{"action":"created","comment":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/comments/79726951","id":79726951,"diff_hunk":"@@ -398,125 +416,100 @@ def __init__(self, traj, reference=None, select='all',\n                         igroup, sel['reference'], sel['mobile'],\n                         len(atoms['reference']), len(atoms['mobile'])))\n \n+        # necessary for throwing error in save, let me know if there is a\n+        # better way\n         self.rmsd = None\n \n-    def run(self, start=None, stop=None, step=None,\n-            mass_weighted=None, ref_frame=None):\n-        \"\"\"Perform RMSD analysis on the trajectory.\n \n-        A number of parameters can be changed from the defaults. The\n-        result is stored as the array :attr:`RMSD.rmsd`.\n+    def _prepare(self):\n+        self._n_atoms = self.mobile_atoms.n_atoms\n \n-        Parameters\n-        ----------\n-        start, stop, step : int (optional)\n-            start and stop frame index with step size\n-        mass_weighted : bool (optional)\n-            overwrite object default to do a mass-weighted RMSD fit\n-        ref_frame : int\n-             frame index to select frame from *reference*\n-        \"\"\"\n-        if mass_weighted is None:\n-            mass_weighted = self.mass_weighted\n-        if ref_frame is None:\n-            ref_frame = self.ref_frame\n-\n-        natoms = self.traj_atoms.n_atoms\n-        trajectory = self.universe.trajectory\n-        traj_atoms = self.traj_atoms\n-\n-        if mass_weighted:\n-            # if performing a mass-weighted alignment/rmsd calculation\n-            weight = self.ref_atoms.masses / self.ref_atoms.masses.mean()\n-            weight = weight.astype(np.float64)\n-        else:\n-            weight = None\n+        self._weights = ((self.ref_atoms.masses / self.ref_atoms.masses.mean())\n+                        if self.mass_weighted else None)\n+\n+        # reference centre of mass system, no longer 1 based indices\n+        current_frame = self.reference.trajectory.ts.frame\n \n-        # reference centre of mass system\n-        current_frame = self.reference.trajectory.ts.frame - 1\n         try:\n             # Move to the ref_frame\n             # (coordinates MUST be stored in case the ref traj is advanced\n             # elsewhere or if ref == mobile universe)\n-            self.reference.trajectory[ref_frame]\n-            ref_com = self.ref_atoms.center_of_mass()\n+            self.reference.trajectory[self.ref_frame]\n+            self._ref_com = self.ref_atoms.center_of_mass()\n             # makes a copy\n-            ref_coordinates = self.ref_atoms.positions - ref_com\n-            if self.groupselections_atoms:\n-                groupselections_ref_coords_64 = [\n-                    self.reference.select_atoms(*s['reference']).positions.astype(np.float64) for s in\n+            self._ref_coordinates = self.ref_atoms.positions - self._ref_com\n+            if self._groupselections_atoms:\n+                self._groupselections_ref_coords_64 = [(self.reference.\n+                    select_atoms(*s['reference']).\n+                    positions.astype(np.float64)) for s in\n                     self.groupselections]\n         finally:\n             # Move back to the original frame\n             self.reference.trajectory[current_frame]\n-        ref_coordinates_64 = ref_coordinates.astype(np.float64)\n \n-        # allocate the array for selection atom coords\n-        traj_coordinates = traj_atoms.positions.copy()","path":"package/MDAnalysis/analysis/rms.py","position":250,"original_position":250,"commit_id":"730588c3380b4ea555f9e63503403aa1542d8b9f","original_commit_id":"730588c3380b4ea555f9e63503403aa1542d8b9f","user":{"login":"orbeckst","id":237980,"avatar_url":"https://avatars.githubusercontent.com/u/237980?v=3","gravatar_id":"","url":"https://api.github.com/users/orbeckst","html_url":"https://github.com/orbeckst","followers_url":"https://api.github.com/users/orbeckst/followers","following_url":"https://api.github.com/users/orbeckst/following{/other_user}","gists_url":"https://api.github.com/users/orbeckst/gists{/gist_id}","starred_url":"https://api.github.com/users/orbeckst/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/orbeckst/subscriptions","organizations_url":"https://api.github.com/users/orbeckst/orgs","repos_url":"https://api.github.com/users/orbeckst/repos","events_url":"https://api.github.com/users/orbeckst/events{/privacy}","received_events_url":"https://api.github.com/users/orbeckst/received_events","type":"User","site_admin":false},"body":"If you allocate an array for mobile coordinates you could avoid recreating it in `_single_step()`.