def OnUpdatePlot(self, evt):
elements_str = self.elem_ctrl.GetPhilValue()
elements = elements_str.replace(",", " ").split()
from cctbx.eltbx import chemical_elements
allowed_list = chemical_elements.proper_upper_list()
for elem in elements:
if (len(elem) > 2):
raise Sorry(
"You must enter standard chemical element symbols (H, Zn, etc.)."
)
if (not elem.upper() in allowed_list):
raise Sorry(
"The symbol '%s' is not a recognized chemical element." %
elem)
range_min = self.range_min.GetPhilValue()
range_max = self.range_max.GetPhilValue()
range_type = self.range_choice.GetStringSelection().lower()
table = self.table_choice.GetStringSelection().lower()
if (range_max <= range_min):
raise Sorry("The range maximum must be greater than the minimum")
self.GetParent().update_plot(elements=elements,
range_type=range_type,
range=(range_min, range_max),
table=table,
include_fp=True)
def run(args, out=sys.stdout):
usage_string = """
mmtbx.water_screen model.pdb data.mtz [options ...]
Utility to flag waters that may actually be elemental ions, based on local
environment, electron density maps, and atomic properties.
"""
import mmtbx.ions.identify
import mmtbx.command_line
cmdline = mmtbx.command_line.load_model_and_data(
args=args,
master_phil=master_phil(),
out=out,
process_pdb_file=True,
set_wavelength_from_model_header=True,
set_inelastic_form_factors="sasaki",
create_fmodel=True,
prefer_anomalous=True)
fmodel = cmdline.fmodel
xray_structure = cmdline.xray_structure
params = cmdline.params
if (params.use_svm):
if (params.elements is Auto):
raise Sorry(
"You must specify elements to consider when using the SVM " +
"prediction method.")
pdb_hierarchy = cmdline.pdb_hierarchy
geometry = cmdline.geometry
make_header("Inspecting water molecules", out=out)
manager_class = None
if (params.use_svm):
manager_class = mmtbx.ions.svm.manager
manager = mmtbx.ions.identify.create_manager(
pdb_hierarchy=pdb_hierarchy,
fmodel=fmodel,
geometry_restraints_manager=geometry,
wavelength=params.input.wavelength,
params=params,
verbose=params.debug,
nproc=params.nproc,
log=out,
manager_class=manager_class)
manager.show_current_scattering_statistics(out=out)
candidates = Auto
if (params.elements is not Auto) and (params.elements is not None):
from cctbx.eltbx import chemical_elements
lu = chemical_elements.proper_upper_list()
elements = params.elements.replace(",", " ")
candidates = elements.split()
for elem in candidates:
if (elem.upper() not in lu):
raise Sorry("Unrecognized element '%s'" % elem)
results = manager.analyze_waters(out=out,
debug=params.debug,
candidates=candidates)
return results, pdb_hierarchy
def anonymize_ions(pdb_hierarchy, log=sys.stdout):
"""
Convert any elemental ions in the PDB hierarchy to water, resetting the
occupancy and scaling the B-factor. The atom segids will be set to the old
resname. NOTE: this does not change the corresponding scatterer in the xray
structure, but a new xray structure can be obtained by calling
hierarchy.extract_xray_structure(crystal_symmetry).
Parameters
----------
pdb_hierarchy : iotbx.pdb.hierarchy.root
log : file, optional
Returns
-------
iotbx.pdb.hierarchy.root
New pdb hierarchy with its ions anonymized
int
Number of atoms that were anonymized.
"""
ion_resnames = set(chemical_elements.proper_upper_list())
for resname in server.params["_lib_charge.resname"]:
if resname not in WATER_RES_NAMES:
ion_resnames.add(resname)
n_converted = 0
pdb_hierarchy = pdb_hierarchy.deep_copy()
for model in pdb_hierarchy.models():
for chain in model.chains():
for residue_group in chain.residue_groups():
for atom_group in residue_group.atom_groups():
if atom_group.resname.strip() in ion_resnames:
atoms = atom_group.atoms()
id_strs = []
for atom in atoms:
elem = atom.element.strip()
if elem in ["H", "D"]:
atomic_number = 1
elif elem in ["HE"]:
atomic_number = 2
else:
atomic_number = sasaki.table(
elem).atomic_number()
id_strs.append(atom.id_str())
atom.segid = atom_group.resname
atom.name = " O "
atom.element = "O"
atom.charge = ""
atom.occupancy = 1.0
atom.b = atom.b * (10 / atomic_number)
atom_group.resname = "HOH"
for atom, id_str in zip(atoms, id_strs):
print("%s --> %s, B-iso = %.2f" %
(id_str, atom.id_str(), atom.b),
file=log)
n_converted += 1
return pdb_hierarchy, n_converted
def run (args, out=sys.stdout) :
usage_string = """
mmtbx.water_screen model.pdb data.mtz [options ...]
Utility to flag waters that may actually be elemental ions, based on local
environment, electron density maps, and atomic properties.
"""
import mmtbx.ions.identify
import mmtbx.command_line
cmdline = mmtbx.command_line.load_model_and_data(
args=args,
master_phil=master_phil(),
out=out,
process_pdb_file=True,
set_wavelength_from_model_header=True,
set_inelastic_form_factors="sasaki",
create_fmodel=True,
prefer_anomalous=True)
fmodel = cmdline.fmodel
xray_structure = cmdline.xray_structure
params = cmdline.params
if (params.use_svm) :
if (params.elements is Auto) :
raise Sorry("You must specify elements to consider when using the SVM "+
"prediction method.")
pdb_hierarchy = cmdline.pdb_hierarchy
geometry = cmdline.geometry
make_header("Inspecting water molecules", out=out)
manager_class = None
if (params.use_svm) :
manager_class = mmtbx.ions.svm.manager
manager = mmtbx.ions.identify.create_manager(
pdb_hierarchy = pdb_hierarchy,
fmodel = fmodel,
geometry_restraints_manager = geometry,
wavelength = params.input.wavelength,
params = params,
verbose = params.debug,
nproc = params.nproc,
log = out,
manager_class = manager_class)
manager.show_current_scattering_statistics(out=out)
candidates = Auto
if (params.elements is not Auto) and (params.elements is not None) :
from cctbx.eltbx import chemical_elements
lu = chemical_elements.proper_upper_list()
elements = params.elements.replace(",", " ")
candidates = elements.split()
for elem in candidates :
if (elem.upper() not in lu) :
raise Sorry("Unrecognized element '%s'" % elem)
results = manager.analyze_waters(
out = out,
debug = params.debug,
candidates = candidates)
return results, pdb_hierarchy
def anonymize_ions(pdb_hierarchy, log=sys.stdout):
"""
Convert any elemental ions in the PDB hierarchy to water, resetting the
occupancy and scaling the B-factor. The atom segids will be set to the old
resname. NOTE: this does not change the corresponding scatterer in the xray
structure, but a new xray structure can be obtained by calling
hierarchy.extract_xray_structure(crystal_symmetry).
Parameters
----------
pdb_hierarchy : iotbx.pdb.hierarchy.root
log : file, optional
Returns
-------
iotbx.pdb.hierarchy.root
New pdb hierarchy with its ions anonymized
int
Number of atoms that were anonymized.
"""
ion_resnames = set(chemical_elements.proper_upper_list())
for resname in server.params["_lib_charge.resname"]:
if resname not in WATER_RES_NAMES:
ion_resnames.add(resname)
n_converted = 0
pdb_hierarchy = pdb_hierarchy.deep_copy()
for model in pdb_hierarchy.models():
for chain in model.chains():
for residue_group in chain.residue_groups():
for atom_group in residue_group.atom_groups():
if atom_group.resname.strip() in ion_resnames:
atoms = atom_group.atoms()
id_strs = []
for atom in atoms:
elem = atom.element.strip()
if elem in ["H", "D"]:
atomic_number = 1
elif elem in ["HE"]:
atomic_number = 2
else:
atomic_number = sasaki.table(elem).atomic_number()
id_strs.append(atom.id_str())
atom.segid = atom_group.resname
atom.name = " O "
atom.element = "O"
atom.charge = ""
atom.occupancy = 1.0
atom.b = atom.b * (10 / atomic_number)
atom_group.resname = "HOH"
for atom, id_str in zip(atoms, id_strs):
print >> log, "%s --> %s, B-iso = %.2f" % (id_str, atom.id_str(), atom.b)
n_converted += 1
return pdb_hierarchy, n_converted
def validate_params(params):
from cctbx.eltbx import chemical_elements
all_elems = chemical_elements.proper_upper_list()
if (params.element is None):
raise Sorry("Element symbol not specified.")
