[![](https://img.shields.io/github/v/tag/bioexcel/biobb_pdb_tools?label=Version)](https://GitHub.com/bioexcel/biobb_pdb_tools/tags/) [![](https://img.shields.io/pypi/v/biobb-pdb-tools.svg?label=Pypi)](https://pypi.python.org/pypi/biobb-pdb-tools/) [![](https://img.shields.io/conda/vn/bioconda/biobb_pdb_tools?label=Conda)](https://anaconda.org/bioconda/biobb_pdb_tools) [![](https://img.shields.io/conda/dn/bioconda/biobb_pdb_tools?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_pdb_tools) [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_pdb_tools?tab=tags) [![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_pdb_tools:5.2.1--pyhdfd78af_0) [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_pdb_tools) [![](https://img.shields.io/pypi/pyversions/biobb-pdb-tools.svg?label=Python%20Versions)](https://pypi.org/project/biobb-pdb-tools/) [![](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0) [![](https://img.shields.io/badge/Open%20Source%3f-Yes!-blue)](https://github.com/bioexcel/biobb_pdb_tools) [![](https://readthedocs.org/projects/biobb-pdb-tools/badge/?version=latest&label=Docs)](https://biobb-pdb-tools.readthedocs.io/en/latest/?badge=latest) [![](https://img.shields.io/website?down_message=Offline&label=Biobb%20Website&up_message=Online&url=https%3A%2F%2Fmmb.irbbarcelona.org%2Fbiobb%2F)](https://mmb.irbbarcelona.org/biobb/) [![](https://img.shields.io/badge/Youtube-tutorials-blue?logo=youtube&logoColor=red)](https://www.youtube.com/@BioExcelCoE/search?query=biobb) [![](https://zenodo.org/badge/DOI/10.1038/s41597-019-0177-4.svg)](https://doi.org/10.1038/s41597-019-0177-4) [![](https://img.shields.io/endpoint?color=brightgreen&url=https%3A%2F%2Fapi.juleskreuer.eu%2Fcitation-badge.php%3Fshield%26doi%3D10.1038%2Fs41597-019-0177-4)](https://www.nature.com/articles/s41597-019-0177-4#citeas) [![](https://docs.bioexcel.eu/biobb_pdb_tools/junit/testsbadge.svg)](https://docs.bioexcel.eu/biobb_pdb_tools/junit/report.html) [![](https://docs.bioexcel.eu/biobb_pdb_tools/coverage/coveragebadge.svg)](https://docs.bioexcel.eu/biobb_pdb_tools/coverage/) [![](https://docs.bioexcel.eu/biobb_pdb_tools/flake8/flake8badge.svg)](https://docs.bioexcel.eu/biobb_pdb_tools/flake8/) [![](https://img.shields.io/github/last-commit/bioexcel/biobb_pdb_tools?label=Last%20Commit)](https://github.com/bioexcel/biobb_pdb_tools/commits/master) [![](https://img.shields.io/github/issues/bioexcel/biobb_pdb_tools.svg?color=brightgreen&label=Issues)](https://GitHub.com/bioexcel/biobb_pdb_tools/issues/) [![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu) [![](https://www.bestpractices.dev/projects/8847/badge)](https://www.bestpractices.dev/projects/8847) [](https://bestpractices.coreinfrastructure.org/projects/8847/badge) [//]: # (The previous line invisible link is for compatibility with the howfairis script https://github.com/fair-software/howfairis-github-action/tree/main wich uses the old bestpractices URL) # biobb_pdb_tools ## Introduction biobb_pdb_tools is a swiss army knife for manipulating and editing PDB files. The latest documentation of this package can be found in our readthedocs site: [latest API documentation](http://biobb-pdb-tools.readthedocs.io/en/latest/). ### Version v5.2.1 2025.2 ### Installation Using PIP: > **Important:** PIP only installs the package. All the dependencies must be installed separately. To perform a complete installation, please use ANACONDA, DOCKER or SINGULARITY. * Installation: pip install "biobb_pdb_tools>=5.2.1" * Usage: [Python API documentation](https://biobb-pdb-tools.readthedocs.io/en/latest/modules.html) Using ANACONDA: * Installation: conda install -c bioconda "biobb_pdb_tools>=5.2.1" * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-pdb-tools.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-pdb-tools.readthedocs.io/en/latest/command_line.html) Using DOCKER: * Installation: docker pull quay.io/biocontainers/biobb_pdb_tools:5.2.1--pyhdfd78af_0 * Usage: docker run quay.io/biocontainers/biobb_pdb_tools:5.2.1--pyhdfd78af_0 Using SINGULARITY: **MacOS users**: it's strongly recommended to avoid Singularity and use **Docker** as containerization system. * Installation: singularity pull --name biobb_pdb_tools.sif https://depot.galaxyproject.org/singularity/biobb_pdb_tools:5.2.1--pyhdfd78af_0 * Usage: singularity exec biobb_pdb_tools.sif The command list and specification can be found at the [Command Line documentation](https://biobb-pdb-tools.readthedocs.io/en/latest/command_line.html). ### Copyright & Licensing This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU Horizon Europe [101093290](https://cordis.europa.eu/project/id/101093290), EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)). * (c) 2015-2026 [Barcelona Supercomputing Center](https://www.bsc.es/) * (c) 2015-2026 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/) Licensed under the [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details. ![](https://bioexcel.eu/wp-content/uploads/2019/04/Bioexcell_logo_1080px_transp.png "Bioexcel")