[](https://GitHub.com/bioexcel/biobb_pdb_tools/tags/)
[](https://pypi.python.org/pypi/biobb-pdb-tools/)
[](https://anaconda.org/bioconda/biobb_pdb_tools)
[](https://anaconda.org/bioconda/biobb_pdb_tools)
[](https://quay.io/repository/biocontainers/biobb_pdb_tools?tab=tags)
[](https://depot.galaxyproject.org/singularity/biobb_pdb_tools:5.0.0--pyhdfd78af_0)
[](https://github.com/bioexcel/biobb_pdb_tools)
[](https://pypi.org/project/biobb-pdb-tools/)
[](https://opensource.org/licenses/Apache-2.0)
[](https://github.com/bioexcel/biobb_pdb_tools)
[](https://biobb-pdb-tools.readthedocs.io/en/latest/?badge=latest)
[](https://mmb.irbbarcelona.org/biobb/)
[](https://www.youtube.com/@BioExcelCoE/search?query=biobb)
[](https://doi.org/10.1038/s41597-019-0177-4)
[](https://www.nature.com/articles/s41597-019-0177-4#citeas)
[](https://docs.bioexcel.eu/biobb_pdb_tools/junit/report.html)
[](https://docs.bioexcel.eu/biobb_pdb_tools/coverage/)
[](https://docs.bioexcel.eu/biobb_pdb_tools/flake8/)
[](https://github.com/bioexcel/biobb_pdb_tools/commits/master)
[](https://GitHub.com/bioexcel/biobb_pdb_tools/issues/)
[](https://fair-software.eu)
[](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
v5.0.0 2024.2
### 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>=5.0.0"
* Usage: [Python API documentation](https://biobb-pdb-tools.readthedocs.io/en/latest/modules.html)
Using ANACONDA:
* Installation:
conda install -c bioconda "biobb_pdb_tools>=5.0.0"
* 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:5.0.0--pyhdfd78af_0
* Usage:
docker run quay.io/biocontainers/biobb_pdb_tools:5.0.0--pyhdfd78af_0 <command>
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:5.0.0--pyhdfd78af_0
* Usage:
singularity exec biobb_pdb_tools.sif <command>
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 H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).
* (c) 2015-2024 [Barcelona Supercomputing Center](https://www.bsc.es/)
* (c) 2015-2024 [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.
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