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  • 204a511f09 Parallelize gif generation Kevin Wu 2022-09-10 19:16:22 -07:00
  • 28d8054685 Process inputs in order and with consistent color Kevin Wu 2022-09-10 19:03:53 -07:00
  • b10672b29c Misc fixes and QOL improvements Kevin Wu 2022-09-10 18:37:58 -07:00
  • 4965de7c39 Initial code for easily generating png from pdb Kevin Wu 2022-09-10 18:12:58 -07:00
  • cb292f6f16 Fix issue with runnning single-item batches Kevin Wu 2022-09-10 13:20:12 -07:00
  • 24e76458eb Reorganize sampling code, add support for writing full sampling history Kevin Wu 2022-09-10 13:02:55 -07:00
  • 3b5d219a65 Update some plotting Kevin Wu 2022-09-10 11:23:40 -07:00
  • 0c6e6657b4 Doc updates Kevin Wu 2022-09-10 11:02:29 -07:00
  • 88243e3157 More detailed logging Kevin Wu 2022-09-10 10:41:23 -07:00
  • 775981b02f Reduce default thread count for tmscore calculation Kevin Wu 2022-09-10 10:40:52 -07:00
  • 1e2d78b87a Better error handling in tmaling Kevin Wu 2022-09-10 10:32:50 -07:00
  • ef80a288a8 README updates Kevin Wu 2022-09-09 15:07:43 -07:00
  • ceb2505a96 Update amlt ignore Kevin Wu 2022-09-09 14:37:14 -07:00
  • d53d4779fb Make cache file determination logic more consistent Kevin Wu 2022-09-09 14:36:30 -07:00
  • 97fdcaf34e Renable cache Kevin Wu 2022-09-09 14:31:51 -07:00
  • 1c0a066dab Re-enable cache to a file named by hash Kevin Wu 2022-09-09 14:31:38 -07:00
  • bf8268f402 Code to checksum all py files in a dir. Useful for checking repo state Kevin Wu 2022-09-09 14:29:35 -07:00
  • 86ce1cbddd Remove old config files Kevin Wu 2022-09-09 14:15:51 -07:00
  • b24b83d445 RAEDME updates Kevin Wu 2022-09-09 14:15:44 -07:00
  • 60ae4ce244 README updates Kevin Wu 2022-09-09 14:09:32 -07:00
  • a27d6948ff Add progressbar to tmscore calculation Kevin Wu 2022-09-09 14:04:44 -07:00
  • 6a5fb6e90e Formatting Kevin Wu 2022-09-09 14:02:27 -07:00
  • 14bc15f2f6 More documentation Kevin Wu 2022-09-09 14:02:19 -07:00
  • 25bffb7a95 Pass through sample_length function Kevin Wu 2022-09-09 13:58:51 -07:00
  • 96794d3d78 When sampling, do not just hardcode sequence length Kevin Wu 2022-09-09 13:56:12 -07:00
  • 3edc076259 Amlt dry runs Kevin Wu 2022-09-09 13:35:18 -07:00
  • 448d947527 Doc udpates Kevin Wu 2022-09-09 13:34:39 -07:00
  • aa2815bad2 Reduce verbosity of warning messages Kevin Wu 2022-09-09 13:14:56 -07:00
  • 27294e5216 Tweak sampling to work with updated models and params Kevin Wu 2022-09-09 13:11:12 -07:00
  • 6a15991a4b Option to load only train set Kevin Wu 2022-09-09 13:06:28 -07:00
  • c10e23efe9 Improve handling of angle determination when loading pretrained models Kevin Wu 2022-09-09 12:53:32 -07:00
  • fde2494bdf Doc update Kevin Wu 2022-09-09 12:03:50 -07:00
  • f2f526cb59 More typing tweaks Kevin Wu 2022-09-09 11:49:43 -07:00
