def read_ccd():
print 'Reading components.cif ...'
sys.stdout.flush()
components = CifFileReader()
all_residues = components.read('components.cif')
print 'Reading aa-variants-v1.cif ...'
amino_variants = components.read('aa-variants-v1.cif')
return itertools.chain(all_residues.iteritems(), amino_variants.iteritems())
sys.path.insert(0, '..')
import utils
# to install mmCif: pip install git+git://github.com/glenveegee/PDBeCIF
from mmCif.mmcifIO import CifFileReader
ORDERS = dict(SING=1, DOUB=2, TRIP=3)
if __name__ == '__main__':
print 'This program regenerates the `residue_bonds` database using the "Chemical Component '
print 'Dictionary" and "Protonation Variants Dictionary" from http://www.wwpdb.org/data/ccd'
print 'These files are not included in the repository and must be downloaded manually.\n'
print 'Reading components.cif ...'
sys.stdout.flush()
components = CifFileReader()
all_residues = components.read('components.cif')
print 'Reading aa-variants-v1.cif ...'
amino_variants = components.read('aa-variants-v1.cif')
residues = []
db = utils.CompressedJsonDbm('residue_bonds', 'n')
for resname, data in itertools.chain(all_residues.iteritems(),
amino_variants.iteritems()):
if '_chem_comp_bond' not in data:
print '\nskipped %s (no bonds)' % resname
continue
