Package Recipe 'openstructure'

recipe openstructure

Open-Source Computational Structural Biology Framework.

Homepage:: https://openstructure.org
Documentation:: https://openstructure.org/docs
Developer docs:: https://git.scicore.unibas.ch/schwede/openstructure
License:: LGPL / LGPL-3.0-or-later
Recipe:: /openstructure/meta.yaml
Links:: biotools: openstructure, doi: 10.1107/S0907444913007051

This project aims to provide an open-source, modular, flexible, molecular modelling and visualization environment. It is targeted at interested method developers in the field of structural bioinformatics.

package openstructure¶

Versions:

2.11.1-0, 2.11.0-1, 2.11.0-0, 2.10.0-3, 2.10.0-2, 2.10.0-1, 2.10.0-0, 2.9.3-0

Depends:

on fftw >=3.3.10,<4.0a0
on glew >=2.1.0,<2.2.0a0
on glfw >=3.4,<4.0a0
on libboost >=1.86.0,<1.87.0a0
on libboost-python >=1.86.0,<1.87.0a0
on libegl >=1.7.0,<2.0a0
on libgcc >=13
on libgfortran
on libgfortran5 >=13.4.0
on libgl >=1.7.0,<2.0a0
on libgles >=1.7.0,<2.0a0
on libglvnd >=1.7.0,<2.0a0
on libglx >=1.7.0,<2.0a0
on libopengl >=1.7.0,<2.0a0
on libpng >=1.6.50,<1.7.0a0
on libsqlite >=3.50.4,<4.0a0
on libstdcxx >=13
on libtiff >=4.7.0,<4.8.0a0
on libxcb >=1.17.0,<2.0a0
on libzlib >=1.3.1,<2.0a0
on mesalib >=25.0.5,<25.1.0a0
on networkx >=3.4.2,<4.0a0
on numpy >=1.26.4,<2.0a0
on ocl-icd >=2.3.3,<3.0a0
on ocl-icd-system
on openmm >=8.3.1,<9.0a0
on pandas >=2.3.1,<3.0a0
on parasail >=2.6.2,<3.0a0
on pyqt >=5.15.11,<5.16.0a0
on python >=3.10,<3.11.0a0 *_cpython
on python_abi 3.10.* *_cp310
on qt >=5.15.15,<5.16.0a0
on scipy >=1.13.1,<2.0a0
on voronota >=1.29.4415,<2.0a0

Additional platforms:

linux-aarch64, osx-arm64

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 openstructure

to add into an existing workspace instead, run:

pixi add openstructure

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 openstructure

Alternatively, to install into a new environment, run:

conda create -n envname openstructure

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/openstructure:<tag>

(see openstructure/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:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/openstructure/README.html)