diff --git a/README.md b/README.md index ca942e1..c5731fe 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ [![Documentation badge](https://img.shields.io/badge/docs-latest-brightgreen.svg)](https://ppiref.readthedocs.io/en/latest/?badge=latest) [![arXiv badge](https://img.shields.io/badge/arXiv-2310.18515-b31b1b.svg)](https://arxiv.org/abs/2310.18515) -[![Zenodo badge](https://zenodo.org/badge/DOI/10.5281/zenodo.10700674.svg)](https://doi.org/10.5281/zenodo.10700674) +[![Zenodo badge](https://zenodo.org/badge/DOI/10.5281/zenodo.12587821.svg)](https://doi.org/10.5281/zenodo.12587821) [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) [![Python package](https://github.com/anton-bushuiev/PPIRef/actions/workflows/python-package.yml/badge.svg)](https://github.com/anton-bushuiev/PPIRef/actions/workflows/python-package.yml) ![Python Versions](https://img.shields.io/badge/Python-3.9%20%7C%203.10%20%7C%203.11-green.svg) @@ -42,7 +42,7 @@ Download the dataset using the package (in Python). from ppiref.utils.misc import download_from_zenodo from ppiref.split import read_fold from ppiref.utils.ppi import PPI -download_from_zenodo('ppi_6A.zip') +download_from_zenodo('ppi_6A.zip') # or for example 'pdb_redo_ppi_10A.zip' for all 10-Angstrom PPIs from PDB-REDO > Downloading: 100%|██████████| 6.94G/6.94G [10:19<00:00, 11.2MiB/s] > Extracting: 100%|██████████| 831382/831382 [02:36<00:00, 5313.49files/s] ``` @@ -88,8 +88,8 @@ The repository is under development. Please do not hesitate to contact us or cre - [x] PPIRef (6A interfaces) on Zenodo - [ ] PPIRef (10A interfaces) on Zenodo (expected in June 2024) -- [ ] PPIRef version based on the [PDB-REDO database](https://pdb-redo.eu/) for higher-quality side chains in the structures (expected in June 2024) -- [ ] Docstrings +- [x] PPIRef version based on the [PDB-REDO database](https://pdb-redo.eu/) for higher-quality side chains in the structures (expected in June 2024) +- [x] Docstrings **Enhancements** diff --git a/docs/ppiref_dataset.ipynb b/docs/ppiref_dataset.ipynb index baf1f6c..455082d 100644 --- a/docs/ppiref_dataset.ipynb +++ b/docs/ppiref_dataset.ipynb @@ -35,7 +35,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "The PPIRef dataset is available on [Zenodo](https://zenodo.org/records/10700674). We recommended downloading it and putting under `PPIRef/ppiref/data/ppiref`. This can be done automatically by running the following command to download all 6A interfaces in .pdb files (see the \"Installation\" section on how to install the ppiref package):" + "The PPIRef dataset is available on [Zenodo](https://zenodo.org/records/12587821). We recommended downloading it and putting under `PPIRef/ppiref/data/ppiref`. This can be done automatically by running the following command to download all 6A interfaces in .pdb files (see the \"Installation\" section on how to install the ppiref package):" ] }, { diff --git a/ppiref/utils/misc.py b/ppiref/utils/misc.py index 5781be8..3b53289 100644 --- a/ppiref/utils/misc.py +++ b/ppiref/utils/misc.py @@ -41,7 +41,7 @@ def get_partition(lst: list, beg: float, end: float): def download_from_zenodo( file: str, - project_url: str = 'https://zenodo.org/records/10700674/files/', + project_url: str = 'https://zenodo.org/records/12587821/files/', destination_folder: Union[Path, str] = None ) -> None: """