Actually use name set/get

MDANSE/Src/MDANSE/Chemistry/ChemicalEntity.py

@@ -115,7 +115,7 @@ class _ChemicalEntity(metaclass=abc.ABCMeta):
     def __init__(self):
         self._parent = None
 
-        self._name = ""
+        self.name = ""
 
     def __getstate__(self):
         return self.__dict__
@@ -162,7 +162,7 @@ def name(self):
 
     @name.setter
     def name(self, name):
-        self._name = name
+        self._name = str(name)
 
     @abc.abstractmethod
     def serialize(self, h5_file):
@@ -485,7 +485,7 @@ def __init__(
         if self._symbol not in ATOMS_DATABASE:
             raise UnknownAtomError("The atom {} is unknown".format(self.symbol))
 
-        self._name = name if name else symbol
+        self.name = name if name else symbol
 
         self._bonds = bonds if bonds else []
 
@@ -642,7 +642,7 @@ def name(self) -> str:
 
     @name.setter
     def name(self, name: str) -> None:
-        self._name = name
+        self.name = str(name)
 
     @property
     def symbol(self) -> str:
@@ -794,7 +794,7 @@ def __init__(self, name: str, atoms: list[Atom], parentless: bool = False):
         """
         super(AtomCluster, self).__init__()
 
-        self._name = name
+        self.name = name
 
         self._parentless = parentless
 
@@ -836,7 +836,7 @@ def copy(self) -> "AtomCluster":
         """
         atoms = [atom.copy() for atom in self._atoms]
 
-        ac = AtomCluster(self._name, atoms, self._parentless)
+        ac = AtomCluster(self.name, atoms, self._parentless)
 
         if not self._parentless:
             for at in ac._atoms:
@@ -933,7 +933,7 @@ def serialize(self, h5_contents: dict[str, list[list[str]]]) -> tuple[str, int]:
             at_indexes = list(range(len(self._atoms)))
 
         h5_contents.setdefault("atom_clusters", []).append(
-            [str(at_indexes), repr(self._name)]
+            [str(at_indexes), repr(self.name)]
         )
 
         for at in self._atoms:
@@ -960,7 +960,7 @@ def __init__(self, code: str, name: str):
 
         self._code = code
 
-        self._name = name
+        self.name = name
 
         self._build(code)
 
@@ -1121,7 +1121,7 @@ def serialize(self, h5_contents: dict[str, list[list[str]]]) -> tuple[str, int]:
             at_indexes = list(range(len(self._atoms)))
 
         h5_contents.setdefault("molecules", []).append(
-            [str(at_indexes), repr(self._code), repr(self._name)]
+            [str(at_indexes), repr(self._code), repr(self.name)]
         )
 
         for at in self._atoms.values():
@@ -1169,7 +1169,7 @@ def __init__(self, code: str, name: str, variant: Union[str, None] = None):
 
         self._code = code
 
-        self._name = name
+        self.name = name
 
         self._variant = variant
 
@@ -1362,7 +1362,7 @@ def serialize(self, h5_contents: dict[str, list[list[str]]]) -> tuple[str, int]:
             at_indexes = list(range(len(self._atoms)))
 
         h5_contents.setdefault("residues", []).append(
-            [str(at_indexes), repr(self._code), repr(self._name), repr(self._variant)]
+            [str(at_indexes), repr(self._code), repr(self.name), repr(self._variant)]
         )
 
         for at in self._atoms.values():
@@ -1396,7 +1396,7 @@ def __init__(self, code: str, name: str, variant: Union[str, None] = None):
 
         self._code = code
 
-        self._name = name
+        self.name = name
 
         self._variant = variant
 
@@ -1590,7 +1590,7 @@ def serialize(self, h5_contents: dict[str, list[list[str]]]) -> tuple[str, int]:
             at_indexes = list(range(len(self._atoms)))
 
         h5_contents.setdefault("nucleotides", []).append(
-            [str(at_indexes), repr(self._code), repr(self._name), repr(self._variant)]
+            [str(at_indexes), repr(self._code), repr(self.name), repr(self._variant)]
         )
 
         for at in self._atoms.values():
@@ -1611,7 +1611,7 @@ def __init__(self, name: str):
 
         super(NucleotideChain, self).__init__()
 
