def generate_magnessium_inputs(file_base="mg_frag", anonymize=True):
"""
Creates a fake model and reflection data for a structure containing magnesium
ions.
Parameters
----------
file_base : str, optional
anonymize : bool, optional
Replace all ions in the returned pdb file with waters.
Returns
-------
mtz_path : str
pdb_path : str
"""
pdb_file = write_pdb_input_magnessium_binding(file_base=file_base)
mtz_file = generate_mtz_file(file_base=file_base, d_min=1.5)
assert os.path.isfile(pdb_file) and os.path.isfile(mtz_file)
if anonymize:
pdb_in = any_file(pdb_file)
hierarchy = pdb_in.file_object.hierarchy
hierarchy, n = anonymize_ions(hierarchy, log=null_out())
pdb_file = file_base + "_hoh.pdb"
hierarchy.write_pdb_file(
file_name=pdb_file,
crystal_symmetry=pdb_in.file_object.crystal_symmetry())
assert os.path.isfile(pdb_file)
return os.path.abspath(mtz_file), os.path.abspath(pdb_file)
def generate_magnessium_inputs (file_base="mg_frag", anonymize=True) :
"""
Creates a fake model and reflection data for a structure containing magnesium
ions.
Parameters
----------
file_base : str, optional
anonymize : bool, optional
Replace all ions in the returned pdb file with waters.
Returns
-------
mtz_path : str
pdb_path : str
"""
pdb_file = write_pdb_input_magnessium_binding (file_base=file_base)
mtz_file = generate_mtz_file(
file_base=file_base,
d_min=1.5)
assert os.path.isfile(pdb_file) and os.path.isfile(mtz_file)
if anonymize:
pdb_in = any_file(pdb_file)
hierarchy = pdb_in.file_object.hierarchy
hierarchy, n = anonymize_ions(hierarchy, log=null_out())
pdb_file = file_base + "_hoh.pdb"
hierarchy.write_pdb_file(
file_name=pdb_file,
crystal_symmetry=pdb_in.file_object.crystal_symmetry())
assert os.path.isfile(pdb_file)
return os.path.abspath(mtz_file), os.path.abspath(pdb_file)
def generate_zinc_inputs(file_base="zn_frag", anonymize=True, wavelength=None):
"""
Generate both a PDB file and an MTZ file for the zinc-bound structure,
with the zinc optionally replaced by solvent after F(model) was
calculated. Zinc is simulated as an anomalous scatterer at 1.54 A.
Parameters
----------
file_base : str, optional
anonymize : bool, optional
Replace all ions in the returned pdb file with waters.
Returns
-------
mtz_path : str
pdb_path : str
"""
anom = None
if (wavelength is None):
fp = -1.3
fdp = 0.47
anom = [
group_args(selection="element ZN", fp=fp, fdp=fdp),
]
pdb_file = write_pdb_input_zinc_binding(file_base=file_base)
mtz_file = generate_mtz_file(file_base=file_base,
d_min=1.9,
anomalous_scatterers=anom,
wavelength=wavelength)
assert os.path.isfile(pdb_file) and os.path.isfile(mtz_file)
if anonymize:
pdb_in = any_file(pdb_file)
hierarchy = pdb_in.file_object.hierarchy
hierarchy, n = anonymize_ions(hierarchy, log=null_out())
pdb_file = file_base + "_hoh.pdb"
hierarchy.write_pdb_file(
file_name=pdb_file,
crystal_symmetry=pdb_in.file_object.crystal_symmetry())
assert os.path.isfile(pdb_file)
return os.path.abspath(mtz_file), os.path.abspath(pdb_file)
def generate_zinc_inputs (file_base="zn_frag", anonymize=True,
wavelength=None) :
"""
Generate both a PDB file and an MTZ file for the zinc-bound structure,
with the zinc optionally replaced by solvent after F(model) was
calculated. Zinc is simulated as an anomalous scatterer at 1.54 A.
