def exercise_get_atom_selections (verbose=False) :
pdb_in = """\
CRYST1 15.000 15.000 15.000 90.00 90.00 90.00 P 212121
HETATM 115 O HOH A 18 3.000 5.000 5.000 1.00 10.00 O
HETATM 115 O HOH A 19 5.000 5.000 8.000 1.00 10.00 O
HETATM 115 O HOH A 20 5.000 5.000 8.000 1.00 10.00 O
END"""
log = null_out()
if (verbose) :
log = sys.stdout
processed_pdb_files_srv = utils.process_pdb_file_srv(log=log)
processed_pdb_file, pdb_inp = processed_pdb_files_srv.process_pdb_files(
raw_records=pdb_in.splitlines())
selections1 = utils.get_atom_selections(
all_chain_proxies=processed_pdb_file.all_chain_proxies,
xray_structure=processed_pdb_file.xray_structure(),
selection_strings=["resseq 18", "resseq 19", "resseq 20"],
parameter_name="refine.occupancy")
try :
selections2 = utils.get_atom_selections(
all_chain_proxies=processed_pdb_file.all_chain_proxies,
xray_structure=processed_pdb_file.xray_structure(),
selection_strings=["resseq 18:19", "resseq 19:20"],
parameter_name="refine.occupancy")
except Sorry, s :
assert (str(s) == """\
One or more overlapping selections for refine.occupancy:
resseq 18:19
resseq 19:20""")
def _rotate_about_axis(self):
raap = self.params.rotate_about_axis
sites_cart = self.xray_structure.sites_cart()
if ([raap.axis, raap.atom_selection, raap.angle].count(None) == 0):
axis = []
try:
for a in raap.axis.split():
axis.append(float(a))
except Exception:
sel = utils.get_atom_selections(
iselection=False,
all_chain_proxies=self.all_chain_proxies,
selection_strings=raap.axis,
xray_structure=self.xray_structure)[0]
axis = [i for i in sites_cart.select(sel).as_double()]
if (len(axis) != 6):
raise Sorry("Bad selection rotate_about_axis.axis: %s" %
str(raap.axis))
p1 = scitbx.matrix.col(axis[:3])
p2 = scitbx.matrix.col(axis[3:])
raa = p1.rt_for_rotation_around_axis_through(point=p2,
angle=raap.angle,
deg=True)
#
sel = utils.get_atom_selections(
iselection=False,
all_chain_proxies=self.all_chain_proxies,
selection_strings=raap.atom_selection,
xray_structure=self.xray_structure)[0]
if (sel.count(True) == 0):
raise Sorry("Empty selection rotate_about_axis.selection: %s" %
str(raap.atom_selection))
sites_cart_rotated = raa * sites_cart.select(sel)
self.xray_structure.set_sites_cart(
sites_cart.set_selected(sel, sites_cart_rotated))
def exercise_get_atom_selections(verbose=False):
pdb_in = """\
CRYST1 15.000 15.000 15.000 90.00 90.00 90.00 P 212121
HETATM 115 O HOH A 18 3.000 5.000 5.000 1.00 10.00 O
HETATM 115 O HOH A 19 5.000 5.000 8.000 1.00 10.00 O
HETATM 115 O HOH A 20 5.000 5.000 8.000 1.00 10.00 O
END"""
log = null_out()
if (verbose):
log = sys.stdout
model = mmtbx.model.manager(
model_input = iotbx.pdb.input(lines=pdb_in.splitlines(), source_info=None),
process_input = True)
processed_pdb_files_srv = utils.process_pdb_file_srv(log=log)
processed_pdb_file, pdb_inp = processed_pdb_files_srv.process_pdb_files(
raw_records=pdb_in.splitlines())
selections1 = utils.get_atom_selections(
model = model,
selection_strings=["resseq 18", "resseq 19", "resseq 20"],
parameter_name="refine.occupancy")
try :
selections2 = utils.get_atom_selections(
model = model,
selection_strings=["resseq 18:19", "resseq 19:20"],
parameter_name="refine.occupancy")
except Sorry, s :
assert (str(s) == """\
One or more overlapping selections for refine.occupancy:
resseq 18:19
resseq 19:20""")
def occupancy_selections(
model,
add_water = False,
other_individual_selection_strings = None,
other_constrained_groups = None,
remove_selection = None,
as_flex_arrays = True,
constrain_correlated_3d_groups = False,
log = None):
# set up defaults
if(other_individual_selection_strings is not None and
len(other_individual_selection_strings) == 0):
other_individual_selection_strings = None
if(other_constrained_groups is not None and
len(other_constrained_groups) == 0):
