def test_cif():
for filename in ['files/cif_struct.cif', 'files/cif_cart_struct.cif']:
p1 = CifFile(filename).get_struct()
assert p1.cell is not None
assert p1.cryst_const is not None
assert p1.symbols is not None
assert p1.coords is not None
assert p1.coords_frac is not None
# test writing
filename = os.path.join(testdir, 'test_write_cif.cif')
io.write_cif(filename, p1)
p2 = CifFile(filename).get_struct()
np.testing.assert_array_almost_equal(p1.coords_frac, p2.coords_frac)
np.testing.assert_array_almost_equal(p1.coords, p2.coords)
np.testing.assert_array_almost_equal(p1.cryst_const, p2.cryst_const)
np.testing.assert_array_almost_equal(p1.cell, p2.cell)
assert p1.symbols == p2.symbols
def test_cif_parse():
tools.skip_if_pkg_missing('CifFile')
for filename in ['files/cif_struct.cif', 'files/cif_cart_struct.cif']:
p1 = CifFile(filename).get_struct()
assert p1.cell is not None
assert p1.cryst_const is not None
assert p1.symbols is not None
assert p1.coords is not None
assert p1.coords_frac is not None
# test writing
filename = os.path.join(testdir, 'test_write_cif.cif')
io.write_cif(filename, p1)
p2 = CifFile(filename).get_struct()
np.testing.assert_array_almost_equal(p1.coords_frac, p2.coords_frac)
np.testing.assert_array_almost_equal(p1.coords, p2.coords)
np.testing.assert_array_almost_equal(p1.cryst_const, p2.cryst_const)
np.testing.assert_array_almost_equal(p1.cell, p2.cell)
assert p1.symbols == p2.symbols
#!/usr/bin/env python
# Read badly formatted PDB file (i.e. generated by Gromacs' genbox tool) and
# write to CIF file. Use this if openbabel doesn't do the job properly. It may
# complain that columns 77-78 are empty and reads the atom symbols wrong.
# pwtools.parse.PDBFile is more forgiving.
import sys
from pwtools import io
def help(prog):
print("""
usage
-----
{} input.pdb [output.cif]
""".format(prog))
if __name__ == '__main__':
argv = sys.argv
prog = argv[0]
if (len(argv) not in [2,3]) or (argv[1] in ['-h', '--help']):
help(prog)
sys.exit()
infile = argv[1]
if len(argv) == 3:
outfile = argv[2]
else:
outfile = infile + '.cif'
io.write_cif(outfile, io.read_pdb(infile))
# Read badly formatted PDB file (i.e. generated by Gromacs' genbox tool) and
# write to CIF file. Use this if openbabel doesn't do the job properly. It may
# complain that columns 77-78 are empty and reads the atom symbols wrong.
# pwtools.parse.PDBFile is more forgiving.
import sys
from pwtools import io
def help(prog):
print("""
usage
-----
{} input.pdb [output.cif]
""".format(prog))
if __name__ == '__main__':
argv = sys.argv
prog = argv[0]
if (len(argv) not in [2, 3]) or (argv[1] in ['-h', '--help']):
help(prog)
sys.exit()
infile = argv[1]
if len(argv) == 3:
outfile = argv[2]
else:
outfile = infile + '.cif'
io.write_cif(outfile, io.read_pdb(infile))