{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":323429813,"defaultBranch":"main","name":"RDMC","ownerLogin":"xiaoruiDong","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2020-12-21T19:30:29.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/35771233?v=4","public":true,"private":false,"isOrgOwned":false},"refInfo":{"name":"","listCacheKey":"v0:1717192728.0","currentOid":""},"activityList":{"items":[{"before":"a1db373b9ae66c6c5c3f299db8e53b04dc81abde","after":"ccba58438f88ba2f968c8bd7287bd2f770783569","ref":"refs/heads/v1.0/dev","pushedAt":"2024-07-16T14:22:08.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"xiaoruiDong","name":"Xiaorui Dong","path":"/xiaoruiDong","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/35771233?s=80&v=4"},"commit":{"message":"Merge pull request #100 from shihchengli/add_notebook_test\n\nAdd notebooks to test in CI","shortMessageHtmlLink":"Merge pull request #100 from shihchengli/add_notebook_test"}},{"before":"2058cdbe55f21cf3b9ca77f900c7b93e8398d607","after":"7d20e9476949d704c55dab6e7b14a6e8f0ed1517","ref":"refs/heads/add_protonation_functions","pushedAt":"2024-06-04T17:19:13.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"jonwzheng","name":"Jonathan Zheng","path":"/jonwzheng","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/30244073?s=80&v=4"},"commit":{"message":"added hint typing for protonation functs","shortMessageHtmlLink":"added hint typing for protonation functs"}},{"before":"8e9f0fd329a4413a8a5bbc1c2467cdb3f7d864d8","after":"2058cdbe55f21cf3b9ca77f900c7b93e8398d607","ref":"refs/heads/add_protonation_functions","pushedAt":"2024-06-04T16:56:24.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"jonwzheng","name":"Jonathan Zheng","path":"/jonwzheng","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/30244073?s=80&v=4"},"commit":{"message":"Add code and test for checking if mol is symmetric to a substructure","shortMessageHtmlLink":"Add code and test for checking if mol is symmetric to a substructure"}},{"before":"f37913afd0292ea77af174e28dffdb14bea4adaf","after":"8e9f0fd329a4413a8a5bbc1c2467cdb3f7d864d8","ref":"refs/heads/add_protonation_functions","pushedAt":"2024-05-31T22:18:37.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"jonwzheng","name":"Jonathan Zheng","path":"/jonwzheng","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/30244073?s=80&v=4"},"commit":{"message":"clean up uncharge_mol code with more rigorous check for implicit vs explicit H","shortMessageHtmlLink":"clean up uncharge_mol code with more rigorous check for implicit vs e…"}},{"before":null,"after":"f37913afd0292ea77af174e28dffdb14bea4adaf","ref":"refs/heads/add_protonation_functions","pushedAt":"2024-05-31T21:58:48.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"jonwzheng","name":"Jonathan Zheng","path":"/jonwzheng","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/30244073?s=80&v=4"},"commit":{"message":"working version of uncharge_mol","shortMessageHtmlLink":"working version of uncharge_mol"}},{"before":"4c969d847bfbc0039514d06d372bfe44d93572e9","after":"99bef5bbb75ed43942683874c330708e9272526d","ref":"refs/heads/v1.0/manuscript","pushedAt":"2024-05-31T16:05:31.000Z","pushType":"push","commitsCount":4,"pusher":{"login":"xiaoruiDong","name":"Xiaorui Dong","path":"/xiaoruiDong","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/35771233?s=80&v=4"},"commit":{"message":"check equivalent reactions considering resonance structures","shortMessageHtmlLink":"check equivalent reactions considering resonance structures"}},{"before":"1968443adc6cf9fe0f94a88b6f1eb49ef1abc8b6","after":"4c969d847bfbc0039514d06d372bfe44d93572e9","ref":"refs/heads/v1.0/manuscript","pushedAt":"2024-05-31T03:54:54.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"xiaoruiDong","name":"Xiaorui Dong","path":"/xiaoruiDong","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/35771233?s=80&v=4"},"commit":{"message":"Add GetMolWeight and get_mol_weight","shortMessageHtmlLink":"Add GetMolWeight and get_mol_weight"}},{"before":"9394e5273cb64c50cd9b60888aa3901fb4e052c8","after":"1968443adc6cf9fe0f94a88b6f1eb49ef1abc8b6","ref":"refs/heads/v1.0/manuscript","pushedAt":"2024-05-30T19:25:28.