def exercise():
from mmtbx.regression.make_fake_anomalous_data import generate_zinc_inputs
base = "tst_pick_approx_zn"
mtz_file, pdb_file = generate_zinc_inputs(file_base=base, anonymize=True)
time.sleep(2)
args = [
"\"%s\"" % pdb_file,
"\"%s\"" % mtz_file, "wavelength=1.54", "nproc=1", "elements=CA,ZN",
"use_phaser=False"
]
result = easy_run.fully_buffered("mmtbx.water_screen %s" %
" ".join(args)).raise_if_errors()
n_zn = 0
for line in result.stdout_lines:
if "Probable cation: ZN+2" in line:
n_zn += 1
if n_zn != 1:
print "\n".join(result.stdout_lines)
raise RuntimeError("Expected 1 ZN+2, found %d" % n_zn)
os.remove(pdb_file)
os.remove(mtz_file)
# "zn_frag_hoh.pdb" => "zn_frag_fmodel.eff"
os.remove(os.path.splitext(pdb_file)[0][:-4] + ".pdb")
os.remove(os.path.splitext(pdb_file)[0][:-4] + "_fmodel.eff")
print "OK"
def exercise():
wavelength = 1.025
mtz_file, pdb_file = generate_zinc_inputs(anonymize=False)
null_out = libtbx.utils.null_out()
cmdline = mmtbx.command_line.load_model_and_data(args=[
pdb_file, mtz_file, "wavelength={}".format(wavelength),
"use_phaser=False", "use_svm=True"
],
master_phil=master_phil(),
out=null_out,
process_pdb_file=True,
create_fmodel=True,
prefer_anomalous=True)
os.remove(pdb_file)
os.remove(mtz_file)
os.remove(os.path.splitext(pdb_file)[0] + "_fmodel.eff")
cmdline.xray_structure.set_inelastic_form_factors(
photon=cmdline.params.input.wavelength, table="sasaki")
cmdline.fmodel.update_xray_structure(cmdline.xray_structure,
update_f_calc=True)
manager = ions.identify.create_manager(
pdb_hierarchy=cmdline.pdb_hierarchy,
fmodel=cmdline.fmodel,
geometry_restraints_manager=cmdline.geometry,
wavelength=cmdline.params.input.wavelength,
params=cmdline.params,
nproc=cmdline.params.nproc,
log=null_out)
manager.validate_ions(out=null_out)
for atom_props in manager.atoms_to_props.values():
i_seq = atom_props.i_seq
chem_env = ChemicalEnvironment(
i_seq, manager.find_nearby_atoms(i_seq, far_distance_cutoff=3.5),
manager)
scatter_env = ScatteringEnvironment(
i_seq,
manager,
fo_density=manager.get_map_gaussian_fit("mFo", i_seq),
fofc_density=manager.get_map_gaussian_fit("mFo-DFc", i_seq),
anom_density=manager.get_map_gaussian_fit("anom", i_seq),
)
vector = ion_vector(chem_env, scatter_env)
resname = ion_class(chem_env)
assert vector is not None
assert resname != ""
print "OK"
def exercise () :
from mmtbx.regression.make_fake_anomalous_data import generate_zinc_inputs
base = "tst_validate_zn"
mtz_file, pdb_file = generate_zinc_inputs(file_base=base, anonymize=False)
time.sleep(2)
args = ["\"%s\"" % pdb_file, "\"%s\"" % mtz_file, "wavelength=1.54",
"nproc=1"]
result = easy_run.fully_buffered("mmtbx.validate_ions %s" % " ".join(args)
).raise_if_errors()
n_zn, n_bad = 0, 0
for line in result.stdout_lines:
if "| ZN" in line:
n_zn += 1
if "!!!" in line:
n_bad += 1
assert n_zn == 1 and n_bad == 2
for ext in [".pdb", ".mtz", "_fmodel.eff"]:
os.remove(base + ext)
print "OK"
def exercise():
wavelength = 1.025
mtz_file, pdb_file = generate_zinc_inputs(anonymize=True)
args = [
"input.pdb.file_name=" + pdb_file,
"input.xray_data.file_name=" + mtz_file,
"wavelength={}".format(wavelength),
]
fully_buffered(
"phenix.python -m mmtbx.ions.svm.dump_sites " + " ".join(args),
