{"action":"created","issue":{"url":"https://api.github.com/repos/biopython/biopython/issues/455","repository_url":"https://api.github.com/repos/biopython/biopython","labels_url":"https://api.github.com/repos/biopython/biopython/issues/455/labels{/name}","comments_url":"https://api.github.com/repos/biopython/biopython/issues/455/comments","events_url":"https://api.github.com/repos/biopython/biopython/issues/455/events","html_url":"https://github.com/biopython/biopython/issues/455","id":53583643,"number":455,"title":"PDB Entity.copy() mangles disordered atoms.","user":{"login":"macraild","id":10427991,"avatar_url":"https://avatars.githubusercontent.com/u/10427991?v=3","gravatar_id":"","url":"https://api.github.com/users/macraild","html_url":"https://github.com/macraild","followers_url":"https://api.github.com/users/macraild/followers","following_url":"https://api.github.com/users/macraild/following{/other_user}","gists_url":"https://api.github.com/users/macraild/gists{/gist_id}","starred_url":"https://api.github.com/users/macraild/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/macraild/subscriptions","organizations_url":"https://api.github.com/users/macraild/orgs","repos_url":"https://api.github.com/users/macraild/repos","events_url":"https://api.github.com/users/macraild/events{/privacy}","received_events_url":"https://api.github.com/users/macraild/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":7,"created_at":"2015-01-07T00:49:06Z","updated_at":"2016-11-10T09:40:14Z","closed_at":null,"body":"Disordered atoms dont inherit `disordered_get_list()` when a parent entity is copied. Eg:\n\n```\n>>> pdbl = Bio.PDB.PDBList(server='http://www.rcsb.org/pdb/files')\n>>> pdbParser = Bio.PDB.PDBParser()\n>>> struct_4LGR = pdbParser.get_structure('4LGR', pdbl.retrieve_pdb_file('4LGR'))\nDownloading PDB structure '4LGR'...\n>>> Bio.PDB.PPBuilder().build_peptides(struct_4LGR)\n[<Polypeptide start=5 end=33>, <Polypeptide start=36 end=259>, <Polypeptide start=2 end=123>]\n>>> Bio.PDB.PPBuilder().build_peptides(struct_4LGR.copy())\nTraceback (most recent call last):\n  File \"<stdin>\", line 1, in <module>\n  File \"/usr/lib/python2.6/site-packages/Bio/PDB/Polypeptide.py\", line 357, in build_peptides\n    and is_connected(prev_res, next_res):\n  File \"/usr/lib/python2.6/site-packages/Bio/PDB/Polypeptide.py\", line 417, in _is_connected\n    nlist=n.disordered_get_list()\nAttributeError: 'Atom' object has no attribute 'disordered_get_list'\n```\n"},"comment":{"url":"https://api.github.com/repos/biopython/biopython/issues/comments/259644547","html_url":"https://github.com/biopython/biopython/issues/455#issuecomment-259644547","issue_url":"https://api.github.com/repos/biopython/biopython/issues/455","id":259644547,"user":{"login":"schwarz-ben","id":23376831,"avatar_url":"https://avatars.githubusercontent.com/u/23376831?v=3","gravatar_id":"","url":"https://api.github.com/users/schwarz-ben","html_url":"https://github.com/schwarz-ben","followers_url":"https://api.github.com/users/schwarz-ben/followers","following_url":"https://api.github.com/users/schwarz-ben/following{/other_user}","gists_url":"https://api.github.com/users/schwarz-ben/gists{/gist_id}","starred_url":"https://api.github.com/users/schwarz-ben/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/schwarz-ben/subscriptions","organizations_url":"https://api.github.com/users/schwarz-ben/orgs","repos_url":"https://api.github.com/users/schwarz-ben/repos","events_url":"https://api.github.com/users/schwarz-ben/events{/privacy}","received_events_url":"https://api.github.com/users/schwarz-ben/received_events","type":"User","site_admin":false},"created_at":"2016-11-10T09:40:13Z","updated_at":"2016-11-10T09:40:13Z","body":"Hi, \r\n   \r\n   First of all I want to thank you for the great job you are doing with biopython.\r\n\r\n  In connection with the problem exposed here.\r\nWhen copying a structure, applying a transformation, then saving : I first ran in the problem exposed by macraild. Using the \"trick\" he proposed on jan 8 2015 I was able to have my script working without complaining, but I realized afterwards that the atoms with alternate locations were not affected by the transformation : they simply stayed in place.\r\n\r\n    Any idea how I can solve the problem ?\r\n\r\n      --Ben\r\n\r\n(using pytho2.7 on ubuntu, biopython version as found in __init__.py : 1.66)\r\n"}}
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