294 Commits

Author	SHA1	Message	Date
Kevin Wu	5c95c4ab47	Report num parameters	2023-10-22 00:15:17 -07:00
Kevin Wu	c9e36e2acb	Typo fix	2023-09-17 18:49:42 -07:00
Kevin Wu	8e784add04	Speed up sampling by truncating input padding regions.	2023-09-17 12:18:44 -07:00
Kevin Wu	612efe49fb	Better handling of inputs	2023-09-07 14:47:45 -07:00
Kevin Wu	b9706eaf20	Script to add oxygen to backbone	2023-09-05 22:54:54 -07:00
Kevin Wu	902b0301d2	Write out the names of all files used in training splits	2023-03-30 13:51:13 -07:00
Kevin Wu	6dbb3117f6	Improved error handling	2023-03-29 10:41:27 -07:00
Kevin Wu	96d6bf2bef	Parallelize aa splicing	2023-03-09 15:55:48 -08:00
Kevin Wu	dd7560611a	Basic script to splice AA sidechains on	2023-03-08 20:49:43 -08:00
Kevin Wu	5dc974b72f	Also save metadata	2023-02-13 23:40:19 -08:00
Kevin Wu	52db3a274a	Save reconst scores to json	2023-02-13 23:12:47 -08:00
Kevin Wu	5debc4f733	Add a script to do partial reconstruction	2023-02-13 19:56:51 -08:00
Kevin Wu	5ecd655128	Support for reading in pdb2git scores	2023-02-09 21:27:26 -08:00
Kevin Wu	02dcfa85fe	Visual tweaks	2023-02-09 18:15:39 -08:00
Kevin Wu	ec2e5e9902	MDS plotting code	2023-02-08 12:49:13 -08:00
Kevin Wu	5b1ff15994	Formatting updates	2023-02-08 10:50:33 -08:00
Kevin Wu	1409aae763	Allow less verbose labeling	2023-02-07 16:21:45 -08:00
Kevin Wu	111e27ada1	Plotting tweaks	2023-02-07 12:02:15 -08:00
Kevin Wu	e27d8b581f	Mor eplotting code	2023-02-04 17:49:27 -08:00
Kevin Wu	a55059e654	Parallelize computation of seocndary structures	2022-12-16 12:45:56 -08:00
Kevin Wu	79f7913e64	Remove old code	2022-12-09 15:46:49 -08:00
Kevin Wu	09f9f15e37	Support for specifying dataset in training script	2022-12-08 11:04:36 -08:00
Kevin Wu	98e9165531	Misc. cleanup	2022-11-23 22:36:51 -08:00
Kevin Wu	93f0db0d8a	AF stuffs	2022-11-18 12:59:34 -08:00
Kevin Wu	23c235c52e	Ability to write raw counts of ss	2022-11-18 11:59:25 -08:00
Kevin Wu	3626b9a8ad	Omegafold spread load more evenly across GPUs	2022-11-17 14:10:41 -08:00
Kevin Wu	d7481e995e	Update omegafold wrapper	2022-11-17 12:22:48 -08:00
Kevin Wu	a90a1a00b2	More checks	2022-11-17 11:53:06 -08:00
Kevin Wu	ace4bd906f	Fix bug with overglobbing	2022-11-17 11:44:37 -08:00
Kevin Wu	40ffb3bbe3	Rename script	2022-11-17 10:58:45 -08:00
Kevin Wu	dd96b1a9a9	Formatting updates	2022-11-17 10:35:32 -08:00
Kevin Wu	70542630fe	Tweak selftm to be more flexible on inputs	2022-11-17 10:35:17 -08:00
Kevin Wu	5609bd3ce2	ProteinMPNN wrapper	2022-11-16 23:59:14 -08:00
Kevin Wu	5a685a097d	Parallelize writing sampled PDB files	2022-11-16 13:33:44 -08:00
Kevin Wu	14e8bad7c0	Addtl reporting	2022-11-11 14:58:02 -08:00
Kevin Wu	b49554880f	Add docs	2022-11-10 13:50:54 -08:00
Kevin Wu	e24e434c28	Ability to configure upper frequency for plotting	2022-11-09 13:20:36 -08:00
Kevin Wu	8be6f49d0b	Progressbar improvements	2022-11-09 11:09:02 -08:00
Kevin Wu	734d8c68c5	Flesh out autoregressive sampling script	2022-11-09 11:05:27 -08:00
Kevin Wu	fde3632c1d	Updates to defaults	2022-11-08 22:03:40 -08:00
Kevin Wu	f044114dae	Bugfix for model not learning	2022-11-08 21:56:18 -08:00
Kevin Wu	52a4b48449	More checks and defaults updates	2022-11-08 21:32:41 -08:00
Kevin Wu	d9773dfb6c	Up the default batch size	2022-11-08 21:04:08 -08:00
Kevin Wu	fdb8b786e2	Initial script for sampling from AR model	2022-11-08 20:54:19 -08:00
Kevin Wu	dd671adbe4	Update some defaults	2022-11-07 15:06:28 -08:00
Kevin Wu	fc00d30b43	AR model take as input the total seq length	2022-11-07 14:50:55 -08:00
Kevin Wu	e13a17384c	Provide missing values	2022-11-07 14:20:44 -08:00
Kevin Wu	07377b7fb4	Enable LR scheduler for AR model	2022-11-07 14:13:37 -08:00
Kevin Wu	4956f42cb8	Update default values for AR training	2022-11-07 13:55:47 -08:00
Kevin Wu	4ae35c7c66	Script for training autoregressive model	2022-11-07 13:46:58 -08:00