{"action":"created","issue":{"url":"https://api.github.com/repos/markovmodel/variational/issues/3","labels_url":"https://api.github.com/repos/markovmodel/variational/issues/3/labels{/name}","comments_url":"https://api.github.com/repos/markovmodel/variational/issues/3/comments","events_url":"https://api.github.com/repos/markovmodel/variational/issues/3/events","html_url":"https://github.com/markovmodel/variational/pull/3","id":97732138,"number":3,"title":"Add basisset vitalini","user":{"login":"fvitalini","id":13469315,"avatar_url":"https://avatars.githubusercontent.com/u/13469315?v=3","gravatar_id":"","url":"https://api.github.com/users/fvitalini","html_url":"https://github.com/fvitalini","followers_url":"https://api.github.com/users/fvitalini/followers","following_url":"https://api.github.com/users/fvitalini/following{/other_user}","gists_url":"https://api.github.com/users/fvitalini/gists{/gist_id}","starred_url":"https://api.github.com/users/fvitalini/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fvitalini/subscriptions","organizations_url":"https://api.github.com/users/fvitalini/orgs","repos_url":"https://api.github.com/users/fvitalini/repos","events_url":"https://api.github.com/users/fvitalini/events{/privacy}","received_events_url":"https://api.github.com/users/fvitalini/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":8,"created_at":"2015-07-28T15:15:18Z","updated_at":"2015-07-28T16:31:20Z","closed_at":"2015-07-28T15:25:46Z","pull_request":{"url":"https://api.github.com/repos/markovmodel/variational/pulls/3","html_url":"https://github.com/markovmodel/variational/pull/3","diff_url":"https://github.com/markovmodel/variational/pull/3.diff","patch_url":"https://github.com/markovmodel/variational/pull/3.patch"},"body":""},"comment":{"url":"https://api.github.com/repos/markovmodel/variational/issues/comments/125672402","html_url":"https://github.com/markovmodel/variational/pull/3#issuecomment-125672402","issue_url":"https://api.github.com/repos/markovmodel/variational/issues/3","id":125672402,"user":{"login":"franknoe","id":6495810,"avatar_url":"https://avatars.githubusercontent.com/u/6495810?v=3","gravatar_id":"","url":"https://api.github.com/users/franknoe","html_url":"https://github.com/franknoe","followers_url":"https://api.github.com/users/franknoe/followers","following_url":"https://api.github.com/users/franknoe/following{/other_user}","gists_url":"https://api.github.com/users/franknoe/gists{/gist_id}","starred_url":"https://api.github.com/users/franknoe/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/franknoe/subscriptions","organizations_url":"https://api.github.com/users/franknoe/orgs","repos_url":"https://api.github.com/users/franknoe/repos","events_url":"https://api.github.com/users/franknoe/events{/privacy}","received_events_url":"https://api.github.com/users/franknoe/received_events","type":"User","site_admin":false},"created_at":"2015-07-28T16:31:19Z","updated_at":"2015-07-28T16:31:19Z","body":"Am 28/07/15 um 18:26 schrieb fvitalini:\n>\n> Il giorno 28/lug/2015, alle ore 17:35, Frank Noe \n> <notifications@github.com> ha scritto:\n>\n> > Am 28/07/15 um 17:26 schrieb fvitalini:\n> > >\n> > > @ Frank:\n> > >\n> > > * psi /phi time series should be in degrees or radiants?\n> > >\n> > Good question. I would do this: Use a parameter radians=True in the\n> > __init__ of the Ramachandran basis set and the Ramachandran product\n> > basis sets. Then in the calculation function you evaluate the input as\n> > radians if radians=True, otherwise in degrees.\n>\n> Ok I will include it, but I would use degrees as default as GROMACS \n> output is in degrees.\nBut our package is not Gromacs-specific. In mdtraj, pyEMMA and numpy \nradians are the default, so this is for future compatibility.\n>\n>\n> > >\n> > > * at the current status we treat the input files as bumpy array of\n> > > shape (T, X) with T = number of time steps and X= 2*number of\n> > > residues. Shouldn't this lead us to memory issues?\n> > >\n> > It could, but it's not the problem of this class to sort these issues\n> > out. We could always read large trajectories in small chunks and feed\n> > them to the basis set class. In EMMA it's done exactly like this,\n> > because the exact same issue can appear with TICA (which is essentially\n> > a variational approach). Doing this chunking is not something you need\n> > to solve, because we have the infrastructure for a long-time solution.\n>\n> OK\n>\n>\n> >\n> > As long as we have just residue basis sets the input is not really a\n> > problem anyway. Even for 100 residues and 1 million frames we would \n> only\n> > have about one GB of memory, which is modest. A stronger problem can\n> > arises from the output of the basis set, because if you consider all\n> > product pairs with full excitation you can get an astronomic number of\n> > dimensions. At the moment we just have to keep it small.\n> > >\n> > > *\n> > >\n> > >\n> > > * I have sent you a pull request to add my commits (that I created\n> > > to branch in a fork at my name). Feliks instead had previously\n> > > created a branch directly from the original repository. What do\n> > > you prefer and can you check if the two of us have all the correct\n> > > permissions?\n> > >\n> > Pull request is perfect! But you can also create a branch in the main\n> > repo and then make a pull request to the master branch. In the end it's\n> > the same.\n> > >\n> > > General question: how do we treat errors?\n> > >\n> > Are you talking about estimation errors in the timescales? You can \n> still\n> > do bootstrapping and feed the estimators in this package with the\n> > bootstrapped trajectories.\n>\n> No we intended numerical errors. For example GROMACS output sometimes \n> gives angles of 180.00000001 that up to now I was manually setting \n> back to 180. Is there an agreement on how to treat these errors?\nAh. I think that's not a problem because the basis functions are \ncoarse-grained anyway. But I think you can not exclude that the input \ngoes over the +-180 degree boundary and you'd have to map it back. For \nexample you could get 540 degrees as an input. So something like ((X + \n180.0) % 360.0 - 180.0)\n>\n> > >\n> > > —\n> > > Reply to this email directly or view it on GitHub\n> > > \n> <https://github.com/markovmodel/variational/pull/3#issuecomment-125653872>.\n> > >\n> >\n> >\n> > --\n> >\n> > ----------------------------------------------\n> > Prof. Dr. Frank Noe\n> > Head of Computational Molecular Biology group\n> > Freie Universitaet Berlin\n> >\n> > Phone: (+49) (0)30 838 75354\n> > Web: research.franknoe.de\n> > Mail: Arnimallee 6, 14195 Berlin, Germany\n> > ----------------------------------------------\n> >\n> > —\n> > Reply to this email directly or view it on GitHub.\n> >\n>\n> —\n> Reply to this email directly or view it on GitHub \n> <https://github.com/markovmodel/variational/pull/3#issuecomment-125670810>.\n>\n\n\n-- \n\n----------------------------------------------\nProf. Dr. Frank Noe\nHead of Computational Molecular Biology group\nFreie Universitaet Berlin\n\nPhone: (+49) (0)30 838 75354\nWeb:   research.franknoe.de\nMail:  Arnimallee 6, 14195 Berlin, Germany\n----------------------------------------------\n\n"}}