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  • d463a3eb60 More fixes Kevin Wu 2022-09-22 15:54:59 -07:00
  • 7407188dcf Misc. bugfixes Kevin Wu 2022-09-22 15:51:20 -07:00
  • 8e17395a13 Initial incorporation of raw coordinate training Kevin Wu 2022-09-22 15:46:47 -07:00
  • d5a70c2d75 Support for coordinate based datasets Kevin Wu 2022-09-22 14:52:30 -07:00
  • b0c5f28fee Also pre-cache coordinates Kevin Wu 2022-09-22 14:24:53 -07:00
  • fa52ec1a2d Code to extract backbone coords from pdb Kevin Wu 2022-09-22 14:07:05 -07:00
  • 32ea22d056 Import cleanup Kevin Wu 2022-09-22 12:17:10 -07:00
  • 52775ec7ec Simple script to generate randomly sampled angles Kevin Wu 2022-09-22 10:29:51 -07:00
  • 1bc3a5a0f1 Add KLdivergence Kevin Wu 2022-09-21 11:48:47 -07:00
  • b252b60b23 More plotting fixes Kevin Wu 2022-09-21 11:14:03 -07:00
  • 71d5b5a288 Plotting tweaks Kevin Wu 2022-09-21 10:39:18 -07:00
  • f27e3ea531 Code refactor Kevin Wu 2022-09-21 10:14:34 -07:00
  • a76d8a9dc8 Yay plotting tweaks Kevin Wu 2022-09-21 09:58:35 -07:00
  • 066186ae43 More plotting tweaks Kevin Wu 2022-09-20 21:55:08 -07:00
  • 921e1c7dfa Merge branch 'main' of github.com:microsoft/protdiff into main Kevin Wu 2022-09-20 21:36:26 -07:00
  • ac7a8f06dc Plotting tweaks Kevin Wu 2022-09-20 21:36:19 -07:00
  • 9e5ddc6155 Create codeql-analysis.yml alt-ellyse 2022-09-20 17:16:58 -07:00
  • fe8c969722 Report Spearman's correlations Kevin Wu 2022-09-20 16:09:47 -07:00
  • 75d5d4bde1 Ability to filter structres by tmscore Kevin Wu 2022-09-20 13:37:36 -07:00
  • 12de5e2280 Initial code to get clustering of PDB structures Kevin Wu 2022-09-20 13:18:21 -07:00
  • 1b6dfbf991 Update clean set again Kevin Wu 2022-09-19 17:32:39 -07:00
  • 2d5664147d Update clean/noisy example Kevin Wu 2022-09-19 17:22:51 -07:00
  • 7a19115455 Report more metrics Kevin Wu 2022-09-19 16:44:03 -07:00
  • 0604f7e8d9 Code formatting Kevin Wu 2022-09-19 14:20:11 -07:00
  • bcd5fe4700 Use 8 instead of 10 structures for consistency in scTM Kevin Wu 2022-09-19 14:19:32 -07:00
  • 0b467cb322 Report percentage designable for each length category Kevin Wu 2022-09-19 14:14:17 -07:00
  • cd353bddfc Write alpha/beta counts Kevin Wu 2022-09-19 11:05:22 -07:00
  • d0bf1ca21d Tweak plotting, write csv file Kevin Wu 2022-09-19 10:55:38 -07:00
  • bcd0e846d7 Fix issue with sampling Kevin Wu 2022-09-15 15:28:45 -07:00
  • ad8b5a458a Remove debug code Kevin Wu 2022-09-15 15:11:52 -07:00
  • 671c444ff5 Plotting improvements Kevin Wu 2022-09-15 15:10:58 -07:00
  • 9cb7bca32f Ability to only do secondary structures for sequences of a max len Kevin Wu 2022-09-15 14:55:58 -07:00
  • ed3a4eff87 Simplfy some code, plot against test instead of train Kevin Wu 2022-09-15 14:44:37 -07:00
