# 使用 Homebrew, apt, MacPorts, Nix 安装 gemmi 查看 gemmi 的安装路径、可执行文件、元数据以及面向 AI 代理工作流的安全说明。 ## 安装 ```sh sudo av install brew:gemmi ``` 其他安装命令: ### macOS - Homebrew (100%): ```sh brew install gemmi ``` 证据: local Homebrew formula metadata - MacPorts (94%): ```sh sudo port install gemmi ``` 证据: 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 ``` 证据: 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 ``` 证据: nixpkgs package indexes: pkgs/by-name/ge/gemmi/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 ## 软件包事实 - **软件包键:** brew:gemmi - **软件包管理器:** Homebrew - **软件包管理器页面:** - **版本:** 0.7.5 - **来源摘要:** Macromolecular crystallography library and utilities - **主页:** - **仓库:** - **上游文档:** - **许可证:** MPL-2.0 - **源码归档:** - **最后更新:** 2026-06-21T00:20:16Z - **已生成:** 2026-07-08T18:08:21+00:00 ## 可执行文件 - gemmi (cli) - gemmi (别名) ## 构建依赖 - cmake ## 安装行为 - post-install 钩子: 未定义 - Bottle: 可用 于 arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux ## 版本和新鲜度 - 页面生成时间: 2026-07-08 - 管理器版本: 0.7.5 - 管理器更新时间: 2026-06-21 - 本地数据: OK - 上游仓库: https://github.com/project-gemmi/gemmi - 检测到的最新版本: v0.7.5 (当前) ## 项目历史与用法 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. ### 项目历史 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. ### 采用历史 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. ### 使用方式 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. ### 为什么软件包爱好者会关心 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. ### 时间线 - 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. ### 来源 - - - - - ## 安全说明 library-like package without higher-risk signals. - **Geiger 风险:** 绿色 / 低 - library-like package without higher-risk signals ## 源数据库详情 - **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 ## 其他软件包管理器记录 - 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 ## 相关链接 - [Source-control packages](https://www.automicvault.com/zh-hans/pkg/source-control-tools/) - Belongs to a source-control command family. - [Terminal utility packages](https://www.automicvault.com/zh-hans/pkg/terminal-utilities/) - Matched terminal and command-line workflow metadata. - [Networking and protocol packages](https://www.automicvault.com/zh-hans/pkg/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata. - [Scientific computing packages](https://www.automicvault.com/zh-hans/pkg/scientific-computing-tools/) - Matched scientific computing metadata. - [cmake](https://www.automicvault.com/zh-hans/pkg/brew/cmake/) - Build dependency declared by Homebrew. - [biosig](https://www.automicvault.com/zh-hans/pkg/brew/biosig/) - Shares av.db curated category or tags: c-plus-plus, cli, science. - [ccfits](https://www.automicvault.com/zh-hans/pkg/brew/ccfits/) - Shares av.db curated category or tags: c-plus-plus, cli, science. - [clhep](https://www.automicvault.com/zh-hans/pkg/brew/clhep/) - Shares av.db curated category or tags: c-plus-plus, cli, science. - [clp](https://www.automicvault.com/zh-hans/pkg/brew/clp/) - Shares av.db curated category or tags: c-plus-plus, cli, science. - [dcmtk](https://www.automicvault.com/zh-hans/pkg/brew/dcmtk/) - Shares av.db curated category or tags: c-plus-plus, cli, science. - [freeling](https://www.automicvault.com/zh-hans/pkg/brew/freeling/) - Shares av.db curated category or tags: c-plus-plus, cli, science. - [freesasa](https://www.automicvault.com/zh-hans/pkg/brew/freesasa/) - Shares av.db curated category or tags: cli, science, structural-biology. - [g2o](https://www.automicvault.com/zh-hans/pkg/brew/g2o/) - Shares av.db curated category or tags: c-plus-plus, cli, science. - [kim-api](https://www.automicvault.com/zh-hans/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) ## 来源 - 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