I have trouble retrieving coordinates from molecules that I read in using io.MoleculeReader. Here is a relevant code fragment (here I use a molecule from the database, but I tried sdf/mol2 formats, and encounter the exact same issue).
>>> import ccdc
>>> from ccdc import io
>>> reader = io.MoleculeReader( "CSD" )
>>> mol = reader.molecule( "ABEBUF" )
>>> print mol.to_string()
39 41 2 0 0
Generated from the CSD
1 O1 1.9287 5.1676 1.7209 O.2 1 RES1 0.0000
>>> mol.atoms.coordinates # returns None, hence no output
>>> mol.atoms._atom.site().orth() # from source code
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "<snip>/ccdc/_lib/PackingSimilarityLib.py", line 693, in __repr__
def __repr__(self): return _PackingSimilarityLib.Point___repr__(self)
RuntimeError: PackingSimilarity is available to CSD-Materials and CSD-Enterprise users.
To enable this functionality contact email@example.com
I honestly do not know whether we are CSD-Materials or CSD-Enterprise users, but the online documentation indicates that this functionality is available to all users (https://downloads.ccdc.cam.ac.uk/documentation/API/release_notes.html#licensed-features).
This is on CentOS7 64bit. Unfortunately, I have not installed the package myself, and hence cannot give you any exact details, but I am guessing that installation was done using pip.
Can you let me know what the problem is, and how to resolve it?
Best wishes, Gabor