{"action":"created","issue":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/792","repository_url":"https://api.github.com/repos/MDAnalysis/mdanalysis","labels_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/792/labels{/name}","comments_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/792/comments","events_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/792/events","html_url":"https://github.com/MDAnalysis/mdanalysis/pull/792","id":142183833,"number":792,"title":"WIP: Contact improvements","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},"labels":[{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/labels/Component-Analysis","name":"Component-Analysis","color":"0088ee"},{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/labels/help%20wanted","name":"help wanted","color":"fef222"},{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/labels/refactoring","name":"refactoring","color":"b0b0b0"},{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/labels/Work%20in%20progress","name":"Work in progress","color":"e11d21"}],"state":"open","locked":false,"assignee":{"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},"milestone":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/milestones/8","html_url":"https://github.com/MDAnalysis/mdanalysis/milestones/0.15.0","labels_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/milestones/8/labels","id":1591417,"number":8,"title":"0.15.0","description":"Fixes, enhancements and deprecations for the new topology system.","creator":{"login":"dotsdl","id":1326811,"avatar_url":"https://avatars.githubusercontent.com/u/1326811?v=3","gravatar_id":"","url":"https://api.github.com/users/dotsdl","html_url":"https://github.com/dotsdl","followers_url":"https://api.github.com/users/dotsdl/followers","following_url":"https://api.github.com/users/dotsdl/following{/other_user}","gists_url":"https://api.github.com/users/dotsdl/gists{/gist_id}","starred_url":"https://api.github.com/users/dotsdl/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dotsdl/subscriptions","organizations_url":"https://api.github.com/users/dotsdl/orgs","repos_url":"https://api.github.com/users/dotsdl/repos","events_url":"https://api.github.com/users/dotsdl/events{/privacy}","received_events_url":"https://api.github.com/users/dotsdl/received_events","type":"User","site_admin":false},"open_issues":8,"closed_issues":19,"state":"open","created_at":"2016-02-18T19:21:16Z","updated_at":"2016-03-23T13:08:27Z","due_on":"2016-04-01T07:00:00Z","closed_at":null},"comments":8,"created_at":"2016-03-20T17:26:02Z","updated_at":"2016-03-25T11:53:54Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/792","html_url":"https://github.com/MDAnalysis/mdanalysis/pull/792","diff_url":"https://github.com/MDAnalysis/mdanalysis/pull/792.diff","patch_url":"https://github.com/MDAnalysis/mdanalysis/pull/792.patch"},"body":"This continues the work in #708.  I have stripped down `Contacts` to the absolute bare essential (besides `single_frame` everything is gone, renamed or moved to it's own function). I think this results in a cleaner implementation in the end and also one that is more flexible. I'm aware that I might have removed useful functionality but I'm happy to add that again if someone explains to me why they need it.\r\n\r\nI've created a ipython notebook in the root-directory where I outlined the normal fraction of native contacts analysis and a new analysis for an easy binary decision algorithm if a protein is folded or two partners are bound. I plan to keep this notebook always at the top comment and remove it before I merge. I would like some help if this is all the usage that people want and what use cases are currently missing as example, or if they can't be done with the class right now)\r\n\r\nThe plots are now removed as well because I don't think the `plot_qavg` contained a lot of content (basically only a complicated way to visualize `np.mean(q)`). The timeseries plot is removed because with arbitrary functions allowed as methods it might now represent accurately the data that is plotted. \r\n\r\nChanges made in this Pull Request:\r\n -  removed all untested code from `Contacts`\r\n -  Contacts now accepts arbitrary functions as method kwarg\r\n -  old contact analysis classes are moved to be deprecated soon\r\n\r\nPR Checklist\r\n------------\r\n - [ ] Tests?\r\n - [ ] Docs?\r\n - [ ] CHANGELOG updated?\r\n - [ ] Issue raised/referenced?\r\n - [ ] deprecate old contact classes\r\n - [ ] pbc keyword\r\n"},"comment":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/comments/201248307","html_url":"https://github.com/MDAnalysis/mdanalysis/pull/792#issuecomment-201248307","issue_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/792","id":201248307,"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":"2016-03-25T11:53:54Z","updated_at":"2016-03-25T11:53:54Z","body":"> Anyway is this ready to merge?\r\n\r\nNo docs are missing. There is still a bit of work left. I have to do some other stuff for my PhD right now. I hope I have some time next week to get some things done. The big 4 that still need doing are [docs, tests, pbc, deprecations for old classes].\r\n\r\nWhile we are at it. What is a good deprecation release?\r\n\r\n@jandom  Does this still work for you now? I removed quite a lot of things.\r\n\r\n@orbeckst You were against removing the old contact classes because of some missing functionality. Could you tell me what that was and how it was used, the old code is not that easy to understand."}}