{"action":"created","issue":{"url":"https://api.github.com/repos/drugdata/D3R/issues/34","repository_url":"https://api.github.com/repos/drugdata/D3R","labels_url":"https://api.github.com/repos/drugdata/D3R/issues/34/labels{/name}","comments_url":"https://api.github.com/repos/drugdata/D3R/issues/34/comments","events_url":"https://api.github.com/repos/drugdata/D3R/issues/34/events","html_url":"https://github.com/drugdata/D3R/issues/34","id":153350767,"number":34,"title":"Provide definition for new file from genchallengedata.py","user":{"login":"coleslaw481","id":655940,"avatar_url":"https://avatars.githubusercontent.com/u/655940?v=3","gravatar_id":"","url":"https://api.github.com/users/coleslaw481","html_url":"https://github.com/coleslaw481","followers_url":"https://api.github.com/users/coleslaw481/followers","following_url":"https://api.github.com/users/coleslaw481/following{/other_user}","gists_url":"https://api.github.com/users/coleslaw481/gists{/gist_id}","starred_url":"https://api.github.com/users/coleslaw481/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/coleslaw481/subscriptions","organizations_url":"https://api.github.com/users/coleslaw481/orgs","repos_url":"https://api.github.com/users/coleslaw481/repos","events_url":"https://api.github.com/users/coleslaw481/events{/privacy}","received_events_url":"https://api.github.com/users/coleslaw481/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/drugdata/D3R/labels/enhancement","name":"enhancement","color":"84b6eb"}],"state":"open","locked":false,"assignee":{"login":"shuail","id":12241923,"avatar_url":"https://avatars.githubusercontent.com/u/12241923?v=3","gravatar_id":"","url":"https://api.github.com/users/shuail","html_url":"https://github.com/shuail","followers_url":"https://api.github.com/users/shuail/followers","following_url":"https://api.github.com/users/shuail/following{/other_user}","gists_url":"https://api.github.com/users/shuail/gists{/gist_id}","starred_url":"https://api.github.com/users/shuail/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/shuail/subscriptions","organizations_url":"https://api.github.com/users/shuail/orgs","repos_url":"https://api.github.com/users/shuail/repos","events_url":"https://api.github.com/users/shuail/events{/privacy}","received_events_url":"https://api.github.com/users/shuail/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/drugdata/D3R/milestones/1","html_url":"https://github.com/drugdata/D3R/milestones/1.0.0%20Release","labels_url":"https://api.github.com/repos/drugdata/D3R/milestones/1/labels","id":1676916,"number":1,"title":"1.0.0 Release","description":"This release contains fixes for \r\n\r\nissue #14 -- addition of celppreports\r\n","creator":{"login":"coleslaw481","id":655940,"avatar_url":"https://avatars.githubusercontent.com/u/655940?v=3","gravatar_id":"","url":"https://api.github.com/users/coleslaw481","html_url":"https://github.com/coleslaw481","followers_url":"https://api.github.com/users/coleslaw481/followers","following_url":"https://api.github.com/users/coleslaw481/following{/other_user}","gists_url":"https://api.github.com/users/coleslaw481/gists{/gist_id}","starred_url":"https://api.github.com/users/coleslaw481/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/coleslaw481/subscriptions","organizations_url":"https://api.github.com/users/coleslaw481/orgs","repos_url":"https://api.github.com/users/coleslaw481/repos","events_url":"https://api.github.com/users/coleslaw481/events{/privacy}","received_events_url":"https://api.github.com/users/coleslaw481/received_events","type":"User","site_admin":false},"open_issues":2,"closed_issues":9,"state":"open","created_at":"2016-03-31T20:20:30Z","updated_at":"2016-05-06T14:42:22Z","due_on":null,"closed_at":null},"comments":10,"created_at":"2016-05-05T23:47:38Z","updated_at":"2016-05-06T20:12:51Z","closed_at":null,"body":"Provide definition for readme.txt and wiki for this new file:\r\nlargest-&lt;target id&gt;_&lt;candidate id&gt;-&lt;candidateligand id&gt;-lig.pdb"},"comment":{"url":"https://api.github.com/repos/drugdata/D3R/issues/comments/217546680","html_url":"https://github.com/drugdata/D3R/issues/34#issuecomment-217546680","issue_url":"https://api.github.com/repos/drugdata/D3R/issues/34","id":217546680,"user":{"login":"mkgilson","id":16845120,"avatar_url":"https://avatars.githubusercontent.com/u/16845120?v=3","gravatar_id":"","url":"https://api.github.com/users/mkgilson","html_url":"https://github.com/mkgilson","followers_url":"https://api.github.com/users/mkgilson/followers","following_url":"https://api.github.com/users/mkgilson/following{/other_user}","gists_url":"https://api.github.com/users/mkgilson/gists{/gist_id}","starred_url":"https://api.github.com/users/mkgilson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mkgilson/subscriptions","organizations_url":"https://api.github.com/users/mkgilson/orgs","repos_url":"https://api.github.com/users/mkgilson/repos","events_url":"https://api.github.com/users/mkgilson/events{/privacy}","received_events_url":"https://api.github.com/users/mkgilson/received_events","type":"User","site_admin":false},"created_at":"2016-05-06T20:12:51Z","updated_at":"2016-05-06T20:12:51Z","body":"I'm not sure exactly what changes would need to be made.  