  • e84bd412e9 Reorganize typing literals Kevin Wu 2022-09-09 11:46:38 -07:00
  • 0b095dbbda Remove installation of biopython Kevin Wu 2022-09-09 10:50:19 -07:00
  • 7dccdb215f Remove dependencies on biopython Kevin Wu 2022-09-09 10:46:37 -07:00
  • 485fcb83a3 Output logging messages to stdout and to file Kevin Wu 2022-09-09 10:19:28 -07:00
  • 49a6bc349f Amlt tweak Kevin Wu 2022-09-09 09:52:04 -07:00
  • 12c863c881 Move some doctests to unit tests Kevin Wu 2022-09-08 23:02:18 -07:00
  • 2f53f4f6df Save plots Kevin Wu 2022-09-08 22:55:25 -07:00
  • 75a097fe4b Barplot of requisite angles/distances Kevin Wu 2022-09-08 22:52:34 -07:00
  • 35a4c6f666 Misc. updates Kevin Wu 2022-09-08 22:24:57 -07:00
  • c0f04da1be Suppress warnings Kevin Wu 2022-09-08 19:59:39 -07:00
  • 406d23664e Bugfix Kevin Wu 2022-09-08 19:51:55 -07:00
  • adb31bbd6e Better control over caching (disable by default) Kevin Wu 2022-09-08 18:14:03 -07:00
  • a3c0f717b4 Logging to file Kevin Wu 2022-09-08 18:04:12 -07:00
  • 6669c3597b More plots of noising process Kevin Wu 2022-09-08 17:49:57 -07:00
  • eb1efe9146 Update noised structure Kevin Wu 2022-09-08 17:30:09 -07:00
  • cecd2ea433 Add images of noised and clean protein backbones Kevin Wu 2022-09-08 17:27:09 -07:00
  • 39f0f6334c More debugging/visualization args Kevin Wu 2022-09-08 16:08:38 -07:00
  • 4a9e781d87 Fix issue where we would repeatedly zero-center and shfiting values over time Kevin Wu 2022-09-08 16:02:40 -07:00
  • 9b4815b3d6 Remove functionality for shifting to [0, 2pi) Kevin Wu 2022-09-08 15:40:19 -07:00
  • 7fcdfb83db Automatically determine which values to set if not given Kevin Wu 2022-09-08 15:34:46 -07:00
  • aadd94a8d0 Remove some old files Kevin Wu 2022-09-08 15:18:38 -07:00
  • 34a821784f Fix cath again Kevin Wu 2022-09-08 15:11:19 -07:00
  • 6f32e0dd43 Fix cath download scripts Kevin Wu 2022-09-08 15:03:35 -07:00
  • 49d9c5e2d0 Add data download directions to README Kevin Wu 2022-09-08 14:48:00 -07:00
  • bfe703944c Merge branch 'main' of https://github.com/microsoft/protdiff into main Kevin Wu 2022-09-08 14:39:15 -07:00
  • 13a639eba3 Add black badget Kevin Wu 2022-09-08 14:39:04 -07:00
  • 154ad2476e Create pylint.yml Kevin Wu 2022-09-08 14:36:12 -07:00
  • 78dbf9c219 Remove more unused code Kevin Wu 2022-09-08 14:29:50 -07:00
  • 339f2ab26f Fix failing data unit tests Kevin Wu 2022-09-08 14:25:43 -07:00
  • a809146c91 More readme updates Kevin Wu 2022-09-08 14:23:10 -07:00
  • 458061e409 README updates Kevin Wu 2022-09-08 14:20:20 -07:00
  • 62cf565ed5 Amulet script updates Kevin Wu 2022-09-08 14:17:22 -07:00
  • b30d16aa8d Remove deprecated tests Kevin Wu 2022-09-08 14:12:27 -07:00
  • 4e979032b8 Redefine datasets Kevin Wu 2022-09-08 14:00:12 -07:00
  • c3d9ef6bf0 Remove some unused args in config json Kevin Wu 2022-09-08 13:42:22 -07:00