).raise_if_errors()
os.remove(pdb_file)
os.remove(os.path.splitext(pdb_file)[0][:-4] + ".pdb")
os.remove(mtz_file)
# "zn_frag_hoh.pdb" => "zn_frag_fmodel.eff"
os.remove(os.path.splitext(pdb_file)[0][:-4] + "_fmodel.eff")
sites_path = os.path.splitext(pdb_file)[0] + "_sites.pkl"
sites = load(sites_path)
os.remove(sites_path)
assert len(sites) == 7
for chem_env, scatter_env in sites:
assert chem_env is not None
assert scatter_env is not None
for name in chem_env.__slots__:
if getattr(chem_env, name) is None:
print "Error: chem_env.{} is not set".format(name)
sys.exit()
for name in scatter_env.__slots__:
# f' is not set by phaser
if name in ["fp"]:
continue
# Only check f'' for heavy metals
if name != "fpp" or ion_class(chem_env) != "HOH":
if getattr(scatter_env, name) is None:
print "Error: scatter_env.{} is not set".format(name)
sys.exit()
print "OK"
def exercise():
wavelength = 1.025
mtz_file, pdb_file = generate_zinc_inputs(anonymize=True)
args = [
"input.pdb.file_name=" + pdb_file,
"input.xray_data.file_name=" + mtz_file,
"wavelength={}".format(wavelength),
]
fully_buffered(
"phenix.python -m mmtbx.ions.svm.dump_sites " +
" ".join(args), ).raise_if_errors()
os.remove(pdb_file)
os.remove(os.path.splitext(pdb_file)[0][:-4] + ".pdb")
os.remove(mtz_file)
# "zn_frag_hoh.pdb" => "zn_frag_fmodel.eff"
os.remove(os.path.splitext(pdb_file)[0][:-4] + "_fmodel.eff")
sites_path = os.path.splitext(pdb_file)[0] + "_sites.pkl"
sites = load(sites_path)
os.remove(sites_path)
assert len(sites) == 7
for chem_env, scatter_env in sites:
assert chem_env is not None
assert scatter_env is not None
for name in chem_env.__slots__:
if getattr(chem_env, name) is None:
print "Error: chem_env.{} is not set".format(name)
sys.exit()
for name in scatter_env.__slots__:
# f' is not set by phaser
if name in ["fp"]:
continue
# Only check f'' for heavy metals
if name != "fpp" or ion_class(chem_env) != "HOH":
if getattr(scatter_env, name) is None:
print "Error: scatter_env.{} is not set".format(name)
sys.exit()
print "OK"
def exercise () :
from mmtbx.regression.make_fake_anomalous_data import generate_zinc_inputs
base = "tst_pick_approx_zn"
mtz_file, pdb_file = generate_zinc_inputs(file_base=base, anonymize = True)
time.sleep(2)
args = ["\"%s\"" % pdb_file, "\"%s\"" % mtz_file, "wavelength=1.54",
"nproc=1", "elements=CA,ZN", "use_phaser=False"]
result = easy_run.fully_buffered("mmtbx.water_screen %s" % " ".join(args)
).raise_if_errors()
n_zn = 0
for line in result.stdout_lines:
if "Probable cation: ZN+2" in line:
n_zn += 1
if n_zn != 1:
print "\n".join(result.stdout_lines)
raise RuntimeError("Expected 1 ZN+2, found %d" % n_zn)
os.remove(pdb_file)
os.remove(mtz_file)
# "zn_frag_hoh.pdb" => "zn_frag_fmodel.eff"
os.remove(os.path.splitext(pdb_file)[0][:-4] + ".pdb")
os.remove(os.path.splitext(pdb_file)[0][:-4] + "_fmodel.eff")
print "OK"
def exercise():
wavelength = 1.025
mtz_file, pdb_file = generate_zinc_inputs(anonymize = False)
null_out = libtbx.utils.null_out()
cmdline = mmtbx.command_line.load_model_and_data(
args = [pdb_file, mtz_file, "wavelength={}".format(wavelength),
"use_phaser=False"],
master_phil = master_phil(),
out = null_out,
