{"id":20915657,"url":"https://github.com/markovmodel/mdshare","last_synced_at":"2025-05-13T10:33:23.866Z","repository":{"id":26924211,"uuid":"111822080","full_name":"markovmodel/mdshare","owner":"markovmodel","description":"Get access to our MD data files.","archived":false,"fork":false,"pushed_at":"2023-11-22T15:15:36.000Z","size":133,"stargazers_count":25,"open_issues_count":4,"forks_count":5,"subscribers_count":3,"default_branch":"master","last_synced_at":"2024-10-30T19:23:51.037Z","etag":null,"topics":["trajectories"],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"lgpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/markovmodel.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2017-11-23T14:58:34.000Z","updated_at":"2024-01-12T07:43:58.000Z","dependencies_parsed_at":"2023-01-14T05:37:29.343Z","dependency_job_id":null,"html_url":"https://github.com/markovmodel/mdshare","commit_stats":null,"previous_names":[],"tags_count":9,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/markovmodel%2Fmdshare","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/markovmodel%2Fmdshare/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/markovmodel%2Fmdshare/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/markovmodel%2Fmdshare/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/markovmodel","download_url":"https://codeload.github.com/markovmodel/mdshare/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":225206750,"owners_count":17438185,"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":["trajectories"],"created_at":"2024-11-18T16:17:12.851Z","updated_at":"2024-11-18T16:17:13.724Z","avatar_url":"https://github.com/markovmodel.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# mdshare\nGet access to our MD data files.\n\n[![CircleCI](https://circleci.com/gh/markovmodel/mdshare/tree/master.svg?style=svg)](https://circleci.com/gh/markovmodel/mdshare/tree/master)\n[![Codacy Badge](https://api.codacy.com/project/badge/Grade/b9a86155b4e84bf3b397bad0c04e42a9)](https://www.codacy.com/app/cwehmeyer/mdshare?utm_source=github.com\u0026amp;utm_medium=referral\u0026amp;utm_content=markovmodel/mdshare\u0026amp;utm_campaign=Badge_Grade)\n\nThis is a downloader for molecular dynamics (MD) data from a public FTP server at FU Berlin. See [here](https://markovmodel.github.io/mdshare/) for a full list of available datasets and terms of use.\n\n## Example\nThis code will download a file (if it does not already exist locally) with a featurized set of three alanine dipeptide MD trajectories and store its content of three `numpy.ndarray` objects (each of `shape=[250000, 2], dtype=numpy.float32`) in the list `trajs`:\n\n```python\nimport mdshare\nimport numpy as np\n\nlocal_filename = mdshare.fetch('alanine-dipeptide-3x250ns-backbone-dihedrals.npz')\nwith np.load(local_filename) as fh:\n    trajs = [fh[key] for key in sorted(fh.keys())]\n```\n\nBy default, the `mdshare.fetch()` function will look in and download to the current directory (function parameter `working_directory='.'`). If you instead set this parameter to `None` ...\n\n```python\nlocal_filename = mdshare.fetch(\n    'alanine-dipeptide-3x250ns-backbone-dihedrals.npz',\n    working_directory=None)\n```\n\n... the file will be downloaded to a temporary directory. In both cases, the function will return the path to the downloaded file.\n\nShould the requested file already be present in the `working_directory`, the download is skipped.\n\nUsing `mdshare.catalogue()` to view the files and filesizes of the available trajectories ...\n\n```python\nmdshare.catalogue()\n```\n\n... produces the output:\n\n```text\nRepository: http://ftp.imp.fu-berlin.de/pub/cmb-data/\nFiles:\nalanine-dipeptide-0-250ns-nowater.xtc                  42.9 MB\nalanine-dipeptide-1-250ns-nowater.xtc                  42.9 MB\nalanine-dipeptide-2-250ns-nowater.xtc                  42.9 MB\nalanine-dipeptide-3x250ns-backbone-dihedrals.npz        6.0 MB\nalanine-dipeptide-3x250ns-heavy-atom-distances.npz    135.0 MB\n[...]\nContainers:\nmdshare-test.tar.gz                                   193.0 bytes\npyemma-tutorial-livecoms.tar.gz                       123.9 MB\n```\n\nUsing `mdshare.search(filename_pattern)` to select for a given group of files ...\n\n```python\npentapeptide_xtcs = mdshare.search('penta*xtc')\nprint(pentapeptide_xtcs)\n```\n\n... produces the output:\n\n```python\n['pentapeptide-00-500ns-impl-solv.xtc',\n 'pentapeptide-01-500ns-impl-solv.xtc',\n 'pentapeptide-02-500ns-impl-solv.xtc',\n...\n 'pentapeptide-22-500ns-impl-solv.xtc',\n 'pentapeptide-23-500ns-impl-solv.xtc',\n 'pentapeptide-24-500ns-impl-solv.xtc']\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmarkovmodel%2Fmdshare","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmarkovmodel%2Fmdshare","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmarkovmodel%2Fmdshare/lists"}