{"action":"created","issue":{"url":"https://api.github.com/repos/Acellera/htmd/issues/46","repository_url":"https://api.github.com/repos/Acellera/htmd","labels_url":"https://api.github.com/repos/Acellera/htmd/issues/46/labels{/name}","comments_url":"https://api.github.com/repos/Acellera/htmd/issues/46/comments","events_url":"https://api.github.com/repos/Acellera/htmd/issues/46/events","html_url":"https://github.com/Acellera/htmd/issues/46","id":158735793,"number":46,"title":"reconstructAdaptiveTraj  TypeError: object of type 'Sim' has no len()","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":{"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},"milestone":null,"comments":7,"created_at":"2016-06-06T17:52:05Z","updated_at":"2016-06-07T10:35:26Z","closed_at":null,"body":"Hello guys,\r\n\r\nNot sure what I'm doing wrong.\r\n\r\nThanks,\r\nNoelia\r\n\r\n```\r\nmol, chain, pathlist = reconstructAdaptiveTraj(sims, 55)\r\n\r\n/path/to/acellera/test/python/lib/python3.5/site-packages/pyEMMA-2.2-py3.5-linux-x86_64.egg/pyemma/util/_ext/shimmodule.py:131: PyEMMA_DeprecationWarning: Access to a moved module 'pyemma.msm.flux' detected! Please use 'msmtools.flux' in the future.\r\n  category=PyEMMA_DeprecationWarning)\r\n/path/to/acellera/test/python/lib/python3.5/site-packages/pyEMMA-2.2-py3.5-linux-x86_64.egg/pyemma/util/_ext/shimmodule.py:131: PyEMMA_DeprecationWarning: Access to a moved module 'pyemma.msm.generation' detected! Please use 'msmtools.generation' in the future.\r\n  category=PyEMMA_DeprecationWarning)\r\n/path/to/acellera/test/python/lib/python3.5/site-packages/pyEMMA-2.2-py3.5-linux-x86_64.egg/pyemma/util/_ext/shimmodule.py:131: PyEMMA_DeprecationWarning: Access to a moved module 'pyemma.msm.analysis' detected! Please use 'msmtools.analysis' in the future.\r\n  category=PyEMMA_DeprecationWarning)\r\n/path/to/acellera/test/python/lib/python3.5/site-packages/pyEMMA-2.2-py3.5-linux-x86_64.egg/pyemma/util/_ext/shimmodule.py:131: PyEMMA_DeprecationWarning: Access to a moved module 'pyemma.msm.dtraj' detected! Please use 'msmtools.dtraj' in the future.\r\n  category=PyEMMA_DeprecationWarning)\r\n/path/to/acellera/test/python/lib/python3.5/site-packages/pyEMMA-2.2-py3.5-linux-x86_64.egg/pyemma/util/_ext/shimmodule.py:131: PyEMMA_DeprecationWarning: Access to a moved module 'pyemma.msm.estimation' detected! Please use 'msmtools.estimation' in the future.\r\n  category=PyEMMA_DeprecationWarning)\r\n\r\n---------------------------------------------------------------------------\r\nTypeError                                 Traceback (most recent call last)\r\n<ipython-input-29-a90feffab4cf> in <module>()\r\n      1 #len(sims)\r\n----> 2 mol, chain, pathlist = reconstructAdaptiveTraj(sims, 55)\r\n\r\n/path/to/acellera/test/python/lib/python3.5/site-packages/htmd/adaptive/adaptive.py in reconstructAdaptiveTraj(simlist, trajID)\r\n    418     for i, c in enumerate(chain):\r\n    419         tmpmol = Molecule(sim.molfile)\r\n--> 420         tmpmol.read(c[0])\r\n    421         endpiece = c[1]\r\n    422         fileloc = np.vstack(tmpmol.fileloc)\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)\r\n    634             firstfile = filename[0]\r\n    635         else:\r\n--> 636             if len(filename) != 4 and not os.path.exists(filename):\r\n    637                 raise FileNotFoundError('File {} was not found.'.format(filename))\r\n    638             firstfile = filename\r\n\r\nTypeError: object of type 'Sim' has no len()\r\n\r\n\r\n```"},"comment":{"url":"https://api.github.com/repos/Acellera/htmd/issues/comments/224242723","html_url":"https://github.com/Acellera/htmd/issues/46#issuecomment-224242723","issue_url":"https://api.github.com/repos/Acellera/htmd/issues/46","id":224242723,"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":"2016-06-07T10:35:26Z","updated_at":"2016-06-07T10:35:26Z","body":"If you feel like it :D You should make a non-adaptive set first though. I did not do it before because I did not know how to set up simulations and HTMD building did not exist yet. It should be a piece of cake now really."}}
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