Addressing Molli Functionality of Arbitrary Property Assignment

molli/chem/atom.py

@@ -409,6 +409,11 @@ class Atom:
         # repr=lambda x: x.name,
     )
 
+    mdata = attrs.field(
+        default=attrs.Factory(dict),
+        repr=False
+    )
+
     def evolve(self, **changes):
         return attrs.evolve(self, **changes)
 
@@ -443,6 +448,12 @@ def __eq__(self, other: AtomLike):
     def __hash__(self) -> int:
         return id(self)
 
+    def __getitem__(self, key):
+        return self.mdata[key]
+
+    def __setitem__(self, key, val):
+        self.mdata[key] = val
+
     @property
     def implicit_valence(self) -> int:
         return IMPLICIT_VALENCE[self.element.group]
@@ -648,7 +659,7 @@ class Promolecule:
     for API compatibility reasons.
     """
 
-    __slots__ = ("_atoms", "_atom_index_cache", "_name", "charge", "mult")
+    __slots__ = ("_atoms", "_atom_index_cache", "_name", "charge", "mult", "mdata")
 
     def __init__(
         self,
@@ -660,6 +671,7 @@ def __init__(
         copy_atoms: bool = False,
         charge: int = None,
         mult: int = None,
+        mdata: dict = None,
         **kwds,  # mostly just for subclassing compatibility
     ):
         """
@@ -671,6 +683,7 @@ def __init__(
         self.name = name
         self.charge = charge or 0
         self.mult = mult or 1
+        self.mdata = mdata
 
         match other:
             case None:

molli/chem/bond.py

@@ -94,6 +94,11 @@ class Bond:
         converter=float,
     )
 
+    mdata: dict = attrs.field(
+        default=attrs.Factory(dict),
+        repr=False
+    )
+
     def evolve(self, **changes):
         return attrs.evolve(self, **changes)
 
@@ -170,6 +175,12 @@ def __mod__(self, a: Atom) -> Atom:
         else:
             raise ValueError("Atom is not a part of this bond")
 
+    def __getitem__(self, key):
+        return self.mdata[key]
+
+    def __setitem__(self, key, val):
+        self.mdata[key] = val
+
     @property
     def expected_length(self) -> float:
         r1 = self.a1.cov_radius_1

molli_test/test_chem_molecule.py

@@ -72,5 +72,36 @@ def test_del_atom(self):
         self.assertEqual(mol.n_bonds, nb - 3) # atom 0 is connected to 3 bonds
         self.assertEqual(mol._atomic_charges.shape, (na - 1,))
 
+    def test_mdata_instance(self):
 
-
+        mol = ml.Molecule.load_mol2(ml.files.dendrobine_mol2)
+        a1 = mol.atoms[0]
+        b1 = mol.atoms[0]
+
+        a1['str'] = '5'
+        a1['int'] = 1
+        a1['float'] = 1.1
+        a1['tuple'] = (1,1)
+        a1['list'] = [2,3]
+        a1['dict'] = {2: 'a', 3: 'b'}
+
+        self.assertIsInstance(a1['str'], str)
+        self.assertIsInstance(a1['int'], int)
+        self.assertIsInstance(a1['float'], float)
+        self.assertIsInstance(a1['tuple'], tuple)
+        self.assertIsInstance(a1['list'], list)
+        self.assertIsInstance(a1['dict'], dict)
+
+        b1['str'] = '5'
+        b1['int'] = 1
+        b1['float'] = 1.1
+        b1['tuple'] = (1,1)
+        b1['list'] = [2,3]
+        b1['dict'] = {2: 'a', 3: 'b'}
+
+        self.assertIsInstance(b1['str'], str)
+        self.assertIsInstance(b1['int'], int)
+        self.assertIsInstance(b1['float'], float)
+        self.assertIsInstance(b1['tuple'], tuple)
+        self.assertIsInstance(b1['list'], list)
+        self.assertIsInstance(b1['dict'], dict)