{"action":"opened","issue":{"url":"https://api.github.com/repos/choderalab/perses/issues/49","labels_url":"https://api.github.com/repos/choderalab/perses/issues/49/labels{/name}","comments_url":"https://api.github.com/repos/choderalab/perses/issues/49/comments","events_url":"https://api.github.com/repos/choderalab/perses/issues/49/events","html_url":"https://github.com/choderalab/perses/issues/49","id":119580182,"number":49,"title":"Remaining issues in the GeometryEngine stuff","user":{"login":"pgrinaway","id":4674712,"avatar_url":"https://avatars.githubusercontent.com/u/4674712?v=3","gravatar_id":"","url":"https://api.github.com/users/pgrinaway","html_url":"https://github.com/pgrinaway","followers_url":"https://api.github.com/users/pgrinaway/followers","following_url":"https://api.github.com/users/pgrinaway/following{/other_user}","gists_url":"https://api.github.com/users/pgrinaway/gists{/gist_id}","starred_url":"https://api.github.com/users/pgrinaway/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pgrinaway/subscriptions","organizations_url":"https://api.github.com/users/pgrinaway/orgs","repos_url":"https://api.github.com/users/pgrinaway/repos","events_url":"https://api.github.com/users/pgrinaway/events{/privacy}","received_events_url":"https://api.github.com/users/pgrinaway/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-11-30T21:02:05Z","updated_at":"2015-11-30T21:02:05Z","closed_at":null,"body":"Currently, there are a couple issues with the GeometryEngine, in particular relating to the implementation that uses all angle and torsion potentials when choosing a torsion.\r\n\r\n* Sometimes, the proposal potential results in some `nan`s somehow making their way to the rejection sampler. When a uniform random number is drawn with `nan` as the upper limit, `numpy` throws an exception. Looking into why this is still happening despite replacing `nan`s with `inf`.\r\n\r\n* The speed is a bit of an issue. I've discovered through profiling that this is a result of the conversion between internal and cartesian coordinates. This can probably be accelerated a lot via vectorization or something of the sort."}}