Bump to 0.0.2

BioinfoMachineLearning · Jan 15, 2025 · b9e4c25 · b9e4c25
1 parent afc9750
commit b9e4c25
Show file tree

Hide file tree

Showing 3 changed files with 56 additions and 42 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -5,7 +5,7 @@ exclude: "^forks/"
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v5.0.0
     hooks:
       # list of supported hooks: https://pre-commit.com/hooks.html
       - id: trailing-whitespace
@@ -22,28 +22,28 @@ repos:
 
   # python code formatting
   - repo: https://github.com/psf/black
-    rev: 23.1.0
+    rev: 24.10.0
     hooks:
       - id: black
         args: [--line-length, "99"]
 
   # python import sorting
   - repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
         args: ["--profile", "black", "--filter-files"]
 
   # python upgrading syntax to newer version
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.1
+    rev: v3.19.1
     hooks:
       - id: pyupgrade
         args: [--py38-plus]
 
   # python docstring formatting
   - repo: https://github.com/myint/docformatter
-    rev: v1.7.4
+    rev: v1.7.5
     hooks:
       - id: docformatter
         args:
@@ -57,7 +57,7 @@ repos:
 
   # python docstring coverage checking
   - repo: https://github.com/econchick/interrogate
-    rev: 1.5.0 # or master if you're bold
+    rev: 1.7.0 # or master if you're bold
     hooks:
       - id: interrogate
         args:
@@ -73,7 +73,7 @@ repos:
 
   # python check (PEP8), programming errors and code complexity
   - repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
+    rev: 7.1.1
     hooks:
       - id: flake8
         args:
@@ -87,28 +87,28 @@ repos:
 
   # python security linter
   - repo: https://github.com/PyCQA/bandit
-    rev: "1.7.5"
+    rev: "1.8.2"
     hooks:
       - id: bandit
         args: ["-s", "B101"]
 
   # yaml formatting
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.0-alpha.6
+    rev: v4.0.0-alpha.8
     hooks:
       - id: prettier
         types: [yaml]
         exclude: "environment.yaml"
 
   # shell scripts linter
   - repo: https://github.com/shellcheck-py/shellcheck-py
-    rev: v0.9.0.2
+    rev: v0.10.0.1
     hooks:
       - id: shellcheck
 
   # md formatting
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.16
+    rev: 0.7.21
     hooks:
       - id: mdformat
         args: ["--number"]
@@ -121,7 +121,7 @@ repos:
 
   # word spelling linter
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.4
+    rev: v2.3.0
     hooks:
       - id: codespell
         args:
@@ -130,13 +130,13 @@ repos:
 
   # jupyter notebook cell output clearing
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.6.1
+    rev: 0.8.1
     hooks:
       - id: nbstripout
 
   # jupyter notebook linting
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.6.3
+    rev: 1.9.1
     hooks:
       - id: nbqa-black
         args: ["--line-length=99"]

diff --git a/README.md b/README.md
@@ -12,7 +12,7 @@
 
 <!-- [![Conference](http://img.shields.io/badge/AnyConference-year-4b44ce.svg)](https://papers.nips.cc/paper/2020) -->
 
-[![Data DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14478459.svg)](https://doi.org/10.5281/zenodo.14478459)
+[![Data DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14660031.svg)](https://doi.org/10.5281/zenodo.14660031)
 
 <img src="./img/FlowDock.png" width="600">
 
@@ -85,7 +85,7 @@ cd ../
 
 ```bash
 # pretrained FlowDock weights
-wget https://zenodo.org/records/14478459/files/flowdock_checkpoints.tar.gz
+wget https://zenodo.org/records/14660031/files/flowdock_checkpoints.tar.gz
 tar -xzf flowdock_checkpoints.tar.gz
 rm flowdock_checkpoints.tar.gz
 ```
@@ -99,19 +99,19 @@ tar -xzf flowdock_data_cache.tar.gz
 rm flowdock_data_cache.tar.gz
 
 # cached data for PDBBind, Binding MOAD, DockGen, and the PDB-based van der Mers (vdM) dataset
-wget https://zenodo.org/records/14478459/files/flowdock_pdbbind_data.tar.gz
+wget https://zenodo.org/records/14660031/files/flowdock_pdbbind_data.tar.gz
 tar -xzf flowdock_pdbbind_data.tar.gz
 rm flowdock_pdbbind_data.tar.gz
 
-wget https://zenodo.org/records/14478459/files/flowdock_moad_data.tar.gz
+wget https://zenodo.org/records/14660031/files/flowdock_moad_data.tar.gz
 tar -xzf flowdock_moad_data.tar.gz
 rm flowdock_moad_data.tar.gz
 
-wget https://zenodo.org/records/14478459/files/flowdock_dockgen_data.tar.gz
+wget https://zenodo.org/records/14660031/files/flowdock_dockgen_data.tar.gz
 tar -xzf flowdock_dockgen_data.tar.gz
 rm flowdock_dockgen_data.tar.gz
 