other_constrained_groups = None
if(remove_selection is not None and len(remove_selection) == 0):
remove_selection = None
result = model.get_hierarchy().occupancy_groups_simple(
common_residue_name_class_only = None,
always_group_adjacent = False,
ignore_hydrogens = False)
exchangable_hd_pairs = mmtbx.utils.combine_hd_exchangable(hierarchy =
model.get_hierarchy())
if(len(exchangable_hd_pairs)==0 and result is not None):
occupancy_regroupping(
pdb_hierarchy = model.get_hierarchy(),
cgs = result)
result = mmtbx.utils.remove_selections(selection = result,
other = exchangable_hd_pairs,
size = model.get_number_of_atoms())
result.extend(exchangable_hd_pairs)
# extract group-[0,1]-constrained atoms withing a residue
pogl = extract_partial_occupancy_selections(hierarchy = model.get_hierarchy())
rm_duplicate_with_pogl = []
for t_ in pogl:
for t__ in t_:
for t___ in t__:
rm_duplicate_with_pogl.append(t___)
result = mmtbx.utils.remove_selections(selection = result, other = pogl,
size = model.get_number_of_atoms())
result.extend(pogl)
# add partial occupancies
occupancies = model.get_xray_structure().scatterers().extract_occupancies()
sel = (occupancies != 1.) & (occupancies != 0.)
result = add_occupancy_selection(
result = result,
size = model.get_number_of_atoms(),
selection = sel,
hd_special = None)
# check user's input
all_sel_strgs = []
if(other_individual_selection_strings is not None):
all_sel_strgs = all_sel_strgs + other_individual_selection_strings
if(other_constrained_groups is not None):
for other_constrained_group in other_constrained_groups:
for other_constrained_group in other_constrained_groups:
if(len(other_constrained_group.selection)>0):
all_sel_strgs = all_sel_strgs + other_constrained_group.selection
if(len(all_sel_strgs) > 0):
for sel_str in all_sel_strgs:
sel_str_sel = get_atom_selections(
model = model,
selection_strings = [sel_str],
iselection = True,
one_selection_array = True)
if(sel_str_sel.size() == 0):
raise Sorry("Empty selection: %s"%sel_str)
#
if([other_individual_selection_strings,
other_constrained_groups].count(None) == 0):
sel1 = get_atom_selections(
model = model,
selection_strings = other_individual_selection_strings,
iselection = True,
one_selection_array = True)
for other_constrained_group in other_constrained_groups:
for other_constrained_group in other_constrained_groups:
for cg_sel_strs in other_constrained_group.selection:
sel2 = get_atom_selections(
model = model,
selection_strings = cg_sel_strs,
iselection = True,
one_selection_array = True)
if(sel1.intersection(sel2).size() > 0):
raise Sorry("Duplicate selection: same atoms selected for individual and group occupancy refinement.")
# check user's input and apply remove_selection to default selection
if(remove_selection is not None):
sel1 = get_atom_selections(
model = model,
selection_strings = remove_selection,
iselection = True,
one_selection_array = True)
if(sel1.size() == 0): # XXX check all and not total.
raise Sorry("Empty selection: remove_selection.")
if(other_individual_selection_strings is not None):
sel2 = get_atom_selections(
model = model,
selection_strings = other_individual_selection_strings,
iselection = True,
one_selection_array = True)
if(sel1.intersection(sel2).size() > 0):
raise Sorry("Duplicate selection: occupancies of same atoms selected to be fixed and to be refined.")
if(other_constrained_groups is not None):
for other_constrained_group in other_constrained_groups:
for cg_sel_strs in other_constrained_group.selection:
sel2 = get_atom_selections(
model = model,
selection_strings = cg_sel_strs,
iselection = True,
one_selection_array = True)
if(sel1.intersection(sel2).size() > 0):
raise Sorry("Duplicate selection: occupancies of same atoms selected to be fixed and to be refined.")