elif (not params.element.upper() in all_elems):
raise Sorry("Element symbol '%s' not recognized." % params.element)
if (params.n_sites is None):
raise Sorry("Number of sites not specified.")
if ([params.fdp, params.energy, params.wavelength].count(None) != 2):
print[params.fdp, params.energy, params.wavelength]
raise Sorry("Please specify either an X-ray wavelength or energy " +
"(but not both), or the expected f''.")
if ([params.n_res, params.mw].count(None) != 1):
raise Sorry("Please specify either the number of residues or the " +
"approximate molecular weight (but not both).")
return True
def exercise():
lc = chemical_elements.proper_caps_list()
assert len(lc) == 111
assert lc[:3] == ["H", "He", "Li"]
lu = chemical_elements.proper_upper_list()
assert len(lu) == len(lc)
assert lu[:3] == ["H", "HE", "LI"]
for c,u in zip(lc,lu): assert c.upper() == u
sc = chemical_elements.proper_caps_set()
assert len(sc) == len(lc)
assert list(sc) == list(stl.set.stl_string(lc))
su = chemical_elements.proper_upper_set()
assert len(su) == len(lc)
assert list(su) == list(stl.set.stl_string(lu))
su = chemical_elements.proper_and_isotopes_upper_set()
assert len(su) == len(lc) + 2
assert list(su) == list(stl.set.stl_string(lu+["D", "T"]))
print("OK")
def exercise(): lc = chemical_elements.proper_caps_list() assert len(lc) == 111 assert lc[:3] == ["H", "He", "Li"] lu = chemical_elements.proper_upper_list() assert len(lu) == len(lc) assert lu[:3] == ["H", "HE", "LI"] for c,u in zip(lc,lu): assert c.upper() == u sc = chemical_elements.proper_caps_set() assert len(sc) == len(lc) assert list(sc) == list(stl.set.stl_string(lc)) su = chemical_elements.proper_upper_set() assert len(su) == len(lc) assert list(su) == list(stl.set.stl_string(lu)) su = chemical_elements.proper_and_isotopes_upper_set() assert len(su) == len(lc) + 2 assert list(su) == list(stl.set.stl_string(lu+["D", "T"])) print "OK"
def CheckFormat (self, value) :
from cctbx.eltbx import chemical_elements
allowed = chemical_elements.proper_upper_list()
ctrl = self.GetWindow()
style = ctrl.GetWxtbxStyle()
elem_strings = strings.parse_strings(value)
if (self.single_element) and (len(elem_strings) > 1) :
raise ValueError("Only a single element may be specified here!")
for elem in elem_strings :
elem = elem.upper() # used in Phaser EP
if (elem == "AX" or elem == "RX") and (style & WXTBX_ELEMENTS_CTRL_ALLOW_AX) :
pass
elif (elem in clusters) and (style & WXTBX_ELEMENTS_CTRL_ALLOW_CLUSTERS):
pass
elif (not elem in allowed) :
raise ValueError("'%s' is not a valid element symbol." % elem)
if (self.single_element) :
return elem_strings[0]
else :
return elem_strings
def CheckFormat(self, value):
from cctbx.eltbx import chemical_elements
allowed = chemical_elements.proper_upper_list() + list(clusters)
ctrl = self.GetWindow()
style = ctrl.GetWxtbxStyle()
elem_strings = strings.parse_strings(value)
if (self.single_element) and (len(elem_strings) > 1):
raise ValueError("Only a single element may be specified here!")
