36 Commits

Author	SHA1	Message	Date
Ben Perry	2cd8c52d9f	adding batch size patch to catch low N edge cases	2026-05-04 12:18:27 -04:00
Ben Perry	ebacb8e45c	removing legacy download code from setup_databases.sh	2026-05-04 11:39:39 -04:00
Ben Perry	a0cf8b472c	adding alternative HF endpoint as documentation	2026-05-04 11:18:25 -04:00
Ben Perry	e38651c4a6	removing rogue git merge conflict text	2026-04-19 23:29:00 -04:00
Benjamin Perry	74ee907dcf	updating temp_dir flag to passthrough to MMSeqs for HPC	2026-04-11 11:25:21 -04:00
Benjamin Perry	902c2f065d	adding --jax_compilation_cache_dir flag to avoid model recompilation across runs	2026-04-10 22:29:00 -04:00
Benjamin Perry	e79c6db693	Merge branch 'feature/rna-nhmmer'	2026-04-10 16:41:51 -04:00
Benjamin Perry	5abb19b7b8	deleting unneeded scripts for benchmarking for clean repo	2026-04-10 15:50:27 -04:00
Benjamin Perry	77ac2217e4	updating help docs for setup databases	2026-04-10 15:49:45 -04:00
Benjamin Perry	d4e3910dcb	adding setup_databases with simpler flags	2026-04-10 15:31:07 -04:00
Benjamin Perry	fca97294d4	final setup db script	2026-04-10 15:21:50 -04:00
Benjamin Perry	f61a919772	modifying setup to only grab .zst files	2026-04-10 10:01:42 -04:00
Benjamin Perry	71560437c1	updating device passing arg	2026-04-07 23:41:44 -04:00
Benjamin Perry	9a6174ea70	fixing gpu cli arg for run model	2026-04-07 23:37:47 -04:00
Benjamin Perry	a7fd4a5b08	adding absolute path	2026-04-07 19:57:42 -04:00
Benjamin Perry	3e69663016	updating hmmer paths	2026-04-07 19:46:01 -04:00
Benjamin Perry	92e53c77cf	adding new dockerfile with hmmer compatability	2026-04-07 19:34:41 -04:00
Benjamin Perry	f1752ed393	adding fixed alphafold3.mmcif parser	2026-04-07 18:30:43 -04:00
Benjamin Perry	7720b28833	updating setup databases with rna option	2026-04-07 17:19:36 -04:00
Benjamin Perry	fcce4fcf5a	fixing modal database script to include config from python	2026-04-07 17:15:25 -04:00
Benjamin Perry	57be42894a	adding final testing scripts for RNA mode	2026-04-06 22:47:45 -04:00
Benjamin Perry	f0e51e4603	adding RNA search functionality	2026-04-06 12:59:38 -04:00
Benjamin Perry	fca90950d3	adding MMseqs vs. NHMMER options to alphafast run script and database download	2026-03-18 13:16:57 -04:00
Benjamin Perry	7aa6cdc423	adding temporary test of mmseqs RNA/DNA search + NHmmer fallback	2026-03-17 20:04:24 -04:00
Ben Perry	83815ff767	iniital testing scripts for dna/rna support	2026-03-16 14:08:16 -04:00
Ben Perry	840b2cc46c	updating README and CLI install instructions	2026-03-16 11:06:01 -04:00
Ben Perry	4336d7678c	switching over to hf cli	2026-03-16 10:55:35 -04:00
Ben Perry	b1c2290546	removing inline python scripting	2026-03-16 10:50:25 -04:00
Ben Perry	6b57ce6181	testing hf download flag	2026-03-16 10:43:25 -04:00
Ben Perry	2323d0c25d	changing find to work with symlinks	2026-03-05 09:27:19 -05:00
Ben Perry	86b9cc2ff2	adding guard to only have N GPUs if less than N + 1 inputs requested. Additionally, fixing logdir and model weights path pointers	2026-03-03 10:01:14 -05:00
Benjamin Perry	262ed23c44	fixing production version of run_alphafast.sh to also use one-time af3 model setup for folding	2026-02-28 16:56:34 -05:00
Benjamin Perry	109dda415a	updating model dir path to match /data/ directory path	2026-02-28 12:30:35 -05:00
Benjamin Perry	91e068887a	updating paths in docker to data/ instead of root/ to avoid root perms issue	2026-02-27 21:34:44 -05:00
Ben Perry	e40eb852a7	adding user ID flag to fix root owned output files on some setups	2026-02-27 14:55:40 -05:00
Ben Perry	625a3839ef	initial commit	2026-02-17 14:10:40 -05:00