recipe fpocketr

CLI tool to find, characterize, and visualize RNA-ligand binding pockets.

Homepage:

https://github.com/Weeks-UNC/fpocketR

License:

MIT

Recipe:

/fpocketr/meta.yaml

Links:

doi: 10.1101/2025.03.13.643147

fpocketR is an RNA-specific wrapper for fpocket 4.0, providing CLI tools to find, characterize, and visualize RNA binding pockets for drug-like ligands. Only available for x86_64 architectures on linux and MacOS.

package fpocketr

(downloads) docker_fpocketr

versions:

1.3.4-0

depends biopython:

1.83

depends fpocket:

4.0.3.*

depends pandas:

depends prody:

2.3.0

depends pymol-open-source:

2.5

depends python:

>=3.11,<3.12

depends rdkit:

2023.9.6

depends scipy:

1.12.0

depends seaborn:

depends trimesh:

4.2.0

requirements:

additional platforms:

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 fpocketr

and update with::

   mamba update fpocketr

To create a new environment, run:

mamba create --name myenvname fpocketr

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/fpocketr:<tag>

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

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Link to this page

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