Some minor fixes suggested by QuantifiedCode.

.checkignore

@@ -0,0 +1,3 @@
+mdtraj/utils/external
+mdtraj/utils/six
+mdtraj/utils/unit

mdtraj/core/trajectory.py

@@ -140,9 +140,9 @@ def _parse_topology(top):
     topology : md.Topology
     """
 
-    try:
+    if isinstance(top, string_types):
         ext = _get_extension(top)
-    except:
+    else:
         ext = None  # might not be a string
 
     if isinstance(top, string_types) and (ext in ['.pdb', '.pdb.gz', '.h5','.lh5']):

mdtraj/formats/hdf5.py

@@ -922,7 +922,7 @@ def tell(self):
         return int(self._frame_index)
 
     def _validate(self):
-        raise NotImplemented
+        raise NotImplementedError()
 
         # check that all of the shapes are consistent
         # check that everything has units

mdtraj/formats/hoomdxml.py

@@ -76,7 +76,7 @@ def load_hoomdxml(filename, top=None):
         xy = float(box.attrib['xy'])
         xz = float(box.attrib['xz'])
         yz = float(box.attrib['yz'])
-    except:
+    except (ValueError, KeyError):
         xy = 0.0
         xz = 0.0
         yz = 0.0

mdtraj/formats/pdb/pdbfile.py

@@ -83,7 +83,7 @@ def _is_url(url):
     """
     try:
         return urlparse(url).scheme in _VALID_URLS
-    except:
+    except (AttributeError, TypeError):
         return False
 
 

mdtraj/formats/pdb/pdbstructure.py

@@ -205,7 +205,8 @@ def _load(self, input_stream):
                 for pos in (11,16,21,26):
                     try:
                         atoms.append(int(pdb_line[pos:pos+5]))
-                    except:
+                    except ValueError:
+                        # Optional field, don't worry if it isn't defined
                         pass
 
                 self._current_model.connects.append(atoms)
@@ -679,11 +680,11 @@ def __init__(self, pdb_line, pdbstructure=None):
         else:
             try:
                 self.serial_number = int(pdb_line[6:11])
-            except:
+            except ValueError:
                 try:
                     self.serial_number = int(pdb_line[6:11], 16)
                     pdbstructure._atom_numbers_are_hex = True
-                except:
+                except ValueError:
                     # Just give it the next number in sequence.
                     self.serial_number = pdbstructure._next_atom_number
         self.name_with_spaces = pdb_line[12:16]
@@ -706,11 +707,11 @@ def __init__(self, pdb_line, pdbstructure=None):
         else:
             try:
                 self.residue_number = int(pdb_line[22:26])
-            except:
+            except ValueError:
                 try:
                     self.residue_number = int(pdb_line[22:26], 16)
                     pdbstructure._residue_numbers_are_hex = True
-                except:
+                except ValueError:
                     # When VMD runs out of hex values it starts filling in the residue ID field with ****
                     # Look at the most recent atoms to figure out whether this is a new residue or not.
                     if pdbstructure._current_model is None or pdbstructure._current_model._current_chain is None or pdbstructure._current_model._current_chain._current_residue is None:
@@ -733,11 +734,11 @@ def __init__(self, pdb_line, pdbstructure=None):
         z = float(pdb_line[46:54])
         try:
             occupancy = float(pdb_line[54:60])
-        except:
+        except ValueError:
             occupancy = 1.0
         try:
             temperature_factor = float(pdb_line[60:66])
-        except:
+        except ValueError:
             temperature_factor = 0.0
         self.locations = {}
         loc = Atom.Location(alternate_location_indicator, np.array([x,y,z]), occupancy, temperature_factor, self.residue_name_with_spaces)