process_pdb_file = True,
create_fmodel = True,
prefer_anomalous = True
)
os.remove(pdb_file)
os.remove(mtz_file)
cmdline.xray_structure.set_inelastic_form_factors(
photon = cmdline.params.input.wavelength,
table = "sasaki"
)
cmdline.fmodel.update_xray_structure(
cmdline.xray_structure,
update_f_calc = True
)
manager = ions.identify.create_manager(
pdb_hierarchy = cmdline.pdb_hierarchy,
fmodel = cmdline.fmodel,
geometry_restraints_manager = cmdline.geometry,
wavelength = cmdline.params.input.wavelength,
params = cmdline.params,
nproc = cmdline.params.nproc,
log = null_out
)
manager.validate_ions(
out = null_out
)
fo_map = manager.get_map("mFo")
fofc_map = manager.get_map("mFo-DFc")
for atom_props in manager.atoms_to_props.values():
chem_env = environment.ChemicalEnvironment(
atom_props.i_seq,
manager.find_nearby_atoms(atom_props.i_seq, far_distance_cutoff = 3.5),
manager
)
new_chem_env = loads(dumps(chem_env))
for attr in dir(chem_env):
if attr == "atom":
# The two won't be directly comparable, but we will trust atom_labels is
# tested fully in its own module
assert chem_env.atom.id_str() == new_chem_env.atom.id_str()
elif not attr.startswith("_") and \
not isinstance(getattr(chem_env, attr), MethodType):
assert getattr(chem_env, attr) == getattr(new_chem_env, attr)
scatter_env = environment.ScatteringEnvironment(
atom_props.i_seq, manager, fo_map, fofc_map
)
new_scatter_env = loads(dumps(scatter_env))
for attr in dir(scatter_env):
if not attr.startswith("_") and \
not isinstance(getattr(scatter_env, attr), MethodType):
assert getattr(scatter_env, attr) == getattr(new_scatter_env, attr)
del fo_map
del fofc_map
print "OK"
def exercise():
wavelength = 1.025
mtz_file, pdb_file = generate_zinc_inputs(anonymize = False)
null_out = libtbx.utils.null_out()
cmdline = mmtbx.command_line.load_model_and_data(
args = [pdb_file, mtz_file, "wavelength={}".format(wavelength),
"use_phaser=False", "use_svm=True"],
master_phil = master_phil(),
out = null_out,
process_pdb_file = True,
create_fmodel = True,
prefer_anomalous = True
)
os.remove(pdb_file)
os.remove(mtz_file)
os.remove(os.path.splitext(pdb_file)[0] + "_fmodel.eff")
cmdline.xray_structure.set_inelastic_form_factors(
photon = cmdline.params.input.wavelength,
table = "sasaki"
)
cmdline.fmodel.update_xray_structure(
cmdline.xray_structure,
update_f_calc = True
)
manager = ions.identify.create_manager(
pdb_hierarchy = cmdline.pdb_hierarchy,
fmodel = cmdline.fmodel,
geometry_restraints_manager = cmdline.geometry,
wavelength = cmdline.params.input.wavelength,
params = cmdline.params,
nproc = cmdline.params.nproc,
log = null_out
)
manager.validate_ions(
out = null_out
)
for atom_props in manager.atoms_to_props.values():
i_seq = atom_props.i_seq
chem_env = ChemicalEnvironment(
i_seq,
manager.find_nearby_atoms(i_seq, far_distance_cutoff = 3.5),
manager
)
scatter_env = ScatteringEnvironment(
i_seq, manager,
fo_density = manager.get_map_gaussian_fit("mFo", i_seq),
fofc_density = manager.get_map_gaussian_fit("mFo-DFc", i_seq),
anom_density = manager.get_map_gaussian_fit("anom", i_seq),
)
vector = ion_vector(chem_env, scatter_env)
resname = ion_class(chem_env)
assert vector is not None
assert resname != ""
print "OK"
