{"action":"created","issue":{"url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/514","labels_url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/514/labels{/name}","comments_url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/514/comments","events_url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/514/events","html_url":"https://github.com/markovmodel/PyEMMA/pull/514","id":103746312,"number":514,"title":"Add distances ca exclude neighbors","user":{"login":"gph82","id":7518004,"avatar_url":"https://avatars.githubusercontent.com/u/7518004?v=3","gravatar_id":"","url":"https://api.github.com/users/gph82","html_url":"https://github.com/gph82","followers_url":"https://api.github.com/users/gph82/followers","following_url":"https://api.github.com/users/gph82/following{/other_user}","gists_url":"https://api.github.com/users/gph82/gists{/gist_id}","starred_url":"https://api.github.com/users/gph82/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gph82/subscriptions","organizations_url":"https://api.github.com/users/gph82/orgs","repos_url":"https://api.github.com/users/gph82/repos","events_url":"https://api.github.com/users/gph82/events{/privacy}","received_events_url":"https://api.github.com/users/gph82/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-08-28T16:05:03Z","updated_at":"2015-09-18T11:50:09Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/markovmodel/PyEMMA/pulls/514","html_url":"https://github.com/markovmodel/PyEMMA/pull/514","diff_url":"https://github.com/markovmodel/PyEMMA/pull/514.diff","patch_url":"https://github.com/markovmodel/PyEMMA/pull/514.patch"},"body":"This addresses #487 . I did not go with the kwargs implementation, dunno if it can be kwarg and a default simultaneously. Also, I changed add_distances_ca so that the definition of neighbor is done with the residue indices and not the atom indices. This way, the starting geometry can be an all atom geometry. "},"comment":{"url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/comments/141427212","html_url":"https://github.com/markovmodel/PyEMMA/pull/514#issuecomment-141427212","issue_url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/514","id":141427212,"user":{"login":"gph82","id":7518004,"avatar_url":"https://avatars.githubusercontent.com/u/7518004?v=3","gravatar_id":"","url":"https://api.github.com/users/gph82","html_url":"https://github.com/gph82","followers_url":"https://api.github.com/users/gph82/followers","following_url":"https://api.github.com/users/gph82/following{/other_user}","gists_url":"https://api.github.com/users/gph82/gists{/gist_id}","starred_url":"https://api.github.com/users/gph82/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gph82/subscriptions","organizations_url":"https://api.github.com/users/gph82/orgs","repos_url":"https://api.github.com/users/gph82/repos","events_url":"https://api.github.com/users/gph82/events{/privacy}","received_events_url":"https://api.github.com/users/gph82/received_events","type":"User","site_admin":false},"created_at":"2015-09-18T11:50:09Z","updated_at":"2015-09-18T11:50:09Z","body":"mdtraj can load pdb.gz files, which made this PR easier. This can be merged now, I think"}}