{"action":"created","issue":{"url":"https://api.github.com/repos/mdtraj/mdtraj/issues/1058","repository_url":"https://api.github.com/repos/mdtraj/mdtraj","labels_url":"https://api.github.com/repos/mdtraj/mdtraj/issues/1058/labels{/name}","comments_url":"https://api.github.com/repos/mdtraj/mdtraj/issues/1058/comments","events_url":"https://api.github.com/repos/mdtraj/mdtraj/issues/1058/events","html_url":"https://github.com/mdtraj/mdtraj/pull/1058","id":136212927,"number":1058,"title":"[WIP] Created function for imaging molecules","user":{"login":"peastman","id":4379786,"avatar_url":"https://avatars.githubusercontent.com/u/4379786?v=3","gravatar_id":"","url":"https://api.github.com/users/peastman","html_url":"https://github.com/peastman","followers_url":"https://api.github.com/users/peastman/followers","following_url":"https://api.github.com/users/peastman/following{/other_user}","gists_url":"https://api.github.com/users/peastman/gists{/gist_id}","starred_url":"https://api.github.com/users/peastman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/peastman/subscriptions","organizations_url":"https://api.github.com/users/peastman/orgs","repos_url":"https://api.github.com/users/peastman/repos","events_url":"https://api.github.com/users/peastman/events{/privacy}","received_events_url":"https://api.github.com/users/peastman/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":14,"created_at":"2016-02-24T22:52:06Z","updated_at":"2016-03-03T07:53:05Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/mdtraj/mdtraj/pulls/1058","html_url":"https://github.com/mdtraj/mdtraj/pull/1058","diff_url":"https://github.com/mdtraj/mdtraj/pull/1058.diff","patch_url":"https://github.com/mdtraj/mdtraj/pull/1058.patch"},"body":"This implementation should be considered preliminary.  It hasn't been at all thoroughly tested.  I tried it on various PDB files and it always seemed to do something reasonable, but I didn't have anything especially challenging on hand.  I'd really like to see how it handles a long simulation of a large complex, or something like that.  So if you have any good test cases, please try it out.\r\n\r\nI also added a method to Topology for identifying molecules based on bonds.  I needed it for this feature, and since it seemed a generally useful thing to have, I made it pubic.\r\n\r\nIs `image_molecules()` a good name?  Any ideas for a better one?"},"comment":{"url":"https://api.github.com/repos/mdtraj/mdtraj/issues/comments/191639163","html_url":"https://github.com/mdtraj/mdtraj/pull/1058#issuecomment-191639163","issue_url":"https://api.github.com/repos/mdtraj/mdtraj/issues/1058","id":191639163,"user":{"login":"mpharrigan","id":4967059,"avatar_url":"https://avatars.githubusercontent.com/u/4967059?v=3","gravatar_id":"","url":"https://api.github.com/users/mpharrigan","html_url":"https://github.com/mpharrigan","followers_url":"https://api.github.com/users/mpharrigan/followers","following_url":"https://api.github.com/users/mpharrigan/following{/other_user}","gists_url":"https://api.github.com/users/mpharrigan/gists{/gist_id}","starred_url":"https://api.github.com/users/mpharrigan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mpharrigan/subscriptions","organizations_url":"https://api.github.com/users/mpharrigan/orgs","repos_url":"https://api.github.com/users/mpharrigan/repos","events_url":"https://api.github.com/users/mpharrigan/events{/privacy}","received_events_url":"https://api.github.com/users/mpharrigan/received_events","type":"User","site_admin":false},"created_at":"2016-03-03T07:53:05Z","updated_at":"2016-03-03T07:53:05Z","body":"@peastman did you see above that even when I did a couple frames (to get rid of the memory problem) there were some imaging issues\r\n\r\nDid you change any of the imaging code with your recent commits? I can test after we get back from bps conference"}}