  • bead02473a More plotting, including CDF Kevin Wu 2022-09-15 14:30:58 -07:00
  • b494b067d0 Implement sampling sweep of lengths Kevin Wu 2022-09-15 14:07:20 -07:00
  • 9778da606b Add scTM scores histogram by length Kevin Wu 2022-09-15 12:56:02 -07:00
  • 40c3679ce3 Code to write a jointplot of scTM and max training TM Kevin Wu 2022-09-15 11:27:59 -07:00
  • 03dd11d3c1 Make omegafold self tm score less rigid in matchine files Kevin Wu 2022-09-15 10:32:59 -07:00
  • ba5e34ed03 Only fold sequences that are valid Kevin Wu 2022-09-14 22:36:05 -07:00
  • e4ea9a97fb Fix issue where illegal sequences are sometimes generated by ESM Kevin Wu 2022-09-14 22:29:01 -07:00
  • 07eaca272a Fix typo Kevin Wu 2022-09-14 22:28:33 -07:00
  • d1662e54bc Write scTM scores with the name Kevin Wu 2022-09-14 15:06:23 -07:00
  • 0ed8ab8a7b Automatically determine chain ID Kevin Wu 2022-09-14 14:12:13 -07:00
  • cc8072b696 Code to setup calculation of scTM score baselines distribution Kevin Wu 2022-09-14 13:16:15 -07:00
  • 095ea52169 Default zero_center to true Kevin Wu 2022-09-14 12:04:07 -07:00
  • cfbd6aa6a0 Remove colabfold wrappers Kevin Wu 2022-09-14 11:57:12 -07:00
  • f00cfc881b Misc. Kevin Wu 2022-09-13 19:27:31 -07:00
  • 23448d1473 Fix issue with PSEA sometimes querying for the wrong chain ID Kevin Wu 2022-09-13 19:14:53 -07:00
  • 89b5432728 Rename file Kevin Wu 2022-09-13 19:01:27 -07:00
  • 49021c1163 Support for DSSP backend Kevin Wu 2022-09-13 19:00:08 -07:00
  • 5a1dcb2e38 Refactor secondary structure code Kevin Wu 2022-09-13 17:47:01 -07:00
  • dd101c8d3d Filter out "failed" runs of counting Kevin Wu 2022-09-13 17:37:32 -07:00
  • 18c7f05e21 Script to calculate cocurrences of various secondary structures Kevin Wu 2022-09-13 17:23:45 -07:00
  • 48fbd3ef7d Simplfy readme instructions Kevin Wu 2022-09-13 16:39:43 -07:00
  • 8f3cf1ff0a Remove statements that caused model collision Kevin Wu 2022-09-13 14:34:19 -07:00
  • e67a9870b6 Snapshot the model when we do sampling Kevin Wu 2022-09-13 11:52:17 -07:00
  • 97a6028f46 Add tests for model loading/saving Kevin Wu 2022-09-13 11:35:06 -07:00
  • 8a4016be3b Add small model for testing Kevin Wu 2022-09-13 09:46:37 -07:00
  • 5838a40e3d Add mini model for testing Kevin Wu 2022-09-13 09:30:08 -07:00
  • 35bb1d5794 Code to save model after loading from pretrained Kevin Wu 2022-09-13 09:26:58 -07:00
  • ccafcd279d Annotate training ramachandran plot with secondary structures Kevin Wu 2022-09-12 22:09:21 -07:00
  • 6166688c0f Add configurable batch size Kevin Wu 2022-09-12 21:06:52 -07:00
  • b2918dfb09 Code to generate a combo plot for generated angles Kevin Wu 2022-09-12 20:41:44 -07:00
  • 513ffc71bd Refactor plotting code for distribution comparisons Kevin Wu 2022-09-12 20:18:51 -07:00
  • 559a77d63f Reorganize code Kevin Wu 2022-09-12 19:58:30 -07:00
