Add target entities

translate2modelcif.py

@@ -230,28 +230,36 @@ def _get_entities(pdb_file, up_acs):
 
 def _store_as_modelcif(interaction_name, data_json, file_prfx):
     """Mix all the data into a ModelCIF file."""
-    # create target references, ...
-    for cif_ent in data_json["target_entities"]:
-        # 'cif_sequence'
-        ref = modelcif.reference.UniProt(
-            cif_ent["up_id"],
-            cif_ent["up_ac"],
-            # careful: alignments are just that easy because of equal sequences!
-            align_begin=1,
-            align_end=cif_ent["up_seqlen"],
-            isoform=cif_ent["up_isoform"],
-            ncbi_taxonomy_id=cif_ent["up_ncbi_taxid"],
-            organism_scientific=cif_ent["up_organism"],
-            sequence_version_date=cif_ent["up_last_mod"],
-            sequence_crc64=cif_ent["up_crc64"],
-        )
-
     # create system to gather all the data
     system = modelcif.System(
         title=data_json["title"],
         id=interaction_name.upper(),
         model_details=data_json["model_details"],
     )
+    # create target entities, references, ...
+    for cif_ent in data_json["target_entities"]:
+        # ToDo [input]: Get entity description
+        mdlcif_ent = modelcif.Entity(
+            cif_ent["cif_sequence"],
+            description="entity.pdbx_description",
+            references=[
+                modelcif.reference.UniProt(
+                    cif_ent["up_id"],
+                    cif_ent["up_ac"],
+                    # Careful: alignments are just that easy because of equal
+                    # sequences!
+                    align_begin=1,
+                    align_end=cif_ent["up_seqlen"],
+                    isoform=cif_ent["up_isoform"],
+                    ncbi_taxonomy_id=cif_ent["up_ncbi_taxid"],
+                    organism_scientific=cif_ent["up_organism"],
+                    sequence_version_date=cif_ent["up_last_mod"],
+                    sequence_crc64=cif_ent["up_crc64"],
+                )
+            ],
+        )
+        system.entities.append(mdlcif_ent)
+        system.target_entities.append(mdlcif_ent)
     # audit_authors
     system.authors.extend(data_json["audit_authors"])
 
@@ -320,4 +328,4 @@ if __name__ == "__main__":
 #  LocalWords:  sqe olc ACDEFGHIKLMNPQRSTVWY RuntimeError upkb txt pylint iter
 #  LocalWords:  rspns unicode startswith sline len elif NCBI TaxID ncbi taxid
 #  LocalWords:  seqlen crc ISOFORM DT dt flds isoforms isoform ent LoadPDB
-#  LocalWords:  mdlcf
+#  LocalWords:  mdlcf mdlcif