-wget https://zenodo.org/records/14478459/files/flowdock_pdbsidechain_data.tar.gz
+wget https://zenodo.org/records/14660031/files/flowdock_pdbsidechain_data.tar.gz
 tar -xzf flowdock_pdbsidechain_data.tar.gz
 rm flowdock_pdbsidechain_data.tar.gz
 ```
@@ -123,7 +123,7 @@ rm flowdock_pdbsidechain_data.tar.gz
 <details>
 
 **NOTE:** The following steps (besides downloading PDBBind and Binding MOAD's PDB files) are only necessary if one wants to fully process each of the following datasets manually.
-Otherwise, preprocessed versions of each dataset can be found on [Zenodo](https://zenodo.org/records/14478459).
+Otherwise, preprocessed versions of each dataset can be found on [Zenodo](https://zenodo.org/records/14660031).
 
 Download data
 
@@ -283,29 +283,49 @@ Download baseline method predictions and results
 
 ```bash
 # cached predictions and evaluation metrics for reproducing structure prediction paper results
-wget https://zenodo.org/records/14478459/files/chai_baseline_method_predictions.tar.gz
+wget https://zenodo.org/records/14660031/files/alphafold3_baseline_method_predictions.tar.gz
+tar -xzf alphafold3_baseline_method_predictions.tar.gz
+rm alphafold3_baseline_method_predictions.tar.gz
+
+wget https://zenodo.org/records/14660031/files/chai_baseline_method_predictions.tar.gz
 tar -xzf chai_baseline_method_predictions.tar.gz
 rm chai_baseline_method_predictions.tar.gz
 
-wget https://zenodo.org/records/14478459/files/diffdock_baseline_method_predictions.tar.gz
+wget https://zenodo.org/records/14660031/files/diffdock_baseline_method_predictions.tar.gz
 tar -xzf diffdock_baseline_method_predictions.tar.gz
 rm diffdock_baseline_method_predictions.tar.gz
 
-wget https://zenodo.org/records/14478459/files/dynamicbind_baseline_method_predictions.tar.gz
+wget https://zenodo.org/records/14660031/files/dynamicbind_baseline_method_predictions.tar.gz
 tar -xzf dynamicbind_baseline_method_predictions.tar.gz
 rm dynamicbind_baseline_method_predictions.tar.gz
 
-wget https://zenodo.org/records/14478459/files/flowdock_baseline_method_predictions.tar.gz
+wget https://zenodo.org/records/14660031/files/flowdock_baseline_method_predictions.tar.gz
 tar -xzf flowdock_baseline_method_predictions.tar.gz
 rm flowdock_baseline_method_predictions.tar.gz
 
-wget https://zenodo.org/records/14478459/files/flowdock_hp_baseline_method_predictions.tar.gz
+wget https://zenodo.org/records/14660031/files/flowdock_aft_baseline_method_predictions.tar.gz
+tar -xzf flowdock_aft_baseline_method_predictions.tar.gz
+rm flowdock_aft_baseline_method_predictions.tar.gz
+
+wget https://zenodo.org/records/14660031/files/flowdock_esmfold_baseline_method_predictions.tar.gz
+tar -xzf flowdock_esmfold_baseline_method_predictions.tar.gz
+rm flowdock_esmfold_baseline_method_predictions.tar.gz
+
+wget https://zenodo.org/records/14660031/files/flowdock_hp_baseline_method_predictions.tar.gz
 tar -xzf flowdock_hp_baseline_method_predictions.tar.gz
 rm flowdock_hp_baseline_method_predictions.tar.gz
 
-wget https://zenodo.org/records/14478459/files/neuralplexer_baseline_method_predictions.tar.gz
+wget https://zenodo.org/records/14660031/files/neuralplexer_baseline_method_predictions.tar.gz
 tar -xzf neuralplexer_baseline_method_predictions.tar.gz
 rm neuralplexer_baseline_method_predictions.tar.gz
+
+wget https://zenodo.org/records/14660031/files/vina_p2rank_baseline_method_predictions.tar.gz
+tar -xzf vina_p2rank_baseline_method_predictions.tar.gz
+rm vina_p2rank_baseline_method_predictions.tar.gz
+
+wget https://zenodo.org/records/14660031/files/rfaa_baseline_method_predictions.tar.gz
+tar -xzf rfaa_baseline_method_predictions.tar.gz
+rm rfaa_baseline_method_predictions.tar.gz
 ```
 
 Reproduce paper result figures
@@ -384,12 +404,9 @@ If you use the code or data associated with this package or otherwise find this
 
 ```bibtex
 @article{morehead2024flowdock,
-      title={FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction},
-      author={Alex Morehead and Jianlin Cheng},
-      year={2024},
-      eprint={2412.10966},
-      archivePrefix={arXiv},
-      primaryClass={cs.LG},
-      url={https://arxiv.org/abs/2412.10966},
+  title={FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction},
+  author={Morehead, Alex and Cheng, Jianlin},
+  journal={arXiv preprint arXiv:2412.10966},
+  year={2024}
 }
 ```
diff --git a/citation.bib b/citation.bib
@@ -1,9 +1,6 @@
 @article{morehead2024flowdock,
-      title={FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction}, 
-      author={Alex Morehead and Jianlin Cheng},
-      year={2024},
-      eprint={2412.10966},
-      archivePrefix={arXiv},
-      primaryClass={cs.LG},
-      url={https://arxiv.org/abs/2412.10966},
-}
+  title={FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction},
+  author={Morehead, Alex and Cheng, Jianlin},
+  journal={arXiv preprint arXiv:2412.10966},
+  year={2024}
+}