Minor fixes

translate2modelcif.py

 #! /usr/local/bin/ost
 """Translate models from Tara/ Xabi from PDB + extra data into ModelCIF."""
 # ToDo [internal]: Add software group for ColabFold and AF2-Multimer
+# ToDo [internal]: get DB versions in - https://colabfold.mmseqs.com, scroll
+# down to "Database Information"
 
 import argparse
 import datetime
@@ -202,6 +204,8 @@ def _check_interaction_extra_files_present(model_dir):
     cnfg = os.path.join(model_dir, "config.json")
     _check_file(cnfg)
 
+    return cnfg
+
 
 def _check_model_extra_files_present(model_dir, pdb_file):
     """Check that all files needed to process this model are present."""
@@ -228,7 +232,7 @@ def _get_audit_authors():
     )
 
 
-def _get_protocol_steps_and_software():
+def _get_protocol_steps_and_software(cnfg_file):
     """Create the list of protocol steps with software and parameters used."""
     protocol = []
 
@@ -271,7 +275,8 @@ def _get_protocol_steps_and_software():
         "version": "1.2.0",
     }
     # get parameters
-    step["software_parameters"] = {}
+    with open(cnfg_file, encoding="utf8") as jfh:
+        step["software_parameters"] = json.load(jfh)
     protocol.append(step)
 
     # model selection step
@@ -301,7 +306,7 @@ def _get_model_details(gene_names):
     return (
         f"Dimer model generated for {' and '.join(gene_names)}, produced "
         + "using AlphaFold-Multimer (AlphaFold v2.2.0) as implemented by "
-        + "ColabFold (v1.2.0) which uses MMseqs2 for MSA generation (UniRef90 "
+        + "ColabFold (v1.2.0) which uses MMseqs2 for MSA generation (UniRef30 "
         + "+ Environmental)."
     )
 
@@ -309,7 +314,7 @@ def _get_model_details(gene_names):
 def _get_model_group_name():
     """Get a name for a model group."""
 
-    return "Crosslinked Heterodimer Multimer v2 Models"
+    return "Crosslinked Heterodimer ALphaFold-Multimer v2 Models"
 
 
 def _get_sequence(chn):
@@ -525,6 +530,18 @@ def _get_modelcif_protocol(protocol_steps, target_entities, model):
                     doi=js_step["software"]["citation"]["doi"],
                 ),
             )
+            # if js_step['software_parameters']:
+            #    params = []
+            #    # ToDo [internal]: handle lists!
+            #    for k, v in js_step['software_parameters'].items():
+            #        print(k, v.__class__)
+            #        params.append(
+            #            modelcif.SoftwareParameter(k, v)
+            #        )
+            #    sftwre = modelcif.SoftwareGroup(
+            #        elements=(sftwre,), parameters=params
+            #    )
+
         if js_step["input"] == "target_sequences":
             input_data = modelcif.data.DataGroup(target_entities)
         elif js_step["input"] == "model":
@@ -616,12 +633,13 @@ def _store_as_modelcif(interaction_name, data_json, ost_ent, file_prfx):
     print(f" ({timer()-pstart:.2f}s)")
 
 
-def _create_interaction_json():
+def _create_interaction_json(cnfg_file):
     """Create a dictionary (mimicking JSON) that contains data which is the same
     for all models."""
     data = {}
 
     data["audit_authors"] = _get_audit_authors()
+    data["protocol"] = _get_protocol_steps_and_software(cnfg_file)
 
     return data
 
@@ -630,7 +648,6 @@ def _create_model_json(data, pdb_file, up_acs):
     """Create a dictionary (mimicking JSON) that contains all the data."""
 
     data["target_entities"], ost_ent = _get_entities(pdb_file, up_acs)
-    data["protocol"] = _get_protocol_steps_and_software()
     gns = []
     for i in data["target_entities"]:
         gns.append(i["up_gn"])
@@ -651,9 +668,9 @@ def _main():
     # get UniProtKB ACs from directory name
     up_acs = interaction.split("-")
 
-    _check_interaction_extra_files_present(opts.model_dir)
+    cnfg = _check_interaction_extra_files_present(opts.model_dir)
 
-    mdlcf_json = _create_interaction_json()
+    mdlcf_json = _create_interaction_json(cnfg)
 
     # iterate model directory
     for fle in os.listdir(opts.model_dir):