Merge pull request #81 from padix-key/master

Fixed dir() function and coord initialization for AtomArray and AtomArrayStack

src/biotite/structure/__init__.py

@@ -15,7 +15,7 @@
 An `Atom` contains data for a single atom, it stores the annotations as
 scalar values and the coordinates as length 3 `ndarray`.
 An `AtomArray` stores data for an entire structure model containing *n*
-atoms. Therefore the annotations are represented as `ndarray`s of
+atoms. Therefore the annotations are represented as `ndarray` objects of
 length *n*, so called annotation arrays. The coordinates are a (n x 3)
 `ndarray`.
 `AtomArrayStack` stores data for *m* models. Each `AtomArray` in

src/biotite/structure/atoms.py

@@ -333,8 +333,10 @@ def __dir__(self):
         attr = super().__dir__()
         attr.append("coord")
         attr.append("bonds")
+        attr.append("box")
         for name in self._annot.keys():
             attr.append(name)
+        return attr
 
     def __eq__(self, item):
         """
@@ -819,7 +821,7 @@ def __init__(self, depth, length):
         if depth == None or length == None:
             self._coord = None
         else:
-            self._coord = np.zeros((depth, length, 3), dtype=float)
+            self._coord = np.full((depth, length, 3), np.nan, dtype=float)
 
     def get_array(self, index):
         """