def exercise_01(verbose):
if (verbose): log = sys.stdout
else: log = StringIO()
pdb_file = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/ala_hd.pdb", test=os.path.isfile)
model = get_model(pdb_file, log)
model.de_deuterate()
assert (len(model.hd_group_selections()) == 0)
ph = model.get_hierarchy()
atoms = ph.atoms()
assert (atoms.extract_element().count('D') == 0)
assert (model.get_hd_selection().count(True) == 7)
def exercise_04(verbose):
if (verbose): log = sys.stdout
else: log = StringIO()
model = get_model(file_name=None, log=log, pdb_str=pdb_str_1)
model.de_deuterate()
assert (len(model.hd_group_selections()) == 0)
ph = model.get_hierarchy()
atoms = ph.atoms()
assert (atoms.extract_element().count('D') == 0)
assert (model.get_hd_selection().count(True) == 15)
atom_names = [x.strip() for x in atoms.extract_name()]
assert ('D' not in atom_names)
assert ('DG' not in atom_names)
def exercise_05(verbose):
if (verbose): log = sys.stdout
else: log = StringIO()
model = get_model(file_name=None, log=log, pdb_str=pdb_str_2)
#model.get_hierarchy().write_pdb_file(file_name="haha.pdb")
model.de_deuterate()
assert (len(model.hd_group_selections()) == 0)
ph = model.get_hierarchy()
atoms = ph.atoms()
assert (atoms.extract_element().count('D') == 0)
#print(model.get_hd_selection().count(True))
assert (model.get_hd_selection().count(True) == 35)
assert (model.selection('resname DOD').count(True) == 0)