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Added a separate AlignmentRunner for handling seq_emb mode. 

- In `seq_emb` mode, the AlignmentRunner works only on generating templates.
This commit is contained in:
Sachin Kadyan 2022-10-28 15:32:40 -04:00
parent 380947c429
commit 8c94482aa0
1 changed files with 20 additions and 11 deletions
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31
run_pretrained_openfold.py
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@ -73,17 +73,26 @@ def precompute_alignments(tags, seqs, alignment_dir, args):
os.makedirs(local_alignment_dir)
alignment_runner = data_pipeline.AlignmentRunner(
jackhmmer_binary_path=args.jackhmmer_binary_path,
hhblits_binary_path=args.hhblits_binary_path,
hhsearch_binary_path=args.hhsearch_binary_path,
uniref90_database_path=args.uniref90_database_path,
mgnify_database_path=args.mgnify_database_path,
bfd_database_path=args.bfd_database_path,
uniclust30_database_path=args.uniclust30_database_path,
pdb70_database_path=args.pdb70_database_path,
no_cpus=args.cpus,
)
if args.use_single_seq_mode:
alignment_runner = data_pipeline.AlignmentRunner(
jackhmmer_binary_path=args.jackhmmer_binary_path,
hhsearch_binary_path=args.hhsearch_binary_path,
uniref90_database_path=args.uniref90_database_path,
pdb70_database_path=args.pdb70_database_path,
no_cpus=args.cpus,
)
else:
alignment_runner = data_pipeline.AlignmentRunner(
jackhmmer_binary_path=args.jackhmmer_binary_path,
hhblits_binary_path=args.hhblits_binary_path,
hhsearch_binary_path=args.hhsearch_binary_path,
uniref90_database_path=args.uniref90_database_path,
mgnify_database_path=args.mgnify_database_path,
bfd_database_path=args.bfd_database_path,
uniclust30_database_path=args.uniclust30_database_path,
pdb70_database_path=args.pdb70_database_path,
no_cpus=args.cpus,
)
alignment_runner.run(
tmp_fasta_path, local_alignment_dir
)