\r\n```python\r\nself._mobile_coordinates64 = self.mobile_atoms.positions.copy().astype(np.float64)\r\n```\r\n\r\nand then (numpy will cast to float64 because the type of `self._mobile_coordinates` is fixed) do inplace ops:\r\n```python\r\nself._mobile_coordinates64[:] = self.mobile_atoms.positions\r\nself._mobile_coordinates64 -= mobile_com\r\n```","created_at":"2016-09-20T22:29:27Z","updated_at":"2016-09-20T22:48:44Z","html_url":"https://github.com/MDAnalysis/mdanalysis/pull/934#discussion_r79726951","pull_request_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/934","_links":{"self":{"href":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/comments/79726951"},"html":{"href":"https://github.com/MDAnalysis/mdanalysis/pull/934#discussion_r79726951"},"pull_request":{"href":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/934"}}},"pull_request":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/934","id":81229630,"html_url":"https://github.com/MDAnalysis/mdanalysis/pull/934","diff_url":"https://github.com/MDAnalysis/mdanalysis/pull/934.diff","patch_url":"https://github.com/MDAnalysis/mdanalysis/pull/934.patch","issue_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/934","number":934,"state":"open","locked":false,"title":"RMSD 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},"body":"Fixes #893 \r\n\r\nChanges made in this Pull Request:\r\n - Pure refactor, only design changes\r\n- Split up run method into prepare and single frame\r\n\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","created_at":"2016-08-13T23:30:56Z","updated_at":"2016-09-20T22:48:45Z","closed_at":null,"merged_at":null,"merge_commit_sha":"e31cfb878e08f5af0f7cdce4d9f40236d480a09d","assignee":{"login":"orbeckst","id":237980,"avatar_url":"https://avatars.githubusercontent.com/u/237980?v=3","gravatar_id":"","url":"https://api.github.com/users/orbeckst","html_url":"https://github.com/orbeckst","followers_url":"https://api.github.com/users/orbeckst/followers","following_url":"https://api.github.com/users/orbeckst/following{/other_user}","gists_url":"https://api.github.com/users/orbeckst/gists{/gist_id}","starred_url":"https://api.github.com/users/orbeckst/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/orbeckst/subscriptions","organizations_url":"https://api.github.com/users/orbeckst/orgs","repos_url":"https://api.github.com/users/orbeckst/repos","events_url":"https://api.github.com/users/orbeckst/events{/privacy}","received_events_url":"https://api.github.com/users/orbeckst/received_events","type":"User","site_admin":false},"assignees":[{"login":"orbeckst","id":237980,"avatar_url":"https://avatars.githubusercontent.com/u/237980?v=3","gravatar_id":"","url":"https://api.github.com/users/orbeckst","html_url":"https://github.com/orbeckst","followers_url":"https://api.github.com/users/orbeckst/followers","following_url":"https://api.github.com/users/orbeckst/following{/other_user}","gists_url":"https://api.github.com/users/orbeckst/gists{/gist_id}","starred_url":"https://api.github.com/users/orbeckst/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/orbeckst/subscriptions","organizations_url":"https://api.github.com/users/orbeckst/orgs","repos_url":"https://api.github.com/users/orbeckst/repos","events_url":"https://api.github.com/users/orbeckst/events{/privacy}","received_events_url":"https://api.github.com/users/orbeckst/received_events","type":"User","site_admin":false},{"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":{"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":18,"closed_issues":41,"state":"open","created_at":"2016-04-19T08:42:42Z","updated_at":"2016-09-18T15:16:14Z","due_on":null,"closed_at":null},"commits_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/934/commits","review_comments_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/934/comments","review_comment_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/comments{/number}","comments_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/934/comments","statuses_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/statuses/730588c3380b4ea555f9e63503403aa1542d8b9f","head":{"label":"jdetle:RMSD","ref":"RMSD","sha":"730588c3380b4ea555f9e63503403aa1542d8b9f","user":{"login":"jdetle","id":10944582,"avatar_url":"https://avatars.githubusercontent.com/u/10944582?v=3","gravatar_id":"","url":"https://api.github.com/users/jdetle","h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