  • f361b6bcc2 Remove old code Kevin Wu 2022-09-08 13:42:09 -07:00
  • 1f060bd63e Evaluation of which angles are needed to reconstruct a protein Kevin Wu 2022-09-08 10:40:17 -07:00
  • 0214b64db6 UPdate the NERF reconstruction code to return path to file it writes. This allows it to signal failure with an empty string Kevin Wu 2022-09-08 10:38:45 -07:00
  • 2bb9108c67 Relax tolerance Kevin Wu 2022-09-07 22:34:51 -07:00
  • 827504f3c9 Typo fix Kevin Wu 2022-09-07 22:32:07 -07:00
  • 4d6a5ab321 Implement a float-tolerant comparison check Kevin Wu 2022-09-07 22:29:31 -07:00
  • 15d99c77ec Disable some checks onmodulo with wrapped range - may fail due to rounding error Kevin Wu 2022-09-07 22:17:54 -07:00
  • 0c09cda312 More detailed logging Kevin Wu 2022-09-07 22:14:05 -07:00
  • e32b81e37c Add biotite dependency Kevin Wu 2022-09-07 22:10:29 -07:00
  • 42283df480 Fix nan errors in data loader Kevin Wu 2022-09-07 21:56:39 -07:00
  • 364e8cc47f Fixes for using new featurization in data loader Kevin Wu 2022-09-07 21:51:57 -07:00
  • a352af6624 Make wrapped mean tolerante of nan values Kevin Wu 2022-09-07 21:37:16 -07:00
  • 377ab9ae07 Better error handling Kevin Wu 2022-09-07 19:21:21 -07:00
  • cbe9a53a38 Unused code for getting secondary structures Kevin Wu 2022-09-07 18:32:30 -07:00
  • b7b72b7aee Add bond info Kevin Wu 2022-09-07 18:05:46 -07:00
  • 0e14869130 Additional tests Kevin Wu 2022-09-07 17:56:36 -07:00
  • 85f0a1788e Set b factors Kevin Wu 2022-09-07 17:39:49 -07:00
  • 5915afd2af Configurable centering of coords Kevin Wu 2022-09-07 17:33:24 -07:00
  • 2310246848 Test that NERF can reconstruct backbones Kevin Wu 2022-09-07 17:16:40 -07:00
  • 29735be0dd Ease directory checks Kevin Wu 2022-09-07 17:00:08 -07:00
  • 35065ec005 Fix offset in setting tau angle Kevin Wu 2022-09-07 16:51:45 -07:00
  • ea66a91c91 More angles support Kevin Wu 2022-09-07 16:49:14 -07:00
  • d915c46cba More support for distances Kevin Wu 2022-09-07 16:30:17 -07:00
  • 29eafbaa8e Additional angle support Kevin Wu 2022-09-07 16:26:58 -07:00
  • 940054d8d8 Flexibility in setting additional angles Kevin Wu 2022-09-07 16:09:45 -07:00
  • 95c8bf9f21 Initial support for setting an array of bond angles/distances Kevin Wu 2022-09-07 15:56:14 -07:00
  • 12c3bbc680 New code to get angles using biotite backend Kevin Wu 2022-09-07 15:34:34 -07:00
  • e5140030e0 Set occupancy Kevin Wu 2022-09-07 15:02:00 -07:00
  • b212b06d53 Import typo fixes Kevin Wu 2022-09-07 14:51:53 -07:00
  • d08626a938 Remove unused nerf backends Kevin Wu 2022-09-07 14:48:23 -07:00
  • 36d2aa0fb3 Test personal nerf implementation -- better but still has issues Kevin Wu 2022-09-07 14:45:27 -07:00
  • 0c4e3c8b13 Simplify implementation of building by NERF Kevin Wu 2022-09-07 14:39:50 -07:00