Merge pull request #352 from padix-key/master

Fix attribute access Atom, AtomArray and AtomArrayStack

src/biotite/structure/atoms.py

@@ -265,7 +265,9 @@ def __getattr__(self, attr):
             return self._bonds
         if attr == "box":
             return self._box
-        elif attr in self._annot:
+        # Call method of 'object' superclass to avoid infinite recursive
+        # calls of '__getattr__()'
+        elif attr in super().__getattribute__("_annot"):
             return self._annot[attr]
         else:
             raise AttributeError(
@@ -301,7 +303,7 @@ def __setattr__(self, attr, value):
                 )
             if value.shape[-1] != 3:
                 raise TypeError("Expected 3 coordinates for each atom")
-            self._coord = value.astype(np.float32, copy=False)
+            super().__setattr__("_coord", value.astype(np.float32, copy=False))
 
         elif attr == "bonds":
             if isinstance(value, BondList):
@@ -310,41 +312,37 @@ def __setattr__(self, attr, value):
                         f"Array length is {self._array_length}, "
                         f"but bond list has {value.get_atom_count()} atoms"
                     )
-                self._bonds = value
+                super().__setattr__("_bonds", value)
             elif value is None:
                 # Remove bond list
-                self._bonds = None
+                super().__setattr__("_bonds", None)
             else:
                 raise TypeError("Value must be 'BondList'")
 
         elif attr == "box":
-            if value is None:
-                self._box = None
-            elif isinstance(self, AtomArray):
-                if value.ndim != 2:
-                    raise ValueError(
-                        "A 2-dimensional ndarray is expected "
-                        "for an AtomArray"
-                )
-            elif isinstance(self, AtomArrayStack):
-                if value.ndim != 3:
-                    raise ValueError(
-                        "A 3-dimensional ndarray is expected "
-                        "for an AtomArrayStack"
-                )
             if isinstance(value, np.ndarray):
+                if isinstance(self, AtomArray):
+                    if value.ndim != 2:
+                        raise ValueError(
+                            "A 2-dimensional ndarray is expected "
+                            "for an AtomArray"
+                    )
+                else:   # AtomArrayStack
+                    if value.ndim != 3:
+                        raise ValueError(
+                            "A 3-dimensional ndarray is expected "
+                            "for an AtomArrayStack"
+                    )
                 if value.shape[-2:] != (3,3):
                     raise TypeError("Box must be a 3x3 matrix (three vectors)")
-                self._box = value.astype(np.float32, copy=False)
+                box = value.astype(np.float32, copy=False)
+                super().__setattr__("_box", box)
             elif value is None:
                 # Remove box
-                self._box = None
+                super().__setattr__("_box", None)
             else:
                 raise TypeError("Box must be ndarray of floats or None")
 
-        # This condition is required, since otherwise 
-        # call of the next one would result
-        # in indefinite calls of __setattr__
         elif attr == "_annot":
             super().__setattr__(attr, value)
         elif attr in self._annot:
@@ -514,16 +512,14 @@ def shape(self):
         return ()
 
     def __getattr__(self, attr):
-        if attr in self._annot:
+        if attr in super().__getattribute__("_annot"):
             return self._annot[attr]
         else:
             raise AttributeError(
                 f"'{type(self).__name__}' object has no attribute '{attr}'"
             )
 
     def __setattr__(self, attr, value):
-        # First condition is required, to avoid indefinite calls of
-        # __getattr__()
         if attr == "_annot":
             super().__setattr__(attr, value)
         elif attr == "coord":

tests/structure/test_atoms.py

@@ -2,9 +2,10 @@
 # under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
 # information.
 
-import biotite.structure as struc
+import pickle
 import numpy as np
 import pytest
+import biotite.structure as struc
 
 
 @pytest.fixture
@@ -176,4 +177,20 @@ def test_array_from_atoms(atom_list):
         atom.some_annotation = 42
     array = struc.array(atom_list)
     assert np.all(array.some_annotation == np.full(array.array_length(), 42))
-    assert np.issubdtype(array.some_annotation.dtype, np.integer)
+    assert np.issubdtype(array.some_annotation.dtype, np.integer)
+
+
+def test_pickle(atom, array, stack):
+    """
+    Check if pickling and unpickling works.
+    This test is necessary since the classes implement the
+    :meth:`__getattr__()` and :meth:`__setattr__()` methods.
+    """
+    test_atom = pickle.loads(pickle.dumps(atom))
+    assert test_atom == atom
+
+    test_array = pickle.loads(pickle.dumps(array))
+    assert test_array == array
+
+    test_stack = pickle.loads(pickle.dumps(stack))
+    assert test_stack == stack