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  • 3f88b808d6 Typo fixes Kevin Wu 2022-09-07 14:36:54 -07:00
  • d34eeda8de Cache cartesian coords Kevin Wu 2022-09-07 14:32:39 -07:00
  • 82aa390b3d Add implementation of NERF builder Kevin Wu 2022-09-07 14:26:06 -07:00
  • 149fe8a72b Simplify dihedral calculation code and add tests Kevin Wu 2022-09-07 12:21:57 -07:00
  • b9c749eae2 Initial working dihedral reversal Kevin Wu 2022-09-07 11:43:17 -07:00
  • 6768384e21 Implement two additional backends for internal coordinates to XYZ. Not working. Kevin Wu 2022-09-06 23:18:35 -07:00
  • 6d58517cbd Throw error if cannot sample value Kevin Wu 2022-09-06 19:44:44 -07:00
  • 7e898b7704 Add 1crn Kevin Wu 2022-09-06 19:29:24 -07:00
  • 51825e801b Config updates Kevin Wu 2022-09-07 01:38:02 +00:00
  • 8e86d625b2 Notebook debugging why reconstructed proteins look so bad Kevin Wu 2022-09-07 01:21:15 +00:00
  • b2da16fd22 More robust handling of values in creating new chain Kevin Wu 2022-09-07 01:14:28 +00:00
  • 818add061d Add py3dmol dependency Kevin Wu 2022-09-07 00:41:03 +00:00
  • d21ab3a6d8 Simplfy some path logic Kevin Wu 2022-09-07 00:34:02 +00:00
  • 79b2fbe60d epoch timing and type annotations Kevin Wu 2022-09-06 23:31:24 +00:00
  • 718783ad3e Dryrun toggle Kevin Wu 2022-09-06 23:16:50 +00:00
  • 9822022e66 Expose sequence length dataset args in training script Kevin Wu 2022-09-06 23:02:53 +00:00
  • 84bb7dbcc5 Implement minimum sequence cutoff Kevin Wu 2022-09-06 15:19:23 -07:00
  • 5c4c6d50a1 Options to control how we trim examples that are too long Kevin Wu 2022-09-06 13:09:29 -07:00
  • 9c8ec98234 Script to calculate sctms cores Kevin Wu 2022-09-06 11:21:23 -07:00
  • 176c57e9e5 Misc. tweaks Kevin Wu 2022-09-06 11:15:07 -07:00
  • 3f552cc204 Make ESM outdir specifiable Kevin Wu 2022-09-04 13:14:15 -07:00
  • a1edd2c36e Separate out the outputs for colabfold Kevin Wu 2022-09-04 13:13:58 -07:00
  • b33ecede32 Basic script to split inputs across GPUS for colabfold Kevin Wu 2022-09-04 13:01:20 -07:00
  • 74fab4370a Calculate pdb scores Kevin Wu 2022-09-02 18:03:22 -07:00
  • 20dafc3689 Rewrite sampling code Kevin Wu 2022-09-02 17:54:51 -07:00
  • 7c2bb3bbd8 Minor fix for typing (tensor vs np array) in sampling code Kevin Wu 2022-09-02 14:59:10 -07:00
  • d2f6a45f4e Basic tests for tmalign wrapper Kevin Wu 2022-09-02 14:13:51 -07:00
  • d5087c2172 Move most tests for modulo with wrapped range as unit tests Kevin Wu 2022-09-02 13:34:59 -07:00
  • ffaffc5d1f Cleanup old code Kevin Wu 2022-09-01 23:10:49 +00:00
  • d18318b1cf black Kevin Wu 2022-09-01 15:34:37 -07:00
  • 00ea19dcce Write descriptive sequence names in fasta Kevin Wu 2022-09-01 15:14:07 -07:00
  • 2d32054500 Flesh out the residues generation script to handle entire folders Kevin Wu 2022-09-01 14:59:19 -07:00
  • cd30f99176 Add TMscores plot Kevin Wu 2022-09-01 10:30:00 -07:00
  • ddb6d05fde Convenience functions to get masked means Kevin Wu 2022-08-31 16:00:32 -07:00
