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Fixes for inference alignment generation

This commit is contained in:
Christina Floristean 2023-11-02 13:43:48 -04:00
parent 5eacd8b689
commit f94ee668e5
1 changed files with 17 additions and 17 deletions
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34
run_pretrained_openfold.py
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@ -68,34 +68,34 @@ def precompute_alignments(tags, seqs, alignment_dir, args):
os.path.join(alignment_dir, tag),
)
if args.use_precomputed_alignments is None and not os.path.isdir(local_alignment_dir):
if args.use_precomputed_alignments is None:
logger.info(f"Generating alignments for {tag}...")
os.makedirs(local_alignment_dir)
os.makedirs(local_alignment_dir, exist_ok=True)
if "multimer" in args.config_preset:
template_searcher = hmmsearch.Hmmsearch(
binary_path=args.hmmsearch_binary_path,
hmmbuild_binary_path=args.hmmbuild_binary_path,
database_path=args.pdb_seqres_database_path,
)
else:
template_searcher = hhsearch.HHSearch(
binary_path=args.hhsearch_binary_path,
databases=[args.pdb70_database_path],
)
# In seqemb mode, use AlignmentRunner only to generate templates
if args.use_single_seq_mode:
alignment_runner = data_pipeline.AlignmentRunner(
jackhmmer_binary_path=args.jackhmmer_binary_path,
uniref90_database_path=args.uniref90_database_path,
template_searcher=template_searcher,
no_cpus=args.cpus,
)
embedding_generator = EmbeddingGenerator()
embedding_generator.run(tmp_fasta_path, alignment_dir)
else:
is_multimer = "multimer" in args.config_preset
if is_multimer:
template_searcher = hmmsearch.Hmmsearch(
binary_path=args.hmmsearch_binary_path,
hmmbuild_binary_path=args.hmmbuild_binary_path,
database_path=args.pdb_seqres_database_path,
)
else:
template_searcher = hhsearch.HHSearch(
binary_path=args.hhsearch_binary_path,
databases=[args.pdb70_database_path],
)
alignment_runner = data_pipeline.AlignmentRunner(
jackhmmer_binary_path=args.jackhmmer_binary_path,
hhblits_binary_path=args.hhblits_binary_path,
@ -107,7 +107,7 @@ def precompute_alignments(tags, seqs, alignment_dir, args):
uniprot_database_path=args.uniprot_database_path,
template_searcher=template_searcher,
use_small_bfd=args.bfd_database_path is None,
no_cpus=args.cpus_per_task
no_cpus=args.cpus
)
alignment_runner.run(
@ -244,7 +244,7 @@ def main(args):
tags, seqs = parse_fasta(data)
if ((not is_multimer) and len(tags) != 1):
if not is_multimer and len(tags) != 1:
print(
f"{fasta_path} contains more than one sequence but "
f"multimer mode is not enabled. Skipping..."