fix(#293): skip full-db paths for reduced_dbs

alphapulldown/scripts/create_individual_features.py

@@ -68,7 +68,7 @@ AF3_DATABASES = {
     "rna_central": "rnacentral_active_seq_id_90_cov_80_linclust.fasta",
 }
 
-AF2_DATABASE_FLAGS = {
+AF2_FULL_DATABASE_FLAGS = {
     "uniref90_database_path": "uniref90",
     "uniref30_database_path": "uniref30",
     "mgnify_database_path": "mgnify",
@@ -81,6 +81,16 @@ AF2_DATABASE_FLAGS = {
     "obsolete_pdbs_path": "obsolete_pdbs",
 }
 
+AF2_REDUCED_DATABASE_FLAGS = {
+    "uniref90_database_path": "uniref90",
+    "mgnify_database_path": "mgnify",
+    "small_bfd_database_path": "small_bfd",
+    "uniprot_database_path": "uniprot",
+    "pdb_seqres_database_path": "pdb_seqres",
+    "template_mmcif_dir": "template_mmcif_dir",
+    "obsolete_pdbs_path": "obsolete_pdbs",
+}
+
 AF3_DATABASE_FLAGS = {
     "uniref90_database_path": "uniref90",
     "mgnify_database_path": "mgnify",
@@ -90,7 +100,11 @@ AF3_DATABASE_FLAGS = {
     "template_mmcif_dir": "template_mmcif_dir",
 }
 
-DATABASE_PATH_FLAGS = frozenset(AF2_DATABASE_FLAGS) | frozenset(AF3_DATABASE_FLAGS)
+DATABASE_PATH_FLAGS = (
+    frozenset(AF2_FULL_DATABASE_FLAGS)
+    | frozenset(AF2_REDUCED_DATABASE_FLAGS)
+    | frozenset(AF3_DATABASE_FLAGS)
+)
 
 # =================== Flags ===================
 flags.DEFINE_enum(
@@ -180,9 +194,7 @@ def create_arguments(local_custom_template_db=None):
     Optionally override template paths with a local custom template DB."""
     validate_data_pipeline_flags()
 
-    required_database_flags = (
-        AF3_DATABASE_FLAGS if FLAGS.data_pipeline == 'alphafold3' else AF2_DATABASE_FLAGS
-    )
+    required_database_flags = get_required_database_flags()
 
     # When using MMseqs2 (current implementation uses remote servers), database paths are not needed
     # Note: Current MMseqs2 implementation uses remote servers via DEFAULT_API_SERVER
@@ -202,6 +214,20 @@ def create_arguments(local_custom_template_db=None):
         FLAGS.template_mmcif_dir = os.path.join(local_custom_template_db, "pdb_mmcif", "mmcif_files")
         FLAGS.obsolete_pdbs_path = os.path.join(local_custom_template_db, "pdb_mmcif", "obsolete.dat")
 
+
+def get_required_database_flags():
+    """Return the database flags required by the selected pipeline and preset."""
+    if FLAGS.data_pipeline == "alphafold3":
+        return AF3_DATABASE_FLAGS
+
+    if FLAGS.db_preset == "reduced_dbs":
+        required_flags = dict(AF2_REDUCED_DATABASE_FLAGS)
+        if FLAGS.use_hhsearch:
+            required_flags["pdb70_database_path"] = "pdb70"
+        return required_flags
+
+    return AF2_FULL_DATABASE_FLAGS
+
 def check_template_date():
     """Check if the max_template_date is provided."""
     if not FLAGS.max_template_date:

test/integration/test_create_individual_features.py

@@ -760,6 +760,66 @@ class TestCreateIndividualFeaturesComprehensive:
         assert FLAGS.obsolete_pdbs_path is None
         logger.info("AF3 argument creation only kept AF3-relevant database paths")
 
+    def test_create_arguments_reduced_dbs_clears_unused_af2_databases(self):
+        """Test that reduced_dbs only sets the AF2 paths it actually needs."""
+        logger.info("Testing reduced_dbs argument creation without full-db leftovers")
+
+        from absl import flags
+        FLAGS = flags.FLAGS
+        FLAGS(['test'])
+
+        FLAGS.use_mmseqs2 = False
+        FLAGS.data_pipeline = "alphafold2"
+        FLAGS.db_preset = "reduced_dbs"
+        FLAGS.use_hhsearch = False
+        FLAGS.data_dir = "/test/db"
+        FLAGS.uniref90_database_path = None
+        FLAGS.mgnify_database_path = None
+        FLAGS.small_bfd_database_path = None
+        FLAGS.uniprot_database_path = None
+        FLAGS.pdb_seqres_database_path = None
+        FLAGS.template_mmcif_dir = None
+        FLAGS.obsolete_pdbs_path = None
+        FLAGS.uniref30_database_path = "/stale/uniref30"
+        FLAGS.bfd_database_path = "/stale/bfd"
+        FLAGS.pdb70_database_path = "/stale/pdb70"
+
+        create_features.create_arguments()
+
+        assert FLAGS.uniref90_database_path == "/test/db/uniref90/uniref90.fasta"
+        assert FLAGS.mgnify_database_path == "/test/db/mgnify/mgy_clusters_2022_05.fa"
+        assert FLAGS.small_bfd_database_path == "/test/db/small_bfd/bfd-first_non_consensus_sequences.fasta"
+        assert FLAGS.uniprot_database_path == "/test/db/uniprot/uniprot.fasta"
+        assert FLAGS.pdb_seqres_database_path == "/test/db/pdb_seqres/pdb_seqres.txt"
+        assert FLAGS.template_mmcif_dir == "/test/db/pdb_mmcif/mmcif_files"
+        assert FLAGS.obsolete_pdbs_path == "/test/db/pdb_mmcif/obsolete.dat"
+        assert FLAGS.uniref30_database_path is None
+        assert FLAGS.bfd_database_path is None
+        assert FLAGS.pdb70_database_path is None
+        logger.info("Reduced-dbs argument creation cleared unused full-database paths")
+
+    def test_create_arguments_reduced_dbs_keeps_pdb70_for_hhsearch(self):
+        """Test that reduced_dbs still sets pdb70 when HHsearch templates are requested."""
+        logger.info("Testing reduced_dbs HHsearch argument creation")
+
+        from absl import flags
+        FLAGS = flags.FLAGS
+        FLAGS(['test'])
+
+        FLAGS.use_mmseqs2 = False
+        FLAGS.data_pipeline = "alphafold2"
+        FLAGS.db_preset = "reduced_dbs"
+        FLAGS.use_hhsearch = True
+        FLAGS.data_dir = "/test/db"
+        FLAGS.pdb70_database_path = None
+
+        create_features.create_arguments()
+
+        assert FLAGS.pdb70_database_path == "/test/db/pdb70/pdb70"
+        assert FLAGS.bfd_database_path is None
+        assert FLAGS.uniref30_database_path is None
+        logger.info("Reduced-dbs HHsearch argument creation kept pdb70 without restoring full BFD")
+
     def test_mmseqs2_without_data_dir(self):
         """Test that MMseqs2 works without data_dir flag."""
         logger.info("Testing MMseqs2 without data_dir flag")