  • cffc794833 Automatically un-shift the sampled data if data was originally shifted Kevin Wu 2022-08-31 16:00:12 -07:00
  • fdb3c2bf96 Ability to disable shfiting to zero center Kevin Wu 2022-08-31 15:23:10 -07:00
  • 1b06fd2c53 Gypo bugfix Kevin Wu 2022-08-31 15:03:03 -07:00
  • decc2bc7d0 Fix logging Kevin Wu 2022-08-31 13:41:35 -07:00
  • e756ab1cb3 Enable fast = True by default Kevin Wu 2022-08-31 13:41:10 -07:00
  • 170fcfa097 -fast flag support for TMalign Kevin Wu 2022-08-31 13:29:49 -07:00
  • 641f7e04f9 Easy access to a dataset's constituent pdb files Kevin Wu 2022-08-31 13:19:26 -07:00
  • 49342050f3 Add parallelized tmscore calculation max across set Kevin Wu 2022-08-31 13:18:02 -07:00
  • 84f75fc2a5 Remove old unused code Kevin Wu 2022-08-31 13:06:13 -07:00
  • 85d9b8ee35 Wrapper for TMalign Kevin Wu 2022-08-31 11:15:17 -07:00
  • bd7ffdd7f2 Update yaml Kevin Wu 2022-08-30 23:21:46 -07:00
  • f323ccf680 Update amlt yaml Kevin Wu 2022-08-30 23:16:19 -07:00
  • 6a8ade12d6 Disable zero centering by default, add config with zero centering Kevin Wu 2022-08-30 23:16:05 -07:00
  • c979fcef2b Support for axis argument in wrapped mean, use wrapped mean for offset Kevin Wu 2022-08-30 19:30:38 -07:00
  • acc4abdb5a update documentation for wrapped mean function Kevin Wu 2022-08-30 19:27:11 -07:00
  • 80bb4b8c9f Test wrapped mean function Kevin Wu 2022-08-30 19:26:02 -07:00
  • 187b924386 Fix issue with wrapping around pi with subclasses Kevin Wu 2022-08-30 18:58:29 -07:00
  • 5837b10cea Enable togging of zero centering of features Kevin Wu 2022-08-30 16:04:48 -07:00
  • 622e32fcfd Code to zero center means in cath dataset Kevin Wu 2022-08-30 15:42:16 -07:00
  • 48f40df827 Auto set outout filename Kevin Wu 2022-08-30 09:34:25 -07:00
  • 80d5854d48 Basic script to go from pdb to residues Kevin Wu 2022-08-29 18:46:47 -07:00
  • 3475f86d0b Update Kevin Wu 2022-08-29 17:25:04 -07:00
  • 56058f344e Update sampled proteins with sweep across angles to set Kevin Wu 2022-08-29 17:24:48 -07:00
  • e4274925d2 Code documentation updates Kevin Wu 2022-08-29 17:23:27 -07:00
  • 450c503338 Improved logging Kevin Wu 2022-08-29 17:19:21 -07:00
  • 27599ab274 Update sampling of non-predicted values to use empirical distribution Kevin Wu 2022-08-29 16:34:37 -07:00
  • 822ca5ca95 Fix error with unused parameters Kevin Wu 2022-08-29 10:13:02 -07:00
  • a19595fd52 Relative embedding json Kevin Wu 2022-08-29 07:42:57 +00:00
  • a195ad708b Disable some reporting -- causes weird subclassing issues Kevin Wu 2022-08-29 07:32:51 +00:00
  • 757bbad912 Add script to install inverse conda env Kevin Wu 2022-08-28 23:14:05 -07:00
  • e821d16d8d Add initial generation of PDB structure Kevin Wu 2022-08-28 22:41:21 -07:00
  • 6c0e429342 Add listing of constants Kevin Wu 2022-08-28 20:42:15 -07:00
  • 4611c02682 Log feature mean/var Kevin Wu 2022-08-28 20:36:48 -07:00