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"xiaoruiDong","name":"Xiaorui Dong","path":"/xiaoruiDong","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/35771233?s=80&v=4"},"commit":{"message":"Use native atom.GetSymbol in get_element_symbol","shortMessageHtmlLink":"Use native atom.GetSymbol in get_element_symbol"}},{"before":"16719aaee2ef55926e32eb9a83c64a5bdcc9de0a","after":"9394e5273cb64c50cd9b60888aa3901fb4e052c8","ref":"refs/heads/v1.0/manuscript","pushedAt":"2024-05-30T18:37:35.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"xiaoruiDong","name":"Xiaorui Dong","path":"/xiaoruiDong","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/35771233?s=80&v=4"},"commit":{"message":"Add coords to H when using explicit mode of get_closed_shell_mol","shortMessageHtmlLink":"Add coords to H when using explicit mode of get_closed_shell_mol"}},{"before":"0c2804436a5515fd7e1be28740dd0f8eab760ee1","after":"16719aaee2ef55926e32eb9a83c64a5bdcc9de0a","ref":"refs/heads/v1.0/manuscript","pushedAt":"2024-05-30T16:35:55.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"xiaoruiDong","name":"Xiaorui Dong","path":"/xiaoruiDong","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/35771233?s=80&v=4"},"commit":{"message":"Utilize rdtools.reaction.analysis for a few methods in Reaction","shortMessageHtmlLink":"Utilize rdtools.reaction.analysis for a few methods in Reaction"}},{"before":"3ffa5b2525d561b30aadc3a5c9d4aec32408c2a2","after":"0c2804436a5515fd7e1be28740dd0f8eab760ee1","ref":"refs/heads/v1.0/manuscript","pushedAt":"2024-05-30T16:32:26.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"xiaoruiDong","name":"Xiaorui Dong","path":"/xiaoruiDong","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/35771233?s=80&v=4"},"commit":{"message":"Add a reaction analysis module","shortMessageHtmlLink":"Add a reaction analysis module"}},{"before":"c8a8bbab1db4cd9864614e4e382f0f5bc3241ace","after":"3ffa5b2525d561b30aadc3a5c9d4aec32408c2a2","ref":"refs/heads/v1.0/manuscript","pushedAt":"2024-05-30T03:25:29.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"xiaoruiDong","name":"Xiaorui Dong","path":"/xiaoruiDong","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/35771233?s=80&v=4"},"commit":{"message":"Fixup: correct usage related to get_closed_shell_mol","shortMessageHtmlLink":"Fixup: correct usage related to get_closed_shell_mol"}},{"before":"c6e4345a7eb3d27c869d0d7a5fc16095108f8bbe","after":"c8a8bbab1db4cd9864614e4e382f0f5bc3241ace","ref":"refs/heads/v1.0/manuscript","pushedAt":"2024-05-29T21:11:28.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"xiaoruiDong","name":"Xiaorui Dong","path":"/xiaoruiDong","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/35771233?s=80&v=4"},"commit":{"message":"update mol_from_xyz\n\n1. Change the argument name from forced_rdmc to original, to indicate using the \"original\" xyz2mol implementation rather than the RDKit's newer implementation; 2. Add the sanitization step into the function call for the xyz2mol backend.","shortMessageHtmlLink":"update mol_from_xyz"}},{"before":"71e4b6e6c926bb4f54570b01d41a1b2bb49a0668","after":"c6e4345a7eb3d27c869d0d7a5fc16095108f8bbe","ref":"refs/heads/v1.0/manuscript","pushedAt":"2024-05-29T16:24:38.000Z","pushType":"push","commitsCount":4,"pusher":{"login":"xiaoruiDong","name":"Xiaorui Dong","path":"/xiaoruiDong","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/35771233?s=80&v=4"},"commit":{"message":"Update get_dehydrogenated_mol with substructmatch and only_on_atoms\n\nThis speeds up the searching for Hs and heavy atoms. only_on_atoms allow only operating on specific atoms. Unit tests are also improved to test the number of Hydrogen atoms and the argument of \"only_on_atoms\"","shortMessageHtmlLink":"Update get_dehydrogenated_mol with substructmatch and only_on_atoms"}},{"before":"d3a96c7f25ebd41c3c2bb6f0b81acaa16ec7757b","after":"71e4b6e6c926bb4f54570b01d41a1b2bb49a0668","ref":"refs/heads/v1.0/manuscript","pushedAt":"2024-05-09T17:50:43.