• RE: unable to access coordinates

    Dear Richard,

    many thanks for your help! I can confirm that the patch solves the problem.

    Best wishes, Gabor

     

  • unable to access coordinates

    Hello,

    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
    >>> ccdc.__version__
    '1.5.0'
    >>> from ccdc import io
    >>> reader = io.MoleculeReader( "CSD" )
    >>> mol = reader.molecule( "ABEBUF" )
    >>> print mol.to_string()
    @<TRIPOS>MOLECULE
    ABEBUF
        39    41     2     0     0
    SMALL
    NO_CHARGES
    ****
    Generated from the CSD
    @<TRIPOS>ATOM
         1 O1       1.9287   5.1676   1.7209   O.2       1 RES1   0.0000
    ...
    >>> mol.atoms[0]
    Atom(O1)
    >>> mol.atoms[0].coordinates # returns None, hence no output
    >>> mol.atoms[0]._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 admin@ccdc.cam.ac.uk

    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