Parameters
----------
file_base : str, optional
anonymize : bool, optional
Replace all ions in the returned pdb file with waters.
Returns
-------
mtz_path : str
pdb_path : str
"""
anom = None
if (wavelength is None) :
fp = -1.3
fdp = 0.47
anom = [ group_args(selection="element ZN", fp=fp, fdp=fdp), ]
pdb_file = write_pdb_input_zinc_binding(file_base=file_base)
mtz_file = generate_mtz_file(
file_base=file_base,
d_min=1.9,
anomalous_scatterers=anom,
wavelength=wavelength)
assert os.path.isfile(pdb_file) and os.path.isfile(mtz_file)
if anonymize:
pdb_in = any_file(pdb_file)
hierarchy = pdb_in.file_object.hierarchy
hierarchy, n = anonymize_ions(hierarchy, log=null_out())
pdb_file = file_base + "_hoh.pdb"
hierarchy.write_pdb_file(
file_name=pdb_file,
crystal_symmetry=pdb_in.file_object.crystal_symmetry())
assert os.path.isfile(pdb_file)
return os.path.abspath(mtz_file), os.path.abspath(pdb_file)
def generate_calcium_inputs(file_base="ca_frag", anonymize=True):
"""
Generate both a PDB file and an MTZ file for the calcium-bound structure,
with the calcium optionally replaced by solvent after F(model) was
calculated. Calcium is simulated as an anomalous scatterer at 1.025 A.
(This method is also a suitable template for generating any other model/data
files for specific structures.)
Parameters
----------
file_base : str, optional
anonymize : bool, optional
Replace all ions in the returned pdb file with waters.
Returns
-------
mtz_path : str
pdb_path : str
"""
pdb_file = write_pdb_input_calcium_binding(file_base=file_base)
mtz_file = generate_mtz_file(file_base=file_base,
d_min=1.5,
anomalous_scatterers=[
group_args(selection="element CA",
fp=0.25,
fdp=0.5)
])
assert (os.path.isfile(pdb_file)) and (os.path.isfile(mtz_file))
if anonymize:
pdb_in = any_file(pdb_file)
hierarchy = pdb_in.file_object.hierarchy
hierarchy, n = anonymize_ions(hierarchy, log=null_out())
pdb_file = file_base + "_hoh.pdb"
hierarchy.write_pdb_file(
file_name=pdb_file,
crystal_symmetry=pdb_in.file_object.crystal_symmetry())
assert os.path.isfile(pdb_file)
return os.path.abspath(mtz_file), os.path.abspath(pdb_file)
def generate_calcium_inputs (file_base="ca_frag", anonymize=True) :
"""
Generate both a PDB file and an MTZ file for the calcium-bound structure,
with the calcium optionally replaced by solvent after F(model) was
calculated. Calcium is simulated as an anomalous scatterer at 1.025 A.
(This method is also a suitable template for generating any other model/data
files for specific structures.)
Parameters
----------
file_base : str, optional
anonymize : bool, optional
Replace all ions in the returned pdb file with waters.
Returns
-------
mtz_path : str
pdb_path : str
"""
pdb_file = write_pdb_input_calcium_binding(file_base=file_base)
mtz_file = generate_mtz_file(
file_base=file_base,
d_min=1.5,
anomalous_scatterers=[
group_args(selection="element CA", fp=0.25, fdp=0.5)
])
assert (os.path.isfile(pdb_file)) and (os.path.isfile(mtz_file))
if anonymize:
pdb_in = any_file(pdb_file)
hierarchy = pdb_in.file_object.hierarchy
hierarchy, n = anonymize_ions(hierarchy, log=null_out())
pdb_file = file_base + "_hoh.pdb"
hierarchy.write_pdb_file(
file_name=pdb_file,
crystal_symmetry=pdb_in.file_object.crystal_symmetry())
assert os.path.isfile(pdb_file)
return os.path.abspath(mtz_file), os.path.abspath(pdb_file)