result = mmtbx.utils.remove_selections(selection = result, other = sel1,
size = model.get_number_of_atoms())
#
if(other_individual_selection_strings is not None):
sel = get_atom_selections(
model = model,
selection_strings = other_individual_selection_strings,
iselection = True,
one_selection_array = True)
result = mmtbx.utils.remove_selections(selection = result, other = sel,
size = model.get_number_of_atoms())
result = add_occupancy_selection(
result = result,
size = model.get_number_of_atoms(),
selection = sel,
hd_special = None)
if(other_constrained_groups is not None):
for other_constrained_group in other_constrained_groups:
cg_sel = []
for cg_sel_strs in other_constrained_group.selection:
sel = get_atom_selections(
model = model,
selection_strings = cg_sel_strs,
iselection = True,
one_selection_array = True)
result = mmtbx.utils.remove_selections(selection = result, other = sel,
size = model.get_number_of_atoms())
if(sel.size() > 0):
cg_sel.append(list(sel))
if(len(cg_sel) > 0):
result.append(cg_sel)
if(add_water):
water_selection = get_atom_selections(
model = model,
selection_strings = ['water'],
iselection = True,
allow_empty_selection = True,
one_selection_array = True)
result = add_occupancy_selection(
result = result,
size = model.get_number_of_atoms(),
selection = water_selection,
hd_special = None)
list_3d_as_bool_selection(
list_3d=result, size=model.get_number_of_atoms())
if(len(result) == 0): result = None
if(as_flex_arrays and result is not None):
result_ = []
for gsel in result:
result__ = []
for sel in gsel:
result__.append(flex.size_t(sel))
result_.append(result__)
result = result_
if (constrain_correlated_3d_groups) and (len(result) > 0):
result = assemble_constraint_groups_3d(
xray_structure=model.get_xray_structure(),
pdb_atoms=model.get_atoms(),
constraint_groups=result,
log=log)
return result
def run(args, command_name = "phenix.tls"):
if(len(args) == 0): args = ["--help"]
usage_fmt = "%s pdb_file [parameters: file or command line string]"
des_fmt = "Example: %s model.pdb fit_tls_to.selection='%s' fit_tls_to.selection='%s'"
command_line = (iotbx_option_parser(
usage = usage_fmt % command_name,
description = banner)
.option("--show_defaults",
action="store_true",
help="Do not output to the screen (except errors).")
.option("--silent",
action="store_true",
help="Suppress output to the screen.")
).process(args=args)
#
log = sys.stdout
if(not command_line.options.silent):
utils.print_header("TLS tools", out = log)
if(command_line.options.show_defaults):
master_params.show(out = log)
print >> log
return
if(not command_line.options.silent):
print >> log, banner
#
processed_args = utils.process_command_line_args(args = command_line.args,
master_params = master_params, log = log)
reflection_files = processed_args.reflection_files
if(processed_args.crystal_symmetry is None):
raise Sorry("No crystal symmetry found.")
if(len(processed_args.pdb_file_names) == 0):
raise Sorry("No PDB file found.")
params = processed_args.params
if(not command_line.options.silent):
utils.print_header("Input parameters", out = log)
params.show(out = log)
params = params.extract()
#
if(processed_args.crystal_symmetry.unit_cell() is None or
processed_args.crystal_symmetry.space_group() is None):
raise Sorry("No CRYST1 record found.")
mmtbx_pdb_file = utils.pdb_file(
pdb_file_names = processed_args.pdb_file_names,
cif_objects = processed_args.cif_objects,
crystal_symmetry = processed_args.crystal_symmetry,
log = log)
#
if(not command_line.options.silent):
utils.print_header("TLS groups from PDB file header", out = log)
pdb_inp_tls = mmtbx.tls.tools.tls_from_pdb_inp(
remark_3_records = mmtbx_pdb_file.pdb_inp.extract_remark_iii_records(3),
pdb_hierarchy = mmtbx_pdb_file.pdb_inp.construct_hierarchy())
#
tls_groups = []
if(pdb_inp_tls.tls_present):
if(pdb_inp_tls.error_string is not None):
raise Sorry(pdb_inp_tls.error_string)
mmtbx_pdb_file.set_ppf()
xray_structure = get_xrs_helper(mmtbx_pdb_file = mmtbx_pdb_file, log = log,
silent = command_line.options.silent)
pdb_tls = mmtbx.tls.tools.extract_tls_from_pdb(
pdb_inp_tls = pdb_inp_tls,
all_chain_proxies = mmtbx_pdb_file.processed_pdb_file.all_chain_proxies,
xray_structure = xray_structure)
tls_groups = pdb_tls.pdb_inp_tls.tls_params
#
tls_selections_strings = []
#
if(len(tls_groups) == 0 and not command_line.options.silent):
print >> log, "No TLS groups found in PDB file header."
