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  • 18c865338d Update README.md with DOI main Kevin Wu 2023-12-12 09:55:03 -08:00
  • a6c3862353 Unused script cleanup v0.0.1 Kevin Wu 2023-12-12 09:51:51 -08:00
  • 69cd4f57eb Remove debugging plots Kevin Wu 2023-12-12 09:46:48 -08:00
  • 37d0a6da88 REplace reconstruction barplot with boxplot. Kevin Wu 2023-12-12 09:22:18 -08:00
  • ac28993b0a Add plot of designability by secondary structure Kevin Wu 2023-10-29 20:09:47 -07:00
  • 36e83beec2 Relaxation plots Kevin Wu 2023-10-25 22:04:16 -07:00
  • e3c18d1a11 Improvements to TMscore script interface Kevin Wu 2023-10-22 21:30:20 -07:00
  • fb5bc22929 Ability to specify threads Kevin Wu 2023-10-22 16:28:08 -07:00
  • d0dcbc3b6c Wrapper to run FASPR Kevin Wu 2023-10-22 16:27:31 -07:00
  • 5c95c4ab47 Report num parameters Kevin Wu 2023-10-22 00:15:17 -07:00
  • c5dc66c90a Add usage for VDW Kevin Wu 2023-10-21 19:51:38 -07:00
  • 88bdb63574 Tweak tmalign library to have basic functionality as a script Kevin Wu 2023-10-21 15:29:38 -07:00
  • d402f6655d Simple wrapper for pyrosetta structure relaxation Kevin Wu 2023-10-21 13:59:58 -07:00
  • c29a9a7422 Update plots Kevin Wu 2023-09-29 17:23:19 -07:00
  • a5c35330a7 Update plot labels Kevin Wu 2023-09-29 17:05:10 -07:00
  • b168f294d4 Swap panel ordering Kevin Wu 2023-09-27 23:04:24 -07:00
  • 36c36101a1 Update scissor effect plots Kevin Wu 2023-09-27 22:40:01 -07:00
  • d35cd38f86 Update test set denoising result Kevin Wu 2023-09-27 21:04:48 -07:00
  • 3f910a61e8 Update plots Kevin Wu 2023-09-24 17:27:11 -07:00
  • 1528d844ba Add plDDT plots Kevin Wu 2023-09-24 17:23:26 -07:00
  • b1cb68729d Update generation time plots Kevin Wu 2023-09-19 23:21:02 -07:00
  • 21ef7d1a31 Update lever plots Kevin Wu 2023-09-19 00:41:14 -07:00
  • b709372f97 Update UMAP plots Kevin Wu 2023-09-17 20:34:59 -07:00
  • 110b6ec577 Update visualization Kevin Wu 2023-09-17 19:29:06 -07:00
  • c9e36e2acb Typo fix Kevin Wu 2023-09-17 18:49:42 -07:00
  • a028edbbf3 Plot update Kevin Wu 2023-09-17 16:47:28 -07:00
  • 64a9726c14 Plot update Kevin Wu 2023-09-17 16:19:45 -07:00
  • 4ccb15b07f Plot update Kevin Wu 2023-09-17 16:19:14 -07:00
  • f472731d50 Add plot looking at sctm vs len continuous Kevin Wu 2023-09-17 16:16:16 -07:00
  • 5fc12767e8 Add plot describing generation time Kevin Wu 2023-09-17 14:26:36 -07:00
  • 8e784add04 Speed up sampling by truncating input padding regions. Kevin Wu 2023-09-17 12:18:44 -07:00
  • b59a937c9a Lever effect analysis. Kevin Wu 2023-09-09 20:49:33 -07:00
  • a2cf8b57cd Update plots Kevin Wu 2023-09-09 20:39:33 -07:00
  • 95b2a00f26 GIT UMAP plots Kevin Wu 2023-09-09 20:38:14 -07:00
