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Using the CCDC Python API

The full CSD and the CCDC Python API are installed on both cposs and xenon. Please refer to the CCDC Python API user guide for full details.

Members of the group have written many useful scripts, which are in the /home/cposs/Python_utilities/ folder on either cluster. These include:

  • convertcif2res.py which converts starting.cif to starting.res
  • convertres2cif.py which converts starting.res to starting.cif
  • find_h_bonds.py which searches for specific SMILES strings in a crystal structure, and measures specific distances between them. Can be adapted to find a variety of intermolecular contacts in your CSP output.
  • find_params.py and find_molecular_params.py which search for specific SMILES strings and output a variety of intramolecular and intermolecular quantities
  • spacegroup.py which outputs the space group of temp.res, and can be called from find_spacegroup
  • relabelling_res is a folder containing all the files necessary to change the atom labels for a crystal structure to standardized labels. This is very useful after a DFTB3-D3 optimization, in which the final symmetry inspection by Platon usually ends up with a complete dogs dinner of atom labelling!
  • powder_and_similarity.py which converts temp.res to temp.cif, writes out the powder patter (as identifier.xye) between defined 2theta values with a defined wavelength, and runs CrystalPackingSimilarity between the structure and a reference structure with a 25 molecule coordination and including hydrogens.

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