64 Commits

Author	SHA1	Message	Date
Kevin Wu	12fa730caf	Vectorize some code, fix some bugs	2023-04-13 10:54:44 -07:00
Kevin Wu	1b8a85213b	Code + tests to graft on AA residues	2023-03-06 16:20:56 -08:00
Kevin Wu	24590bf817	Format updates	2022-11-08 14:41:39 -08:00
Kevin Wu	d1ccb7477f	Additional tests	2022-11-07 22:23:01 -08:00
Kevin Wu	a29fc8ca2c	Additional tests	2022-11-07 14:41:19 -08:00
Kevin Wu	d4646309e5	More tests	2022-10-31 15:30:35 -07:00
Kevin Wu	fabfb694cc	Fix some tests	2022-10-31 15:10:20 -07:00
Kevin Wu	e767a4f49a	More tests	2022-10-31 11:16:49 -07:00
Kevin Wu	732d6d7787	More tests	2022-10-31 10:57:50 -07:00
Kevin Wu	5e8b215c8d	Tests for pairwise distance loss	2022-10-30 19:41:55 -07:00
Kevin Wu	821488454e	Test that backbone building works with nan padding	2022-10-30 12:57:02 -07:00
Kevin Wu	3e4380cc50	More thorough tests	2022-10-30 12:26:16 -07:00
Kevin Wu	e1cd243be6	Batched nerf building	2022-10-21 15:08:17 -07:00
Kevin Wu	f62efd40f9	Additional testing for vectorized dihedral placement	2022-10-21 13:29:06 -07:00
Kevin Wu	9a994514c3	Vectorize calculation of NERF	2022-10-21 11:52:59 -07:00
Kevin Wu	0be75b5bc4	Implement NERF reconstruction with pytorch	2022-10-18 15:07:44 -07:00
Kevin Wu	fe7418e7e3	Make sure repeated running sampling code is reproducible	2022-10-13 10:22:22 -07:00
Kevin Wu	ecde05cb50	Fix for loading lightning module without lighttning	2022-10-04 20:01:37 -07:00
Kevin Wu	3f5408fe05	Add failing test case for loading without pytorch lightning	2022-10-04 19:46:27 -07:00
Kevin Wu	6ac88f7a44	Separate out base model from pytorch ligthning model	2022-10-04 19:36:09 -07:00
Kevin Wu	7e37d03563	Remove unused files	2022-09-29 03:22:25 -07:00
Kevin Wu	39d1999078	Fix test for data keys	2022-09-28 09:35:03 -07:00
Kevin Wu	070b7b8442	Fix tests importing	2022-09-27 13:58:22 -07:00
Kevin Wu	868d8781bf	Remove "kevin" from all files outside of scripts and jupyter	2022-09-25 23:23:44 -07:00
Kevin Wu	97a6028f46	Add tests for model loading/saving	2022-09-13 11:35:06 -07:00
Kevin Wu	8a4016be3b	Add small model for testing	2022-09-13 09:46:37 -07:00
Kevin Wu	ba8f0d7831	Remove use of sequence-models	2022-09-12 17:17:08 -07:00
Kevin Wu	1c0a066dab	Re-enable cache to a file named by hash	2022-09-09 14:31:38 -07:00
Kevin Wu	12c863c881	Move some doctests to unit tests	2022-09-08 23:02:18 -07:00
Kevin Wu	4a9e781d87	Fix issue where we would repeatedly zero-center and shfiting values over time	2022-09-08 16:02:40 -07:00
Kevin Wu	339f2ab26f	Fix failing data unit tests	2022-09-08 14:25:43 -07:00
Kevin Wu	b30d16aa8d	Remove deprecated tests	2022-09-08 14:12:27 -07:00
Kevin Wu	a352af6624	Make wrapped mean tolerante of nan values	2022-09-07 21:37:16 -07:00
Kevin Wu	5915afd2af	Configurable centering of coords	2022-09-07 17:33:24 -07:00
Kevin Wu	2310246848	Test that NERF can reconstruct backbones	2022-09-07 17:16:40 -07:00
Kevin Wu	d08626a938	Remove unused nerf backends	2022-09-07 14:48:23 -07:00
Kevin Wu	149fe8a72b	Simplify dihedral calculation code and add tests	2022-09-07 12:21:57 -07:00
Kevin Wu	b9c749eae2	Initial working dihedral reversal	2022-09-07 11:43:17 -07:00
Kevin Wu	d2f6a45f4e	Basic tests for tmalign wrapper	2022-09-02 14:13:51 -07:00
Kevin Wu	d5087c2172	Move most tests for modulo with wrapped range as unit tests	2022-09-02 13:34:59 -07:00
Kevin Wu	ffaffc5d1f	Cleanup old code	2022-09-01 23:10:49 +00:00
Kevin Wu	80bb4b8c9f	Test wrapped mean function	2022-08-30 19:26:02 -07:00
Kevin Wu	e9eb860b55	More tests	2022-08-26 22:48:55 +00:00
Kevin Wu	5a1764ce06	Typo fix	2022-08-26 22:11:02 +00:00
Kevin Wu	5b78ca5472	Basic unit tests for data loaders	2022-08-26 22:10:44 +00:00
Kevin Wu	96c2367c83	Tests for KL divergence code	2022-08-26 21:40:41 +00:00
Kevin Wu	1881f833c4	Add failing test. Dihedral reversal not really workingz	2022-08-24 23:39:53 +00:00
Kevin Wu	a287e93c02	Initial reversal of dihedral angle. Seems to work for simple test cases	2022-08-24 23:21:42 +00:00
Kevin Wu	faef8c97f8	Comprehensive tests for radian smooth L1 loss	2022-08-12 19:28:22 +00:00
Kevin Wu	85d2d2a64a	Basic tests for variance schedules	2022-08-11 21:19:16 +00:00