else:
for i_seq, tls_group in enumerate(tls_groups):
tls_selections_strings.append(tls_group.selection_string)
if(not command_line.options.silent):
print >> log, "TLS group %d: %s" % (i_seq+1, tls_group.selection_string)
mmtbx.tls.tools.show_tls_one_group(tlso = tls_group, out = log)
print >> log
#
if(len(tls_selections_strings) > 0 and len(params.selection) > 0):
raise Sorry("Two TLS selection sources found: PDB file header and parameters.")
if(len(params.selection) > 0):
tls_selections_strings = params.selection
xray_structure = get_xrs_helper(mmtbx_pdb_file = mmtbx_pdb_file, log = log,
silent = command_line.options.silent)
if([params.combine_tls, params.extract_tls].count(True) > 1):
raise Sorry("Cannot simultaneously pereform: combine_tls and extract_tls")
if([params.combine_tls, params.extract_tls].count(True) > 0):
if(len(tls_selections_strings)==0):
raise Sorry("No TLS selections found.")
#
if(len(tls_selections_strings)):
if(not command_line.options.silent):
utils.print_header("TLS groups selections", out = log)
selections = utils.get_atom_selections(
all_chain_proxies = mmtbx_pdb_file.processed_pdb_file.all_chain_proxies,
selection_strings = tls_selections_strings,
xray_structure = xray_structure)
if(not command_line.options.silent):
print >> log, "Number of TLS groups: ", len(selections)
print >> log, "Number of atoms: %d" % xray_structure.scatterers().size()
n_atoms_in_tls = 0
for sel_a in selections:
n_atoms_in_tls += sel_a.size()
if(not command_line.options.silent):
print >> log, "Number of atoms in TLS groups: %d" % n_atoms_in_tls
print >> log
assert len(tls_selections_strings) == len(selections)
if(not command_line.options.silent):
for sel_a, sel_s in zip(selections,tls_selections_strings):
print >> log, "Selection string:\n%s" % sel_s
print >> log, "selects %d atoms." % sel_a.size()
print >> log
print >> log, "Ready-to-use in phenix.refine:\n"
for sel_a, sel_s in zip(selections,tls_selections_strings):
print >> log, sel_s
#
ofn = params.output_file_name
if(ofn is None):
ofn = os.path.splitext(os.path.basename(processed_args.pdb_file_names[0]))[0]
if(len(processed_args.pdb_file_names) > 1):
ofn = ofn+"_el_al"
if(params.combine_tls):
ofn = ofn+"_combine_tls.pdb"
elif(params.extract_tls):
ofn = ofn+"_extract_tls.pdb"
else: ofn = None
if(ofn is not None):
ofo = open(ofn, "w")
#
if(params.extract_tls):
utils.print_header(
"Fit TLS matrices to B-factors of selected sets of atoms", out = log)
tlsos = mmtbx.tls.tools.generate_tlsos(
selections = selections,
xray_structure = xray_structure,
value = 0.0)
for rt,rl,rs in [[1,0,1],[1,1,1],[0,1,1],
[1,0,0],[0,1,0],[0,0,1],[1,1,1],
[0,0,1]]*10:
tlsos = mmtbx.tls.tools.tls_from_uanisos(
xray_structure = xray_structure,
selections = selections,
tlsos_initial = tlsos,
number_of_macro_cycles = 10,
max_iterations = 100,
refine_T = rt,
refine_L = rl,
refine_S = rs,
enforce_positive_definite_TL = params.enforce_positive_definite_TL,
verbose = -1,
out = log)
mmtbx.tls.tools.show_tls(tlsos = tlsos, out = log)
u_cart_from_tls = mmtbx.tls.tools.u_cart_from_tls(
sites_cart = xray_structure.sites_cart(),
selections = selections,
tlsos = tlsos)
unit_cell = xray_structure.unit_cell()
for i_seq, sc in enumerate(xray_structure.scatterers()):
if(u_cart_from_tls[i_seq] != (0,0,0,0,0,0)):
u_star_tls = adptbx.u_cart_as_u_star(unit_cell,
tuple(u_cart_from_tls[i_seq]))
sc.u_star = tuple(flex.double(sc.u_star) - flex.double(u_star_tls))
for sel in selections:
xray_structure.convert_to_isotropic(selection = sel)
mmtbx.tls.tools.remark_3_tls(tlsos = tlsos,
selection_strings = tls_selections_strings, out = ofo)
#
if(params.combine_tls):
utils.print_header("Combine B_tls with B_residual", out = log)
mmtbx.tls.tools.combine_tls_and_u_local(xray_structure = xray_structure,
tls_selections = selections, tls_groups = tls_groups)
print >> log, "All done."
