def run(prefix):
"""
Exercise standard (cctbx-based restraints) optimization (no data required).
"""
xrs_good, xrs_poor, f_obs, r_free_flags = run_tests.setup_helix_example()
run_tests.run_cmd(
prefix=prefix,
args=["restraints=cctbx mode=opt use_convergence_test=False"],
mtz_name="")
# Check results
pdb_inp = iotbx.pdb.input(
file_name=os.path.join(prefix, "m00_poor_refined.pdb"))
model_1 = mmtbx.model.manager(model_input=pdb_inp,
build_grm=True,
log=null_out())
s1 = model_1.geometry_statistics().result()
assert s1.bond.mean < 0.005
##########################
xrs_good, xrs_poor, f_obs, r_free_flags = run_tests.setup_helix_example()
run_tests.run_cmd(
prefix=prefix,
args=["restraints=cctbx mode=opt use_convergence_test=False"])
# Check results
pdb_inp = iotbx.pdb.input(
file_name=os.path.join(prefix, "m00_poor_refined.pdb"))
model_2 = mmtbx.model.manager(model_input=pdb_inp,
build_grm=True,
log=null_out())
s2 = model_2.geometry_statistics().result()
assert s2.bond.mean < 0.005
###########################
assert approx_equal(s1.bond.mean, s2.bond.mean, 0.0001)
def run(prefix):
"""
Exercise standard (cctbx-based restraints) refinement with all defaults.
"""
xrs_good, xrs_poor, f_obs, r_free_flags = run_tests.setup_helix_example()
run_tests.run_cmd(prefix, args=["restraints=cctbx"])
# Check results
xrs_refined = iotbx.pdb.input(file_name=os.path.join(
prefix, "m00_poor_refined.pdb")).xray_structure_simple()
d = flex.sqrt((xrs_good.sites_cart() - xrs_poor.sites_cart()).dot())
assert flex.mean(d) > 0.10
d = flex.sqrt((xrs_good.sites_cart() - xrs_refined.sites_cart()).dot())
assert flex.mean(d) < 0.05
# Check R-factors
r_start, r_final = None, None
ofo = open("%s.log" % prefix, "r")
for l in ofo.readlines():
if (l.strip().endswith("n_fev: 0")):
r_start = float(l.split()[2])
if (l.strip().startswith("Best r_work:")):
r_final = float(l.split()[2])
assert r_start > 0.1
assert r_final < 0.04
# Make sure output model actually corresponds to reported R-factor
fmodel = mmtbx.f_model.manager(f_obs=f_obs,
r_free_flags=r_free_flags,
xray_structure=xrs_refined)
fmodel.update_all_scales()
assert fmodel.r_work() < 0.04
assert abs(r_final - fmodel.r_work()) < 0.0005, abs(r_final -
fmodel.r_work())
def run(prefix):
"""
Exercise refine_sites=False.
"""
xrs_good, xrs_poor, f_obs, r_free_flags = run_tests.setup_helix_example()
run_tests.run_cmd(prefix, args=["restraints=cctbx", "refine_sites=False"])
xrs_start = iotbx.pdb.input(file_name=os.path.join(
qr_unit_tests, "data_files", "m00_poor.pdb")).xray_structure_simple()
xrs_refined = iotbx.pdb.input(file_name=os.path.join(
prefix, "m00_poor_refined.pdb")).xray_structure_simple()
d = flex.sqrt((xrs_start.sites_cart() - xrs_refined.sites_cart()).dot())
assert approx_equal(d.min_max_mean().as_tuple(), [0, 0, 0])
def run(prefix="tst_06"):
"""
Exercise altlocs.
"""
run_tests.assert_folder_is_empty(prefix=prefix)
xrs_good, xrs_poor, f_obs, r_free_flags = run_tests.setup_helix_example(
pdb_name="altlocs.pdb", mtz_name="altlocs.mtz")
r = run_tests.run_cmd(prefix,
args=["restraints=cctbx"],
pdb_name="altlocs.pdb",
mtz_name="altlocs.mtz")
#assert r.stdout_lines == \
# ['Sorry: Alternative conformations are not supported.']
run_tests.clean_up(prefix, mtz_name="altlocs.mtz")
def run(prefix):
"""
Exercise standard (cctbx-based restraints) optimization.
Assert mode=opt is approximately equivalent to data_weight=0.
"""
xrs_good, xrs_poor, f_obs, r_free_flags = run_tests.setup_helix_example()
# Run optimization
run_tests.run_cmd(prefix, args=["restraints=cctbx", "mode=opt"])
assert get_bond_rmsd(file_name=os.path.join(qr_unit_tests, "data_files",
"m00_poor.pdb")) > 0.1
assert get_bond_rmsd(
file_name=os.path.join(prefix, "m00_poor_refined.pdb")) < 0.0009
#Run refinement without data term
run_tests.run_cmd(prefix, args=["restraints=cctbx", "data_weight=0"])
assert get_bond_rmsd(
file_name=os.path.join(prefix, "m00_poor_refined.pdb")) < 0.0009