Reading .CIFs

If you have a .CIF file, use amd.CifReader to extract the crystals. Here are some common patterns when reading .CIFs:

# loop over the reader and get AMDs (k=100) of crystals
amds = []
for p_set in amd.CifReader('file.cif'):
    amds.append(amd.AMD(p_set, 100))

# create list of crystals in a .cif
crystals = list(amd.CifReader('file.cif'))

# Use folder=True to read all cifs in a folder
crystals = list(amd.CifReader(folder_path, folder=True))

# if you need the file names as well
import os
crystals = [amd.CifReader(os.path.join(folder_path, file)).read_one(), file
            for file in os.listdir(folder_path)]

The CifReader 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.CifReader or amd.periodicset.PeriodicSet for more.

Reading options

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

amd.CifReader('file.cif',                  # path to file/folder
              reader='ase',                # backend cif parser
              remove_hydrogens=False,      # remove H/D
              disorder='skip',             # handling disorder
              heaviest_component=False,    # just keep the heaviest component in asym unit
              folder=False)                # if path is to a folder

  • reader controls the backend package used to parse the file. The default is ase; to use csd-python-api pass ccdc. The ccdc reader can read any format accepted by ccdc’s EntryReader, though only .CIFs have been tested.

  • 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'.

  • folder will read all crystals from files in a folder. If true, the sets yielded will have a tag/attribute ‘filename’.