diff --git a/colabfold/mmseqs/search.py b/colabfold/mmseqs/search.py index 6455f4ae..580bd260 100644 --- a/colabfold/mmseqs/search.py +++ b/colabfold/mmseqs/search.py @@ -211,8 +211,7 @@ def mmseqs_search_monomer( def mmseqs_search_pair( dbbase: Path, base: Path, - uniref_db: Path = Path("uniref30_2302_db"), - spire_db: Path = Path("spire_ctg10_2401_db"), + db: Path = Path("uniref30_2302_db"), mmseqs: Path = Path("mmseqs"), pair_env: bool = True, prefilter_mode: int = 0, @@ -224,12 +223,12 @@ def mmseqs_search_pair( pairing_strategy: int = 0, unpack: bool = True, ): - if not dbbase.joinpath(f"{uniref_db}.dbtype").is_file(): - raise FileNotFoundError(f"Database {uniref_db} does not exist") + if not dbbase.joinpath(f"{db}.dbtype").is_file(): + raise FileNotFoundError(f"Database {db} does not exist") if ( ( - not dbbase.joinpath(f"{uniref_db}.idx").is_file() - and not dbbase.joinpath(f"{uniref_db}.idx.index").is_file() + not dbbase.joinpath(f"{db}.idx").is_file() + and not dbbase.joinpath(f"{db}.idx.index").is_file() ) or os.environ.get("MMSEQS_IGNORE_INDEX", False) ): @@ -242,10 +241,8 @@ def mmseqs_search_pair( dbSuffix2 = ".idx" if pair_env: - db = spire_db output = ".env.paired.a3m" else: - db = uniref_db output = ".paired.a3m" # fmt: off @@ -493,7 +490,7 @@ def main(): mmseqs=args.mmseqs, dbbase=args.dbbase, base=args.base, - uniref_db=args.db1, + db=args.db1, prefilter_mode=args.prefilter_mode, s=args.s, db_load_mode=args.db_load_mode, @@ -509,8 +506,7 @@ def main(): mmseqs=args.mmseqs, dbbase=args.dbbase, base=args.base, - uniref_db=args.db1, - spire_db=args.db4, + db=args.db4, prefilter_mode=args.prefilter_mode, s=args.s, db_load_mode=args.db_load_mode,