#
if(ofn is not None):
utils.print_header("Write output PDB file %s"%ofn, out = log)
utils.write_pdb_file(
xray_structure = xray_structure,
pdb_hierarchy = mmtbx_pdb_file.processed_pdb_file.all_chain_proxies.pdb_hierarchy,
out = ofo)
ofo.close()
print >> log, "All done."
def run(args, command_name="phenix.tls"):
if (len(args) == 0): args = ["--help"]
usage_fmt = "%s pdb_file [parameters: file or command line string]"
des_fmt = "Example: %s model.pdb fit_tls_to.selection='%s' fit_tls_to.selection='%s'"
command_line = (iotbx_option_parser(
usage=usage_fmt % command_name, description=banner).option(
"--show_defaults",
action="store_true",
help="Do not output to the screen (except errors).").option(
"--silent",
action="store_true",
help="Suppress output to the screen.")).process(args=args)
#
log = sys.stdout
if (not command_line.options.silent):
utils.print_header("TLS tools", out=log)
if (command_line.options.show_defaults):
master_params.show(out=log)
print(file=log)
return
if (not command_line.options.silent):
print(banner, file=log)
#
processed_args = utils.process_command_line_args(
args=command_line.args, master_params=master_params, log=log)
reflection_files = processed_args.reflection_files
if (processed_args.crystal_symmetry is None):
raise Sorry("No crystal symmetry found.")
if (len(processed_args.pdb_file_names) == 0):
raise Sorry("No PDB file found.")
params = processed_args.params
if (not command_line.options.silent):
utils.print_header("Input parameters", out=log)
params.show(out=log)
params = params.extract()
#
if (processed_args.crystal_symmetry.unit_cell() is None
or processed_args.crystal_symmetry.space_group() is None):
raise Sorry("No CRYST1 record found.")
pdb_combined = iotbx.pdb.combine_unique_pdb_files(
file_names=processed_args.pdb_file_names)
pdb_combined.report_non_unique(out=log)
if (len(pdb_combined.unique_file_names) == 0):
raise Sorry("No coordinate file given.")
raw_records = pdb_combined.raw_records
try:
pdb_inp = iotbx.pdb.input(source_info=None,
lines=flex.std_string(raw_records))
except ValueError as e:
raise Sorry("Model format (PDB or mmCIF) error:\n%s" % str(e))
model = mmtbx.model.manager(
model_input=pdb_inp,
restraint_objects=processed_args.cif_objects,
crystal_symmetry=processed_args.crystal_symmetry,
log=log)
if (not command_line.options.silent):
utils.print_header("TLS groups from PDB file header", out=log)
pdb_inp_tls = mmtbx.tls.tools.tls_from_pdb_inp(
remark_3_records=model._model_input.extract_remark_iii_records(3),
pdb_hierarchy=model.get_hierarchy())
#
tls_groups = []
if (pdb_inp_tls.tls_present):
if (pdb_inp_tls.error_string is not None):
raise Sorry(pdb_inp_tls.error_string)
pdb_tls = mmtbx.tls.tools.extract_tls_from_pdb(pdb_inp_tls=pdb_inp_tls,
model=model)
tls_groups = pdb_tls.pdb_inp_tls.tls_params
#
tls_selections_strings = []
#
if (len(tls_groups) == 0 and not command_line.options.silent):
print("No TLS groups found in PDB file header.", file=log)
else:
for i_seq, tls_group in enumerate(tls_groups):
tls_selections_strings.append(tls_group.selection_string)
if (not command_line.options.silent):
print("TLS group %d: %s" %
(i_seq + 1, tls_group.selection_string),
file=log)
mmtbx.tls.tools.show_tls_one_group(tlso=tls_group, out=log)
print(file=log)
#
if (len(tls_selections_strings) > 0 and len(params.selection) > 0):
raise Sorry(
"Two TLS selection sources found: PDB file header and parameters.")
if (len(params.selection) > 0):
tls_selections_strings = params.selection
if ([params.combine_tls, params.extract_tls].count(True) > 1):
raise Sorry(
"Cannot simultaneously pereform: combine_tls and extract_tls")
if ([params.combine_tls, params.extract_tls].count(True) > 0):
if (len(tls_selections_strings) == 0):
raise Sorry("No TLS selections found.")
