# gemmi を Homebrew, apt, MacPorts, Nix でインストール gemmi のインストール経路、実行ファイル、メタデータ、AI エージェント向けセキュリティノートを確認します。 ## インストール ```sh sudo av install brew:gemmi ``` 追加のインストールコマンド: ### macOS - Homebrew (100%): ```sh brew install gemmi ``` 証拠: local Homebrew formula metadata - MacPorts (94%): ```sh sudo port install gemmi ``` 証拠: MacPorts ports tree: science/gemmi/Portfile from https://api.github.com/repos/macports/macports-ports/git/trees/master?recursive=1 ### Linux - Debian apt (92%): ```sh sudo apt install gemmi ``` 証拠: Debian stable package indexes: gemmi from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz - Nix (92%): ```sh nix profile install nixpkgs#gemmi ``` 証拠: nixpkgs package indexes: pkgs/by-name/ge/gemmi/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 ## パッケージ情報 - **パッケージキー:** brew:gemmi - **パッケージマネージャ:** Homebrew - **パッケージマネージャページ:** - **バージョン:** 0.7.5 - **ソース概要:** Macromolecular crystallography library and utilities - **ホームページ:** - **リポジトリ:** - **上流ドキュメント:** - **ライセンス:** MPL-2.0 - **ソースアーカイブ:** - **最終更新:** 2026-06-21T00:20:16Z - **生成日時:** 2026-07-08T18:08:21+00:00 ## 実行可能ファイル - gemmi (cli) - gemmi (エイリアス) ## ビルド依存関係 - cmake ## インストール挙動 - post-install フック: 未定義 - Bottle: 利用可能 対象 arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux ## バージョンと鮮度 - ページ生成日: 2026-07-08 - マネージャ版: 0.7.5 - マネージャ更新日: 2026-06-21 - ローカルデータ: OK - 上流リポジトリ: https://github.com/project-gemmi/gemmi - 検出された最新: v0.7.5 (最新) ## プロジェクトの歴史と使われ方 Gemmi is a C++ library and command-line toolkit for structural biology, especially macromolecular crystallography. It handles mmCIF, PDB, MTZ, CCP4/MRC maps, crystallographic symmetry, reflection data, and related file formats, with Python bindings and additional interfaces around the same core library. ### プロジェクトの歴史 Gemmi's repository begins in 2017 and its documentation identifies it as a joint project of Global Phasing Ltd and CCP4. The project name is both a reference to Gemmi Pass and an expansion of General MacroMolecular I/O, reflecting its emphasis on file formats and data structures used by crystallographers. The project matured from a parser and utility collection into a broad structural-biology library. Its README and documentation describe C++14 code, Python bindings, a developing Fortran interface, partial WebAssembly bindings, web tools, and the `gemmi` command with many subcommands for validation, conversion, map handling, reflection data, and model analysis. In 2022, Gemmi was published in the Journal of Open Source Software as 'GEMMI: A library for structural biology,' giving the project a citable software reference for scientific users. ### 採用の歴史 Gemmi's adoption is anchored in crystallography infrastructure. The README names CCP4 and Global Phasing as institutional homes, while the JOSS paper and project documentation frame it as reusable infrastructure for programs that need fast, standards-aware handling of CIF-family files, structural models, maps, and reflection data. Package availability in Homebrew, Debian, Ubuntu, MacPorts, and Nix makes Gemmi accessible outside specialist crystallography distributions, which matters for reproducible pipelines and notebooks that mix command-line conversion with Python analysis. ### 使われ方 Practitioners use Gemmi as a library when writing structural-biology software and as a CLI when inspecting, validating, converting, or extracting data from coordinate, CIF, MTZ, and CCP4/MRC files. The `gemmi` program includes subcommands such as `validate`, `grep`, `convert`, `cif2mtz`, `mtz2cif`, `map`, `sfcalc`, and `xds2mtz`. Python users use the bindings for scripting and data analysis, while package maintainers care about the shared C++ core because it supports both standalone utilities and embedded scientific workflows. ### パッケージ好きにとっての重要性 Gemmi is package-nerd interesting because it turns hard scientific file-format support into one installable toolkit. It is small compared with full crystallography suites but intersects with many of them, so it often appears in environments where users need command-line conversion, Python bindings, and citation-grade provenance. ### タイムライン - 2017: Initial public repository commits. - 2018: Early 0.1.x releases appear. - 2022-05-04: Gemmi is published in the Journal of Open Source Software. - 2020s: Documentation expands around the `gemmi` command, Python API, C++ API, WebAssembly tools, and structural-biology workflows. ### Related projects - Gemmi is related to CCP4, Global Phasing software, wwPDB/mmCIF tooling, MTZ and CCP4/MRC map workflows, GemmiMOL, and scientific Python pipelines for