add radical smiles support

cctk/array.py

@@ -1,6 +1,7 @@
 import numpy as np
 import copy
 
+
 class OneIndexedArray(np.ndarray):
     """
     Wrapper for ``np.ndarray`` that's indexed from one, not zero, to store atomic numbers and geometries.
@@ -28,7 +29,7 @@ def __getitem__(self, index):
             return super().__getitem__(new_index)
         elif isinstance(index, int):
             if index > 0:
-                return super().__getitem__(index-1)
+                return super().__getitem__(index - 1)
             elif index == 0:
                 raise IndexError("this is a 1-indexed array: no element 0!")
             elif index < 0:
@@ -37,7 +38,7 @@ def __getitem__(self, index):
             if index[0] is None:
                 return super().__getitem__((index[0], index[1]))
             elif index[0] > 0:
-                return super().__getitem__((index[0]-1, index[1]))
+                return super().__getitem__((index[0] - 1, index[1]))
             elif index[0] == 0:
                 raise IndexError("this is a 1-indexed array: no element 0!")
             elif index[0] < 0:
@@ -76,11 +77,13 @@ def __setitem__(self, index, value):
         if isinstance(index, int):
             if index > 0:
                 if self.ndim == 1:
-                    super().__setitem__(index-1, value)
+                    super().__setitem__(index - 1, value)
                 elif self.ndim == 2:
                     super().__setitem__(index, value)
                 else:
-                    raise TypeError("this datatype is only defined for 1D and 2D ndarrays")
+                    raise TypeError(
+                        "this datatype is only defined for 1D and 2D ndarrays"
+                    )
             elif index == 0:
                 raise IndexError("this is a 1-indexed array: no element 0!")
             elif index < 0:
@@ -89,7 +92,7 @@ def __setitem__(self, index, value):
             if index[0] is None:
                 super().__setitem__((index[0], index[1]), value)
             elif index[0] > 0:
-                super().__setitem__((index[0]-1, index[1]), value)
+                super().__setitem__((index[0] - 1, index[1]), value)
             elif index[0] == 0:
                 raise IndexError("this is a 1-indexed array: no element 0!")
             elif index[0] < 0:
@@ -122,10 +125,11 @@ def __setitem__(self, index, value):
                 super().__setitem__(index, value)
         else:
             super().__setitem__(index, value)
-#            raise IndexError(f"invalid index {index} for OneIndexedArray")
+
+    #            raise IndexError(f"invalid index {index} for OneIndexedArray")
 
     def __iter__(self):
-        for idx in range(1,len(self)+1):
+        for idx in range(1, len(self) + 1):
             yield self.__getitem__(idx)
 
     def __hash__(self):

cctk/file.py

@@ -78,4 +78,3 @@ def read_file(filename, lazy=False):
         with open(filename, "r") as filehandle:
             lines = filehandle.read().splitlines()
             return lines
-