#
if (len(tls_selections_strings)):
if (not command_line.options.silent):
utils.print_header("TLS groups selections", out=log)
selections = utils.get_atom_selections(
model=model, selection_strings=tls_selections_strings)
if (not command_line.options.silent):
print("Number of TLS groups: ", len(selections), file=log)
print("Number of atoms: %d" % model.get_number_of_atoms(),
file=log)
n_atoms_in_tls = 0
for sel_a in selections:
n_atoms_in_tls += sel_a.size()
if (not command_line.options.silent):
print("Number of atoms in TLS groups: %d" % n_atoms_in_tls,
file=log)
print(file=log)
assert len(tls_selections_strings) == len(selections)
if (not command_line.options.silent):
for sel_a, sel_s in zip(selections, tls_selections_strings):
print("Selection string:\n%s" % sel_s, file=log)
print("selects %d atoms." % sel_a.size(), file=log)
print(file=log)
print("Ready-to-use in phenix.refine:\n", file=log)
for sel_a, sel_s in zip(selections, tls_selections_strings):
print(sel_s, file=log)
#
ofn = params.output_file_name
if (ofn is None):
ofn = os.path.splitext(
os.path.basename(processed_args.pdb_file_names[0]))[0]
if (len(processed_args.pdb_file_names) > 1):
ofn = ofn + "_el_al"
if (params.combine_tls):
ofn = ofn + "_combine_tls.pdb"
elif (params.extract_tls):
ofn = ofn + "_extract_tls.pdb"
else:
ofn = None
if (ofn is not None):
ofo = open(ofn, "w")
#
if (params.extract_tls):
utils.print_header(
"Fit TLS matrices to B-factors of selected sets of atoms", out=log)
tlsos = mmtbx.tls.tools.generate_tlsos(
selections=selections,
xray_structure=model.get_xray_structure(),
value=0.0)
for rt, rl, rs in [[1, 0, 1], [1, 1, 1], [0, 1, 1], [1, 0, 0],
[0, 1, 0], [0, 0, 1], [1, 1, 1], [0, 0, 1]] * 10:
tlsos = mmtbx.tls.tools.tls_from_uanisos(
xray_structure=model.get_xray_structure(),
selections=selections,
tlsos_initial=tlsos,
number_of_macro_cycles=10,
max_iterations=100,
refine_T=rt,
refine_L=rl,
refine_S=rs,
enforce_positive_definite_TL=params.
enforce_positive_definite_TL,
verbose=-1,
out=log)
mmtbx.tls.tools.show_tls(tlsos=tlsos, out=log)
u_cart_from_tls = mmtbx.tls.tools.u_cart_from_tls(
sites_cart=model.get_sites_cart(),
selections=selections,
tlsos=tlsos)
unit_cell = model.get_xray_structure().unit_cell()
for i_seq, sc in enumerate(model.get_xray_structure().scatterers()):
if (u_cart_from_tls[i_seq] != (0, 0, 0, 0, 0, 0)):
u_star_tls = adptbx.u_cart_as_u_star(
unit_cell, tuple(u_cart_from_tls[i_seq]))
sc.u_star = tuple(
flex.double(sc.u_star) - flex.double(u_star_tls))
for sel in selections:
model.get_xray_structure().convert_to_isotropic(selection=sel)
mmtbx.tls.tools.remark_3_tls(tlsos=tlsos,
selection_strings=tls_selections_strings,
out=ofo)
#
if (params.combine_tls):
utils.print_header("Combine B_tls with B_residual", out=log)
mmtbx.tls.tools.combine_tls_and_u_local(
xray_structure=model.get_xray_structure(),
tls_selections=selections,
tls_groups=tls_groups)
print("All done.", file=log)
#
if (ofn is not None):
utils.print_header("Write output PDB file %s" % ofn, out=log)
model.set_sites_cart_from_xrs()
pdb_str = model.model_as_pdb()
ofo.write(pdb_str)
ofo.close()
print("All done.", file=log)
def selection(self, selection_strings):
return utils.get_atom_selections(iselection = False,
all_chain_proxies= self.all_chain_proxies,
selection_strings= selection_strings,
xray_structure = self.xray_structure)[0]
def selection(self, selection_strings):
return utils.get_atom_selections(
iselection=False,
all_chain_proxies=self.all_chain_proxies,
