{"action":"created","comment":{"url":"https://api.github.com/repos/NMRExchangeFormat/NEF/pulls/comments/82037404","pull_request_review_id":2972768,"id":82037404,"diff_hunk":"@@ -9,18 +9,53 @@ organised by data category (saveframe).\n \n ### General issues\n \n-  1. Residue and Atom names\n-\n-    Residues are identified by three strings ('chain_code', 'sequence_code',\n-    'residue_type') that always are used together. Atoms are identified by a\n-    residue identifier plus the atom name as a fourth string.\n+  1. Requirements for NEF compatibility\n+\n+    The NEF format tries to support as many kinds of data as possible in a\n+    simple file format. But we can clearly not require any program to\n+    read and understand data that it does not normally support, be it complex or\n+    crosslinked sequences, non-standard residues or residue variants, OR/AND\n+    restraint logic, anonymous atom assignments, particular restraint types,\n+    etc. If a program does support a certain type of data,\n+    it is required to read and write such data correctly to/from NEF. If it\n+    does not, it is free to skip such data, or convert them to something it can\n+    deal with if this can be done appropriately.","path":"specification/Overview.md","position":19,"original_position":19,"commit_id":"5a0d7a44023421a42d804aeff525b0e0e7a0e875","original_commit_id":"5a0d7a44023421a42d804aeff525b0e0e7a0e875","user":{"login":"rhfogh","id":9820176,"avatar_url":"https://avatars.githubusercontent.com/u/9820176?v=3","gravatar_id":"","url":"https://api.github.com/users/rhfogh","html_url":"https://github.com/rhfogh","followers_url":"https://api.github.com/users/rhfogh/followers","following_url":"https://api.github.com/users/rhfogh/following{/other_user}","gists_url":"https://api.github.com/users/rhfogh/gists{/gist_id}","starred_url":"https://api.github.com/users/rhfogh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rhfogh/subscriptions","organizations_url":"https://api.github.com/users/rhfogh/orgs","repos_url":"https://api.github.com/users/rhfogh/repos","events_url":"https://api.github.com/users/rhfogh/events{/privacy}","received_events_url":"https://api.github.com/users/rhfogh/received_events","type":"User","site_admin":false},"body":"That would be a change to the current consensus, as I understand it. What you say is indeed desirable. But the way it was discussed, it was agreed that we could not require programs in general to keep and re-export data that they did not use. Let alone to interpret data that their programs are not equipped to handle, like non-stereospecifically assigned nuclei for programs that can not handle them. \r\nAn inferior but more realistic solution would be to use a combination of the input file and output file for software B. As long as we are talking about program-specific fields, it should not be too hard to write a merge utility.","created_at":"2016-10-05T18:21:08Z","updated_at":"2016-10-05T18:21:08Z","html_url":"https://github.com/NMRExchangeFormat/NEF/pull/70#discussion_r82037404","pull_request_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/pulls/70","_links":{"self":{"href":"https://api.github.com/repos/NMRExchangeFormat/NEF/pulls/comments/82037404"},"html":{"href":"https://github.com/NMRExchangeFormat/NEF/pull/70#discussion_r82037404"},"pull_request":{"href":"https://api.github.com/repos/NMRExchangeFormat/NEF/pulls/70"}}},"pull_request":{"url":"https://api.github.com/repos/NMRExchangeFormat/NEF/pulls/70","id":87341280,"html_url":"https://github.com/NMRExchangeFormat/NEF/pull/70","diff_url":"https://github.com/NMRExchangeFormat/NEF/pull/70.diff","patch_url":"https://github.com/NMRExchangeFormat/NEF/pull/70.patch","issue_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/issues/70","number":70,"state":"open","locked":false,"title":"New isotope specification system","user":{"login":"rhfogh","id":9820176,"avatar_url":"https://avatars.githubusercontent.com/u/9820176?v=3","gravatar_id":"","url":"https://api.github.com/users/rhfogh","html_url":"https://github.com/rhfogh","followers_url":"https://api.github.com/users/rhfogh/followers","following_url":"https://api.github.com/users/rhfogh/following{/other_user}","gists_url":"https://api.github.com/users/rhfogh/gists{/gist_id}","starred_url":"https://api.github.com/users/rhfogh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rhfogh/subscriptions","organizations_url":"https://api.github.com/users/rhfogh/orgs","repos_url":"https://api.github.com/users/rhfogh/repos","events_url":"https://api.github.com/users/rhfogh/events{/privacy}","received_events_url":"https://api.github.com/users/rhfogh/received_events","type":"User","site_admin":false},"body":"New system for specifying elements and isotopes\r\n\r\n- Elements with one-letter names ('H', 'C', ...) have the element deduced from the first letter of the name.