{"action":"created","issue":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/542","labels_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/542/labels{/name}","comments_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/542/comments","events_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/542/events","html_url":"https://github.com/MDAnalysis/mdanalysis/pull/542","id":116863369,"number":542,"title":"Feature blankuniverse","user":{"login":"richardjgowers","id":9249543,"avatar_url":"https://avatars.githubusercontent.com/u/9249543?v=3","gravatar_id":"","url":"https://api.github.com/users/richardjgowers","html_url":"https://github.com/richardjgowers","followers_url":"https://api.github.com/users/richardjgowers/followers","following_url":"https://api.github.com/users/richardjgowers/following{/other_user}","gists_url":"https://api.github.com/users/richardjgowers/gists{/gist_id}","starred_url":"https://api.github.com/users/richardjgowers/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/richardjgowers/subscriptions","organizations_url":"https://api.github.com/users/richardjgowers/orgs","repos_url":"https://api.github.com/users/richardjgowers/repos","events_url":"https://api.github.com/users/richardjgowers/events{/privacy}","received_events_url":"https://api.github.com/users/richardjgowers/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/labels/review","name":"review","color":"bfdadc"},{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/labels/topology-building","name":"topology-building","color":"bfdadc"},{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/labels/Work%20in%20progress","name":"Work in progress","color":"e11d21"}],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":7,"created_at":"2015-11-13T22:10:30Z","updated_at":"2015-12-09T17:08:50Z","closed_at":"2015-12-09T17:08:50Z","pull_request":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/542","html_url":"https://github.com/MDAnalysis/mdanalysis/pull/542","diff_url":"https://github.com/MDAnalysis/mdanalysis/pull/542.diff","patch_url":"https://github.com/MDAnalysis/mdanalysis/pull/542.patch"},"body":"Currently it's a pain to create a blank Universe to fill up with data then save.  This adds the classmethod `Universe.create_dummy` which lets you create a Universe of arbitrary size:\r\n\r\n``` python\r\nnew_u = mda.Universe.create_dummy(20)\r\n\r\nfor i, atom in enumerate(new_u.atoms):\r\n    atom.name = 'Congaman{}'.format(i+1)\r\nnew_u.atoms.resnames = 'Congaline'\r\n\r\nnew_coords = np.stack([np.zeros(20), np.zeros(20), np.arange(20)]).T\r\nnew_u.trajectory.ts.positions = new_coords\r\n```\r\nIt's different from Merge because that merges existing populated structures, this just creates them from nothing.\r\n\r\n\r\nAlso allows reading a trajectory without having any topology information except the number of atoms:\r\n\r\n``` python\r\nu = mda.Universe(1000, 'mytraj.trr', topology_format='dummy')\r\n```\r\n\r\nAnd then obviously your atoms names etc are all defaults."},"comment":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/comments/163326726","html_url":"https://github.com/MDAnalysis/mdanalysis/pull/542#issuecomment-163326726","issue_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/542","id":163326726,"user":{"login":"richardjgowers","id":9249543,"avatar_url":"https://avatars.githubusercontent.com/u/9249543?v=3","gravatar_id":"","url":"https://api.github.com/users/richardjgowers","html_url":"https://github.com/richardjgowers","followers_url":"https://api.github.com/users/richardjgowers/followers","following_url":"https://api.github.com/users/richardjgowers/following{/other_user}","gists_url":"https://api.github.com/users/richardjgowers/gists{/gist_id}","starred_url":"https://api.github.com/users/richardjgowers/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/richardjgowers/subscriptions","organizations_url":"https://api.github.com/users/richardjgowers/orgs","repos_url":"https://api.github.com/users/richardjgowers/repos","events_url":"https://api.github.com/users/richardjgowers/events{/privacy}","received_events_url":"https://api.github.com/users/richardjgowers/received_events","type":"User","site_admin":false},"created_at":"2015-12-09T17:08:50Z","updated_at":"2015-12-09T17:08:50Z","body":"So this will end up looking very different soon, so I'm closing this, but I'll revive the idea soon!"}}