{"action":"created","issue":{"url":"https://api.github.com/repos/chemfiles/chemfiles/issues/35","repository_url":"https://api.github.com/repos/chemfiles/chemfiles","labels_url":"https://api.github.com/repos/chemfiles/chemfiles/issues/35/labels{/name}","comments_url":"https://api.github.com/repos/chemfiles/chemfiles/issues/35/comments","events_url":"https://api.github.com/repos/chemfiles/chemfiles/issues/35/events","html_url":"https://github.com/chemfiles/chemfiles/issues/35","id":172203164,"number":35,"title":"Support for biological molecules","user":{"login":"pgbarletta","id":5693483,"avatar_url":"https://avatars.githubusercontent.com/u/5693483?v=3","gravatar_id":"","url":"https://api.github.com/users/pgbarletta","html_url":"https://github.com/pgbarletta","followers_url":"https://api.github.com/users/pgbarletta/followers","following_url":"https://api.github.com/users/pgbarletta/following{/other_user}","gists_url":"https://api.github.com/users/pgbarletta/gists{/gist_id}","starred_url":"https://api.github.com/users/pgbarletta/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pgbarletta/subscriptions","organizations_url":"https://api.github.com/users/pgbarletta/orgs","repos_url":"https://api.github.com/users/pgbarletta/repos","events_url":"https://api.github.com/users/pgbarletta/events{/privacy}","received_events_url":"https://api.github.com/users/pgbarletta/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/chemfiles/chemfiles/labels/enhancement","name":"enhancement","color":"84b6eb"}],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":11,"created_at":"2016-08-19T19:27:38Z","updated_at":"2016-09-27T22:37:25Z","closed_at":"2016-09-22T12:34:41Z","body":"I'm wondering if there's  some space for an **AminoAcid** class. Objects of this class would be linked to each Frame object and 'contain' many objects of the Atom class. That is, a more 'OpenBabel' way of treating biological molecules and a more intuitive one.\r\n\r\nI'm currently developing C++ software to use on biological molecules. Chemfiles is the only library that supports the major molecular dynamics trajectory formats and PDB format at the same time.  But the lack of a Residue concept is critical. On the other hand, OpenBabel can't read netcdf and my soft became considerably slower when I made the change from chemfiles."},"comment":{"url":"https://api.github.com/repos/chemfiles/chemfiles/issues/comments/250019632","html_url":"https://github.com/chemfiles/chemfiles/issues/35#issuecomment-250019632","issue_url":"https://api.github.com/repos/chemfiles/chemfiles/issues/35","id":250019632,"user":{"login":"Luthaf","id":6141587,"avatar_url":"https://avatars.githubusercontent.com/u/6141587?v=3","gravatar_id":"","url":"https://api.github.com/users/Luthaf","html_url":"https://github.com/Luthaf","followers_url":"https://api.github.com/users/Luthaf/followers","following_url":"https://api.github.com/users/Luthaf/following{/other_user}","gists_url":"https://api.github.com/users/Luthaf/gists{/gist_id}","starred_url":"https://api.github.com/users/Luthaf/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Luthaf/subscriptions","organizations_url":"https://api.github.com/users/Luthaf/orgs","repos_url":"https://api.github.com/users/Luthaf/repos","events_url":"https://api.github.com/users/Luthaf/events{/privacy}","received_events_url":"https://api.github.com/users/Luthaf/received_events","type":"User","site_admin":false},"created_at":"2016-09-27T22:37:25Z","updated_at":"2016-09-27T22:37:25Z","body":"> id_ for the Atom class could still be included though. It won't change during the run and would allow a more intuitive way to access atoms coordinates.\r\n\r\nI am more reticent with this: what would be the use case where you have the atom but not the id? My problem is that an Atom should not know about how it is being used, and where it is being stored. More generally, what would be the id of an atom created outside of a Frame? This is perfectly legal now:\r\n\r\n```cpp\r\nauto atom = Atom(\"Zn\");\r\n\r\nauto mass = atom.mass();\r\nauto radius = atom.vdw_radius();\r\n\r\n// Use this data for an analysis algorithm\r\n```"}}
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