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Make template research possible with precomputed MSA #554

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Merged
DimaMolod merged 4 commits into from
Nov 19, 2025
Merged

Make template research possible with precomputed MSA #554

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864d216
Add use_templates option for MSA calculation
Qrouger Nov 18, 2025
8231ad1
Add use_templates flag to make_mmseq_features call
Qrouger Nov 18, 2025
6cb7c6a
Change use_templates parameter to False
Qrouger Nov 18, 2025
eddfa65
Change template flag to re_search_templates_mmseqs2
Qrouger Nov 19, 2025
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17 changes: 16 additions & 1 deletion alphapulldown/objects.py
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Original file line number Diff line number Diff line change
Expand Up @@ -189,6 +189,7 @@ def make_mmseq_features(
output_dir=None,
compress_msa_files=False,
use_precomputed_msa=False,
use_templates=False,
):
"""
A method to use mmseq_remote to calculate MSA.
Expand All @@ -200,7 +201,6 @@ def make_mmseq_features(
msa_mode = "mmseqs2_uniref_env"
keep_existing_results = True
result_dir = output_dir
use_templates = True
result_zip = os.path.join(result_dir, self.description, ".result.zip")
if keep_existing_results and plPath(result_zip).is_file():
logging.info(f"Skipping {self.description} (result.zip)")
Expand All @@ -211,6 +211,21 @@ def make_mmseq_features(
a3m_lines = [plPath(a3m_path).read_text()]
(unpaired_msa, paired_msa, query_seqs_unique, query_seqs_cardinality,
template_features) = unserialize_msa(a3m_lines, self.sequence)

if use_templates == True : #Search templates for precomputed msa
(_, _, _, _, template_features) = get_msa_and_templates(
jobname=self.description,
query_sequences=self.sequence,
a3m_lines=False,
result_dir=plPath(result_dir),
msa_mode='single_sequence',
use_templates=True,
custom_template_path=None,
pair_mode="none",
host_url=DEFAULT_API_SERVER,
user_agent='alphapulldown')


else:
logging.info("You chose to calculate MSA with mmseqs2.\nPlease also cite: "
"Mirdita M, Schütze K, Moriwaki Y, Heo L, Ovchinnikov S and Steinegger M. "
Expand Down
3 changes: 2 additions & 1 deletion alphapulldown/scripts/create_individual_features.py
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Original file line number Diff line number Diff line change
Expand Up @@ -98,6 +98,7 @@
flags.DEFINE_string('obsolete_pdbs_path', None, '')
flags.DEFINE_enum('db_preset', 'full_dbs', ['full_dbs', 'reduced_dbs'], '')
flags.DEFINE_boolean('use_precomputed_msas', False, '')
flags.DEFINE_boolean('re_search_templates_mmseqs2', False, '')
flags.DEFINE_bool("use_mmseqs2", False, "")
flags.DEFINE_bool("save_msa_files", False, "")
flags.DEFINE_bool("skip_existing", False, "")
Expand Down Expand Up @@ -260,7 +261,7 @@ def create_and_save_monomer_objects(monomer, pipeline):
with open(metadata_output_path, "w") as meta_data_outfile:
json.dump(meta_dict, meta_data_outfile)
if FLAGS.use_mmseqs2:
monomer.make_mmseq_features(DEFAULT_API_SERVER=DEFAULT_API_SERVER, output_dir=FLAGS.output_dir, use_precomputed_msa=FLAGS.use_precomputed_msas)
monomer.make_mmseq_features(DEFAULT_API_SERVER=DEFAULT_API_SERVER, output_dir=FLAGS.output_dir, use_precomputed_msa=FLAGS.use_precomputed_msas, use_templates=FLAGS.re_search_templates_mmseqs2)
else:
monomer.make_features(
pipeline=pipeline, output_dir=FLAGS.output_dir,
Expand Down
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