- recipe biobb_structure_utils
Biobb_structure_utils is the Biobb module collection to modify or extract information from a PDB structure file.
- Homepage:
- License:
APACHE / Apache-2.0
- Recipe:
[](https://biobb-structure-utils.readthedocs.io/en/latest/?badge=latest) [](https://opensource.org/licenses/Apache-2.0)
# biobb_structure_utils
Biobb_structure_utils is the Biobb module collection to modify or extract information from a PDB structure file, such as pulling out a particular model or chain, removing water molecules or ligands, or renumbering or sorting atoms or residues. Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over popular bioinformatics tools. The latest documentation of this package can be found in our readthedocs site: [latest API documentation](http://biobb_structure_utils.readthedocs.io/en/latest/).
### 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) 2015-2026 [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
- package biobb_structure_utils¶
- Versions:
5.2.1-0,5.2.0-0,5.1.0-0,5.0.0-0,4.2.0-0,4.1.0-0,4.0.0-1,4.0.0-0,3.9.0-0,5.2.1-0,5.2.0-0,5.1.0-0,5.0.0-0,4.2.0-0,4.1.0-0,4.0.0-1,4.0.0-0,3.9.0-0,3.8.0-0,3.7.6-0,3.7.4-0,3.7.3-0,3.7.2-0,3.7.1-0,3.7.0-0,3.6.1-0,3.6.0-0,3.5.3-0,3.5.2-0,3.5.1-0,3.5.0-0,3.0.1-0,3.0.0-0,2.0.0-0- Depends:
on biobb_common
5.2.2on biobb_structure_checking
>=3.13.5on python
>=3.10
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install biobb_structure_utils
to add into an existing workspace instead, run:
pixi add biobb_structure_utils
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install biobb_structure_utils
Alternatively, to install into a new environment, run:
conda create -n envname biobb_structure_utils
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/biobb_structure_utils:<tag>
(see biobb_structure_utils/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/biobb_structure_utils/README.html)
