192 Commits

Author	SHA1	Message	Date
Gustaf Ahdritz	ca810168d9	Add bfloat16 support to DeepSpeed config script	2021-11-29 19:03:40 -05:00
yuzhiguo07	1bfb1e1b2a	Update precompute_alignments_mmseqs.py	2021-11-29 15:11:41 -06:00
Gustaf Ahdritz	78e7996227	Fix bugs in MMseqs DB script	2021-11-29 13:53:27 -05:00
Gustaf Ahdritz	52800ff027	Add alternative fasta file extension	2021-11-22 16:26:05 -05:00
Gustaf Ahdritz	6e5c619c38	Fix bug in alignment precomputation script	2021-11-15 16:16:08 -05:00
Gustaf	8c95493f1a	Update documention for ProteinNet use case	2021-11-10 02:08:58 -05:00
Gustaf	e7b239c9e4	Add missing variable	2021-11-10 02:05:50 -05:00
Gustaf	2c7ce956e8	Add more ProteinNet functionality	2021-11-10 01:53:46 -05:00
Gustaf	22cc45a85a	Begin to add ProteinNet support (WIP)	2021-11-09 23:53:14 -05:00
Gustaf	36f317bef9	Add MMseqs2 MSA generation	2021-11-09 02:57:53 -05:00
Gustaf Ahdritz	1feca912a7	Merge pull request #2 from aqlaboratory/marta-sd/nan-loss ... Fix NaN loss bug + add development env for Nvidians	2021-11-03 12:14:11 -04:00
Marta	6c14c76a1b	add dllogger to conda env	2021-11-02 06:03:49 -07:00
Gustaf Ahdritz	9d4c9357c5	Speed up template featurizer	2021-10-29 23:18:06 -04:00
Gustaf Ahdritz	a9a19b78a9	Fix model checkpointing bug	2021-10-26 16:16:25 -04:00
Gustaf Ahdritz	98b2c663c5	Add description to ProteinNet MSA script	2021-10-26 00:40:37 -04:00
Gustaf Ahdritz	b5f885d0ff	Add ProteinNet support to parser	2021-10-26 00:39:07 -04:00
Gustaf Ahdritz	94ab346e40	Merge pull request #1 from aqlaboratory/mpvenkatesh/changes ... minor fixes	2021-10-24 14:21:28 -04:00
sft-managed	04fa3548e9	minor fixes	2021-10-24 10:21:12 -07:00
Gustaf Ahdritz	5b9cfdafa6	Add script for installing the HH-suite	2021-10-22 18:01:58 -04:00
Gustaf Ahdritz	872787b9f0	Add gradient clipping to DeepSpeed config generator	2021-10-21 20:59:41 -04:00
Gustaf Ahdritz	497670998b	Bring tests up to speed	2021-10-19 23:07:09 -04:00
Gustaf Ahdritz	a6f56d1663	Prettyprint mmCIF cache	2021-10-19 00:14:01 -04:00
Gustaf Ahdritz	238866194b	Add mmCIF cache generation script, remove verbose warnings	2021-10-18 03:14:44 -04:00
Gustaf Ahdritz	5497655c00	Fix faulty symlink command in install script	2021-10-15 17:59:44 -04:00
Gustaf Ahdritz	d48c052cd9	Add training parsers	2021-10-15 17:59:11 -04:00
Gustaf Ahdritz	f4150fa1e2	Tweak run script args, roll back repo to Python 3.7 (for Colab)	2021-10-08 20:27:14 -04:00
Sachin Kadyan	83fa3b901a	Added a wrapper shell script to download all databases by executing each of the individual scripts.	2021-10-08 18:29:27 -04:00
Sachin Kadyan	e8ac431706	Added the shell script to download the uniref90 database.	2021-10-08 18:28:33 -04:00
Sachin Kadyan	a78c044541	Added the shell script to download the uniclust30 database.	2021-10-08 18:28:10 -04:00
Sachin Kadyan	ac8d5677e1	Added the shell script to download the small BFD database.	2021-10-08 18:27:48 -04:00
Sachin Kadyan	44e87083ae	Added the shell script to download the PDB mmCIF database.	2021-10-08 18:27:20 -04:00
Sachin Kadyan	e8226a5804	Added the shell script to download the PDB70 database.	2021-10-08 18:26:40 -04:00
Sachin Kadyan	48df5d188d	Added the shell script to download the Mgnify database for JackHMMer MSA queries.	2021-10-08 17:52:48 -04:00
Sachin Kadyan	365254a7fe	Added the shell script to download the BFD database for HHBlits queries.	2021-10-08 17:36:34 -04:00
Gustaf Ahdritz	9f6b67f37c	Fix another FP16 overflow, finish tests, update util scripts	2021-10-06 18:53:45 -04:00
Gustaf Ahdritz	54317fe469	Add pTM config options, spruce up pretrained script, add test script	2021-09-30 17:55:08 -04:00
Gustaf Ahdritz	2065a6ca22	Add missing license notice	2021-09-27 17:20:21 -04:00
Gustaf Ahdritz	cc6ba53456	Add DeepSpeed config script	2021-09-27 17:19:14 -04:00
Gustaf Ahdritz	754d2ba82e	Add conda env scripts	2021-09-22 01:29:49 -04:00
Gustaf Ahdritz	75c79b79c2	Rename main directory	2021-09-20 19:27:13 -04:00
Gustaf Ahdritz	15895ea94e	Add requirements & minor edits	2021-09-17 18:36:10 -04:00
Gustaf Ahdritz	92f1932e6b	Initial commit	2021-09-17 18:34:59 -04:00