Fix names

Dockerfile

@@ -24,7 +24,8 @@ COPY requirements.txt ${SRC_DIR}
 WORKDIR ${SRC_DIR}
 RUN set -e pipefail; \
     apt-get update -y; \
-    apt-get install -y git pip; \
+    # for development, install venv
+    apt-get install -y git pip python3.8-venv; \
     pip install -r requirements.txt; \
     # for development, install black & PyLint
     pip install black pylint; \

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"
 
@@ -57,7 +56,6 @@ def _parse_args():
 class _GlobalPTM(modelcif.qa_metric.Global, modelcif.qa_metric.PTM):
     """Predicted accuracy according to the TM-score score in [0,1]."""
 
-    # ToDo [input]: Add software
     name = "pTM"
     software = None
 
@@ -220,9 +218,10 @@ def _check_model_extra_files_present(model_dir, pdb_file):
 
 def _get_audit_authors():
     """Return the list of authors that produced this model."""
+    # ToDo: tell Xabi that his name can't have a á in mmCIF
     return (
         "Bartolec T",
-        "Vázquez-Campos X",
+        "Vazquez-Campos X",
         "Johnson M",
         "Norman A",
         "Payne R",
@@ -267,7 +266,7 @@ def _get_protocol_steps_and_software(cnfg_file):
                 "year": 2022,
                 "authors": [
                     "Mirdita M",
-                    "Schütze K",
+                    "Schuetze K",
                     "Moriwaki Y",
                     "Heo L",
                     "Ovchinnikov S",
@@ -294,7 +293,7 @@ def _get_protocol_steps_and_software(cnfg_file):
                 "authors": [
                     "Mirdita M",
                     "Steinegger M",
-                    "Söding J",
+                    "Soeding J",
                 ],
                 "doi": "10.1093/bioinformatics/bty1057",
             },
@@ -321,7 +320,7 @@ def _get_protocol_steps_and_software(cnfg_file):
                     "Antropova N",
                     "Senior A",
                     "Green T",
-                    "Žídek A",
+                    "Zidek A",
                     "Bates R",
                     "Blackwell S",
                     "Yim J",
@@ -613,16 +612,20 @@ 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)
-            # if js_step['software_parameters']:
-            #    params = []
-            #    # ToDo [internal]: handle lists!
-            #    for k, v in js_step['software_parameters'].items():
-            #        params.append(
-            #            modelcif.SoftwareParameter(k, v)
-            #        )
-            #    sftwre = modelcif.SoftwareGroup(
-            #        elements=(sftwre,), parameters=params
-            #    )
+            # ToDo [internal]: add software parameters
+            if js_step['software_parameters']:
+                params = []
+                # ToDo [internal]: handle lists!
+                for k, v in js_step['software_parameters'].items():
+                    params.append(
+                        modelcif.SoftwareParameter(k, v)
+                    )
+                if isinstance(sftwre, modelcif.SoftwareGroup):
+                    sftwre.parameters = params
+                else:
+                    sftwre = modelcif.SoftwareGroup(
+                        elements=(sftwre,), parameters=params
+                    )
 
         if js_step["input"] == "target_sequences":
             input_data = modelcif.data.DataGroup(target_entities)
@@ -710,7 +713,7 @@ def _store_as_modelcif(interaction_name, data_json, ost_ent, file_prfx):
     # write modelcif System to file
     print("    write to disk...", end="", flush=True)
     pstart = timer()
-    with open(f"{file_prfx}.cif", "w", encoding="utf8") as mmcif_fh:
+    with open(f"{file_prfx}.cif", "w", encoding="ascii") as mmcif_fh:
         modelcif.dumper.write(mmcif_fh, [system])
     print(f" ({timer()-pstart:.2f}s)")