{"id":22276260,"url":"https://github.com/grimme-lab/rmsd-tool","last_synced_at":"2026-02-08T12:05:18.153Z","repository":{"id":49526763,"uuid":"302016080","full_name":"grimme-lab/rmsd-tool","owner":"grimme-lab","description":"Tool to calculate the root mean square deviation between molecular 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returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["rmsd","structure-comparison"],"created_at":"2024-12-03T14:14:18.416Z","updated_at":"2026-02-08T12:05:18.104Z","avatar_url":"https://github.com/grimme-lab.png","language":"Fortran","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Root mean square deviation for structural comparison\n\n[![LGPL-3.0](https://img.shields.io/github/license/grimme-lab/rmsd-tool)](COPYING.LESSER)\n[![Release](https://img.shields.io/github/v/release/grimme-lab/rmsd-tool)](https://github.com/grimme-lab/rmsd-tool/releases/latest)\n[![CI](https://github.com/grimme-lab/rmsd-tool/workflows/CI/badge.svg)](https://github.com/grimme-lab/rmsd-tool/actions)\n[![docs](https://github.com/grimme-lab/rmsd-tool/workflows/docs/badge.svg)](https://grimme-lab.github.io/rmsd-tool)\n\n## Installation\n\nTo build this project from the source code in this repository you need to have\n- a Fortran compiler supporting Fortran 2008\n- [meson](https://mesonbuild.com) version 0.53 or newer\n- a build-system backend, *i.e.* [ninja](https://ninja-build.org) version 1.7 or newer\n\nSetup a build with\n\n```\nmeson setup _build\n```\n\nYou can select the Fortran compiler by the `FC` environment variable, currently this project supports GCC and Intel compilers.\nTo compile the project run\n\n```\nmeson compile -C _build\n```\n\nYou can run the projects testsuite with\n\n```\nmeson test -C _build --print-errorlogs\n```\n\nIf the testsuite passes you can install with\n\n```\nmeson configure _build --prefix=/path/to/install\nmeson install -C _build\n```\n\nThis might require administrator access depending on the chosen install prefix.\nNow you are ready to use ``mctc-rmsd``.\n\n\n## Usage\n\nTo calculate the RMSD between two structures use the [``mctc-rmsd(1)``](man/mctc-rmsd.1.adoc) program with\n\n```\nmctc-rmsd struc-a.xyz struc-b.xyz\n```\n\nThe RMSD is calculated relative to the first provided structure.\nMultiple structures can be provided to perform additional RMSD calculations,\n\n```\nmctc-rmsd coord conf-1.xyz conf-2.xyz conf-3.xyz\n```\n\nTo select a subset of atoms use a filter\n\n```\nmctc-rmsd xrd.pdb opt.pdb --filter heavy\n```\n\nThe heavy atom RMSD (excluding all H atoms) is built-in by default.\nNew filter can be defined in the ``mctc.toml`` configuration file in the current directory or in your home directory with:\n\n```toml\n[rmsd.filter]\n# Definition of the built-in heavy atom filter\nheavy.exclude = [\"H\", \"h\"]\n# Include all carbon, nitrogen and oxygen atoms\norganic.include = [6, 7, 8]\n```\n\nFor more details look up [the manual page](man/mctc-rmsd.1.adoc).\n\n\n## License\n\nThis project is free software: you can redistribute it and/or modify it under\nthe terms of the GNU Lesser General Public License as published by\nthe Free Software Foundation, either version 3 of the License, or\n(at your option) any later version.\n\nThis project is distributed in the hope that it will be useful,\nbut without any warranty; without even the implied warranty of\nmerchantability or fitness for a particular purpose.  See the\nGNU Lesser General Public License for more details.\n\nUnless you explicitly state otherwise, any contribution intentionally\nsubmitted for inclusion in this project by you, as defined in the\nGNU Lesser General Public license, shall be licensed as above, without any\nadditional terms or conditions.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgrimme-lab%2Frmsd-tool","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgrimme-lab%2Frmsd-tool","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgrimme-lab%2Frmsd-tool/lists"}