def exercise () :
pdb_file = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/1ywf.pdb",
test=os.path.isfile)
if (pdb_file is None) :
print "phenix_regression not available, skipping test."
return
from iotbx.command_line.pdb_add_conformations import run
out = cStringIO.StringIO()
run([pdb_file], out=out)
assert contains_lines(out.getvalue(), "Modified model: 4254 atoms")
out = cStringIO.StringIO()
run([pdb_file, "atom_selection=\"chain A and not resname HOH\""], out=out)
assert contains_lines(out.getvalue(), "Modified model: 3990 atoms")
run([pdb_file, "new_occ=0.4", "atom_selection=\"resseq 1:275\""], out=out)
from iotbx import file_reader
pdb_in = file_reader.any_file("1ywf_split.pdb", force_type="pdb").file_object
atoms = pdb_in.input.atoms()
occ = atoms.extract_occ()
assert (occ.count(0.6) == occ.count(0.4) == 1858)
out = cStringIO.StringIO()
run([pdb_file, "n_confs=3", "new_occ=0.25"], out=out)
pdb_in = file_reader.any_file("1ywf_split.pdb", force_type="pdb").file_object
assert contains_lines(out.getvalue(), """\
WARNING: zero-occupancy atom:
HETATM 1940 O AHOH A 354 -0.009 56.525 -3.872 0.25 29.17 O\
""")
atoms = pdb_in.input.atoms()
assert (atoms.size() == 6381)
occ = atoms.extract_occ()
assert (occ.count(0.5) == 2126) and (occ.count(0.25) == 4254)
try :
run([pdb_file, "atom_selection=\"chain G\""], out=out)
except Sorry, e :
assert (str(e) == "Empty selection.")
assert contains_lines(out.getvalue(), """\
WARNING: zero-occupancy atom:
HETATM 1940 O AHOH A 354 -0.009 56.525 -3.872 0.25 29.17 O\
""")
atoms = pdb_in.input.atoms()
assert (atoms.size() == 6381)
occ = atoms.extract_occ()
assert (occ.count(0.5) == 2126) and (occ.count(0.25) == 4254)
try :
run([pdb_file, "atom_selection=\"chain G\""], out=out)
except Sorry, e :
assert (str(e) == "Empty selection.")
else :
raise Exception_expected
try :
run([pdb_file, "new_occ=2"], out=out)
except Sorry, e :
assert (str(e) == "new_occ must be between 0 and 1.0")
else :
raise Exception_expected
pdb_file = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/1akg.pdb",
test=os.path.isfile)
try :
run([pdb_file], out=out)
except Sorry, e :
assert (str(e) == """\
Atom group included in selection already has one or more alternate conformers:
ATOM 22 OG ASER 4 -1.752 0.849 3.272 0.50 11.67 O\
""")
else :
def exercise():
pdb_file = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/1ywf.pdb",
test=os.path.isfile)
if (pdb_file is None):
print("phenix_regression not available, skipping test.")
return
from iotbx.command_line.pdb_add_conformations import run
out = StringIO()
run([pdb_file], out=out)
assert contains_lines(out.getvalue(), "Modified model: 4254 atoms")
out = StringIO()
run([pdb_file, "atom_selection=\"chain A and not resname HOH\""], out=out)
assert contains_lines(out.getvalue(), "Modified model: 3990 atoms")
run([pdb_file, "new_occ=0.4", "atom_selection=\"resseq 1:275\""], out=out)
from iotbx import file_reader
pdb_in = file_reader.any_file("1ywf_split.pdb", force_type="pdb").file_object
atoms = pdb_in.input.atoms()
occ = atoms.extract_occ()
assert (occ.count(0.6) == occ.count(0.4) == 1858)
out = StringIO()
run([pdb_file, "n_confs=3", "new_occ=0.25"], out=out)
pdb_in = file_reader.any_file("1ywf_split.pdb", force_type="pdb").file_object
assert contains_lines(out.getvalue(), """\
WARNING: zero-occupancy atom:
HETATM 1940 O AHOH A 354 -0.009 56.525 -3.872 0.25 29.17 O\
""")
atoms = pdb_in.input.atoms()
assert (atoms.size() == 6381)
occ = atoms.extract_occ()
assert (occ.count(0.5) == 2126) and (occ.count(0.25) == 4254)
try :
run([pdb_file, "atom_selection=\"chain G\""], out=out)
except Sorry as e :
assert (str(e) == "Empty selection.")
else :
raise Exception_expected
try :
run([pdb_file, "new_occ=2"], out=out)
except Sorry as e :
assert (str(e) == "new_occ must be between 0 and 1.0")
else :
raise Exception_expected
pdb_file = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/1akg.pdb",
test=os.path.isfile)
try :
run([pdb_file], out=out)
except Sorry as e :
assert (str(e) == """\
Atom group included in selection already has one or more alternate conformers:
ATOM 22 OG ASER 4 -1.752 0.849 3.272 0.50 11.67 O\
""")
else :
raise Exception_expected
run([pdb_file, "atom_selection=\"not name OG\""], out=out)
print("OK")