Foxed gathering entities

convert_to_modelcif.py

@@ -289,8 +289,6 @@ def _store_as_modelcif(
     #        the JSON data/ does the JSON data look different for each mode?
     #      - are the scores only calculated by alpha-analysis.sif or do they
     #        come out of run_multimer_jobs.py? Does this go into its own step?
-    #      - could Jupyter notebooks be included as associated file or do they
-    #        require the pickle files?
     #      - what about including the tabular summary?
     #      - model selection: only if just a certain model is translated to
     #        ModelCIF, or mix it with scoring step?
@@ -442,12 +440,8 @@ def _get_entities(
     structure = PDBParser().get_structure("_".join(cmplx_name), pdb_file)
     cif_json["target_entities"] = []
     already_seen = []
-    # ToDo: skip using chains to make it safe for models with ligands. Chains
-    #       are only used for the chain ID. That can be obtained from the first
-    #       residue in the sequence: seq[0].parent.id
-    for chn, seq in zip(
-        structure.get_chains(), PPBuilder().build_peptides(structure)
-    ):
+    for seq in PPBuilder().build_peptides(structure):
+        chn_id = seq[0].parent.id
         seq = seq.get_sequence()
         seq_md5 = hashlib.md5(seq.encode()).hexdigest()
         cif_ent = {}
@@ -456,10 +450,10 @@ def _get_entities(
         except ValueError:
             pass
         else:
-            cif_json["target_entities"][e_idx]["pdb_chain_id"].append(chn.id)
+            cif_json["target_entities"][e_idx]["pdb_chain_id"].append(chn_id)
             continue
         cif_ent["pdb_sequence"] = seq
-        cif_ent["pdb_chain_id"] = [chn.id]
+        cif_ent["pdb_chain_id"] = [chn_id]
         cif_ent["description"] = sequences[seq_md5]
         cif_json["target_entities"].append(cif_ent)
         already_seen.append(sequences[seq_md5])
@@ -710,5 +704,9 @@ if __name__ == "__main__":
 # ToDo: where to store which model was chosen? Should be in Tara's models.
 # ToDo: make sure all functions come with types
 
+# From former discussions:
+# - including Jupyter notebooks would require adding the pickle files to the
+#   associated files (too much storage needed for that)
+
 #  LocalWords:  ToDo AlphaPulldown PAEs dir struct coevolution MSA py modeling
 #  LocalWords:  multimer sif Jupyter aa MSAs