Missing dependency openbabel

[Dom1L]

Hi,

I tried to read a ligand with SmallMol('ligands.sdf', force_reading=True), but openbabel seems to be missing in the dependency list. With force_reading=False it also fails and suggests to set it True.

I installed moleculekit through conda install -c acellera moleculekit

In [1]: from moleculekit.smallmol.smallmol import SmallMol                                                                                                                               

In [2]: ligs = SmallMol('ligands.sdf', force_reading=True)                                                                                                                               
Reading ligands.sdf with force_reading procedure
---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
<ipython-input-2-f3cfc0eeef37> in <module>
----> 1 ligs = SmallMol('ligands.sdf', force_reading=True)

/shared/dominik/repos/moleculekit/moleculekit/smallmol/smallmol.py in __init__(self, mol, ignore_errors, force_reading, fixHs, removeHs)
     98         self._frame = 0
     99 
--> 100         _mol = self._initializeMolObj(mol, force_reading, ignore_errors)
    101 
    102         if removeHs:

/shared/dominik/repos/moleculekit/moleculekit/smallmol/smallmol.py in _initializeMolObj(self, mol, force_reading, ignore_errors)
    145                 if _mol is None and force_reading:
    146                     logger.warning('Reading {} with force_reading procedure'.format(mol))
--> 147                     sdf = openbabelConvert(mol, name_suffix, 'sdf')
    148                     _mol = Chem.SDMolSupplier(sdf, removeHs=False)[0]
    149                     os.remove(sdf)

/shared/dominik/repos/moleculekit/moleculekit/smallmol/util.py in openbabelConvert(input_file, input_format, output_format)
    213     """
    214 
--> 215     import openbabel
    216     import tempfile
    217     input_format = input_format[1:] if input_format.startswith('.') else input_format

ModuleNotFoundError: No module named 'openbabel'

[Dom1L]

I have also just seen that I should use smallmollib to read .sdf , my fault on this one

[stefdoerr]

You are missing openbabel. ` conda install -c acellera openbabel `

…

On Thu, May 2, 2019 at 5:18 PM Dominik Lemm ***@***.***> wrote: I have also just seen that I should use smallmollib to read .sdf , my fault on this one — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#6 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AB4RLAT75POAEQ247Z5SQGDPTLZ3NANCNFSM4HJ6W6FQ> .

[Dom1L]

I'm aware, but shouldn't it be in the dependencies of the package?

[stefdoerr]

Not until we decide on the hard dependencies. I left out on purpose openbabel and rdkit because they are both a bit tricky dependencies. I can add a "please install openbabel with ..." as I did with rdkit there though.

[Dom1L]

Oh okay I wasn't aware of that.
Just wanted to mention that just in case it slipped through or something. Thanks!