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# This example demonstrates the use of the Python IHM library at a low
# level, to parse an mmCIF file and extract a subset of its data.
# This particular example just extracts the atomic coordinates.
import ihm.format
# Make an object to handle a given mmCIF category in the file; it will
# be called for each line in the loop construct.
class AtomSiteHandler(object):
# If a given keyword is not in the file, or has the special
# mmCIF omitted (.) or unknown (?) value, the corresponding argument
# to __call__ will be given these values:
not_in_file = omitted = None
unknown = ihm.unknown
# Extract the group_PDB, Cartn_x, Cartn_y, Cartn_z keywords from
# the mmCIF category (mmCIF keywords are case-insensitive, but the
# Python arguments here should be lowercase).
def __call__(self, group_pdb, cartn_x, cartn_y, cartn_z):
if group_pdb == 'ATOM':
print("Atom at %s, %s, %s" % (cartn_x, cartn_y, cartn_z))
ash = AtomSiteHandler()
with open('mini.cif') as fh:
# Extract keywords from the _atom_site mmCIF category using the
# AtomSiteHandler defined above
c = ihm.format.CifReader(fh, category_handler={'_atom_site': ash})
# Read the first data block in mini.cif
# (This will return True as long as there are more blocks, so it can
# be put in a while loop instead if you want to read all data blocks.)
c.read_file()
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