Chain type determination changed to _entity_poly.type (#8)

* Fixed chain type determination

* Returned letter converters

* Fixed entity id dictionary key

Author: RJPenic

rna3db/parser.py

@@ -538,8 +538,10 @@ def __init__(
 
         if molecule_type == "RNA":
             self.letters_3to1 = lambda x: modification_handler.rna_letters_3to1(x)
+            self.polymer_type = "polyribonucleotide"
         elif molecule_type == "protein":
             self.letters_3to1 = lambda x: modification_handler.protein_letters_3to1(x)
+            self.polymer_type = "polypeptide"
         else:
             raise ValueError('molecule_type must be one of "RNA" or "protein".')
 
@@ -671,15 +673,19 @@ def chains(self):
                     )
                 )
 
-        # keep only chains that contain at least one 'self.molecule_type'
+        # Get chain/polymer types
+        chain_type = {}
+        for entity_id, poly_type in zip(
+            self.parsed_info["_entity_poly.entity_id"],
+            self.parsed_info["_entity_poly.type"],
+        ):
+            for author_id in id_map[entity_id]:
+                chain_type[author_id] = poly_type
+
+        # keep only chains of the appropriate polymer type
         chains = {}
         for author_chain_id, chain_data in chains_full.items():
-            if any(
-                [
-                    self.molecule_type in chem_comp_type[i.three_letter_code]
-                    for i in chain_data.residues
-                ]
-            ):
+            if self.polymer_type in chain_type[author_chain_id]:
                 chains[author_chain_id] = chain_data
 
         # find starting index of relevant chains