recipe chemfp

chemfp is a set of command-lines tools for generating cheminformatics fingerprints and searching those fingerprints by Tanimoto similarity, as well as a Python library which can be used to build new tools.

These algorithms are designed for the dense, 100-10,000 bit fingerprints which occur in small-molecule/pharmaceutical chemisty. The Tanimoto search algorithms are implemented in C for performance and support both threshold and k-nearest searches.

Fingerprint generation can be done either by extracting existing fingerprint data from an SD file or by using an existing chemistry toolkit. chemfp supports the Python libraries from Open Babel, OpenEye, and RDKit toolkits.

Homepage:

https://chemfp.com

License:

MIT

Recipe:

/chemfp/meta.yaml

Links:

doi: 10.1186/s13321-019-0398-8, usegalaxy-eu: ctb_chemfp_mol2fps

package chemfp

(downloads) docker_chemfp

Versions:
1.6.1-2,  1.6.1-1,  1.6.1-0,  1.6-0,  1.5-0,  1.4-1,  1.4-0,  1.3-1,  1.3-0, 

1.6.1-2,  1.6.1-1,  1.6.1-0,  1.6-0,  1.5-0,  1.4-1,  1.4-0,  1.3-1,  1.3-0,  1.3a1-0,  1.1p1-0

Depends:

  • on libgcc-ng >=10.3.0

  • on openbabel

  • on python >=2.7,<2.8.0a0

  • on python_abi 2.7.* *_cp27mu

  • on rdkit

Additional platforms:

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 chemfp

to add into an existing workspace instead, run:

pixi add chemfp

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 chemfp

Alternatively, to install into a new environment, run:

conda create -n envname chemfp

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/chemfp:<tag>

(see chemfp/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.

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