{"action":"created","comment":{"url":"https://api.github.com/repos/Acellera/htmd/pulls/comments/236308987","pull_request_review_id":178357345,"id":236308987,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDIzNjMwODk4Nw==","diff_hunk":"@@ -525,13 +564,23 @@ def main_parameterize(arguments=None):\n     mol = _prepare_molecule(args)\n \n     # Copy the molecule to preserve initial coordinates\n-    orig_coor = mol.coords.copy()\n+    initial_coords = mol.coords.copy()\n \n     # Select dihedral angles to parameterize\n     selected_dihedrals = _select_dihedrals(mol, args)\n \n-    # Get a reference calculator\n-    qm = _get_reference_calculator(args)\n+    # Get a queue\n+    queue = _get_queue(args)\n+\n+    # Get calculators\n+    qm = _get_qm_calculator(args, queue)\n+    nnp = _get_nnp_calculator(args, queue)\n+    if args.nnp:\n+        ref = nnp","path":"htmd/parameterization/cli.py","position":179,"original_position":179,"commit_id":"b835326c299240e0c252463b00470a2a11dde95b","original_commit_id":"b835326c299240e0c252463b00470a2a11dde95b","user":{"login":"stefdoerr","id":7935362,"node_id":"MDQ6VXNlcjc5MzUzNjI=","avatar_url":"https://avatars3.githubusercontent.com/u/7935362?v=4","gravatar_id":"","url":"https://api.github.com/users/stefdoerr","html_url":"https://github.com/stefdoerr","followers_url":"https://api.github.com/users/stefdoerr/followers","following_url":"https://api.github.com/users/stefdoerr/following{/other_user}","gists_url":"https://api.github.com/users/stefdoerr/gists{/gist_id}","starred_url":"https://api.github.com/users/stefdoerr/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/stefdoerr/subscriptions","organizations_url":"https://api.github.com/users/stefdoerr/orgs","repos_url":"https://api.github.com/users/stefdoerr/repos","events_url":"https://api.github.com/users/stefdoerr/events{/privacy}","received_events_url":"https://api.github.com/users/stefdoerr/received_events","type":"User","site_admin":false},"body":"Call ref calculator instead (as the functions already call it). Ref is too abstract a variable name I think","created_at":"2018-11-26T15:49:30Z","updated_at":"2018-11-26T15:49:31Z","html_url":"https://github.com/Acellera/htmd/pull/816#discussion_r236308987","pull_request_url":"https://api.github.com/repos/Acellera/htmd/pulls/816","author_association":"CONTRIBUTOR","_links":{"self":{"href":"https://api.github.com/repos/Acellera/htmd/pulls/comments/236308987"},"html":{"href":"https://github.com/Acellera/htmd/pull/816#discussion_r236308987"},"pull_request":{"href":"https://api.github.com/repos/Acellera/htmd/pulls/816"}}},"pull_request":{"url":"https://api.github.com/repos/Acellera/htmd/pulls/816","id":233013067,"node_id":"MDExOlB1bGxSZXF1ZXN0MjMzMDEzMDY3","html_url":"https://github.com/Acellera/htmd/pull/816","diff_url":"https://github.com/Acellera/htmd/pull/816.diff","patch_url":"https://github.com/Acellera/htmd/pull/816.patch","issue_url":"https://api.github.com/repos/Acellera/htmd/issues/816","number":816,"state":"open","locked":false,"title":"Fix NNP (a.k.a. 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