  • 612efe49fb Better handling of inputs Kevin Wu 2023-09-07 14:47:45 -07:00
  • e917c2843d Update animation Kevin Wu 2023-09-06 10:36:25 -07:00
  • edb66ac711 Updates to pymol visualization Kevin Wu 2023-09-05 23:25:24 -07:00
  • b9706eaf20 Script to add oxygen to backbone Kevin Wu 2023-09-05 22:54:54 -07:00
  • 818ec9c38d Code to check for van der waals clashes Kevin Wu 2023-09-04 23:04:30 -07:00
  • 68b8d13350 Bump scipy from 1.9.1 to 1.10.0 dependabot/pip/scipy-1.10.0 dependabot[bot] 2023-07-06 23:28:02 +00:00
  • ed7a27d8e4 Add SuperBio link Kevin Wu 2023-06-20 11:47:31 -07:00
  • 49d7b7057e Bump transformers from 4.11.3 to 4.30.0 dependabot/pip/transformers-4.30.0 dependabot[bot] 2023-06-12 21:33:00 +00:00
  • 7f65baf0d4 Scipt-ify lddt Kevin Wu 2023-06-08 11:09:15 -07:00
  • 44e7b9f3b8 Code to calculate lddt Kevin Wu 2023-06-07 15:03:07 -07:00
  • e2d1a86cfd Update README Kevin Wu 2023-04-28 11:57:06 -07:00
  • 12fa730caf Vectorize some code, fix some bugs Kevin Wu 2023-04-13 10:54:44 -07:00
  • 902b0301d2 Write out the names of all files used in training splits Kevin Wu 2023-03-30 13:51:13 -07:00
  • 106b3632ac Update gromacs script to add a constant amount of water Kevin Wu 2023-03-30 13:50:45 -07:00
  • c5a557e8fa Fix inverted filenames Kevin Wu 2023-03-30 12:03:50 -07:00
  • 6dbb3117f6 Improved error handling Kevin Wu 2023-03-29 10:41:27 -07:00
  • 372ec85564 Path fixes Kevin Wu 2023-03-09 23:35:17 -08:00
  • 403e747368 Multi input support for docker wrapper Kevin Wu 2023-03-09 23:02:19 -08:00
  • fe45834ae7 Misc. improvements to file naming Kevin Wu 2023-03-09 22:51:02 -08:00
  • de5659e8be Logging and bugfixes Kevin Wu 2023-03-09 17:44:43 -08:00
  • 03ef32eb96 Misc. fixes Kevin Wu 2023-03-09 16:40:31 -08:00
  • 646e1b655e Ability to speicfy threads in docker Kevin Wu 2023-03-09 16:11:06 -08:00
  • 9ca513f5e1 Threading updates Kevin Wu 2023-03-09 16:02:30 -08:00
  • 96d6bf2bef Parallelize aa splicing Kevin Wu 2023-03-09 15:55:48 -08:00
  • 224d19f5eb Add table of PDB ids to compare Kevin Wu 2023-03-09 14:21:21 -08:00
  • 5de09e00e4 Minor bugfix Kevin Wu 2023-03-08 21:25:49 -08:00
  • dd7560611a Basic script to splice AA sidechains on Kevin Wu 2023-03-08 20:49:43 -08:00
  • ccb7d18d19 Add a docker wrapper for gromacs Kevin Wu 2023-03-07 22:59:44 -08:00
  • bbcf914050 Performance optimziations Kevin Wu 2023-03-07 16:34:22 -08:00
  • 868524699f Docker file for GROMACS Kevin Wu 2023-03-07 15:58:45 -08:00
  • ef740c6d39 Speed tweaks Kevin Wu 2023-03-07 15:58:32 -08:00
  • dfd6842643 Tweaks to accept files Kevin Wu 2023-03-07 15:49:25 -08:00
  • 560f0f6b2c Add mdp files Kevin Wu 2023-03-07 15:03:23 -08:00
  • 5467ffb9d5 Misc. fixes Kevin Wu 2023-03-07 14:52:53 -08:00
