{"action":"created","issue":{"url":"https://api.github.com/repos/pytraj/pytraj/issues/521","labels_url":"https://api.github.com/repos/pytraj/pytraj/issues/521/labels{/name}","comments_url":"https://api.github.com/repos/pytraj/pytraj/issues/521/comments","events_url":"https://api.github.com/repos/pytraj/pytraj/issues/521/events","html_url":"https://github.com/pytraj/pytraj/issues/521","id":93946673,"number":521,"title":"speed: pytraj vs mdtraj with rmsd","user":{"login":"hainm","id":4451957,"avatar_url":"https://avatars.githubusercontent.com/u/4451957?v=3","gravatar_id":"","url":"https://api.github.com/users/hainm","html_url":"https://github.com/hainm","followers_url":"https://api.github.com/users/hainm/followers","following_url":"https://api.github.com/users/hainm/following{/other_user}","gists_url":"https://api.github.com/users/hainm/gists{/gist_id}","starred_url":"https://api.github.com/users/hainm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hainm/subscriptions","organizations_url":"https://api.github.com/users/hainm/orgs","repos_url":"https://api.github.com/users/hainm/repos","events_url":"https://api.github.com/users/hainm/events{/privacy}","received_events_url":"https://api.github.com/users/hainm/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-07-09T03:49:49Z","updated_at":"2015-07-09T04:12:23Z","closed_at":null,"body":"**Note** I have a ipython notebook before but I've just moved some codes from cython to python\r\nto make faster code writing and testing. So just want to compare rmd calculation again.\r\n\r\n```python\r\nIn [68]: traj # pytraj\r\nOut[68]:\r\n<pytraj.Trajectory with 1000 frames: <Topology with 17443 atoms, 5666 residues, \r\n1 mols, 17452 bonds, PBC with box type = truncoct>>\r\n\r\n\r\nIn [69]: t # mdtraj\r\nOut[69]: <mdtraj.Trajectory with 1000 frames, 17443 atoms, 5666 residues, \r\nand unitcells at 0x2aaacc4155c0>\r\n```"},"comment":{"url":"https://api.github.com/repos/pytraj/pytraj/issues/comments/119810142","html_url":"https://github.com/pytraj/pytraj/issues/521#issuecomment-119810142","issue_url":"https://api.github.com/repos/pytraj/pytraj/issues/521","id":119810142,"user":{"login":"hainm","id":4451957,"avatar_url":"https://avatars.githubusercontent.com/u/4451957?v=3","gravatar_id":"","url":"https://api.github.com/users/hainm","html_url":"https://github.com/hainm","followers_url":"https://api.github.com/users/hainm/followers","following_url":"https://api.github.com/users/hainm/following{/other_user}","gists_url":"https://api.github.com/users/hainm/gists{/gist_id}","starred_url":"https://api.github.com/users/hainm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hainm/subscriptions","organizations_url":"https://api.github.com/users/hainm/orgs","repos_url":"https://api.github.com/users/hainm/repos","events_url":"https://api.github.com/users/hainm/events{/privacy}","received_events_url":"https://api.github.com/users/hainm/received_events","type":"User","site_admin":false},"created_at":"2015-07-09T04:12:23Z","updated_at":"2015-07-09T04:12:23Z","body":"it's funny that if `mdtraj` use `pytraj.api.Trajectory` that I wrote a while ago, its rmsd calculation is even faster.\r\n\r\n```python\r\nIn [122]: type(ta)\r\nOut[122]: pytraj.api.Trajectory\r\n\r\nIn [123]: %timeit md.rmsd(ta, ta, 0)\r\n10 loops, best of 3: 55 ms per loop\r\n\r\nIn [124]: type(t)\r\nOut[124]: mdtraj.core.trajectory.Trajectory\r\n\r\nIn [125]: %timeit md.rmsd(t, t, 0)\r\n10 loops, best of 3: 78.9 ms per loop\r\n```"}}