MolVS 0.1.0 Standardization fails on Python 3

[thesketh]

Hi Matt, a bug report for something I've noticed in the latest release.

The standardize_smiles, Standardizer().tautomer_parent and Standardizer().standardize functions all fail because of line 133. These all work okay in 0.0.9

>>> mol = Chem.MolFromSmiles('[Na]OC(=O)c1ccc(C[S+2]([O-])([O-]))cc1')
>>> Standardizer().standardize(mol)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/travis/anaconda3/envs/rdkit/lib/python3.6/site-packages/molvs/standardize.py", line 98, in standardize
    mol = self.normalize(mol)
  File "/home/travis/anaconda3/envs/rdkit/lib/python3.6/site-packages/molvs/normalize.py", line 105, in __call__
    return self.normalize(mol)
  File "/home/travis/anaconda3/envs/rdkit/lib/python3.6/site-packages/molvs/normalize.py", line 124, in normalize
    fragments.append(self._normalize_fragment(fragment))
  File "/home/travis/anaconda3/envs/rdkit/lib/python3.6/site-packages/molvs/normalize.py", line 133, in _normalize_fragment
    for n in six.moves.range(self.max_restarts):
NameError: name 'six' is not defined

I had a look at the file and it seems that the 'import six' line is missing. When this is added, I get another error, but I think this may be a Py2 vs Py3 difference:

>>> Standardizer().standardize(mol)
Traceback (most recent call last):
 File "<stdin>", line 1, in <module>
 File "/home/travis/anaconda3/envs/rdkit/lib/python3.6/site-packages/molvs/standardize.py", line 98, in standardize
   mol = self.normalize(mol)
 File "/home/travis/anaconda3/envs/rdkit/lib/python3.6/site-packages/molvs/normalize.py", line 106, in __call__
   return self.normalize(mol)
 File "/home/travis/anaconda3/envs/rdkit/lib/python3.6/site-packages/molvs/normalize.py", line 125, in normalize
   fragments.append(self._normalize_fragment(fragment))
 File "/home/travis/anaconda3/envs/rdkit/lib/python3.6/site-packages/molvs/normalize.py", line 137, in _normalize_fragment
   product = self._apply_transform(mol, normalization.transform)
 File "/home/travis/anaconda3/envs/rdkit/lib/python3.6/site-packages/molvs/utils.py", line 28, in fget_memoized
   setattr(self, attr_name, fget(self))
 File "/home/travis/anaconda3/envs/rdkit/lib/python3.6/site-packages/molvs/normalize.py", line 42, in transform
   return AllChem.ReactionFromSmarts(self.transform_str.encode('utf8'))
Boost.Python.ArgumentError: Python argument types in
   rdkit.Chem.rdChemReactions.ReactionFromSmarts(bytes)
did not match C++ signature:
   ReactionFromSmarts(char const* SMARTS, boost::python::dict replacements={}, bool useSmiles=False)

When I move ".encode('utf8')" from line 42 it works as expected in Py3, but I think this would probably produce an error on Py2.

Hope this helps, thanks for working on this, it's been really useful!

EDIT: I see that these changes are already reflected in the file on GitHub, it seems that the PyPI version is just a bit out of date

[mcs07]

Weird, the import six line definitely should already be there:
https://github.com/mcs07/MolVS/blob/v0.1.0/molvs/normalize.py#L19

Likewise I think the string encoding for py2/py3 was fixed while ago:
0e96acf#diff-36072b6ed94d3d5dd8829d1effae2cd5

How did you install MolVS? Is it possible you have an older version? What do you see if you do:

>>> import molvs
>>> molvs.__version__
'0.1.0'

Might be worth trying to uninstall and install again.

[thesketh]

Yeah, I was confused too, so I tried the reinstall a few times (pip install molvs==0.1.0 and pip install molvs==0.0.9). I'll try clearing the cached version and see if it makes a difference

[  2:23pm ]  [ travis@mljet:~ ]
 $ pip install molvs==0.1.0
Collecting molvs==0.1.0
  Using cached MolVS-0.1.0-py3-none-any.whl
Requirement already satisfied: six in ./anaconda3/envs/rdkit/lib/python3.6/site-packages (from molvs==0.1.0)
Installing collected packages: molvs
  Found existing installation: MolVS 0.0.9
    Uninstalling MolVS-0.0.9:
      Successfully uninstalled MolVS-0.0.9
Successfully installed molvs-0.1.0
[  2:23pm ]  [ travis@mljet:~ ]
 $ python
Python 3.6.4 |Anaconda, Inc.| (default, Jan 16 2018, 18:10:19)
[GCC 7.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import molvs
>>> molvs.__version__
'0.1.0'
>>> exit()
[  2:23pm ]  [ travis@mljet:~ ]
 $ cat /home/travis/anaconda3/envs/rdkit/lib/python3.6/site-packages/molvs/normalize.py | grep "import six"
[  2:23pm ]  [ travis@mljet:~ ]
 $

[thesketh]

Yeah, even with a forced reinstall I'm getting the same issue, it must just be the PyPI package

[  2:23pm ]  [ travis@mljet:~ ]
 $ pip install -I --no-cache-dir molvs==0.1.0
Collecting molvs==0.1.0
  Downloading MolVS-0.1.0-py3-none-any.whl
Collecting six (from molvs==0.1.0)
  Downloading six-1.11.0-py2.py3-none-any.whl
Installing collected packages: six, molvs
Successfully installed molvs-0.1.0 six-1.11.0
[  2:26pm ]  [ travis@mljet:~ ]
 $ python
Python 3.6.4 |Anaconda, Inc.| (default, Jan 16 2018, 18:10:19)
[GCC 7.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import molvs
>>> molvs.__version__
'0.1.0'
>>> molvs.standardize_smiles('c1ccccc1')
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/travis/anaconda3/envs/rdkit/lib/python3.6/site-packages/molvs/standardize.py", line 305, in standardize_smiles
    mol = Standardizer().standardize(mol)
  File "/home/travis/anaconda3/envs/rdkit/lib/python3.6/site-packages/molvs/standardize.py", line 98, in standardize
    mol = self.normalize(mol)
  File "/home/travis/anaconda3/envs/rdkit/lib/python3.6/site-packages/molvs/normalize.py", line 105, in __call__
    return self.normalize(mol)
  File "/home/travis/anaconda3/envs/rdkit/lib/python3.6/site-packages/molvs/normalize.py", line 124, in normalize
    fragments.append(self._normalize_fragment(fragment))
  File "/home/travis/anaconda3/envs/rdkit/lib/python3.6/site-packages/molvs/normalize.py", line 133, in _normalize_fragment
    for n in six.moves.range(self.max_restarts):
NameError: name 'six' is not defined

[mcs07]

Oh dear, yes there's definitely something wrong specifically with the wheel file on PyPI. I've removed it, so pip should use the source distribution instead, which looks fine to me.

[thesketh]

That's great, thanks for your quick response! Everything seems to be working perfectly now, I'll close this issue

[JoshuaMeyers]

Great, I have just had the same issue and this fixed it. Cheers guys