Reading from the CSD

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

amd.CSDReader accepts refcode(s) and yields the chosen crystals. If None or 'CSD' are passed instead of refcode(s), it reads the whole CSD. If the optional parameter families is True, the refcode(s) given are interpreted as refcode families: any entry whose ID starts with the given string is included.

Here are some common patterns for the CSDReader:

# 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 periodic_set in amd.CSDReader(refcodes, families=True):
    amds.append(amd.AMD(periodic_set, 100))

The CSDReader yields PeriodicSet objects, which can be passed to amd.AMD() or amd.PDD(). The PeriodicSet has attributes .name, .motif, .cell, .types (atomic types), and information about the asymmetric unit to help with AMD and PDD calculations.

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

Optional parameters

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

amd.CSDReader(refcodes=None,
              families=False,
              remove_hydrogens=False,
              disorder='skip',
              heaviest_component=False,
              extract_data=None,
              include_if=None)

  • 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. Only available when reader='ccdc'.

  • extract_data is used to extract more data from crystals.

  • include_if can remove unwanted structures.