{"action":"created","issue":{"url":"https://api.github.com/repos/Acellera/htmd/issues/136","repository_url":"https://api.github.com/repos/Acellera/htmd","labels_url":"https://api.github.com/repos/Acellera/htmd/issues/136/labels{/name}","comments_url":"https://api.github.com/repos/Acellera/htmd/issues/136/comments","events_url":"https://api.github.com/repos/Acellera/htmd/issues/136/events","html_url":"https://github.com/Acellera/htmd/issues/136","id":178477007,"number":136,"title":"support for dcds?","user":{"login":"noeliaferruz","id":12035024,"avatar_url":"https://avatars.githubusercontent.com/u/12035024?v=3","gravatar_id":"","url":"https://api.github.com/users/noeliaferruz","html_url":"https://github.com/noeliaferruz","followers_url":"https://api.github.com/users/noeliaferruz/followers","following_url":"https://api.github.com/users/noeliaferruz/following{/other_user}","gists_url":"https://api.github.com/users/noeliaferruz/gists{/gist_id}","starred_url":"https://api.github.com/users/noeliaferruz/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/noeliaferruz/subscriptions","organizations_url":"https://api.github.com/users/noeliaferruz/orgs","repos_url":"https://api.github.com/users/noeliaferruz/repos","events_url":"https://api.github.com/users/noeliaferruz/events{/privacy}","received_events_url":"https://api.github.com/users/noeliaferruz/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-09-21T22:21:08Z","updated_at":"2016-09-22T08:38:49Z","closed_at":null,"body":"Hi, \r\n\r\nDoes htmd provide support for dcds in any form?\r\n\r\nI converted some pdbs to trajectories so that simlist could read them (i want to cluster them). Unfortunately I could only save them in dcd format. Simlist does not seem to read dcds.\r\nThen I concatenated the dcds to a single one and tried to read it as a molecule: `mol=Molecule('my.dcd')`\r\nOr on top of a molecule pdb: `mol=Molecule('my.pdb'); mol.read('my.dcd')`. But gave me the following:\r\n```---------------------------------------------------------------------------\r\nAttributeError                            Traceback (most recent call last)\r\n<ipython-input-41-71890c41f5e2> in <module>()\r\n      1 mol=Molecule('my.pdb')\r\n----> 2 mol.read('my.dcd')\r\n\r\n\r\n/path/to/acellera/test/python/lib/python3.5/site-packages/htmd/molecule/molecule.py in read(self, filename, type, skip, frames, append, overwrite)\r\n    718             self.coords = np.atleast_3d(np.array(coords, dtype=self._dtypes['coords']))\r\n    719         elif type in _MDTRAJ_EXTS or ext in _MDTRAJ_EXTS:\r\n--> 720             self._readTraj(filename, skip=skip, frames=frames, append=append, mdtraj=True)\r\n    721         else:\r\n    722             raise ValueError('Unknown file type with extension \"{}\".'.format(ext))\r\n\r\n/path/to/acellera/test/python/lib/python3.5/site-packages/htmd/molecule/molecule.py in _readTraj(self, filename, skip, frames, append, mdtraj)\r\n    827             if frames is None:\r\n    828                 if mdtraj:\r\n--> 829                     coords, box, boxangles, step, time = MDTRAJread(f, self.topoloc)\r\n    830                 else:\r\n    831                     coords, box, boxangles, step, time = XTCread(f)\r\n\r\n/path/to/acellera/test/python/lib/python3.5/site-packages/htmd/molecule/readers.py in MDTRAJread(filename, topoloc)\r\n    781         time = traj.time * 1000  # need to go from picoseconds to femtoseconds\r\n    782         step = time / 25  # DO NOT TRUST THIS. I just guess that there are 25 simulation steps in each picosecond\r\n--> 783     box = traj.unitcell_lengths.T * 10\r\n    784     boxangles = traj.unitcell_angles.T\r\n    785     return coords, box, boxangles, step, time\r\n\r\nAttributeError: 'NoneType' object has no attribute 'T'\r\n```\r\nbest,\r\nNoelia\r\n"},"comment":{"url":"https://api.github.com/repos/Acellera/htmd/issues/comments/248843654","html_url":"https://github.com/Acellera/htmd/issues/136#issuecomment-248843654","issue_url":"https://api.github.com/repos/Acellera/htmd/issues/136","id":248843654,"user":{"login":"stefdoerr","id":7935362,"avatar_url":"https://avatars.githubusercontent.com/u/7935362?v=3","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},"created_at":"2016-09-22T08:38:48Z","updated_at":"2016-09-22T08:38:48Z","body":"Yeah it is supposed to read dcds. Simlist should also read dcds. However if you have an xtc in the same folder as the dcds it will only read the xtc to not mix trajectories.\r\n\r\nI see what causes the error. I didn't test the MDtraj reader much after accepting some changes by the PMEMD contributors. Can you send me a tiny dcd example for a test?"}}
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