selection_strings=selection_strings,
xray_structure=self.xray_structure)[0]
def occupancy_selections(
all_chain_proxies,
xray_structure,
add_water = False,
other_individual_selection_strings = None,
other_constrained_groups = None,
remove_selection = None,
as_flex_arrays = True,
constrain_correlated_3d_groups = False,
log = None):
# set up defaults
if(other_individual_selection_strings is not None and
len(other_individual_selection_strings) == 0):
other_individual_selection_strings = None
if(other_constrained_groups is not None and
len(other_constrained_groups) == 0):
other_constrained_groups = None
if(remove_selection is not None and len(remove_selection) == 0):
remove_selection = None
result = all_chain_proxies.pdb_hierarchy.occupancy_groups_simple(
common_residue_name_class_only = None,
always_group_adjacent = False,
ignore_hydrogens = False)
exchangable_hd_pairs = mmtbx.utils.combine_hd_exchangable(hierarchy =
all_chain_proxies.pdb_hierarchy)
if(len(exchangable_hd_pairs)==0 and result is not None):
occupancy_regroupping(
pdb_hierarchy = all_chain_proxies.pdb_hierarchy,
cgs = result)
result = mmtbx.utils.remove_selections(selection = result,
other = exchangable_hd_pairs,
size = xray_structure.scatterers().size())
result.extend(exchangable_hd_pairs)
# extract group-[0,1]-constrained atoms withing a residue
pogl = extract_partial_occupancy_selections(hierarchy = all_chain_proxies.pdb_hierarchy)
rm_duplicate_with_pogl = []
for t_ in pogl:
for t__ in t_:
for t___ in t__:
rm_duplicate_with_pogl.append(t___)
result = mmtbx.utils.remove_selections(selection = result, other = pogl,
size = xray_structure.scatterers().size())
result.extend(pogl)
# add partial occupancies
occupancies = xray_structure.scatterers().extract_occupancies()
sel = (occupancies != 1.) & (occupancies != 0.)
result = add_occupancy_selection(
result = result,
size = xray_structure.scatterers().size(),
selection = sel,
hd_special = None)
# check user's input
all_sel_strgs = []
if(other_individual_selection_strings is not None):
all_sel_strgs = all_sel_strgs + other_individual_selection_strings
if(other_constrained_groups is not None):
for other_constrained_group in other_constrained_groups:
for other_constrained_group in other_constrained_groups:
if(len(other_constrained_group.selection)>0):
all_sel_strgs = all_sel_strgs + other_constrained_group.selection
if(len(all_sel_strgs) > 0):
for sel_str in all_sel_strgs:
sel_str_sel = get_atom_selections(
all_chain_proxies = all_chain_proxies,
selection_strings = [sel_str],
iselection = True,
xray_structure = xray_structure,
one_selection_array = True)
if(sel_str_sel.size() == 0):
raise Sorry("Empty selection: %s"%sel_str)
#
if([other_individual_selection_strings,
other_constrained_groups].count(None) == 0):
sel1 = get_atom_selections(
all_chain_proxies = all_chain_proxies,
selection_strings = other_individual_selection_strings,
iselection = True,
xray_structure = xray_structure,
one_selection_array = True)
for other_constrained_group in other_constrained_groups:
for other_constrained_group in other_constrained_groups:
for cg_sel_strs in other_constrained_group.selection:
sel2 = get_atom_selections(
all_chain_proxies = all_chain_proxies,
selection_strings = cg_sel_strs,
iselection = True,
xray_structure = xray_structure,
one_selection_array = True)
if(sel1.intersection(sel2).size() > 0):
raise Sorry("Duplicate selection: same atoms selected for individual and group occupancy refinement.")