structural biology. ### ソース - - - - - ## セキュリティノート library-like package without higher-risk signals. - **Geiger リスク:** グリーン / 低 - library-like package without higher-risk signals ## ソースデータベース詳細 - **Source Database:** Homebrew formula API - **Tap:** homebrew/core - **Full Name:** gemmi - **Version Scheme:** 0 - **Revision:** 0 - **Bottle Stable Root URL:** - **Deprecated:** no - **Disabled:** no - **Keg Only:** no - **URL Keys:** stable ## 他のパッケージマネージャ記録 - Debian apt - gemmi - 0.6.5+ds-3: normalized package name match | Debian stable package indexes: gemmi from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | library for structural biology - executable | https://project-gemmi.github.io - Debian apt - gemmi-dev - 0.6.5+ds-3: normalized package name match | Debian stable package indexes: gemmi-dev from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | library for structural biology | https://project-gemmi.github.io - Debian apt - python3-gemmi - 0.6.5+ds-3: normalized package name match | Debian stable package indexes: python3-gemmi from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | library for structural biology - Python module | https://project-gemmi.github.io - Nix - gemmi: normalized package name match | nixpkgs package indexes: pkgs/by-name/ge/gemmi/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 - Ubuntu apt - gemmi - 0.6.4+ds-1build1: normalized package name match | Ubuntu 24.04 LTS package indexes: gemmi from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | library for structural biology - executable | https://project-gemmi.github.io - Ubuntu apt - gemmi-dev - 0.6.4+ds-1build1: normalized package name match | Ubuntu 24.04 LTS package indexes: gemmi-dev from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | library for structural biology | https://project-gemmi.github.io - Ubuntu apt - python3-gemmi - 0.6.4+ds-1build1: normalized package name match | Ubuntu 24.04 LTS package indexes: python3-gemmi from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | library for structural biology - Python module | https://project-gemmi.github.io - MacPorts - gemmi: normalized package name match | MacPorts ports tree: science/gemmi/Portfile from https://api.github.com/repos/macports/macports-ports/git/trees/master?recursive=1 ## 関連リンク - [Source-control packages](https://www.automicvault.com/ja/pkg/source-control-tools/) - Belongs to a source-control command family. - [Terminal utility packages](https://www.automicvault.com/ja/pkg/terminal-utilities/) - Matched terminal and command-line workflow metadata. - [Networking and protocol packages](https://www.automicvault.com/ja/pkg/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata. - [Scientific computing packages](https://www.automicvault.com/ja/pkg/scientific-computing-tools/) - Matched scientific computing metadata. - [cmake](https://www.automicvault.com/ja/pkg/brew/cmake/) - Build dependency declared by Homebrew. - [biosig](https://www.automicvault.com/ja/pkg/brew/biosig/) - Shares av.db curated category or tags: c-plus-plus, cli, science. - [ccfits](https://www.automicvault.com/ja/pkg/brew/ccfits/) - Shares av.db curated category or tags: c-plus-plus, cli, science. - [clhep](https://www.automicvault.com/ja/pkg/brew/clhep/) - Shares av.db curated category or tags: c-plus-plus, cli, science. - [clp](https://www.automicvault.com/ja/pkg/brew/clp/) - Shares av.db curated category or tags: c-plus-plus, cli, science. - [dcmtk](https://www.automicvault.com/ja/pkg/brew/dcmtk/) - Shares av.db curated category or tags: c-plus-plus, cli, science. - [freeling](https://www.automicvault.com/ja/pkg/brew/freeling/) - Shares av.db curated category or tags: c-plus-plus, cli, science. - [freesasa](https://www.automicvault.com/ja/pkg/brew/freesasa/) - Shares av.db curated category or tags: cli, science, structural-biology. - [g2o](https://www.automicvault.com/ja/pkg/brew/g2o/) - Shares av.db curated category or tags: c-plus-plus, cli, science. - [kim-api](https://www.automicvault.com/ja/pkg/brew/kim-api/) - Local package facts share a topical domain. Shared terms: c-plus-plus, cli, models, plus, science. ## Combined YAML source View the package source record on GitHub. [combined/gemmi.yml](https://github.com/automic-vault/db/blob/main/combined/gemmi.yml) ## ソース - Nucleus package database - Geiger risk classifier - package-page enrichment - curated package history - package version freshness - av.db category and tag curation - package relationship graph - external package-manager database matches - cross-ecosystem install command graph