:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'biobb_structure_checking' .. highlight: bash biobb_structure_checking ======================== .. conda:recipe:: biobb_structure_checking :replaces_section_title: :noindex: BioBB\_structure\_checking performs MDWeb structure checking set as a command line utility. :homepage: https://github.com/bioexcel/biobb_structure_checking :license: APACHE / Apache Software License :recipe: /`biobb_structure_checking `_/`meta.yaml `_ Biobb\_structure\_checking performs a checking of the quality of a 3D structure intended to facilitate the setup of molecular dynamics simulation of protein or nucleic acids systems. Biobb\_structure\_checking package allows to configure the system \(selection of model\/chains\,alternative location\, addition of disulfide bonds and hydrogen atoms\, side chain mutations\)\, to detect and fix structure errors \(missing side chain atoms\, backbone breaks\, amide assignments\, incorrect chirality\). It works with structures obtained from the Protein Data Bank or user provided. The Biobb\_structure\_checking package provides a command line utility \(https\:\/\/biobb\-structure\-checking.readthedocs.io\/en\/latest\/command\_line\_usage.html\) and a python API \(https\:\/\/biobb\-structure\-checking.readthedocs.io\/en\/latest\/biobb\_structure\_checking.html\). The latest documentation of this package can be found in our readthedocs site\: http\:\/\/biobb\_structure\_checking.readthedocs.io\/en\/latest\/ .. conda:package:: biobb_structure_checking |downloads_biobb_structure_checking| |docker_biobb_structure_checking| :versions: .. raw:: html
3.13.4-03.13.3-03.13.2-03.13.0-03.12.1-03.12.0-03.10.1-03.9.11-13.9.11-0 ``3.13.4-0``,  ``3.13.3-0``,  ``3.13.2-0``,  ``3.13.0-0``,  ``3.12.1-0``,  ``3.12.0-0``,  ``3.10.1-0``,  ``3.9.11-1``,  ``3.9.11-0``,  ``3.9.10-0``,  ``3.9.9-0``,  ``3.9.7-0``,  ``3.9.6-0``,  ``3.9.2-0``,  ``3.9.1-0``,  ``3.8.5-0``,  ``3.7.3-0``,  ``3.7.2-0``,  ``3.7.1-0``,  ``3.5.3-0``,  ``3.5.0-0``,  ``3.0.2-0``,  ``3.0.1-0``,  ``3.0.0-0``,  ``1.0.7-0``,  ``1.0.6-0``,  ``1.0.5-0``,  ``0.0.1-0`` .. raw:: html
:depends biopython: ``>=1.79`` :depends numpy: :depends pip: :depends psutil: :depends python: ``>=3.8`` :depends setuptools: :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`set-up-channels`). While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see `here `_ for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others. Given that you already have a conda environment in which you want to have this package, install with:: mamba install biobb_structure_checking and update with:: mamba update biobb_structure_checking To create a new environment, run:: mamba create --name myenvname biobb_structure_checking with ``myenvname`` being a reasonable name for the environment (see e.g. the `mamba docs `_ for details and further options). Alternatively, use the docker container:: docker pull quay.io/biocontainers/biobb_structure_checking: (see `biobb_structure_checking/tags`_ for valid values for ````) .. |downloads_biobb_structure_checking| image:: https://img.shields.io/conda/dn/bioconda/biobb_structure_checking.svg?style=flat :target: https://anaconda.org/bioconda/biobb_structure_checking :alt: (downloads) .. |docker_biobb_structure_checking| image:: https://quay.io/repository/biocontainers/biobb_structure_checking/status :target: https://quay.io/repository/biocontainers/biobb_structure_checking .. _`biobb_structure_checking/tags`: https://quay.io/repository/biocontainers/biobb_structure_checking?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| badge with the following MarkDown:: [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/biobb_structure_checking/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/biobb_structure_checking/README.html