Reading from the CSD

If csd-python-api is installed, amd can use it to read crystals directly from the CSD.

amd.io.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))

# Create a generic reader, read crystals 'on demand' with CSDReader.entry()
reader = amd.CSDReader()
debxit01 = reader.entry('DEBXIT01')

# looping over this generic reader will yield all CSD entries
for periodic_set in reader:
    ...

# Make list of AMDs for crystals in these families
refcodes = ['ACSALA', 'HXACAN']
amds = []
for structure in amd.CSDReader(refcodes, families=True):
    amds.append(amd.AMD(structure, 100))

The CSDReader returns periodicset.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 .asymmetric_unit and .wyckoff_multiplicities for use in calculations.

Reading options

The amd.io.CSDReader accepts the following parameters (many shared by io.CifReader):

amd.CSDReader(
    refcodes=None,              # list of refcodes (or families) or 'CSD'
    families=False,             # interpret refcodes as families (include if refcode starts with)
    remove_hydrogens=False,     # remove Hydrogens
    disorder='skip',            # handling disorder
    heaviest_component=False    # just keep the heaviest component in asym unit
)

  • As described above, families chooses whether to read refcodes or refcode families.

  • remove_hydrogens removes Hydrogen atoms from the structure.

  • disorder 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.

  • heaviest_component takes the heaviest connected molecule in the motif, intended for removing solvents.

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