Fundamentally, \nwhat I want to get away from is talking about the largest protein.  I'd \nrather talk about the MaxMCSS protein or something like that.\n\nOn 5/6/2016 9:47 AM, shuail wrote:\n> I see the point, yes that makes sense to me! So how about changing the\n> definition to\n>\n> The file contains the 3D coordinate of the atoms for the ligand in the\n> MaxMCSS(\"largest\") candidate?\n>\n> Where the quoted \"largest\" is the hyperlink to the full definition. Do you\n> also suggest to change all \"largest\" to \"MaxMCSS\" in all other filenames?\n> If so, I need to change the code correspondingly.\n>\n> Thanks,\n> Shuai\n>\n> On Fri, May 6, 2016 at 9:23 AM, mkgilson <notifications@github.com> wrote:\n>\n> > Hi Shuai,\n> >\n> >\n> > The problem comes when someone mentions the “largest protein”. This\n> > phrase, on the face of it, means the protein with the greatest molecular\n> > weight. So every time we use this phrase, it is ambiguous and \n> confusing. I\n> > would therefore like to find a different term for the protein with the\n> > ligand with the largest MCSS. Even if the term we choose is not\n> > self-defined, it can be an improvement over “largest protein” by not \n> having\n> > an alternative meaning.\n> >\n> >\n> >\n> > How about “MaxMCSS” and “MinMCSS”?\n> >\n> >\n> >\n> > Mike\n> >\n> >\n> >\n> > From: shuail [mailto:notifications@github.com]\n> > Sent: Friday, May 6, 2016 9:15 AM\n> > To: drugdata/D3R <D3R@noreply.github.com>\n> > Cc: mkgilson <mgilson@ucsd.edu>; Comment <comment@noreply.github.com>\n> > Subject: Re: [drugdata/D3R] Provide definition for new file from\n> > genchallengedata.py (#34)\n> >\n> >\n> >\n> > When I wrote that definition, I think the quoted \"largest\" should be \n> fully\n> > defined at the same page ie in the upper readme file or the hyperlink in\n> > the wiki page similar like other definitions like \"smallest\", \n> \"target\" etc.\n> > So I quoted it to say that we need to refer this to somewhere else \n> to avoid\n> > redefining it. It's not very easy to make it self defined I guess. It is\n> > the largest MCSS comparing with the ligand to be docked, but it's \n> also not\n> > a designed ligand or any ligands in the PDB. It must be the ligand \n> in the\n> > protein which passed the criteria of the blastnfilter. So it comes \n> back to\n> > the definition of the \"largest\" protein...\n> >\n> > Thanks,\n> > Shuai\n> >\n> > On Fri, May 6, 2016 at 7:21 AM, Chris Churas <notifications@github.com>\n> > wrote:\n> >\n> > > The contents of the readme.txt packaged with the challenge data \n> tarfile\n> > is\n> > > on this page:\n> > >\n> > >\n> > \n> https://github.com/drugdata/D3R/wiki/Proposed-structure-of-weekly-CELPP-data-package-for-pose-predictions\n> > >\n> > > The data dictionary with definitions is here:\n> > > https://github.com/drugdata/d3r/wiki/Data-dictionary\n> > >\n> > > —\n> > > You are receiving this because you were assigned.\n> > > Reply to this email directly or view it on GitHub\n> > > <https://github.com/drugdata/D3R/issues/34#issuecomment-217453111>\n> > >\n> >\n> >\n> >\n> > —\n> > You are receiving this because you commented.\n> > Reply to this email directly or view it on GitHub <\n> > https://github.com/drugdata/D3R/issues/34#issuecomment-217487624>\n> >\n> > —\n> > You are receiving this because you were assigned.\n> > Reply to this email directly or view it on GitHub\n> > <https://github.com/drugdata/D3R/issues/34#issuecomment-217489758>\n> >\n>\n> —\n> You are receiving this because you commented.\n> Reply to this email directly or view it on GitHub \n> <https://github.com/drugdata/D3R/issues/34#issuecomment-217495289>\n>\n\n\n-- \nMichael K. Gilson, M.D., Ph.D.\nProfessor, Skaggs School of Pharmacy and Pharmaceutical Sciences\nCo-Director, UCSD Center for Drug Discovery Innovation\nU. C. San Diego\n9500 Gilman Drive\nPharmaceutical Sciences Building, Room 3224\nLa Jolla, CA 92093-0736\nVoice: 858-822-0622\nFax: 858-822-7726\nhttp://gilson.ucsd.edu\nhttp://www.bindingdb.org\nhttp://drugdiscovery.ucsd.edu\nhttp://drugdesigndata.org\n\n"}}