  • 795cbf7656 Support for gmx binary Kevin Wu 2023-03-07 14:50:38 -08:00
  • de5592490d Reorg files Kevin Wu 2023-03-07 14:14:19 -08:00
  • 725afc32bd Add CLI Kevin Wu 2023-03-07 14:09:45 -08:00
  • ac83b15a28 Misc. tweaks Kevin Wu 2023-03-07 11:44:48 -08:00
  • c3c06eb950 Flesh out gromacs script Kevin Wu 2023-03-07 10:45:25 -08:00
  • 1b8a85213b Code + tests to graft on AA residues Kevin Wu 2023-03-06 16:20:56 -08:00
  • 592e4ec32a Add some dummy files containing all residues and a corresponding "folded" structure Kevin Wu 2023-03-06 11:50:58 -08:00
  • 43a6b7a367 Code to describe/save AA side chains as relative sets of angles/distances Kevin Wu 2023-03-06 11:41:21 -08:00
  • f3c3c63f1c Script to do gromacs Kevin Wu 2023-02-14 20:00:57 -08:00
  • 5dc974b72f Also save metadata Kevin Wu 2023-02-13 23:40:19 -08:00
  • 52db3a274a Save reconst scores to json Kevin Wu 2023-02-13 23:12:47 -08:00
  • a162535ad0 Parallelize computation of reconstruction error Kevin Wu 2023-02-13 23:08:10 -08:00
  • 5debc4f733 Add a script to do partial reconstruction Kevin Wu 2023-02-13 19:56:51 -08:00
  • 157aa90941 Centralize code for reconstruction Kevin Wu 2023-02-13 17:58:04 -08:00
  • cb306a3e1b Code to manually set angle means Kevin Wu 2023-02-13 16:18:56 -08:00
  • 6a05cb4104 Skip cache cleaning if not using cache; allow for passing dataset a list of PDB files Kevin Wu 2023-02-13 16:02:06 -08:00
  • 5ecd655128 Support for reading in pdb2git scores Kevin Wu 2023-02-09 21:27:26 -08:00
  • 02dcfa85fe Visual tweaks Kevin Wu 2023-02-09 18:15:39 -08:00
  • a6b7e7f1d5 Bump torch from 1.12 to 1.13.1 dependabot/pip/torch-1.13.1 dependabot[bot] 2023-02-08 20:50:00 +00:00
  • ec2e5e9902 MDS plotting code Kevin Wu 2023-02-08 12:49:13 -08:00
  • c17bc360b5 Add sklearn requirement (for MDS) Kevin Wu 2023-02-08 10:57:38 -08:00
  • 5b1ff15994 Formatting updates Kevin Wu 2023-02-08 10:50:33 -08:00
  • 1409aae763 Allow less verbose labeling Kevin Wu 2023-02-07 16:21:45 -08:00
  • 111e27ada1 Plotting tweaks Kevin Wu 2023-02-07 12:02:15 -08:00
  • 19525239da Update pymol script to use rainbow output Kevin Wu 2023-02-04 18:08:55 -08:00
  • e27d8b581f Mor eplotting code Kevin Wu 2023-02-04 17:49:27 -08:00
  • e3cf719038 Merge pull request #12 from divnori/install-required-packages Kevin Wu 2023-02-04 13:03:39 -08:00
  • 20ffb43109 Added install_requires to setup.py Divya 2023-01-24 18:26:55 -05:00
  • a55059e654 Parallelize computation of seocndary structures Kevin Wu 2022-12-16 12:45:56 -08:00
  • df60612ffa README update Kevin Wu 2022-12-12 11:58:18 -08:00
  • 79f7913e64 Remove old code Kevin Wu 2022-12-09 15:46:49 -08:00
  • 09f9f15e37 Support for specifying dataset in training script Kevin Wu 2022-12-08 11:04:36 -08:00