GitHub PullRequestReviewCommentEvent at 2014-07-23 18:06:35
Repository: mixtape
Actor: mpharrigan
Payload: {"action":"created","comment":{"url":"https://api.github.com/repos/rmcgibbo/mixtape/pulls/comments/15304323","id":15304323,"diff_hunk":"@@ -464,11 +460,25 @@ def partial_transform(self, traj):\n         transform : simultaneously featurize a collection of MD trajectories\n         \"\"\"\n         value = traj.xyz.reshape(len(traj), -1)\n-        if value.shape[1] != self.n_features:\n-            warnings.warn('wrong n_features in RawPositionsFeaturizer')\n         return value\n \n \n+class RawPositionsSuperposeFeaturizer(RawPositionsFeaturizer):\n+    def __init__(self, ref_traj, atom_indices):\n+        super().__init__()\n+\n+        self.ref_traj = ref_traj\n+        self.atom_indices = atom_indices\n+\n+        self.ref_traj.restrict_atoms(atom_indices)\n+\n+    def partial_transform(self, traj):\n+        traj.restrict_atoms(self.atom_indices)","path":"Mixtape/featurizer.py","position":30,"original_position":30,"commit_id":"33d3d5e0b10ec55e10d953fe60f0ee53fda4aa43","original_commit_id":"33d3d5e0b10ec55e10d953fe60f0ee53fda4aa43","user":{"login":"mpharrigan","id":4967059,"avatar_url":"https://avatars.githubusercontent.com/u/4967059?","gravatar_id":"7ad051848cd24ea7aad73311af6755e6","url":"https://api.github.com/users/mpharrigan","html_url":"https://github.com/mpharrigan","followers_url":"https://api.github.com/users/mpharrigan/followers","following_url":"https://api.github.com/users/mpharrigan/following{/other_user}","gists_url":"https://api.github.com/users/mpharrigan/gists{/gist_id}","starred_url":"https://api.github.com/users/mpharrigan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mpharrigan/subscriptions","organizations_url":"https://api.github.com/users/mpharrigan/orgs","repos_url":"https://api.github.com/users/mpharrigan/repos","events_url":"https://api.github.com/users/mpharrigan/events{/privacy}","received_events_url":"https://api.github.com/users/mpharrigan/received_events","type":"User","site_admin":false},"body":"I think that's by design. I only want to return the positions of the atoms specified by atom_indices","created_at":"2014-07-23T18:06:35Z","updated_at":"2014-07-23T18:06:35Z","html_url":"https://github.com/rmcgibbo/mixtape/pull/223#discussion_r15304323","pull_request_url":"https://api.github.com/repos/rmcgibbo/mixtape/pulls/223","_links":{"self":{"href":"https://api.github.com/repos/rmcgibbo/mixtape/pulls/comments/15304323"},"html":{"href":"https://github.com/rmcgibbo/mixtape/pull/223#discussion_r15304323"},"pull_request":{"href":"https://api.github.com/repos/rmcgibbo/mixtape/pulls/223"}}},"pull_request":{"url":"https://api.github.com/repos/rmcgibbo/mixtape/pulls/223","id":18792022,"html_url":"https://github.com/rmcgibbo/mixtape/pull/223","diff_url":"https://github.com/rmcgibbo/mixtape/pull/223.diff","patch_url":"https://github.com/rmcgibbo/mixtape/pull/223.patch","issue_url":"https://api.github.com/repos/rmcgibbo/mixtape/issues/223","number":223,"state":"open","title":"Raw Positions Superpose 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