def write_and_read(self, st, via_cif):
if via_cif:
doc = st.make_mmcif_document()
st = gemmi.make_structure_from_block(doc[0])
out_name = get_path_for_tempfile()
st.write_pdb(out_name)
return read_lines_and_remove(out_name)
def test_read_write(self):
path = full_path('5e5z.mtz')
mtz = gemmi.read_mtz_file(path)
self.assertEqual(mtz.spacegroup.hm, 'P 1 21 1')
out_name = get_path_for_tempfile()
mtz.write_to_file(out_name)
mtz2 = gemmi.read_mtz_file(out_name)
os.remove(out_name)
self.assertEqual(mtz2.spacegroup.hm, 'P 1 21 1')
def test_blank_chain(self):
st = gemmi.read_pdb_string(BLANK_CHAIN_FRAGMENT)
out_name = get_path_for_tempfile()
st.write_minimal_pdb(out_name)
out = read_lines_and_remove(out_name)
# CRYST1 differs (50.000 not 50.00 and added P1).
# ATOM lines have added element names.
trimmed_out = [line[:66] for line in out[1:]]
self.assertEqual(trimmed_out, BLANK_CHAIN_FRAGMENT.splitlines()[1:])
def write_and_read(self, st, via_cif):
if via_cif:
st.setup_entities()
st.assign_label_seq_id()
doc = st.make_mmcif_document()
st = gemmi.make_structure_from_block(doc[0])
out_name = get_path_for_tempfile()
st.write_pdb(out_name)
return read_lines_and_remove(out_name)
def test_read_1pfe_cif(self):
st = gemmi.read_structure(full_path('1pfe.cif.gz'))
self.check_1pfe(st)
# write structure to cif and read it back
out_name = get_path_for_tempfile(suffix='.cif')
st.make_mmcif_document().write_file(out_name)
st2 = gemmi.read_structure(out_name)
os.remove(out_name)
self.check_1pfe(st2)
def test_read_write(self):
path = full_path('5e5z.mtz')
mtz = gemmi.read_mtz_file(path)
self.assertEqual(mtz.spacegroup.hm, 'P 1 21 1')
out_name = get_path_for_tempfile()
mtz.write_to_file(out_name)
mtz2 = gemmi.read_mtz_file(out_name)
os.remove(out_name)
self.assertEqual(mtz2.spacegroup.hm, 'P 1 21 1')
if numpy is not None:
self.assert_numpy_equal(numpy.array(mtz, copy=False), mtz.array)
self.assert_numpy_equal(mtz.array, mtz2.array)
