{"action":"created","issue":{"url":"https://api.github.com/repos/ParmEd/ParmEd/issues/149","labels_url":"https://api.github.com/repos/ParmEd/ParmEd/issues/149/labels{/name}","comments_url":"https://api.github.com/repos/ParmEd/ParmEd/issues/149/comments","events_url":"https://api.github.com/repos/ParmEd/ParmEd/issues/149/events","html_url":"https://github.com/ParmEd/ParmEd/issues/149","id":78164205,"number":149,"title":"Document Structure / AmberParm addition operations","user":{"login":"kyleabeauchamp","id":1900459,"avatar_url":"https://avatars.githubusercontent.com/u/1900459?v=3","gravatar_id":"","url":"https://api.github.com/users/kyleabeauchamp","html_url":"https://github.com/kyleabeauchamp","followers_url":"https://api.github.com/users/kyleabeauchamp/followers","following_url":"https://api.github.com/users/kyleabeauchamp/following{/other_user}","gists_url":"https://api.github.com/users/kyleabeauchamp/gists{/gist_id}","starred_url":"https://api.github.com/users/kyleabeauchamp/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kyleabeauchamp/subscriptions","organizations_url":"https://api.github.com/users/kyleabeauchamp/orgs","repos_url":"https://api.github.com/users/kyleabeauchamp/repos","events_url":"https://api.github.com/users/kyleabeauchamp/events{/privacy}","received_events_url":"https://api.github.com/users/kyleabeauchamp/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-05-19T16:44:01Z","updated_at":"2015-05-21T04:21:04Z","closed_at":null,"body":"The structure addition syntax from #145 looks excellent, but probably could use some examples / documentation on the main docs page when things are ready.  \r\n\r\n```\r\n\r\n#Test a simple merge of A and B (phenol and biphenyl)\r\nphenol = chemistry.amber.AmberParm( 'phenol.prmtop', 'phenol.crd')\r\nbiphenyl = chemistry.amber.AmberParm( 'biphenyl.prmtop', 'biphenyl.crd')\r\nphenol_biphenyl = phenol * 3 + biphenyl * 2\r\ngromacs_topology = chemistry.gromacs.GromacsTopologyFile.from_structure( phenol_biphenyl )\r\nchemistry.gromacs.GromacsTopologyFile.write( gromacs_topology, 'test_merged.top')\r\n\r\n#Let's try that after conversion to GROMACS\r\ngromacs_topology_phenol = chemistry.gromacs.GromacsTopologyFile.from_structure( phenol )\r\ngromacs_topology_biphenyl = chemistry.gromacs.GromacsTopologyFile.from_structure( biphenyl )\r\nphenol_biphenyl = gromacs_topology_phenol  + gromacs_topology_biphenyl\r\nchemistry.gromacs.GromacsTopologyFile.write( phenol_biphenyl, 'test_merged_2.top' )\r\n```"},"comment":{"url":"https://api.github.com/repos/ParmEd/ParmEd/issues/comments/104130121","html_url":"https://github.com/ParmEd/ParmEd/issues/149#issuecomment-104130121","issue_url":"https://api.github.com/repos/ParmEd/ParmEd/issues/149","id":104130121,"user":{"login":"hainm","id":4451957,"avatar_url":"https://avatars.githubusercontent.com/u/4451957?v=3","gravatar_id":"","url":"https://api.github.com/users/hainm","html_url":"https://github.com/hainm","followers_url":"https://api.github.com/users/hainm/followers","following_url":"https://api.github.com/users/hainm/following{/other_user}","gists_url":"https://api.github.com/users/hainm/gists{/gist_id}","starred_url":"https://api.github.com/users/hainm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hainm/subscriptions","organizations_url":"https://api.github.com/users/hainm/orgs","repos_url":"https://api.github.com/users/hainm/repos","events_url":"https://api.github.com/users/hainm/events{/privacy}","received_events_url":"https://api.github.com/users/hainm/received_events","type":"User","site_admin":false},"created_at":"2015-05-21T04:21:04Z","updated_at":"2015-05-21T04:21:04Z","body":"```\r\nphenol_biphenyl = phenol * 3 + biphenyl * 2\r\n```\r\nDoes this vstack coords too?"}}