# check user's input and apply remove_selection to default selection
if(remove_selection is not None):
sel1 = get_atom_selections(
all_chain_proxies = all_chain_proxies,
selection_strings = remove_selection,
iselection = True,
xray_structure = xray_structure,
one_selection_array = True)
if(sel1.size() == 0): # XXX check all and not total.
raise Sorry("Empty selection: remove_selection.")
if(other_individual_selection_strings is not None):
sel2 = get_atom_selections(
all_chain_proxies = all_chain_proxies,
selection_strings = other_individual_selection_strings,
iselection = True,
xray_structure = xray_structure,
one_selection_array = True)
if(sel1.intersection(sel2).size() > 0):
raise Sorry("Duplicate selection: occupancies of same atoms selected to be fixed and to be refined.")
if(other_constrained_groups is not None):
for other_constrained_group in other_constrained_groups:
for cg_sel_strs in other_constrained_group.selection:
sel2 = get_atom_selections(
all_chain_proxies = all_chain_proxies,
selection_strings = cg_sel_strs,
iselection = True,
xray_structure = xray_structure,
one_selection_array = True)
if(sel1.intersection(sel2).size() > 0):
raise Sorry("Duplicate selection: occupancies of same atoms selected to be fixed and to be refined.")
result = mmtbx.utils.remove_selections(selection = result, other = sel1,
size = xray_structure.scatterers().size())
#
if(other_individual_selection_strings is not None):
sel = get_atom_selections(
all_chain_proxies = all_chain_proxies,
selection_strings = other_individual_selection_strings,
iselection = True,
xray_structure = xray_structure,
one_selection_array = True)
result = mmtbx.utils.remove_selections(selection = result, other = sel,
size = xray_structure.scatterers().size())
result = add_occupancy_selection(
result = result,
size = xray_structure.scatterers().size(),
selection = sel,
hd_special = None)
if(other_constrained_groups is not None):
for other_constrained_group in other_constrained_groups:
cg_sel = []
for cg_sel_strs in other_constrained_group.selection:
sel = get_atom_selections(
all_chain_proxies = all_chain_proxies,
selection_strings = cg_sel_strs,
iselection = True,
xray_structure = xray_structure,
one_selection_array = True)
result = mmtbx.utils.remove_selections(selection = result, other = sel,
size = xray_structure.scatterers().size())
if(sel.size() > 0):
cg_sel.append(list(sel))
if(len(cg_sel) > 0):
result.append(cg_sel)
if(add_water):
water_selection = get_atom_selections(
all_chain_proxies = all_chain_proxies,
selection_strings = ['water'],
iselection = True,
xray_structure = xray_structure,
allow_empty_selection = True,
one_selection_array = True)
result = add_occupancy_selection(
result = result,
size = xray_structure.scatterers().size(),
selection = water_selection,
hd_special = None)
list_3d_as_bool_selection(
list_3d=result, size=xray_structure.scatterers().size())
if(len(result) == 0): result = None
if(as_flex_arrays and result is not None):
result_ = []
for gsel in result:
result__ = []
for sel in gsel:
result__.append(flex.size_t(sel))
result_.append(result__)
result = result_
if (constrain_correlated_3d_groups) and (len(result) > 0) :
result = assemble_constraint_groups_3d(
xray_structure=xray_structure,
pdb_atoms=all_chain_proxies.pdb_hierarchy.atoms(),
constraint_groups=result,
log=log)
return result
if (len(tls_selections_strings) > 0 and len(params.selection) > 0):
raise Sorry(
"Two TLS selection sources found: PDB file header and parameters.")
if (len(params.selection) > 0):
tls_selections_strings = params.selection
if ([params.combine_tls, params.extract_tls].count(True) > 1):
raise Sorry(
"Cannot simultaneously pereform: combine_tls and extract_tls")
if ([params.combine_tls, params.extract_tls].count(True) > 0):
if (len(tls_selections_strings) == 0):
raise Sorry("No TLS selections found.")
#
if (len(tls_selections_strings)):
if (not command_line.options.silent):
utils.print_header("TLS groups selections", out=log)
selections = utils.get_atom_selections(
model=model, selection_strings=tls_selections_strings)
if (not command_line.options.silent):
print >> log, "Number of TLS groups: ", len(selections)
print >> log, "Number of atoms: %d" % model.get_number_of_atoms()
n_atoms_in_tls = 0
for sel_a in selections:
n_atoms_in_tls += sel_a.size()
if (not command_line.options.silent):
print >> log, "Number of atoms in TLS groups: %d" % n_atoms_in_tls
print >> log
assert len(tls_selections_strings) == len(selections)
if (not command_line.options.silent):
for sel_a, sel_s in zip(selections, tls_selections_strings):
print >> log, "Selection string:\n%s" % sel_s
print >> log, "selects %d atoms." % sel_a.size()
print >> log
