recipe privateer

The Swiss Army knife for carbohydrate structure validation, refinement and analysis

Homepage:

https://github.com/glycojones/privateer

Documentation:

https://www.ccp4.ac.uk/html/privateer.html

License:

LGPL / LGPL-3.0

Recipe:

/privateer/meta.yaml

Links:

doi: 10.1107/S2053230X24000359, doi: 10.1038/nsmb.3115, doi: 10.3762/bjoc.16.204, doi: 10.1107/S2059798323003510

Privateer is a tool for carbohydrate structure validation, re-refinement and graphical analysis. It carries out automatic assignments of ring conformation (IUPAC nomenclature), anomeric form, absolute configuration and comparison to reference values for validation. It computes omit mFo-DFc maps and calculates a correlation coefficient between model and electron density. For structure refinement, it is able to generate chemical dictionaries with unimodal torsion restraints which will help keep the lowest energy conformation. In terms of graphical analysis, it will produce vector diagrams in SNFG nomenclature (SVG format), which are annotated using the validation information (ring conformation, anomeric form, etc). Privateer is implemented in C++11 and Python3 (via pybind11), and produces Scheme and Python scripts for use with Coot (https://github.com/pemsley/coot).

package privateer

versions:

MKV-2,  MKV-1,  MKV-0

depends ccp4srs:

>=2024.6.14

depends clipper:

>=2.1.20180802,<3.0a0

depends gemmi:

<0.6.0

depends libccp4:

>=8.0.0,<9.0a0

depends libgcc:

>=13

depends libgfortran:

depends libgfortran5:

>=13.3.0

depends libstdcxx:

>=13

depends matplotlib-base:

depends mmdb2:

>=2.0.22,<3.0a0

depends numpy:

1.26.*

depends prettytable:

depends pytest:

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

depends requests:

depends seaborn:

requirements:

additional platforms:

linux-aarch64,  osx-arm64

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see 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 privateer

and update with::

   mamba update privateer

To create a new environment, run:

mamba create --name myenvname privateer

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/privateer:<tag>

(see `privateer/tags`_ for valid values for ``<tag>``)

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/privateer/README.html)