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Add --merge-a3m option to colabfold_search. #769

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Add --merge-a3m option to colabfold_search. #769

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80171da
Add --merge-a3m option to colabfold_search.
tomgoddard Aug 30, 2025
947b10a
Made naming of unmerged .a3m files use job name. The merge code depe…
tomgoddard Sep 4, 2025
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64 changes: 44 additions & 20 deletions colabfold/mmseqs/search.py
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Original file line number Diff line number Diff line change
Expand Up @@ -390,7 +390,10 @@ def main():
help="Database preload mode 0: auto, 1: fread, 2: mmap, 3: mmap+touch",
)
parser.add_argument(
"--unpack", type=int, default=1, choices=[0, 1], help="Unpack results to loose files or keep MMseqs2 databases."
"--unpack", type=int, default=1, choices=[0, 1], help="Unpack results to a3m text files or keep MMseqs2 databases."
)
parser.add_argument(
"--merge-a3m", type=int, default=1, choices=[0, 1], help="Merge unpacked a3m files into a single a3m file."
)
parser.add_argument(
"--threads", type=int, default=64, help="Number of threads to use."
Expand Down Expand Up @@ -522,7 +525,7 @@ def main():
unpack=args.unpack,
)

if args.unpack or args.af3_json:
if args.merge_a3m or args.af3_json:
id = 0
for job_number, (
raw_jobname,
Expand All @@ -537,30 +540,27 @@ def main():
for seq in query_sequences:
with args.base.joinpath(f"{id}.a3m").open("r") as f:
unpaired_msa.append(f.read())
if args.af3_json:
args.base.joinpath(f"{id}.a3m").unlink()

if args.use_env_pairing:
with open(args.base.joinpath(f"{id}.paired.a3m"), 'a') as file_pair:
with open(args.base.joinpath(f"{id}.env.paired.a3m"), 'r') as file_pair_env:
while chunk := file_pair_env.read(10 * 1024 * 1024):
file_pair.write(chunk)
if args.unpack:
args.base.joinpath(f"{id}.env.paired.a3m").unlink()
args.base.joinpath(f"{id}.a3m").unlink()

if len(query_seqs_cardinality) > 1:
with args.base.joinpath(f"{id}.paired.a3m").open("r") as f:
paired_msa.append(f.read())
if args.unpack:
args.base.joinpath(f"{id}.paired.a3m").unlink()
paired = f.read()
if args.merge_a3m:
args.base.joinpath(f"{id}.paired.a3m").unlink()
if args.use_env_pairing:
with open(args.base.joinpath(f"{id}.env.paired.a3m"), 'r') as file_pair_env:
paired += file_pair_env.read()
if args.merge_a3m:
args.base.joinpath(f"{id}.env.paired.a3m").unlink()
paired_msa.append(paired)
id += 1

if args.af3_json:
af3 = AF3Utils(raw_jobname, query_sequences, query_seqs_cardinality, unpaired_msa, paired_msa, other_molecules)
with open(args.base.joinpath(f"{job_number}.json"), 'w') as f:
f.write(json.dumps(af3.content, indent=4))

if args.unpack:
if args.merge_a3m:
msa = msa_to_str(
unpaired_msa, paired_msa, query_sequences, query_seqs_cardinality
)
Expand All @@ -583,10 +583,34 @@ def main():
if args.unpack:
# rename a3m files
for job_number, (raw_jobname, query_sequences, query_seqs_cardinality, other_molecules) in enumerate(queries_unique):
os.rename(
args.base.joinpath(f"{job_number}.a3m"),
args.base.joinpath(f"{safe_filename(raw_jobname)}.a3m"),
)
if args.merge_a3m:
os.rename(
args.base.joinpath(f"{job_number}.a3m"),
args.base.joinpath(f"{safe_filename(raw_jobname)}.a3m"),
)
else:
# Rename unpaired, paired and env paired files.
nseqs = len(query_seqs_cardinality)
for id in range(job_number * nseqs, (job_number+1) * nseqs):
if nseqs > 1:
os.rename(
args.base.joinpath(f"{id}.a3m"),
args.base.joinpath(f"{safe_filename(raw_jobname)}_{id}.a3m"),
)
os.rename(
args.base.joinpath(f"{id}.paired.a3m"),
args.base.joinpath(f"{safe_filename(raw_jobname)}_{id}.paired.a3m"),
)
if args.use_env_pairing:
os.rename(
args.base.joinpath(f"{id}.env.paired.a3m"),
args.base.joinpath(f"{safe_filename(raw_jobname)}_{id}.env.paired.a3m"),
)
else:
os.rename(
args.base.joinpath(f"{id}.a3m"),
args.base.joinpath(f"{safe_filename(raw_jobname)}.a3m"),
)

# rename m8 files
if args.use_templates:
Expand Down
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