amd.io module

Contains I/O tools, including a .CIF reader and CSD reader (csd-python-api only) to extract periodic set representations of crystals which can be passed to calculate.AMD() and calculate.PDD().

These intermediate periodicset.PeriodicSet representations can be written to a .hdf5 file with SetWriter, which can be read back with SetReader. This is much faster than rereading a .CIF and recomputing invariants.

class amd.io.CifReader(path, reader='ase', folder=False, remove_hydrogens=False, disorder='skip', heaviest_component=False, show_warnings=True, extract_data=None, include_if=None)

Bases: amd._reader._Reader

Read all structures in a .CIF with ase or ccdc (csd-python-api only), yielding periodicset.PeriodicSet objects which can be passed to calculate.AMD() or calculate.PDD().

Examples

# Put all crystals in a .CIF in a list
structures = list(amd.CifReader('mycif.cif'))

# Reads just one if the .CIF has just one crystal
periodic_set = amd.CifReader('mycif.cif').read_one()

# If a folder has several .CIFs each with one crystal, use
structures = list(amd.CifReader('path/to/folder', folder=True))

# Make list of AMDs (with k=100) of crystals in a .CIF
amds = [amd.AMD(periodic_set, 100) for periodic_set in amd.CifReader('mycif.cif')]

class amd.io.CSDReader(refcodes=None, families=False, remove_hydrogens=False, disorder='skip', heaviest_component=False, show_warnings=True, extract_data=None, include_if=None)

Bases: amd._reader._Reader

Read Entries from the CSD, yielding periodicset.PeriodicSet objects.

The CSDReader returns periodicset.PeriodicSet objects which can be passed to calculate.AMD() or calculate.PDD().

Examples

Get crystals with 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 by name 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 AMD (with k=100) 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))

entry(refcode: str) → amd.periodicset.PeriodicSet: Read a PeriodicSet given any CSD refcode.

amd.io.crystal_to_periodicset(crystal): ccdc.crystal.Crystal –> amd.periodicset.PeriodicSet. Ignores disorder, missing sites/coords, checks & no options. Is a stripped-down version of the function used in CifReader.

amd.io.cifblock_to_periodicset(block): ase.io.cif.CIFBlock –> amd.periodicset.PeriodicSet. Ignores disorder, missing sites/coords, checks & no options. Is a stripped-down version of the function used in CifReader.