recipe ssm

Secondary-structure matching, tool for fast protein structure alignment

Homepage:

https://www.ccp4.ac.uk

License:

GPL3 / GPL-3.0-or-later AND LGPL-3.0-or-later

Recipe:

/ssm/meta.yaml

Links:

doi: 10.1107/S0907444904026460

SSM is a macromolecular coordinate superposition library, written by Eugene Krissinel of the EBI. The library implements the SSM algorithm of protein structure comparison in three dimensions, which includes an original procedure of matching graphs built on the protein's secondary-structure elements, followed by an iterative three-dimensional alignment of protein backbone Calpha atoms.

package ssm

versions:

1.4-1,  1.4-0

depends libccp4:

>=8.0.0,<9.0a0

depends libgcc:

>=13

depends libstdcxx:

>=13

depends mmdb2:

>=2.0.22,<3.0a0

depends pkg-config:

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 ssm

and update with::

   mamba update ssm

To create a new environment, run:

mamba create --name myenvname ssm

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/ssm:<tag>

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

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