-        self._name = name
+        self.name = name
 
         self._nucleotides = []
 
@@ -1747,7 +1747,7 @@ def bases(self) -> list[Atom]:
 
     def copy(self) -> "NucleotideChain":
         """Copies the instance of NucleotideChain into a new, identical instance."""
-        nc = NucleotideChain(self._name)
+        nc = NucleotideChain(self.name)
 
         nucleotides = [nucl.copy() for nucl in self._nucleotides]
 
@@ -1852,7 +1852,7 @@ def serialize(self, h5_contents: dict[str, list[list[str]]]) -> tuple[str, int]:
             nucl.serialize(h5_contents)
 
         h5_contents.setdefault("nucleotide_chains", []).append(
-            [repr(self._name), str(res_indexes)]
+            [repr(self.name), str(res_indexes)]
         )
 
         return "nucleotide_chains", len(h5_contents["nucleotide_chains"]) - 1
@@ -1902,7 +1902,7 @@ def __init__(self, name: str):
 
         super(PeptideChain, self).__init__()
 
-        self._name = name
+        self.name = name
 
         self._residues = []
 
@@ -2039,7 +2039,7 @@ def backbone(self) -> list[Atom]:
 
     def copy(self) -> "PeptideChain":
         """Copies the instance of NucleotideChain into a new, identical instance."""
-        pc = PeptideChain(self._name)
+        pc = PeptideChain(self.name)
 
         residues = [res.copy() for res in self._residues]
 
@@ -2158,7 +2158,7 @@ def serialize(self, h5_contents: dict[str, list[list[str]]]) -> tuple[str, int]:
             res.serialize(h5_contents)
 
         h5_contents.setdefault("peptide_chains", []).append(
-            [repr(self._name), str(res_indexes)]
+            [repr(self.name), str(res_indexes)]
         )
 
         return "peptide_chains", len(h5_contents["peptide_chains"]) - 1
@@ -2202,7 +2202,7 @@ def __init__(self, name: str = ""):
         """
         super().__init__()
 
-        self._name = name
+        self.name = name
 
         self._peptide_chains = []
 
@@ -2245,7 +2245,7 @@ def backbone(self) -> list[Atom]:
 
     def copy(self) -> "Protein":
         """Copies the instance of Protein into a new, identical instance."""
-        p = Protein(self._name)
+        p = Protein(self.name)
 
         peptide_chains = [pc.copy() for pc in self._peptide_chains]
 
@@ -2370,7 +2370,7 @@ def serialize(self, h5_contents: dict[str, list[list[str]]]) -> tuple[str, int]:
             pc_indexes = list(range(len(self._peptide_chains)))
 
         h5_contents.setdefault("proteins", []).append(
-            [repr(self._name), str(pc_indexes)]
+            [repr(self.name), str(pc_indexes)]
         )
 
         for pc in self._peptide_chains:
@@ -2444,7 +2444,7 @@ def __init__(self, name: str = ""):
 
         self._total_number_of_atoms = 0
 
-        self._name = name
+        self.name = name
 
         self._bonds = []
 
@@ -2618,7 +2618,7 @@ def copy(self) -> "ChemicalSystem":
         :return: Copy of the ChemicalSystem instance
         :rtype: MDANSE.Chemistry.ChemicalEntity.ChemicalSystem
         """
-        cs = ChemicalSystem(self._name)
+        cs = ChemicalSystem(self.name)
 
         cs._parent = self._parent
 
@@ -2758,7 +2758,7 @@ def load(self, h5_filename: Union[str, h5py.File]) -> None:
         except KeyError:
             bonds = []
 
-        self._name = grp.attrs["name"]
+        self.name = grp.attrs["name"]
 
         h5_contents = {}
         for entity_type, v in grp.items():
@@ -2902,7 +2902,7 @@ def serialize(self, h5_file: h5py.File) -> None:
 
         grp = h5_file.create_group("/chemical_system")
 
-        grp.attrs["name"] = self._name
+        grp.attrs["name"] = self.name
 
         h5_contents = {}