert os.path.exists(\n",
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" dg_set_dir\n",
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"), \"Please download the DockGen set from `https://zenodo.org/records/16791095` before proceeding.\"\n",
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"), \"Please download the DockGen set from `https://zenodo.org/records/17536252` before proceeding.\"\n",
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"assert os.path.exists(\n",
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"), \"Please download the (public) CASP15 set from `https://zenodo.org/records/16791095` before proceeding.\"\n",
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"), \"Please download the (public) CASP15 set from `https://zenodo.org/records/17536252` before proceeding.\"\n",
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"\n",
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"CASP15_ANALYSIS_TARGETS_TO_SKIP = [\n",
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‎notebooks/dataset_interaction_analysis_plotting.py‎

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), "Please download the Astex Diverse set from `https://zenodo.org/records/17536252` before proceeding."
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assert os.path.exists(
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pb_set_dir
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), "Please download the PoseBusters Benchmark set from `https://zenodo.org/records/16791095` before proceeding."
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), "Please download the PoseBusters Benchmark set from `https://zenodo.org/records/17536252` before proceeding."
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), "Please download the DockGen set from `https://zenodo.org/records/17536252` before proceeding."
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), "Please download the (public) CASP15 set from `https://zenodo.org/records/17536252` before proceeding."
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‎notebooks/dockgen_method_interaction_analysis_plotting.ipynb‎

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"assert os.path.exists(\n",
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" dg_set_dir\n",
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"), \"Please download the DockGen set from `https://zenodo.org/records/16791095` before proceeding.\"\n",
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"), \"Please download the DockGen set from `https://zenodo.org/records/17536252` before proceeding.\"\n",
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"# Mappings\n",
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"method_mapping = {\n",

‎notebooks/dockgen_method_interaction_analysis_plotting.py‎

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), "Please download the DockGen set from `https://zenodo.org/records/17536252` before proceeding."
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# Mappings
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method_mapping = {

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