{"action":"created","issue":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/759","repository_url":"https://api.github.com/repos/MDAnalysis/mdanalysis","labels_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/759/labels{/name}","comments_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/759/comments","events_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/759/events","html_url":"https://github.com/MDAnalysis/mdanalysis/issues/759","id":139248153,"number":759,"title":"Periodic/Nonperiodic keywords to selections","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/question","name":"question","color":"cc317c"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2016-03-08T11:06:39Z","updated_at":"2016-03-08T11:40:49Z","closed_at":null,"body":"So currently we have some [geometric selections](http://pythonhosted.org/MDAnalysis/documentation_pages/selections.html#geometric) which allow you to select atoms based on absolute and relative positions.  These can work with and without periodic boundary conditions, both are useful at different times.  \r\n\r\nThe use of PBC is currently controlled by flags, which I think we're moving towards removing (#315) so instead a keyword in the selection could be used.\r\n\r\n```\r\nu.select_atoms('A around B 7.0 C protein D')\r\n\r\nu.select_atoms('A point B x y z C distance D')\r\n```\r\nSo with the above selections, there are positions **A** -> **D** where we could put the keyword.  \r\n\r\nPosition **A** would be tricky as the keyword precedes the token, but it could be done.  (`'periodic around 7.0 protein'`)\r\n\r\n**D** is messy for the `around` case as generally anything after **C** gets made into another selection.\r\n\r\nI think **C** reads best.. (`'around 7.0 periodic protein'`)\r\n\r\nSo tl;dr\r\n - add `periodic` keyword?\r\n - what should the default be? (probably same as currently?)\r\n - where to put the `periodic` keyword?"},"comment":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/comments/193744560","html_url":"https://github.com/MDAnalysis/mdanalysis/issues/759#issuecomment-193744560","issue_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/759","id":193744560,"user":{"login":"kain88-de","id":4302678,"avatar_url":"https://avatars.githubusercontent.com/u/4302678?v=3","gravatar_id":"","url":"https://api.github.com/users/kain88-de","html_url":"https://github.com/kain88-de","followers_url":"https://api.github.com/users/kain88-de/followers","following_url":"https://api.github.com/users/kain88-de/following{/other_user}","gists_url":"https://api.github.com/users/kain88-de/gists{/gist_id}","starred_url":"https://api.github.com/users/kain88-de/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kain88-de/subscriptions","organizations_url":"https://api.github.com/users/kain88-de/orgs","repos_url":"https://api.github.com/users/kain88-de/repos","events_url":"https://api.github.com/users/kain88-de/events{/privacy}","received_events_url":"https://api.github.com/users/kain88-de/received_events","type":"User","site_admin":false},"created_at":"2016-03-08T11:40:49Z","updated_at":"2016-03-08T11:40:49Z","body":"I might replace `periodic` with `pbc`"}}