Minor fixes

translate2modelcif.py

@@ -251,7 +251,6 @@ def _get_protocol_steps_and_software(cnfg_file):
     # Must refer to existing data, so we try keywords
     step["output"] = "model"
     # get software
-<<<<<<< HEAD
     step["software"] = [
         {
             "name": "ColabFold",
@@ -543,6 +542,8 @@ def _get_scores(data, prfx):
     with open(scrs_fle, encoding="utf8") as jfh:
         scrs_json = json.load(jfh)
 
+    # ToDo: is dict.update still the way to go when iterating multiple model
+    # directories? Aka, does dict.update overwrite old scores?
     data.update(scrs_json)
 
 
@@ -613,11 +614,10 @@ def _get_modelcif_protocol(protocol_steps, target_entities, model):
                 for sft in js_step["software"]:
                     sftwre.append(_assemble_modelcif_software(sft))
                 sftwre = modelcif.SoftwareGroup(elements=sftwre)
-            # ToDo [internal]: add software parameters
-            if js_step['software_parameters']:
+            if js_step["software_parameters"]:
                 params = []
                 # ToDo [internal]: handle lists!
-                for k, v in js_step['software_parameters'].items():
+                for k, v in js_step["software_parameters"].items():
                     params.append(
                         modelcif.SoftwareParameter(k, v)
                     )
@@ -630,6 +630,7 @@ def _get_modelcif_protocol(protocol_steps, target_entities, model):
 
         if js_step["input"] == "target_sequences":
             input_data = modelcif.data.DataGroup(target_entities)
+        # ToDo: Add databases + versions
         elif js_step["input"] == "model":
             input_data = model
         else: