Get software from file

convert_to_modelcif.py

@@ -318,10 +318,9 @@ def _get_modelcif_ref_dbs(meta_json):
             db_name = db_name.lower()
             # if DB already exists, check URL and version
             if db_name in sdb_dct:
-                print("ALREADY THERE", sdb_dct[db_name])
                 # ToDo: switch URL to the actual URL read from JSON
                 if (
-                    sdb_dct[db_name].version == vdct["version"]
+                    sdb_dct[db_name].version != vdct["version"]
                     or sdb_dct[db_name].url != db_info[db_name]["url"]
                 ):
                     raise RuntimeError(
@@ -376,6 +375,7 @@ def _store_as_modelcif(
     )
 
     # create software list from feature metadata
+    # ToDo: store_as_modelcif should not use __meta__
     sw_dct = _get_software_data(data_json["__meta__"])
 
     # process scores
@@ -730,25 +730,20 @@ def _get_protocol_steps(modelcif_json):
     """Create the list of protocol steps with software and parameters used."""
     protocol = []
     # MSA/ monomer feature generation step
-    # ToDo: get software from modelcif_json
     step = {
         "method_type": "coevolution MSA",
         "step_name": "MSA generation",
         "details": "Create sequence features for corresponding monomers.",
         "input_data_group": "target_sequences",
         "output_data_group": "monomer_pickle_files",
-        "software_group": [
-            "AlphaPulldown",
-            "AlphaFold",
-            "jackhmmer",
-            "hhblits",
-            "hhsearch",
-            "hmmsearch",
-            "hmmbuild",
-            "kalign",
-        ]
+        "software_group": []
         # _ma_protocol_step.protocol_id
     }
+    for sftwr in modelcif_json["__meta__"].values():
+        sftwr = sftwr["software"]
+        for tool in sftwr:
+            if tool not in step["software_group"]:
+                step["software_group"].append(tool)
     protocol.append(step)
 
     # modelling step