{"action":"opened","issue":{"url":"https://api.github.com/repos/isambard-uob/isambard/issues/13","repository_url":"https://api.github.com/repos/isambard-uob/isambard","labels_url":"https://api.github.com/repos/isambard-uob/isambard/issues/13/labels{/name}","comments_url":"https://api.github.com/repos/isambard-uob/isambard/issues/13/comments","events_url":"https://api.github.com/repos/isambard-uob/isambard/issues/13/events","html_url":"https://github.com/isambard-uob/isambard/issues/13","id":356192294,"node_id":"MDU6SXNzdWUzNTYxOTIyOTQ=","number":13,"title":"Finding H-bonds and KIHs with Isambard2","user":{"login":"broncio123","id":17453074,"node_id":"MDQ6VXNlcjE3NDUzMDc0","avatar_url":"https://avatars2.githubusercontent.com/u/17453074?v=4","gravatar_id":"","url":"https://api.github.com/users/broncio123","html_url":"https://github.com/broncio123","followers_url":"https://api.github.com/users/broncio123/followers","following_url":"https://api.github.com/users/broncio123/following{/other_user}","gists_url":"https://api.github.com/users/broncio123/gists{/gist_id}","starred_url":"https://api.github.com/users/broncio123/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/broncio123/subscriptions","organizations_url":"https://api.github.com/users/broncio123/orgs","repos_url":"https://api.github.com/users/broncio123/repos","events_url":"https://api.github.com/users/broncio123/events{/privacy}","received_events_url":"https://api.github.com/users/broncio123/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-09-01T10:37:35Z","updated_at":"2018-09-01T10:37:35Z","closed_at":null,"author_association":"NONE","body":"Hi,\r\n\r\nI'm struggling to find a way with the `ampal` module to get all H-bonds (Sidechain-Sidechain, Sidechain-Mainchain, etc) and Knobs into Holes, given a PDB.\r\n\r\nWith previous `isambard` versions I used to do something like:\r\n\r\n```bash\r\nimport isambard_dev\r\n\r\n# Passed a PDB which already includes hydrogens\t\t\r\np = isambard_dev.ampal.convert_pdb_to_ampal(pdb_path)\r\n\r\nhbonds = isambard_dev.interactions.find_hydrogen_bonds(p)\r\n# Find all H-bonds and select those between sidechain atoms\r\nsc_hbonds = [hb for hb in hbonds if hb.is_sidechain_sidechain == True]\r\n\r\n# Get donor/acceptor info\r\nhb = sc_hbonds[0]\r\ndonor_H = [hb.donor.ampal_parent.id , hb.donor.res_label]\r\nacceptor_O = [hb.acceptor.ampal_parent.id , hb.acceptor.res_label]\r\n```\r\nand \r\n\r\n```bash\r\nkihs = isambard_dev.add_ons.knobs_into_holes.find_kihs(p)\r\n\r\n# Get KIH info\r\nkih = kihs[0]\r\nknob_data = kih.knob.unique_id\r\nhole_data = [kih.hole[x].unique_id for x in range(len(kih.hole))]\r\n```\r\nI would appreciate any help so that I can upgrade my code to Isambard2.\r\n\r\nCheers,\r\nBroncio "}}
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