{"action":"created","comment":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/comments/63043503","id":63043503,"diff_hunk":"@@ -360,44 +339,35 @@ def _read_next_timestep(self, ts=None):\n \n     def _read_frame(self, frame):\n         try:\n-            line = self.frames[frame]\n-        except KeyError:\n+            start = self._start_offsets[frame]\n+            stop = self._stop_offsets[frame]\n+        except IndexError:  # out of range of known frames\n             raise IOError\n-        if line is None:\n-            # single frame file, we already have the timestep\n-            return self.ts\n \n-        # TODO: only open file once and leave the file open; then seek back and\n-        #       forth; should improve performance substantially\n         pos = 0\n         occupancy = np.ones(self._n_atoms)\n-        with util.openany(self.filename, 'rt') as f:\n-            for i in range(line):\n-                next(f)  # forward to frame\n-            for line in f:\n-                if line[:6] == 'ENDMDL':\n-                    break\n-                # NOTE - CRYST1 line won't be found if it comes before the","path":"package/MDAnalysis/coordinates/PDB.py","position":188,"original_position":188,"commit_id":"ea70fd4aece67348fa581169f37ea79859b62b71","original_commit_id":"ea70fd4aece67348fa581169f37ea79859b62b71","user":{"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},"body":"So this issue has been fixed now too","created_at":"2016-05-12T15:40:59Z","updated_at":"2016-05-12T15:40:59Z","html_url":"https://github.com/MDAnalysis/mdanalysis/pull/849#discussion_r63043503","pull_request_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/849","_links":{"self":{"href":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/comments/63043503"},"html":{"href":"https://github.com/MDAnalysis/mdanalysis/pull/849#discussion_r63043503"},"pull_request":{"href":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/849"}}},"pull_request":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/849","id":69820113,"html_url":"https://github.com/MDAnalysis/mdanalysis/pull/849","diff_url":"https://github.com/MDAnalysis/mdanalysis/pull/849.diff","patch_url":"https://github.com/MDAnalysis/mdanalysis/pull/849.patch","issue_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/849","number":849,"state":"open","locked":false,"title":"WIP: First draft of faster pdb reading","user":{"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},"body":"So this is a first attempt at getting PDB iteration faster. (Issue #848)\r\n\r\nThe current implementation is slow because to read a frame it `next()`s a certain number of lines from the start, and then reads from there.  So frames towards the end of file require counting many lines.\r\n\r\nThis approach saves the offset (not line number) of each frame, so `seek` can be used to position the file handle.\r\n\r\nAlso cleaned up frame reading, only happens in one place now!\r\n\r\nI'm not sure about CRYST entries, can these happen multiple times in a pdb file?  And do they happen before/after the MODEL entry (which I'm using to designate the start of a frame)\r\n\r\n@kain88-de try this out with your timing?\r\n","created_at":"2016-05-12T11:25:30Z","updated_at":"2016-05-12T15:40:59Z","closed_at":null,"merged_at":null,"merge_commit_sha":"6f8f7b6d3486c0475ffbb835ec5a9dd0455703cd","assignee":{"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},"milestone":null,"commits_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/849/commits","review_comments_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/849/comments","review_comment_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/comments{/number}","comments_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/849/comments","statuses_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/statuses/ea70fd4aece67348fa581169f37ea79859b62b71","head":{"label":"MDAnalysis:issue-848-fasterpdb","ref":"issue-848-fasterpdb","sha":"ea70fd4aece67348fa581169f37ea79859b62b71","user":{"login":"MDAnalysis","id":11445951,"avatar_url":"https://avatars.githubusercontent.com/u/11445951?v=3","gravatar_id":"","url":"https://api.github.com/users/MDAnalysis","html_url":"https://github.com/MDAnalysis","followers_url":"https://api.github.com/users/MDAnalysis/followers","following_url":"https://api.github.com/users/MDAnalysis/following{/other_user}","gists_url":"https://api.github.com/users/MDAnalysis/gists{/gist_id}","starred_url":"https://api.github.com/users/MDAnalysis/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MDAnalysis/subscriptions","organizations_url":"https://api.github.com/users/MDAnalysis/orgs","repos_url":"https://api.github.com/users/MDAnalysis/repos","events_url":"https://api.github.com/users/MDAnalysis/events{/privacy}","received_events_url":"https://api.github.com/users/MDAnalysis/received_events","type":"Organization","site_admin":false},"repo":{"id":33389183,"name":"mdanalysis","full_name":"MDAnalysis/mdanalysis","owner":{"login":"MDAnalysis","id":11445951,"avatar_url":"https://avatars.githubusercontent.com/u/11445951?v=3","gravatar_id":"","url":"https://api.github.com/users/MDAnalysis","html_url":"https://github.com/MDAnalysis","followers_url":"https://api.github.com/users/MDAnalysis/followers","following_url":"https://api.github.com/users/MDAnalysis/following{/other_user}","gists_url":"https://api.github.com/users/MDAnalysis/gists{/gist_id}","starred_url":"https://api.github.com/users/MDAnalysis/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MDAnalysis/subscriptions","organizations_url":"https://api.github.com/users/MDAnalysis/orgs","repos_url":"https://api.github.com/users/MDAnalysis/repos","events_url":"https://api.github.com/users/MDAnalysis/events{/privacy}","received_events_url":"https://api.github.com/users/MDAnalysis/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/MDAnalysis/mdanalysis","description":"MDAnalysis 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