freesasa を Homebrew, apt, Nix でインストール

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• freesasa

プロジェクトの歴史

The official documentation describes FreeSASA as a C library and C++ command-line tool designed to be simple with defaults while allowing detailed control of calculation parameters. It implements the Lee and Richards algorithm by default and also supports the Shrake and Rupley method.

The project was presented in a 2016 F1000Research paper as an open source C library for SASA calculations with command-line and Python interfaces. Later 2.x releases split the Python bindings into a separate repository, changed parts of the C API, and added structured output formats.

採用の歴史

FreeSASA fits the structural-biology toolchain niche where users need repeatable command-line SASA calculation without depending on older closed or narrowly distributed programs. The project's homepage explicitly targets casual users who want direct PDB-file calculation and advanced users who need C or Python APIs.

The README documents installation through Homebrew and conda-forge channels as well as source builds, reflecting its adoption as both a scientist-facing command and a library package.

使われ方

The basic CLI workflow is to run freesasa on a PDB file with sensible defaults. More advanced use changes algorithms, atomic radii, classifications, output formats, and resolution; the library interface supports calculations directly from coordinates.

Version 2.x made output and embedding more package-friendly by consolidating CLI output format selection, adding JSON and XML output options, and separating the Python module so language bindings can be released independently.

パッケージ好きにとっての重要性

FreeSASA is a compact example of scientific software that packages well: a C ABI, a CLI, optional JSON/XML features, man pages, Doxygen docs, and language bindings. It exposes the usual tradeoff between minimal native dependencies and richer output or parser support.

Its 2.1 line added mmCIF input support using Gemmi, which matters because structural biology packaging increasingly has to handle both legacy PDB workflows and modern mmCIF data.

タイムライン

• 2013-2016: FreeSASA 1.1 documentation records early copyright years for Simon Mitternacht.
• 2016: FreeSASA paper published describing the project as an open source C library with CLI and Python interfaces.
• 2.0: Major API and CLI changes introduced JSON/XML output and a new result tree interface.
• 2.0.3: Python bindings separated into the freesasa-python repository.
• 2.1.0: mmCIF input support added with Gemmi.

Related projects

• freesasa-python provides the separate Python bindings repository used after the 2.0.3 split.
• Gemmi is bundled as a submodule for mmCIF import in the 2.1 line.
• NACCESS is a related SASA tool whose parameter set appears as a sample configuration and compatibility reference in FreeSASA documentation.

ソース

• https://doi.org/10.12688/f1000research.7931.1
• https://freesasa.github.io/
• https://freesasa.github.io/1.1/md_README.html
• https://freesasa.github.io/doxygen/md__Users_n642254_code_proteins_freesasa_README.html
• https://github.com/freesasa/freesasa-python
• https://raw.githubusercontent.com/mittinatten/freesasa/master/CHANGELOG.md
• https://raw.githubusercontent.com/mittinatten/freesasa/master/README.md