  • c45c4cda68 Slurm updates Kevin Wu 2022-09-12 17:44:01 -07:00
  • 258f702fa3 Reorganize slurm scripts Kevin Wu 2022-09-12 17:42:46 -07:00
  • 8c58f3ef50 Remove unnecessary imports Kevin Wu 2022-09-12 17:42:41 -07:00
  • 57278dcfad Fully remove trRosetta angles stuff Kevin Wu 2022-09-12 17:27:55 -07:00
  • e0890e4d8b Remove old notebook Kevin Wu 2022-09-12 17:27:33 -07:00
  • 48ff9fb8fa Merge branch 'main' of github.com:microsoft/protdiff into main Kevin Wu 2022-09-12 17:23:54 -07:00
  • 983db96319 CUDA check Kevin Wu 2022-09-12 17:23:49 -07:00
  • ac5446093d Add slurm training script Kevin Wu 2022-09-12 17:23:01 -07:00
  • ba8f0d7831 Remove use of sequence-models Kevin Wu 2022-09-12 17:17:08 -07:00
  • ceb67d5aed README updates Kevin Wu 2022-09-12 16:55:53 -07:00
  • 715a105692 Add more json configs for further experiments Kevin Wu 2022-09-12 13:59:20 -07:00
  • b195d809c7 Reorganize config jsons Kevin Wu 2022-09-12 13:45:58 -07:00
  • 2f9c68bbba Implement code path to discard too-long sequences Kevin Wu 2022-09-12 13:40:08 -07:00
  • 5e55a04f94 Misc. Kevin Wu 2022-09-12 01:17:53 -07:00
  • 2df9e0397b Ability to do tm scores for only a subset Kevin Wu 2022-09-12 01:16:25 -07:00
  • 9abe71e6d2 Attribute passthrough Kevin Wu 2022-09-12 01:08:20 -07:00
  • d757501c02 Refactor for code sharing Kevin Wu 2022-09-12 00:57:36 -07:00
  • 29e4e327a6 scTM score calculation for omegafold outputs Kevin Wu 2022-09-12 00:40:39 -07:00
  • 25f15145c5 Bugfix Kevin Wu 2022-09-12 00:32:33 -07:00
  • b195a710f9 Toggle parallel running for tmalign max over refs Kevin Wu 2022-09-12 00:14:31 -07:00
  • b8e61c19f9 Fix typing issue Kevin Wu 2022-09-11 21:53:26 -07:00
  • f648cfaccf Minor markdown formatting Kevin Wu 2022-09-11 21:52:42 -07:00
  • 10171fcf9e Fix issue with not reading full fasta input Kevin Wu 2022-09-11 21:48:25 -07:00
  • b7b18f8be9 Redirect stdout Kevin Wu 2022-09-11 21:47:12 -07:00
  • 6e77dbaa48 Code to split omegafold inputs into two Kevin Wu 2022-09-11 21:42:22 -07:00
  • be4ee901fe More readme updates Kevin Wu 2022-09-11 17:54:22 -07:00
  • 34a07851ca README updates Kevin Wu 2022-09-11 17:40:02 -07:00
  • 4918af6890 Update gif to no watermark Kevin Wu 2022-09-11 16:03:00 -07:00
  • cb2e6a0865 Remove core cap Kevin Wu 2022-09-11 15:54:06 -07:00
  • a359ff6502 Support to batch convert folder of PDBs to folder of PNGs Kevin Wu 2022-09-11 15:39:58 -07:00
  • b950b2218a Update installation instructions Kevin Wu 2022-09-11 12:22:13 -07:00
  • 8ff8145595 Add a gif to the readme Kevin Wu 2022-09-10 20:50:55 -07:00
  • c1a9f810a4 README update Kevin Wu 2022-09-10 20:43:19 -07:00
  • 28b55b3705 Add exmple usage Kevin Wu 2022-09-10 19:27:57 -07:00
  • 2c93b97e4c More control over gif creation process Kevin Wu 2022-09-10 19:24:54 -07:00