Reading from the CSD

If csd-python-api is installed, amd can use it to read crystals directly from the CSD. amd.CSDReader accepts a list of CSD refcode(s) and yields the crystals. If None or 'CSD' are passed instead of refcodes, it reads the whole CSD:

# Put crystals with these refcodes in a list
refcodes = ['DEBXIT01', 'DEBXIT05', 'HXACAN01']
structures = list(amd.CSDReader(refcodes))

# Read refcode families (any whose refcode starts with strings in the list)
refcodes = ['ACSALA', 'HXACAN']
structures = list(amd.CSDReader(refcodes, families=True))

# Giving the reader nothing reads from the whole CSD.
for periodic_set in amd.CSDReader():
    ...

CSDReader returns PeriodicSet objects representing the crystals, which can be passed to amd.AMD() or amd.PDD() to calculate their invariants. The PeriodicSet has attributes name, motif, cell, types (atomic numbers), as well as asym_unit and weights for use in AMD/PDD calculations.

Reading options

CSDReader accepts the following parameters (many shared by CifReader):

amd.CSDReader(
    refcodes=None,              # list of refcodes (or families) or 'CSD'
    families=False,             # interpret refcodes as families
    remove_hydrogens=False,     # remove Hydrogens
    disorder='skip',            # how to handle disorder
    heaviest_component=False,   # keep only heaviest molecule
    molecular_centres=False,    # take molecular centres as the motif
    show_warnings=True,         # silence warnings
    verbose=False               # print number of items processed
)

  • families (default False) will interpret the list of strings given as refcode families, i.e. all crystals with refcodes starting with any in the list are read.

  • remove_hydrogens (default False) removes Hydrogen atoms from the structure.

  • disorder (default skip) controls how disordered structures are handled. The default is to skip any crystal with disorder, since disorder conflicts with the periodic set model. To read disordered structures anyway, choose either ordered_sites to remove sites with disorder or all_sites include all sites regardless.

  • show_warnings (default True) chooses whether to print warnings during reading, e.g. from disordered structures or crystals with missing data.

  • verbose (default False) prints a progress bar showing the number of items read so far.

  • heaviest_component (default False) removes all but the heaviest connected molecule in the asymmetric unit, intended for removing solvents.

  • molecular_centres (default False) uses molecular centres of mass instead of atoms as the motif of the periodic set.

See the references amd.io.CSDReader or amd.periodicset.PeriodicSet for more.