  • 16118116e0 Code extract feature mean/var Kevin Wu 2022-08-28 20:25:51 -07:00
  • 4f8a5a6b67 Add reduced model Kevin Wu 2022-08-28 22:45:33 +00:00
  • e399444a01 Parallelize KL divergence over timesteps code Kevin Wu 2022-08-28 14:32:08 -07:00
  • bcd4ac7f11 Simplify some plotting code Kevin Wu 2022-08-28 13:08:18 -07:00
  • bb3d30ce57 Reimplement plotting validation distances at timestep t to dynamically use feature names Kevin Wu 2022-08-28 12:50:44 -07:00
  • 97c7bde6d6 Pass through feature_names and feature_is_angular for noised dset Kevin Wu 2022-08-28 12:49:42 -07:00
  • 2d241a8337 Sample from an even later run Kevin Wu 2022-08-28 12:34:55 -07:00
  • b407a93cc7 Add dihedrals only dataset Kevin Wu 2022-08-28 12:34:45 -07:00
  • f3083bad39 Specify biopython version Kevin Wu 2022-08-28 06:35:18 +00:00
  • d90ca90ae8 Implement linear warmup LR scheduler Kevin Wu 2022-08-27 22:44:07 -07:00
  • 1bd98b0331 Later epoch Kevin Wu 2022-08-27 21:57:56 -07:00
  • f8390074a0 More checks Kevin Wu 2022-08-27 20:47:36 -07:00
  • 3ea6d5465a Simplify implementation of angles only dataset while enabling more flexibility Kevin Wu 2022-08-27 20:41:47 -07:00
  • 37e78f20c0 Add ramachandran plots Kevin Wu 2022-08-27 18:42:36 -07:00
  • 26e2a6cbdd Did not save changes lol oops Kevin Wu 2022-08-27 18:32:00 -07:00
  • cf0ba58713 Add generated Ramachandran plots Kevin Wu 2022-08-27 18:31:53 -07:00
  • 95669c9d43 Code to plot joint KDE (useful for Ramachandran plots) Kevin Wu 2022-08-27 18:20:56 -07:00
  • 3d2662e1a3 More detailed loss plots Kevin Wu 2022-08-27 17:53:41 -07:00
  • 0189ecc026 More flexibility in specifying which model to load Kevin Wu 2022-08-27 17:16:07 -07:00
  • 46e244ce98 More flexibility in specifying what losses to plot Kevin Wu 2022-08-27 17:15:45 -07:00
  • 907daab1e5 Add config json for full run canonical angles no distance Kevin Wu 2022-08-26 23:25:07 +00:00
  • 9c0eaf729d Incorporate angles only dataset to training script Kevin Wu 2022-08-26 22:53:18 +00:00
  • e9eb860b55 More tests Kevin Wu 2022-08-26 22:48:55 +00:00
  • 5a1764ce06 Typo fix Kevin Wu 2022-08-26 22:11:02 +00:00
  • 5b78ca5472 Basic unit tests for data loaders Kevin Wu 2022-08-26 22:10:44 +00:00
  • 972a1dddc8 Initial implemntation of a angles only CATH canonical dataset Kevin Wu 2022-08-26 21:55:29 +00:00
  • 3003026d95 Rerun sampling notebook with latest canonical angle model Kevin Wu 2022-08-26 21:46:36 +00:00
  • bb751fdf0f Plot KL divergence when initializing data loaders for training Kevin Wu 2022-08-26 21:41:40 +00:00
  • 96c2367c83 Tests for KL divergence code Kevin Wu 2022-08-26 21:40:41 +00:00
  • 435eedbd22 Typo bugfix Kevin Wu 2022-08-26 21:09:19 +00:00
  • 68b7b4d25a Misc cosmetic tweaks KL vs time plots Kevin Wu 2022-08-26 21:03:37 +00:00
  • 3b00fd7de2 Implement KL divergence from empirical distributions Kevin Wu 2022-08-26 20:05:14 +00:00
  • 9afa3716f4 Initial code to plot wasserstein distance Kevin Wu 2022-08-26 19:25:59 +00:00