for elem in elem_strings :
elem = elem.upper() # used in Phaser EP
if (elem == "AX" or elem == "RX") and (style & WXTBX_ELEMENTS_CTRL_ALLOW_AX):
pass
elif (elem in clusters) and (style & WXTBX_ELEMENTS_CTRL_ALLOW_CLUSTERS):
pass
elif (not elem in allowed):
raise ValueError("'%s' is not a valid element symbol." % elem)
if (self.single_element):
return elem_strings[0]
else :
return elem_strings
def OnUpdatePlot (self, evt) :
elements_str = self.elem_ctrl.GetPhilValue()
elements = elements_str.replace(",", " ").split()
from cctbx.eltbx import chemical_elements
allowed_list = chemical_elements.proper_upper_list()
for elem in elements :
if (len(elem) > 2) :
raise Sorry(
"You must enter standard chemical element symbols (H, Zn, etc.).")
if (not elem.upper() in allowed_list) :
raise Sorry("The symbol '%s' is not a recognized chemical element." %
elem)
range_min = self.range_min.GetPhilValue()
range_max = self.range_max.GetPhilValue()
range_type = self.range_choice.GetStringSelection().lower()
table = self.table_choice.GetStringSelection().lower()
if (range_max <= range_min) :
raise Sorry("The range maximum must be greater than the minimum")
self.GetParent().update_plot(
elements=elements,
range_type=range_type,
range=(range_min,range_max),
table=table,
include_fp=True)
def collect_ions(pdb_hierarchy):
"""
Collects a list of all ions in pdb_hierarchy.
Parameters
----------
pdb_hierarchy : iotbx.pdb.hierarchy.root
Returns
-------
list of iotbx.pdb.hierarchy.atom
"""
elements = chemical_elements.proper_upper_list()
ions = []
for model in pdb_hierarchy.models():
for chain in model.chains():
for residue_group in chain.residue_groups():
for atom_group in residue_group.atom_groups():
if atom_group.resname.strip() in elements:
atoms = atom_group.atoms()
assert len(atoms) == 1
for atom in atoms:
ions.append(atom)
return ions
def collect_ions(pdb_hierarchy):
"""
Collects a list of all ions in pdb_hierarchy.
Parameters
----------
pdb_hierarchy : iotbx.pdb.hierarchy.root
Returns
-------
list of iotbx.pdb.hierarchy.atom
"""
elements = chemical_elements.proper_upper_list()
ions = []
for model in pdb_hierarchy.models():
for chain in model.chains():
for residue_group in chain.residue_groups():
for atom_group in residue_group.atom_groups():
if atom_group.resname.strip() in elements:
atoms = atom_group.atoms()
assert len(atoms) == 1
for atom in atoms:
ions.append(atom)
return ions
def process_other(self, arg):
if (len(arg) <= 2):
if (arg.upper() in chemical_elements.proper_upper_list()):
return iotbx.phil.parse("element=%s" % arg)
def exercise():
from mmtbx.ions import server as s
import iotbx.pdb.hierarchy
import iotbx.pdb
from cctbx.eltbx import chemical_elements
# Assert that valence parameters exist for all common ions with their
# coordinating atoms
for elem in [
"NA", "MG", "K", "CA", "MN", "FE", "NI", "CO", "CU", "ZN", "CD"
]:
params = s.get_metal_parameters(elem)
assert (len(params.allowed_coordinating_atoms) > 0)
assert (params.charge is not None)
for elem2 in params.allowed_coordinating_atoms:
atom1 = iotbx.pdb.hierarchy.atom()
atom1.name = elem
atom1.element = elem
atom1.charge = "+" + str(params.charge)
atom2 = iotbx.pdb.hierarchy.atom()
atom2.name = elem2
atom2.element = elem2
atom2.charge = "{:+}".format(s.get_charge(elem2))
assert (s.get_valence_params(atom1, atom2) != (None, None))
# Make sure we don't crash on any ion residue names
for elem in chemical_elements.proper_upper_list():
s.get_element(elem)
s.get_charge(elem)
