headless fragmentor error fixed for small or bondless molecules.

fingerprint generation fixed. method renamed.

CIMtools/preprocessing/fingerprint.py

@@ -87,13 +87,13 @@ def fit(self, x, y=None):
         return self
 
     def transform(self, x):
-        x = self._transform_bitset(x)
+        x = self.transform_bitset(x)
         out = zeros((len(x), 2 ** self.fingerprint_size), dtype=bool8)
         for i, j in enumerate(x):
             out[i, j] = True
         return out
 
-    def _transform_bitset(self, x):
+    def transform_bitset(self, x):
         x = iter2array(x, dtype=(MoleculeContainer, CGRContainer))
         mask = 2 ** self.fingerprint_size - 1
         fp_count = self.bits_count
@@ -109,7 +109,7 @@ def _transform_bitset(self, x):
                                            for r in range(0, fp_active, 2)] + prev
 
         out = []
-        for s, row in zip(x, df.itertuples(index=False)):
+        for s, (_, row) in zip(x, df.iterrows()):
             active_bits = set()
             # add atomic bits
             if isinstance(s, MoleculeContainer):

CIMtools/preprocessing/fragmentor.py

@@ -345,14 +345,14 @@ def __parse_header(header):
             head_dict = {int(k[:-1]): v for k, v in (i.split() for i in head_dump.splitlines())}
         except ValueError as e:
             raise ConfigurationError from e
-        if not head_dict:
-            raise ConfigurationError('empty header')
-
         return head_dict
 
     def __load_header(self, header):
-        self.__head_dict = self.__parse_header(header)
-        self.__head_dump = self.__format_header(self.__head_dict)
+        head_dict = self.__parse_header(header)
+        if not head_dict:
+            raise ConfigurationError('empty header')
+        self.__head_dict = head_dict
+        self.__head_dump = self.__format_header(head_dict)
 
     def __prepare_header(self):
         if not self.__head_exec:

setup.py

@@ -22,7 +22,7 @@
 from wheel.bdist_wheel import bdist_wheel
 
 
-version = '4.0.0'
+version = '4.0.1'
 
 platform = get_platform()
 if platform == 'win-amd64':