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"xiaoruiDong","name":"Xiaorui Dong","path":"/xiaoruiDong","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/35771233?s=80&v=4"},"commit":{"message":"Enable mapping H atoms for Reaction\n\nThis is useful if H atoms are not mapped or not included in initialization","shortMessageHtmlLink":"Enable mapping H atoms for Reaction"}},{"before":"4edfa2c6bea1ef20d3f82dc9623ecc63747b022e","after":"d3a96c7f25ebd41c3c2bb6f0b81acaa16ec7757b","ref":"refs/heads/v1.0/manuscript","pushedAt":"2024-05-09T15:17:36.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"xiaoruiDong","name":"Xiaorui Dong","path":"/xiaoruiDong","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/35771233?s=80&v=4"},"commit":{"message":"Add AddConformerWithCoords to MolConfMixin","shortMessageHtmlLink":"Add AddConformerWithCoords to MolConfMixin"}},{"before":"0b10598de00ad04b5b0f845b47aac6285c0fb1ab","after":"4edfa2c6bea1ef20d3f82dc9623ecc63747b022e","ref":"refs/heads/v1.0/manuscript","pushedAt":"2024-05-07T22:12:41.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"xiaoruiDong","name":"Xiaorui Dong","path":"/xiaoruiDong","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/35771233?s=80&v=4"},"commit":{"message":"Easier import for reaction functions","shortMessageHtmlLink":"Easier import for reaction functions"}},{"before":"c97b7c8a1dd469a062d0365364b7de6b3ae7249e","after":"0b10598de00ad04b5b0f845b47aac6285c0fb1ab","ref":"refs/heads/v1.0/manuscript","pushedAt":"2024-05-03T19:42:42.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"xiaoruiDong","name":"Xiaorui Dong","path":"/xiaoruiDong","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/35771233?s=80&v=4"},"commit":{"message":"Add get_fingerprint method to the Reaction","shortMessageHtmlLink":"Add get_fingerprint method to the Reaction"}},{"before":null,"after":"c97b7c8a1dd469a062d0365364b7de6b3ae7249e","ref":"refs/heads/v1.0/manuscript","pushedAt":"2024-05-03T19:37:47.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"xiaoruiDong","name":"Xiaorui Dong","path":"/xiaoruiDong","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/35771233?s=80&v=4"},"commit":{"message":"Update featurizer: add avalon and maccs and reaction featurizer","shortMessageHtmlLink":"Update featurizer: add avalon and maccs and reaction featurizer"}},{"before":"88c4a274e8a9d38fabf26dc4d9520d15142d661b","after":null,"ref":"refs/heads/add_xtb_method","pushedAt":"2024-03-29T15:01:04.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"hwpang","name":"Hao-Wei Pang","path":"/hwpang","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/45482070?s=80&v=4"}},{"before":"d240de455f1ed20538db34fad75272f4ca24077e","after":"a1db373b9ae66c6c5c3f299db8e53b04dc81abde","ref":"refs/heads/v1.0/dev","pushedAt":"2024-03-29T15:00:26.000Z","pushType":"pr_merge","commitsCount":6,"pusher":{"login":"xiaoruiDong","name":"Xiaorui Dong","path":"/xiaoruiDong","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/35771233?s=80&v=4"},"commit":{"message":"Merge pull request #96 from xiaoruiDong/v1.0/cg_refactor\n\nUpdate Notebooks Part 1","shortMessageHtmlLink":"Merge pull request #96 from xiaoruiDong/v1.0/cg_refactor"}},{"before":"3ad9c3b6ea4abdf686ccc9d293e59fd6c8712cc0","after":"16323322598444cc2d8d62a61eb5d300753e7735","ref":"refs/heads/v1.0/cg_refactor","pushedAt":"2024-03-29T14:41:23.000Z","pushType":"push","commitsCount":6,"pusher":{"login":"xiaoruiDong","name":"Xiaorui Dong","path":"/xiaoruiDong","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/35771233?s=80&v=4"},"commit":{"message":"Bugfix: import torsional-diffusion embedder in embedder.__init__","shortMessageHtmlLink":"Bugfix: import torsional-diffusion embedder in embedder.