def _main(args, out=sys.stdout):
"""
Main entry point to this script.
Parameters
----------
args : list of str
List of arguments, should not include the first argument with the
executable name.
out : file, optional
"""
usage_string = """\
phenix.python -m mmtbx.ions.svm.dump_sites model.pdb data.mtz [options ...]
Utility to dump information about the properties of water and ion sites in a
model. This properties include local environment, electron density maps, and
atomic properties.
"""
cmdline = load_model_and_data(
args=args,
master_phil=master_phil(),
out=out,
process_pdb_file=True,
create_fmodel=True,
prefer_anomalous=True,
set_wavelength_from_model_header=True,
set_inelastic_form_factors="sasaki",
usage_string=usage_string,
)
params = cmdline.params
params.use_svm = True
make_header("Inspecting sites", out=out)
manager = ions.identify.create_manager(
pdb_hierarchy=cmdline.pdb_hierarchy,
fmodel=cmdline.fmodel,
geometry_restraints_manager=cmdline.geometry,
wavelength=params.input.wavelength,
params=params,
verbose=params.debug,
nproc=params.nproc,
log=out,
)
manager.show_current_scattering_statistics(out=out)
sites = dump_sites(manager)
out_name = os.path.splitext(
params.input.pdb.file_name[0])[0] + "_sites.pkl"
print("Dumping to", out_name, file=out)
easy_pickle.dump(out_name, sites)
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 _main(args, out=sys.stdout):
"""
Main entry point to this script.
Parameters
----------
args : list of str
List of arguments, should not include the first argument with the
executable name.
out : file, optional
"""
usage_string = """\
phenix.python -m mmtbx.ions.svm.dump_sites model.pdb data.mtz [options ...]
Utility to dump information about the properties of water and ion sites in a
model. This properties include local environment, electron density maps, and
atomic properties.
"""
cmdline = load_model_and_data(
args=args,
master_phil=master_phil(),
out=out,
process_pdb_file=True,
create_fmodel=True,
prefer_anomalous=True,
set_wavelength_from_model_header=True,
set_inelastic_form_factors="sasaki",
usage_string=usage_string,
)
params = cmdline.params
params.use_svm = True
make_header("Inspecting sites", out=out)
manager = ions.identify.create_manager(
pdb_hierarchy=cmdline.pdb_hierarchy,
fmodel=cmdline.fmodel,
geometry_restraints_manager=cmdline.geometry,
wavelength=params.input.wavelength,
params=params,
verbose=params.debug,
nproc=params.nproc,
log=out,
)
manager.show_current_scattering_statistics(out=out)
sites = dump_sites(manager)
out_name = os.path.splitext(params.input.pdb.file_name[0])[0] + "_sites.pkl"
print >> out, "Dumping to", out_name
easy_pickle.dump(out_name, sites)
def exercise():
fns = [generate_calcium_inputs, generate_zinc_inputs]
wavelengths = [1.025, 1.54]
for fn, wavelength in zip(fns, wavelengths):
mtz_file, pdb_file = fn(anonymize=True)
null_out = libtbx.utils.null_out()
cmdline = mmtbx.command_line.load_model_and_data(
args=[
pdb_file, mtz_file, "wavelength={}".format(wavelength),
"use_phaser=True", "use_svm=True"
],
master_phil=master_phil(),
out=null_out,
process_pdb_file=True,
create_fmodel=True,
prefer_anomalous=True,
set_inelastic_form_factors="sasaki",
)
os.remove(pdb_file)
os.remove(mtz_file)
os.remove(os.path.splitext(mtz_file)[0] + "_fmodel.eff")
os.remove(os.path.splitext(mtz_file)[0] + ".pdb")
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_class=ions.svm.manager,
)
# Build a list of properties of each water / ion site
waters = []
for chain in manager.pdb_hierarchy.only_model().chains():
for residue_group in chain.residue_groups():
atom_groups = residue_group.atom_groups()
if (len(atom_groups) > 1): # alt conf, skip
continue
for atom_group in atom_groups:
# Check for non standard atoms in the residue
# Or a label indicating the residue is a water
resname = atom_group.resname.strip().upper()
if (resname in WATER_RES_NAMES):
atoms = atom_group.atoms()
if (len(atoms) == 1
): # otherwise it probably has hydrogens, skip
waters.append(atoms[0].i_seq)
assert len(waters) > 0
atom_props = [AtomProperties(i_seq, manager) for i_seq in waters]
for atom_prop in atom_props:
i_seq = atom_prop.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),
)
resname = ion_class(chem_env)
assert resname != ""
predictions = predict_ion(chem_env,
scatter_env,
elements=["HOH", "ZN", "CA"])
if predictions is None:
print "Could not load SVM classifier"
print "Skipping {}".format(os.path.split(__file__)[1])
return
if resname != predictions[0][0]:
print "Prediction ({}) did not match expected: {}" \
.format(predictions[0][0], resname)
for element, prob in predictions:
print " {}: {:.2f}".format(element, prob)
sys.exit()
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 () :
fns = [generate_calcium_inputs, generate_zinc_inputs]
wavelengths = [1.025, 1.54]
for fn, wavelength in zip(fns, wavelengths):
mtz_file, pdb_file = fn(anonymize = True)
null_out = libtbx.utils.null_out()
cmdline = mmtbx.command_line.load_model_and_data(
args = [pdb_file, mtz_file, "wavelength={}".format(wavelength),
"use_phaser=True", "use_svm=True"],
master_phil = master_phil(),
out = null_out,
process_pdb_file = True,
create_fmodel = True,
prefer_anomalous = True,
set_inelastic_form_factors = "sasaki",
)
os.remove(pdb_file)
os.remove(mtz_file)
os.remove(os.path.splitext(mtz_file)[0] + "_fmodel.eff")
os.remove(os.path.splitext(mtz_file)[0] + ".pdb")
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_class = ions.svm.manager,
)
# Build a list of properties of each water / ion site
waters = []
for chain in manager.pdb_hierarchy.only_model().chains():
for residue_group in chain.residue_groups():
atom_groups = residue_group.atom_groups()
if (len(atom_groups) > 1) : # alt conf, skip
continue
for atom_group in atom_groups :
# Check for non standard atoms in the residue
# Or a label indicating the residue is a water
resname = atom_group.resname.strip().upper()
if (resname in WATER_RES_NAMES) :
atoms = atom_group.atoms()
if (len(atoms) == 1) : # otherwise it probably has hydrogens, skip
waters.append(atoms[0].i_seq)
assert len(waters) > 0
atom_props = [AtomProperties(i_seq, manager) for i_seq in waters]
for atom_prop in atom_props:
i_seq = atom_prop.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),
)
resname = ion_class(chem_env)
assert resname != ""
predictions = predict_ion(chem_env, scatter_env,
elements = ["HOH", "ZN", "CA"])
if predictions is None:
print "Could not load SVM classifier"
print "Skipping {}".format(os.path.split(__file__)[1])
return
if resname != predictions[0][0]:
print "Prediction ({}) did not match expected: {}" \
.format(predictions[0][0], resname)
for element, prob in predictions:
print " {}: {:.2f}".format(element, prob)
sys.exit()
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"