# Make sure we don't crash on any common residue names either
from mmtbx import monomer_library
from mmtbx.rotamer.rotamer_eval import mon_lib_query
mon_lib_srv = monomer_library.server.server()
common_residues = [
getattr(iotbx.pdb, i) for i in dir(iotbx.pdb)
if i.startswith("common_residue_names")
and isinstance(getattr(iotbx.pdb, i), list)
]
common_atoms = {
"H": -1,
"C": 4,
"N": -3,
"O": -2,
"S": -2,
}
for common in common_residues:
for resn in common:
mlq = mon_lib_query(resn, mon_lib_srv)
if mlq is None:
continue
for atom in mlq.atom_dict().values():
elem, charge = s._get_charge_params(resname=resn,
element=atom.type_symbol)
from libtbx import group_args
class GAtom(group_args):
def fetch_labels(self):
return group_args(resname=self.resname)
def id_str(self):
return "gatom=\"{} {}\"".format(
self.resname, self.element)
def charge_as_int(self):
return int(self.charge)
gatom = GAtom(
element=atom.type_symbol,
resname=resn,
charge="0",
)
get_charge_val, get_elem_val = s.get_charge(
gatom), s.get_element(gatom)
if elem in common_atoms:
assert charge == common_atoms[elem]
assert get_charge_val == charge
assert get_elem_val == elem
# And we support all waters
for resn in iotbx.pdb.common_residue_names_water:
assert s.get_element(resn) == "O"
assert s.get_charge(resn) == -2
print "OK"
def exercise () :
from mmtbx.ions import server as s
import iotbx.pdb.hierarchy
import iotbx.pdb
from cctbx.eltbx import chemical_elements
# Assert that valence parameters exist for all common ions with their
# coordinating atoms
for elem in ["NA", "MG", "K", "CA", "MN", "FE", "NI", "CO", "CU", "ZN", "CD"]:
params = s.get_metal_parameters(elem)
assert (len(params.allowed_coordinating_atoms) > 0)
assert (params.charge is not None)
for elem2 in params.allowed_coordinating_atoms :
atom1 = iotbx.pdb.hierarchy.atom()
atom1.name = elem
atom1.element = elem
atom1.charge = "+" + str(params.charge)
atom2 = iotbx.pdb.hierarchy.atom()
atom2.name = elem2
atom2.element = elem2
atom2.charge = "{:+}".format(s.get_charge(elem2))
assert (s.get_valence_params(atom1, atom2) != (None, None))
# Make sure we don't crash on any ion residue names
for elem in chemical_elements.proper_upper_list():
s.get_element(elem)
s.get_charge(elem)
# Make sure we don't crash on any common residue names either
from mmtbx import monomer_library
from mmtbx.rotamer.rotamer_eval import mon_lib_query
mon_lib_srv = monomer_library.server.server()
common_residues = [getattr(iotbx.pdb, i) for i in dir(iotbx.pdb)
if i.startswith("common_residue_names") and
isinstance(getattr(iotbx.pdb, i), list)]
common_atoms = {
"H": -1,
"C": 4,
"N": -3,
"O": -2,
"S": -2,
}
for common in common_residues:
for resn in common:
mlq = mon_lib_query(resn, mon_lib_srv)
if mlq is None:
continue
for atom in mlq.atom_dict().values():
elem, charge = s._get_charge_params(resname = resn,
element = atom.type_symbol)
from libtbx import group_args
class GAtom(group_args):
def fetch_labels(self):
return group_args(resname = self.resname)
def id_str(self):
return "gatom=\"{} {}\"".format(self.resname, self.element)
def charge_as_int(self):
return int(self.charge)
gatom = GAtom(
element = atom.type_symbol,
resname = resn,
charge = "0",
)
get_charge_val, get_elem_val = s.get_charge(gatom), s.get_element(gatom)
if elem in common_atoms:
assert charge == common_atoms[elem]
assert get_charge_val == charge
assert get_elem_val == elem
# And we support all waters
for resn in iotbx.pdb.common_residue_names_water:
assert s.get_element(resn) == "O"
assert s.get_charge(resn) == -2
print "OK"
