{"action":"created","issue":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/863","repository_url":"https://api.github.com/repos/MDAnalysis/mdanalysis","labels_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/863/labels{/name}","comments_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/863/comments","events_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/863/events","html_url":"https://github.com/MDAnalysis/mdanalysis/pull/863","id":157405554,"number":863,"title":"Diffusion Map Refactor","user":{"login":"jdetle","id":10944582,"avatar_url":"https://avatars.githubusercontent.com/u/10944582?v=3","gravatar_id":"","url":"https://api.github.com/users/jdetle","html_url":"https://github.com/jdetle","followers_url":"https://api.github.com/users/jdetle/followers","following_url":"https://api.github.com/users/jdetle/following{/other_user}","gists_url":"https://api.github.com/users/jdetle/gists{/gist_id}","starred_url":"https://api.github.com/users/jdetle/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jdetle/subscriptions","organizations_url":"https://api.github.com/users/jdetle/orgs","repos_url":"https://api.github.com/users/jdetle/repos","events_url":"https://api.github.com/users/jdetle/events{/privacy}","received_events_url":"https://api.github.com/users/jdetle/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/enhancement","name":"enhancement","color":"84b6eb"}],"state":"open","locked":false,"assignee":null,"milestone":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/milestones/9","html_url":"https://github.com/MDAnalysis/mdanalysis/milestones/0.16.0","labels_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/milestones/9/labels","id":1716502,"number":9,"title":"0.16.0","description":"","creator":{"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},"open_issues":11,"closed_issues":7,"state":"open","created_at":"2016-04-19T08:42:42Z","updated_at":"2016-06-06T21:20:49Z","due_on":null,"closed_at":null},"comments":14,"created_at":"2016-05-29T20:53:59Z","updated_at":"2016-06-06T21:21:15Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/863","html_url":"https://github.com/MDAnalysis/mdanalysis/pull/863","diff_url":"https://github.com/MDAnalysis/mdanalysis/pull/863.diff","patch_url":"https://github.com/MDAnalysis/mdanalysis/pull/863.patch"},"body":"Fixes #857\r\n\r\nChanges made in this Pull Request:\r\n- Refactor of @euhruska's work to fit bauhaus style\r\n- Reading and thoroughly understanding the diffusion map methodology presented in these papers is on my agenda. The kernel is asymmetric which is something I was entirely unfamiliar with during the application process. Why weights = np.ones causes a float division error is another thing that is confusing me, but I will figure it out in a bit.\r\n\r\nTODO:\r\nUpdate tests, clarify API, right now it is a specific version of diffusion maps introduced in the lefane and clementi papers. Will clarify in depth in the coming days\r\nPR Checklist\r\n------------\r\n - [x] Tests?\r\n - [x] Docs?\r\n - [x] CHANGELOG updated?\r\n - [x] Issue raised/referenced?\r\n"},"comment":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/comments/224092308","html_url":"https://github.com/MDAnalysis/mdanalysis/pull/863#issuecomment-224092308","issue_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/863","id":224092308,"user":{"login":"jdetle","id":10944582,"avatar_url":"https://avatars.githubusercontent.com/u/10944582?v=3","gravatar_id":"","url":"https://api.github.com/users/jdetle","html_url":"https://github.com/jdetle","followers_url":"https://api.github.com/users/jdetle/followers","following_url":"https://api.github.com/users/jdetle/following{/other_user}","gists_url":"https://api.github.com/users/jdetle/gists{/gist_id}","starred_url":"https://api.github.com/users/jdetle/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jdetle/subscriptions","organizations_url":"https://api.github.com/users/jdetle/orgs","repos_url":"https://api.github.com/users/jdetle/repos","events_url":"https://api.github.com/users/jdetle/events{/privacy}","received_events_url":"https://api.github.com/users/jdetle/received_events","type":"User","site_admin":false},"created_at":"2016-06-06T21:21:15Z","updated_at":"2016-06-06T21:21:15Z","body":"No, I am saying I am seeing the jth coordinate of v_i equal to the the -jth\ncoordinate of v_i. But the vectors have the same norm but components aren't\nnecessarily all of the same sign.\n\nOn Mon, Jun 6, 2016 at 2:14 PM kain88-de <notifications@github.com> wrote:\n\n> Are you saying for an eigenvector *v_i* you are seeing in two different\n> runs *v_i* == *-v_i*?\n> That would be normal this just means that they point in opposite\n> directions (which is OK the eigenvalue problem says nothing about the\n> direction of a vector). Mathematically you can insert *-v_i* into the\n> eigenvalue problem, the minus 1 will cancel out.\n>\n> —\n> You are receiving this because you were mentioned.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/MDAnalysis/mdanalysis/pull/863#issuecomment-224090501>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe/AKcARt7YC45mPcCF9gkYO0C32CVxn-qPks5qJI2pgaJpZM4IpYIS>\n> .\n>\n-- \nHave a wonderful day,\nJohn J. Detlefs\n"}}
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