fix parsing error for strand circularity in oat's new topology reader

analysis/src/oxDNA_analysis_tools/UTILS/data_structures.py

@@ -95,6 +95,9 @@ class System:
             strands (List[Strand]) : A list of Strand objects
     """
 
+    top_file: str
+    strands: List[Strand]
+
     def __init__(self, top_file:str='', strands:List = []):
         self.top_file = top_file
         self.strands = strands
@@ -138,6 +141,12 @@ class Strand:
             circular (bool) : Is this a circular strand? (default : False)
     """
 
+    __from_old: bool
+    id: int
+    monomers: List[Monomer]
+    type: str
+    circular: bool
+
     def __init__(self, id, *initial_data, **kwargs):
         self.__from_old = False
         self.id = id
@@ -149,7 +158,11 @@ def __init__(self, id, *initial_data, **kwargs):
                 setattr(self, key, dictionary[key])
         for key in kwargs:
             setattr(self, key, kwargs[key])
+
+        # the initial values come in as strings, so ones with known types must be set.
         self.id = int(self.id)
+        if isinstance(self.circular, str):
+            self.circular = self.circular.lower() == "true"
 
     def __getitem__(self, key:int):
         return self.monomers[key]

analysis/src/oxDNA_analysis_tools/__init__.py

@@ -1 +1 @@
-__version__ = '2.4.0'
+__version__ = '2.4.2'

analysis/src/oxDNA_analysis_tools/external_force_utils/forces.py

@@ -1,4 +1,5 @@
 #see: https://dna.physics.ox.ac.uk/index.php/Documentation#External_Forces
+# TODO: "group_name" and "id" need to be added as optional parameters to forces
 from typing import Dict, List, Literal
 
 def mutual_trap(particle:int, ref_particle:int, stiff:float, r0:float, PBC:bool, rate:float=0, stiff_rate:float=0) -> Dict:

analysis/src/oxDNA_analysis_tools/oxDNA_PDB.py

@@ -342,12 +342,12 @@ def oxDNA_PDB(conf:Configuration, system:System, out_basename:str, protein_pdb_f
                         if strand.is_old():
                             if nucleotide == strand.monomers[0] and not strand.is_circular():
                                 residue_type = "3"
-                            elif nucleotide == strand.monomers[-1]:
+                            elif nucleotide == strand.monomers[-1] and not strand.is_circular():
                                 residue_type = "5"
                         else:
                             if nucleotide == strand.monomers[0] and not strand.is_circular():
                                 residue_type = "5"
-                            elif nucleotide == strand.monomers[-1]:
+                            elif nucleotide == strand.monomers[-1] and not strand.is_circular():
                                 residue_type = "3"
 
                     nuc_data = {