\r\n- Elements with two-letter names (e.g. Ca, Cd, Zn, ...) must have the element code specified in the _nef_chemical_shift.element column\r\n- Isotopes are normally asumed to be the default form (e.g. 1H for hydrogen, 13C for NMR active carbon, 15N for NMR active nitrogen, etc.). Isotopes that can not be deduced from context (e.g. 2H, different active Cd isotopes) must have their isotope number specified in the _new_chemical_shift.isotope_number column","created_at":"2016-09-29T15:52:31Z","updated_at":"2016-10-05T18:21:08Z","closed_at":null,"merged_at":null,"merge_commit_sha":"bbc348d702b9646c9290d3806154d81d75b71fac","assignee":null,"assignees":[],"milestone":null,"commits_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/pulls/70/commits","review_comments_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/pulls/70/comments","review_comment_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/pulls/comments{/number}","comments_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/issues/70/comments","statuses_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/statuses/5a0d7a44023421a42d804aeff525b0e0e7a0e875","head":{"label":"rhfogh:new_isotope_specification","ref":"new_isotope_specification","sha":"5a0d7a44023421a42d804aeff525b0e0e7a0e875","user":{"login":"rhfogh","id":9820176,"avatar_url":"https://avatars.githubusercontent.com/u/9820176?v=3","gravatar_id":"","url":"https://api.github.com/users/rhfogh","html_url":"https://github.com/rhfogh","followers_url":"https://api.github.com/users/rhfogh/followers","following_url":"https://api.github.com/users/rhfogh/following{/other_user}","gists_url":"https://api.github.com/users/rhfogh/gists{/gist_id}","starred_url":"https://api.github.com/users/rhfogh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rhfogh/subscriptions","organizations_url":"https://api.github.com/users/rhfogh/orgs","repos_url":"https://api.github.com/users/rhfogh/repos","events_url":"https://api.github.com/users/rhfogh/events{/privacy}","received_events_url":"https://api.github.com/users/rhfogh/received_events","type":"User","site_admin":false},"repo":{"id":28093871,"name":"NEF","full_name":"rhfogh/NEF","owner":{"login":"rhfogh","id":9820176,"avatar_url":"https://avatars.githubusercontent.com/u/9820176?v=3","gravatar_id":"","url":"https://api.github.com/users/rhfogh","html_url":"https://github.com/rhfogh","followers_url":"https://api.github.com/users/rhfogh/followers","following_url":"https://api.github.com/users/rhfogh/following{/other_user}","gists_url":"https://api.github.com/users/rhfogh/gists{/gist_id}","starred_url":"https://api.github.com/users/rhfogh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rhfogh/subscriptions","organizations_url":"https://api.github.com/users/rhfogh/orgs","repos_url":"https://api.github.com/users/rhfogh/repos","events_url":"https://api.github.com/users/rhfogh/events{/privacy}","received_events_url":"https://api.github.com/users/rhfogh/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/rhfogh/NEF","description":"NMR Exchange Format official specification","fork":true,"url":"https://api.github.com/repos/rhfogh/NEF","forks_url":"https://api.github.com/repos/rhfogh/NEF/forks","keys_url":"https://api.github.com/repos/rhfogh/NEF/keys{/key_id}","collaborators_url":"https://api.github.com/repos/rhfogh/NEF/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/rhfogh/NEF/teams","hooks_url":"https://api.github.com/repos/rhfogh/NEF/hooks","issue_events_url":"https://api.github.com/repos/rhfogh/NEF/issues/events{/number}","events_url":"https://api.github.com/repos/rhfogh/NEF/events","assignees_url":"https://api.github.com/repos/rhfogh/NEF/assignees{/user}","branches_url":"https://api.github.com/repos/rhfogh/NEF/branches{/branch}","tags_url":"https://api.github.com/repos/rhfogh/NEF/tags","blobs_url":"https://api.github.com/repos/rhfogh/NEF/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/rhfogh/NEF/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/rhfogh/NEF/git/refs{/sha}","trees_url":"https://api.github.com/repos/rhfogh/NEF/git/trees{/sha}","statuses_url":"https://api.github.com/repos/rhfogh/NEF/statuses/{sha}","languages_url":"https://api.github.com/repos/rhfogh/NEF/languages","stargazers_url":"https://api.github.com/repos/rhfogh/NEF/stargazers","contributors_url":"https://api.github.com/repos/rhfogh/NEF/contributors","subscribers_url":"https://api.github.com/repos/rhfogh/NEF/subscribers","subscription_url":"https://api.github.com/repos/rhfogh/NEF/subscription","commits_url":"https://api.github.com/repos/rhfogh/NEF/commits{/sha}","git_commits_url":"https://api.github.com/repos/rhfogh/NEF/git/commits{/sha}","comments_url":"https://api.github.com/repos/rhfogh/NEF/comments{/number}","issue_comment_url":"https://api.github.com/repos/rhfogh/NEF/issues/comments{/number}","contents_url":"https://api.github.com/repos/rhfogh/NEF/contents/{+path}","compare_url":"https://api.github.com/repos/rhfogh/NEF/compare/{base}...{head}","merges_url":"https://api.github.com/repos/rhfogh/NEF/merges","archive_url":"https://api.github.com/repos/rhfogh/NEF/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/rhfogh/NEF/downloads","issues_url":"https://api.github.com/repos/rhfogh/NEF/issues{/number}","pulls_url":"https://api.github.com/repos/rhfogh/NEF/pulls{/number}","milestones_url":"https://api.github.com/repos/rhfogh/NEF/milestones{/number}","notifications_url":"https://api.github.com/repos/rhfogh/NEF/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/rhfogh/NEF/labels{/name}","releases_url":"https://api.github.com/repos/rhfogh/NEF/releases{/id}","deployments_url":"https://api.github.com/repos/rhfogh/NEF/deployments","created_at":"2014-12-16T15:47:17Z","updated_at":"2016-08-02T09:14:18Z","pushed_at":"2016-10-04T10:37:59Z","git_url":"git://github.com/rhfogh/NEF.git","ssh_url":"git@github.com:rhfogh/NEF.git","clone_url":"https://github.com/rhfogh/NEF.git","svn_url":"https://github.com/rhfogh/NEF","homepage":null,"size":7529,"stargazers_count":0,"watchers_count":0,"language":null,"has_issues":false,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":0,"mirror_url":null,"open_issues_count":0,"forks":0,"open_issues":0,"watchers":0,"default_branch":"master"}},"base":{"label":"NMRExchangeFormat:master","ref":"master","sha":"e6d90b88bf918f2881db8617f56525372170c9d3","user":{"login":"NMRExchangeFormat","id":9676490,"avatar_url":"https://avatars.githubusercontent.com/u/9676490?v=3","gravatar_id":"","url":"https://api.github.com/users/NMRExchangeFormat","html_url":"https://github.com/NMRExchangeFormat","followers_url":"https://api.github.com/users/NMRExchangeFormat/followers","following_url":"https://api.github.com/users/NMRExchangeFormat/following{/other_user}","gists_url":"https://api.github.com/users/NMRExchangeFormat/gists{/gist_id}","starred_url":"https://api.github.com/users/NMRExchangeFormat/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/NMRExchangeFormat/subscriptions","organizations_url":"https://api.github.com/users/NMRExchangeFormat/orgs","repos_url":"https://api.github.com/users/NMRExchangeFormat/repos","events_url":"https://api.github.com/users/NMRExchangeFormat/events{/privacy}","received_events_url":"https://api.github.com/users/NMRExchangeFormat/received_events","type":"Organization","site_admin":false},"repo":{"id":28087843,"name":"NEF","full_name":"NMRExchangeFormat/NEF","owner":{"login":"NMRExchangeFormat","id":9676490,"avatar_url":"https://avatars.githubusercontent.com/u/9676490?v=3","gravatar_id":"","url":"https://api.github.com/users/NMRExchangeFormat","html_url":"https://github.com/NMRExchangeFormat","followers_url":"https://api.github.com/users/NMRExchangeFormat/followers","following_url":"https://api.github.com/users/NMRExchangeFormat/following{/other_user}","gists_url":"https://api.github.com/users/NMRExchangeFormat/gists{/gist_id}","starred_url":"https://api.github.com/users/NMRExchangeFormat/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/NMRExchangeFormat/subscriptions","organizations_url":"https://api.github.com/users/NMRExchangeFormat/orgs","repos_url":"https://api.github.com/users/NMRExchangeFormat/repos","events_url":"https://api.github.com/users/NMRExchangeFormat/events{/privacy}","received_events_url":"https://api.github.com/users/NMRExchangeFormat/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/NMRExchangeFormat/NEF","description":"NMR