58 Commits

Author	SHA1	Message	Date
Kevin Wu	8e784add04	Speed up sampling by truncating input padding regions.	2023-09-17 12:18:44 -07:00
Kevin Wu	5a685a097d	Parallelize writing sampled PDB files	2022-11-16 13:33:44 -08:00
Kevin Wu	b49554880f	Add docs	2022-11-10 13:50:54 -08:00
Kevin Wu	8f01d839ec	Improved detection of huggingface hub id	2022-10-05 13:53:15 -07:00
Kevin Wu	ac7406d871	Use automatic cache dir	2022-10-05 12:17:56 -07:00
Kevin Wu	5867534e47	Tweak sample.py to accept a huggingface repo ID	2022-10-05 12:09:51 -07:00
Kevin Wu	270f441721	Sampling CLI tweaks	2022-10-05 11:24:18 -07:00
Kevin Wu	a3f72b1123	Store and load training mean offsets without loading full dataset	2022-10-05 10:37:19 -07:00
Kevin Wu	c1bbcb583d	Bugfix with trying to compute test set metrics when test set isn't loaded	2022-10-04 22:08:14 -07:00
Kevin Wu	f994be0b3e	Initial implementation of a dummy dataset to hold values in lieu of actually loading in dataset	2022-10-04 21:55:05 -07:00
Kevin Wu	135553dc47	Remove some unnecessary code	2022-10-04 21:06:48 -07:00
Kevin Wu	c651f79ed0	use the version of model without lightning for sampling	2022-10-04 20:11:08 -07:00
Kevin Wu	17898dee6c	Updates to Ramachandran plot	2022-09-27 21:54:42 -07:00
Kevin Wu	1074327185	Plotting tweaks	2022-09-27 19:16:19 -07:00
Kevin Wu	aa9a0670ae	Cleanup	2022-09-27 13:52:21 -07:00
Kevin Wu	11ea36b976	Import stuffs	2022-09-27 11:39:11 -07:00
Kevin Wu	50df1d3b52	Add default model to sample script	2022-09-27 10:48:32 -07:00
Kevin Wu	f6b8b8d342	Misc.	2022-09-26 13:32:59 -07:00
Kevin Wu	b252b60b23	More plotting fixes	2022-09-21 11:14:03 -07:00
Kevin Wu	71d5b5a288	Plotting tweaks	2022-09-21 10:39:18 -07:00
Kevin Wu	f27e3ea531	Code refactor	2022-09-21 10:14:34 -07:00
Kevin Wu	ac7a8f06dc	Plotting tweaks	2022-09-20 21:36:19 -07:00
Kevin Wu	ad8b5a458a	Remove debug code	2022-09-15 15:11:52 -07:00
Kevin Wu	671c444ff5	Plotting improvements	2022-09-15 15:10:58 -07:00
Kevin Wu	9cb7bca32f	Ability to only do secondary structures for sequences of a max len	2022-09-15 14:55:58 -07:00
Kevin Wu	ed3a4eff87	Simplfy some code, plot against test instead of train	2022-09-15 14:44:37 -07:00
Kevin Wu	bead02473a	More plotting, including CDF	2022-09-15 14:30:58 -07:00
Kevin Wu	b494b067d0	Implement sampling sweep of lengths	2022-09-15 14:07:20 -07:00
Kevin Wu	89b5432728	Rename file	2022-09-13 19:01:27 -07:00
Kevin Wu	49021c1163	Support for DSSP backend	2022-09-13 19:00:08 -07:00
Kevin Wu	e67a9870b6	Snapshot the model when we do sampling	2022-09-13 11:52:17 -07:00
Kevin Wu	35bb1d5794	Code to save model after loading from pretrained	2022-09-13 09:26:58 -07:00
Kevin Wu	ccafcd279d	Annotate training ramachandran plot with secondary structures	2022-09-12 22:09:21 -07:00
Kevin Wu	6166688c0f	Add configurable batch size	2022-09-12 21:06:52 -07:00
Kevin Wu	b2918dfb09	Code to generate a combo plot for generated angles	2022-09-12 20:41:44 -07:00
Kevin Wu	513ffc71bd	Refactor plotting code for distribution comparisons	2022-09-12 20:18:51 -07:00
Kevin Wu	559a77d63f	Reorganize code	2022-09-12 19:58:30 -07:00
Kevin Wu	5e55a04f94	Misc.	2022-09-12 01:17:53 -07:00
Kevin Wu	2df9e0397b	Ability to do tm scores for only a subset	2022-09-12 01:16:25 -07:00
Kevin Wu	9abe71e6d2	Attribute passthrough	2022-09-12 01:08:20 -07:00
Kevin Wu	d757501c02	Refactor for code sharing	2022-09-12 00:57:36 -07:00
Kevin Wu	24e76458eb	Reorganize sampling code, add support for writing full sampling history	2022-09-10 13:02:55 -07:00
Kevin Wu	88243e3157	More detailed logging	2022-09-10 10:41:23 -07:00
Kevin Wu	775981b02f	Reduce default thread count for tmscore calculation	2022-09-10 10:40:52 -07:00
Kevin Wu	a27d6948ff	Add progressbar to tmscore calculation	2022-09-09 14:04:44 -07:00
Kevin Wu	6a5fb6e90e	Formatting	2022-09-09 14:02:27 -07:00
Kevin Wu	14bc15f2f6	More documentation	2022-09-09 14:02:19 -07:00
Kevin Wu	27294e5216	Tweak sampling to work with updated models and params	2022-09-09 13:11:12 -07:00
Kevin Wu	7dccdb215f	Remove dependencies on biopython	2022-09-09 10:46:37 -07:00
Kevin Wu	74fab4370a	Calculate pdb scores	2022-09-02 18:03:22 -07:00