• RE: Deeper Crystal Search Configuration

    Okey-doke, Dean, I'll rustle something up.  Might take me a couple of days, so please be patient.

    Best wishes

    Richard

  • RE: Deeper Crystal Search Configuration

    Hi Dean,

    we don't have any methods to search by spacegroup symbol or formula, so iterating over hit structures would be the only way to do it.  If you have to do many of these searches it would be fairly simple to make an SQLite database containing terms of interest, then to join the results of a ReducedCellSearch with a query of this database.

    If you like I can provide a prototype of how to go about this.

    Best wishes

    Richard

  • RE: Deeper Crystal Search Configuration

    Hi Dean,

    I'm not entirely clear what you are trying to do here.  Let me know if I've got the wrong end of the stick:

    You run a reduced cell search on the CSD, or another database of structures, retrieving some hits.  You then wish to filter these results according to further criteria, e.g. chemical formula, or space groups.

    You can do a simple filter of the hits, assuming there are not too many of them, simply by iterating over the hits:

    for h in hits:

        c = h.crystal

        if c.spacegroup_symbol == ...

     

    Alternatively you can use any of the search classes except TextNumericSearch on an individual crystal structure.

     

    Hope this is helpful; if not please ask again.

    Richard

     

       

     

  • RE: Counting hydrogen bonds: Crystal() vs. Molecule() behaviour

    Hi Chris.

    The HBond in CATKIT is not found because the default path length range for detecting hydrogen bonds is set to (4, 999), so excluding contacts between separate components of the molecule.  You can include such contacts by setting the path_length_range to (-1, 999), i.e:

    from ccdc import io

    csd = io.MoleculeReader('csd')

    catkit = csd.molecule('CATKIT')

    print catkit.hbonds(path_length_range=(-1, 999))

    (HBond(Atom(N2)-Atom(H2)-Atom(O2)),)

    The value -1 is used to cope with both options to the 'require_hydrogens' parameter of the hbonds() method.  I appreciate that this is not clear from the documentation, and this will be rectified in a forthcoming release.

    I think the default behaviour is somewhat counterintuitive; I shall discuss with colleagues whether the default should be made more permissive.

    Hope this is helpful.

    Richard

     

  • RE: Problem with kekulize() of AFUWEE

    Hi Dave,

    I agree - or rather a friendly chemist agrees - that the structure is a bit rubbish.  The first kekulize misassigns the double bonds in the carbon you mentioned, so the second aromatic assignment does not regard these bonds as aromatic, then the second kekulize does not operate on the same structure as the first.  I agree that this is not ideal behaviour, but it is comprehensible.

    The only solution I can think of is to assign all bond types:

    mol.assign_bond_types('all')

    where the double bond to the phosphorus is detected, the five membered ring is no longer aromatic and the kekulisation works as expected.

    I have mailed the database group to see if they want to fix the bonds in the structure, but this will be too late for the forthcoming November release.

    Best wishes

    Richard

  • RE: Peculiar behaviour of remove_hydrogens

    Hi David,

    I'm afraid you have unearthed a genuine bug.  Discussions are underway here to see if it can be fixed in the forthcoming API version 1.3 release.

    In the meantime you can work around the problem by using the internal API:

    mol = Molecule.from_string(...)

    mol = Molecule(mol.identifier, _molecule=mol._molecule.create_editable_molecule())

    Sorry about this.

     

    Richard

  • RE: Querying the CSD by substructure created "from scratch"

    Thanks, Christian.

    Please carry on raising any difficulties you have, and making suggestions for ways in which we may improve the API.

    Cheers

    Richard

     

  • RE: Void space in crystal structures

    Here's the slightly modified script, testing for 3D coordinates.

    Richard

  • RE: Void space in crystal structures

    I've attached a table of spacegroup, average void space (as a percentage of the unit cell volume), number of observations from the 673,606 structures of CSD V536 with 3D coordinates.  I'll leave it to the crystallographically adept to extract any meaning there is in the table.

    Richard

  • RE: Void space in crystal structures

    I've attached a script which will do this over the whole CSD.  It's running on my desktop at the moment, but I don't expect the results until tomorrow - the void calculation is computationally fairly heavy.

    I'll let you know the results when I get them.

    Richard