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.

Version

v5.3.1 2026.1

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>=5.3.1"
  

• Usage: Python API documentation

Using ANACONDA:

• Installation:

    conda install -c bioconda "biobb_pdb_tools>=5.3.1"
  

• Usage: With conda installation BioBBs can be used with the Python API documentation and the Command Line documentation

Using DOCKER:

• Installation:

    docker pull quay.io/biocontainers/biobb_pdb_tools:5.3.1--pyhdfd78af_0
  

• Usage:

    docker run quay.io/biocontainers/biobb_pdb_tools:5.3.1--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:5.3.1--pyhdfd78af_0
  

• Usage:

    singularity exec biobb_pdb_tools.sif <command>
  

The command list and specification can be found at the Command Line documentation.

Copyright & Licensing

This software has been developed in the MMB group at the BSC & IRB for the European BioExcel, funded by the European Commission (EU Horizon Europe 101093290, EU H2020 823830, EU H2020 675728).

• (c) 2015-2026 Barcelona Supercomputing Center
• (c) 2015-2026 Institute for Research in Biomedicine

Licensed under the Apache License 2.0, see the file LICENSE for details.