Exchange Format official specification","fork":false,"url":"https://api.github.com/repos/NMRExchangeFormat/NEF","forks_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/forks","keys_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/keys{/key_id}","collaborators_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/teams","hooks_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/hooks","issue_events_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/issues/events{/number}","events_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/events","assignees_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/assignees{/user}","branches_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/branches{/branch}","tags_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/tags","blobs_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/git/refs{/sha}","trees_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/git/trees{/sha}","statuses_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/statuses/{sha}","languages_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/languages","stargazers_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/stargazers","contributors_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/contributors","subscribers_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/subscribers","subscription_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/subscription","commits_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/commits{/sha}","git_commits_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/git/commits{/sha}","comments_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/comments{/number}","issue_comment_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/issues/comments{/number}","contents_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/contents/{+path}","compare_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/compare/{base}...{head}","merges_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/merges","archive_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/downloads","issues_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/issues{/number}","pulls_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/pulls{/number}","milestones_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/milestones{/number}","notifications_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/labels{/name}","releases_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/releases{/id}","deployments_url":"https://api.github.com/repos/NMRExchangeFormat/NEF/deployments","created_at":"2014-12-16T13:19:20Z","updated_at":"2016-06-10T18:30:06Z","pushed_at":"2016-09-29T15:52:31Z","git_url":"git://github.com/NMRExchangeFormat/NEF.git","ssh_url":"git@github.com:NMRExchangeFormat/NEF.git","clone_url":"https://github.com/NMRExchangeFormat/NEF.git","svn_url":"https://github.com/NMRExchangeFormat/NEF","homepage":null,"size":7675,"stargazers_count":4,"watchers_count":4,"language":null,"has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":13,"mirror_url":null,"open_issues_count":21,"forks":13,"open_issues":21,"watchers":4,"default_branch":"master"}},"_links":{"self":{"href":"https://api.github.com/repos/NMRExchangeFormat/NEF/pulls/70"},"html":{"href":"https://github.com/NMRExchangeFormat/NEF/pull/70"},"issue":{"href":"https://api.github.com/repos/NMRExchangeFormat/NEF/issues/70"},"comments":{"href":"https://api.github.com/repos/NMRExchangeFormat/NEF/issues/70/comments"},"review_comments":{"href":"https://api.github.com/repos/NMRExchangeFormat/NEF/pulls/70/comments"},"review_comment":{"href":"https://api.github.com/repos/NMRExchangeFormat/NEF/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/NMRExchangeFormat/NEF/pulls/70/commits"},"statuses":{"href":"https://api.github.com/repos/NMRExchangeFormat/NEF/statuses/5a0d7a44023421a42d804aeff525b0e0e7a0e875"}}}}
{"actor":{"display_login":"rhfogh"}}