{"id":27391531,"url":"https://github.com/fragit/fragit-main","last_synced_at":"2025-04-13T20:56:26.156Z","repository":{"id":201268411,"uuid":"4166669","full_name":"FragIt/fragit-main","owner":"FragIt","description":"FragIt main repository","archived":false,"fork":false,"pushed_at":"2025-04-11T22:28:31.000Z","size":542,"stargazers_count":26,"open_issues_count":12,"forks_count":12,"subscribers_count":6,"default_branch":"master","last_synced_at":"2025-04-13T20:56:22.503Z","etag":null,"topics":["fragments","mfcc","molecule","python"],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/FragIt.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGES.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2012-04-28T10:52:04.000Z","updated_at":"2025-04-11T22:21:02.000Z","dependencies_parsed_at":"2023-12-03T00:31:35.415Z","dependency_job_id":"caacfb5f-0eed-4e88-b3e3-88117fd632a7","html_url":"https://github.com/FragIt/fragit-main","commit_stats":{"total_commits":251,"total_committers":3,"mean_commits":83.66666666666667,"dds":"0.015936254980079667","last_synced_commit":"525753478caf1adde7f316ae82ebd928661f3ffd"},"previous_names":["fragit/fragit-main"],"tags_count":32,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/FragIt%2Ffragit-main","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/FragIt%2Ffragit-main/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/FragIt%2Ffragit-main/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/FragIt%2Ffragit-main/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/FragIt","download_url":"https://codeload.github.com/FragIt/fragit-main/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248782279,"owners_count":21160716,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","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":["fragments","mfcc","molecule","python"],"created_at":"2025-04-13T20:56:20.195Z","updated_at":"2025-04-13T20:56:26.149Z","avatar_url":"https://github.com/FragIt.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# FragIt\n\n[![GitHub release](https://img.shields.io/github/release/FragIt/fragit-main.svg?style=flat)](https://github.com/FragIt/fragit-main/releases)\n\nFragIt is a python based tool that allows you to quickly fragment [\"any\"](http://openbabel.org/docs/2.3.0/FileFormats/Overview.html) molecule and use the produced output file(s) as an a starting point for input files in quantum chemistry programs that supports such fragment based methods.\n\nFragIt was made out of the need to quickly benchmark many different molecules while developing new fragment based methods and is now being released in the hope that it is useful for others in their research. You can read about FragIt in the [published paper](http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0044480).\n\nCurrently, FragIt supports the [fragment molecular orbital](http://en.wikipedia.org/wiki/Fragment_Molecular_Orbital) method in [GAMESS](http://www.msg.ameslab.gov/gamess/index.html). FragIt also comes with a standard purpose XYZ writer that dumps each fragment in a separate `.xyz` file. Finally, there is a new XYZ-MFCC writer to support molecular fragmentation with conjugate caps that will yield capped fragments and caps for MFCC. New output writers can be added easily to support other methods and programs.\n\n## Obtaining FragIt\n\nSince you found this file, it is obvious that you also found the source code. You can obtain the latest version from [github](https://www.github.com/FragIt/fragit-main) where [tagged releases](https://github.com/FragIt/fragit-main/releases) are also available.\nYou get the source code by cloning the repository\n\n    git clone https://github.com/FragIt/fragit-main.git\ns\n## Installing FragIt in a Conda Environment With Pip\nThe easiest installation option is to use conda and pip.\nWe have supplied an `environment.yml` file for you to use.\nSimply run\n\n    cd fragit-main\n    conda env create -f environment.yml\n\nwhich creates an environment called fragit.\nAfter activating the `fragit` environment\n\n    conda activate fragit\n\nyou can install fragit using `pip` with the following command\n\n    pip install .\n\n## Installing FragIt Without Conda\nWithout conda, the installation of FragIt becomes slightly more\ntedious and of course system dependent.\nIf you have root access, you can install all dependencies using\nthe system package manager, but if you don't, then you have to\ninstall OpenBabel manually\n(Github user [andersx](https://github.com/andersx) [wrote a guide](http://combichem.blogspot.dk/2013/12/compiling-open-babel-with-python.html) to how that is accomplished.)\nFinally, the recommended installation method for FragIt is to use pip again \n\n    pip install . --user\n\nbut it is also possible using the old school approach (deprecated and not recommended)\n\n    python setup.py build\n    python setup.py install\n\nremember to make sure that environment variables (`PATH` and `PYTHONPATH` at least!) are\nset up correctly or else FragIt will complain that it cannot find itself.\n\n## Running FragIt\n\nin a terminal, you can type\n\n    fragit\n\nto see its help message.\n\nSee the [wiki](https://www.github.com/FragIt/fragit-main/wiki) for more examples of how to use FragIt.\n\n## Requirements\n\nIn order to run FragIt, you *need* the following installed on your system:\n\n* The FragIt source code, look above for information on how to obtain it\n* [Open Babel](http://www.openbabel.org) 3 or newer with [python language bindings](http://openbabel.org/docs/dev/Installation/install.html#compile-language-bindings) enabled.\n* [Numpy](http://numpy.scipy.org) 1.5 or newer.\n* [Python](http://www.python.org) 3.9 (or later).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffragit%2Ffragit-main","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ffragit%2Ffragit-main","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffragit%2Ffragit-main/lists"}