some getters

Author: rtviii

ribctl/assets_project/cache_hmm/taxid_410359_hmm_scanner

@@ -304,18 +304,19 @@ def calculate_position_entropy(aligned_sequences: List[str], position: int) -> f
     return entropy
 
 def get_conservation_scores(fasta_obj: Fasta) -> Dict[int, float]:
+
     """
     Calculate conservation scores for each position in aligned sequences.
     Returns a dictionary mapping structural indices to conservation scores.
     """
     # Get alignment using existing MUSCLE implementation
     aligned_records = muscle_align_N_seq(fasta_obj.records)
-    
+
     # Convert to list of strings for easier processing
     aligned_sequences = [str(record.seq) for record in aligned_records]
 
     # Detect sequence type
-    seq_type = detect_sequence_type(aligned_sequences)
+    seq_type    = detect_sequence_type(aligned_sequences)
     max_entropy = get_max_entropy(seq_type)
 
     # Calculate entropy for each position

ribctl/assets_project/cache_hmm/taxid_410359_seed_seqs

@@ -36,6 +36,19 @@ def taxid(self)->int:
     def profile(self) -> RibosomeStructure:
         return self.assets.profile()
 
+    def get_biopython_chain_by_polymer_class(self, polymer_class: PolymerClass) -> Chain:
+        struct = self.assets.biopython_structure()[0]
+        poly = self.get_poly_by_polyclass(polymer_class)
+        if poly == None:
+            raise KeyError("No polymer found with class: {}".format(polymer_class))
+        return struct.child_dict[0].child_dict[poly.auth_asym_id]
+
+
+
+    def get_biopython_chain_by_auth_asym_id(self, auth_asym_id: str) -> Chain:
+        struct = self.assets.biopython_structure()[0]
+        return struct.child_dict[0].child_dict[auth_asym_id]
+
     def nomenclature_table(self, verbose: bool = False) -> dict[str, dict]:
         prof = self.assets.profile()
         m    = {}