__init__"}},{"before":"858e5561588500ebbf42f466ed6e43659996d1e8","after":"d240de455f1ed20538db34fad75272f4ca24077e","ref":"refs/heads/v1.0/dev","pushedAt":"2024-03-29T13:56:05.000Z","pushType":"pr_merge","commitsCount":149,"pusher":{"login":"xiaoruiDong","name":"Xiaorui Dong","path":"/xiaoruiDong","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/35771233?s=80&v=4"},"commit":{"message":"Merge pull request #94 from xiaoruiDong/v1.0/cg_refactor\n\nAnother Huge PR to refactor the conformer_generation module","shortMessageHtmlLink":"Merge pull request #94 from xiaoruiDong/v1.0/cg_refactor"}},{"before":"3d39d38e49a518888936c14e28215c6402728b0f","after":"3ad9c3b6ea4abdf686ccc9d293e59fd6c8712cc0","ref":"refs/heads/v1.0/cg_refactor","pushedAt":"2024-03-29T05:01:29.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"xiaoruiDong","name":"Xiaorui Dong","path":"/xiaoruiDong","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/35771233?s=80&v=4"},"commit":{"message":"cont'd: Use implicit type hints in oa_reactdiff\n\nI guess I need some rest. Xiaorui","shortMessageHtmlLink":"cont'd: Use implicit type hints in oa_reactdiff"}},{"before":"72e23d8b471167f4bb6edc48b9c448b92f0d68e1","after":"3d39d38e49a518888936c14e28215c6402728b0f","ref":"refs/heads/v1.0/cg_refactor","pushedAt":"2024-03-29T04:59:05.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"xiaoruiDong","name":"Xiaorui Dong","path":"/xiaoruiDong","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/35771233?s=80&v=4"},"commit":{"message":"Format fixes according to pycodestyle","shortMessageHtmlLink":"Format fixes according to pycodestyle"}},{"before":"c715cd099dac7d4512d85eab16dc265e10260d39","after":"72e23d8b471167f4bb6edc48b9c448b92f0d68e1","ref":"refs/heads/v1.0/cg_refactor","pushedAt":"2024-03-29T04:56:47.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"xiaoruiDong","name":"Xiaorui Dong","path":"/xiaoruiDong","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/35771233?s=80&v=4"},"commit":{"message":"Update unit test of Gaussian Writer\n\nDue to an updated strategy for running gaussian xtb job","shortMessageHtmlLink":"Update unit test of Gaussian Writer"}},{"before":"955456bfbe9f900ce2d9c83a915fb6baba27a52c","after":"c715cd099dac7d4512d85eab16dc265e10260d39","ref":"refs/heads/v1.0/cg_refactor","pushedAt":"2024-03-29T04:51:45.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"xiaoruiDong","name":"Xiaorui Dong","path":"/xiaoruiDong","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/35771233?s=80&v=4"},"commit":{"message":"cont'd: Use implicit type hints in oa_reactdiff","shortMessageHtmlLink":"cont'd: Use implicit type hints in oa_reactdiff"}},{"before":"8384370089d1a633d3260b7f318655bb9e0d3415","after":"955456bfbe9f900ce2d9c83a915fb6baba27a52c","ref":"refs/heads/v1.0/cg_refactor","pushedAt":"2024-03-29T04:50:08.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"xiaoruiDong","name":"Xiaorui Dong","path":"/xiaoruiDong","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/35771233?s=80&v=4"},"commit":{"message":"Use implicit type hints in oa_reactdiff","shortMessageHtmlLink":"Use implicit type hints in oa_reactdiff"}},{"before":"fa99c3888909e34f83a5b432ee79d8e84439cebb","after":"8384370089d1a633d3260b7f318655bb9e0d3415","ref":"refs/heads/v1.0/cg_refactor","pushedAt":"2024-03-29T04:43:57.000Z","pushType":"push","commitsCount":7,"pusher":{"login":"xiaoruiDong","name":"Xiaorui Dong","path":"/xiaoruiDong","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/35771233?s=80&v=4"},"commit":{"message":"Add an attempt to add OA-ReactDiff to ts guessers","shortMessageHtmlLink":"Add an attempt to add OA-ReactDiff to ts guessers"}},{"before":"698ed6d0e28e2b075a0a96c6449ccc50878c571e","after":null,"ref":"refs/heads/v1.0/fix","pushedAt":"2024-03-28T20:16:52.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"xiaoruiDong","name":"Xiaorui Dong","path":"/xiaoruiDong","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/35771233?s=80&v=4"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"Y3Vyc29yOnYyOpK7MjAyNC0wNy0xNlQxNDoyMjowOC4wMDAwMDBazwAAAASA3uAB","startCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wNy0xNlQxNDoyMjowOC4wMDAwMDBazwAAAASA3uAB","endCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wMy0yOFQyMDoxNjo1Mi4wMDAwMDBazwAAAAQiIsF7"}},"title":"Activity · xiaoruiDong/RDMC"}