def run(model_filename=None):
import mmtbx.monomer_library.pdb_interpretation as pdb_inter
#print_restraints(database)
if model_filename is not None:
from iotbx import pdb
pdb_inp = pdb.input(model_filename)
pdb_hierarchy = pdb_inp.construct_hierarchy()
#pdb_hierarchy.show()
pdb_processed_file = pdb_inter.run(
args=[model_filename],
assume_hydrogens_all_missing=False,
hard_minimum_nonbonded_distance=0.0,
nonbonded_distance_threshold=None,
substitute_non_crystallographic_unit_cell_if_necessary=True,
)
grm = pdb_processed_file.geometry_restraints_manager()
xrs = pdb_processed_file.xray_structure()
sites_cart = xrs.sites_cart()
site_labels = xrs.scatterers().extract_labels()
pair_proxies = grm.pair_proxies(sites_cart=sites_cart,
site_labels=site_labels)
proxies_info_nonbonded = pair_proxies.nonbonded_proxies.get_sorted(
by_value="delta", sites_cart=sites_cart, site_labels=site_labels)
rc = get_metal_coordination_proxies(
pdb_hierarchy,
pair_proxies.nonbonded_proxies,
)
bonds, angles = get_proxies(rc)
print('\n\tbonds, angles : %d, %d\n\n' % (len(bonds), len(angles)))
def exercise():
if (not libtbx.env.has_module("mmtbx")):
print "Skipping exercise(): mmtbx module not available"
return
if (libtbx.env.find_in_repositories(relative_path="chem_data") is None):
print "Skipping exercise(): chem_data directory not available"
return
from mmtbx.monomer_library import pdb_interpretation
file_name = "phe_tst_adp_aniso_restraints.pdb"
open(file_name, "w").write(phe_pdb)
out = StringIO()
processed_pdb_file = pdb_interpretation.run(
args = [file_name],
strict_conflict_handling = False,
log = out)
geo = processed_pdb_file.geometry_restraints_manager()
xray_structure = processed_pdb_file.xray_structure()
xray_structure.scatterers().flags_set_grads(state=False)
xray_structure.scatterers().flags_set_grad_u_iso(
iselection=xray_structure.use_u_iso().iselection())
xray_structure.scatterers().flags_set_grad_u_aniso(
iselection=xray_structure.use_u_aniso().iselection())
adp_rm = cctbx.adp_restraints.adp_aniso_restraints(
xray_structure = xray_structure,
restraints_manager = geo,
use_hd = False)
assert approx_equal(flex.mean(adp_rm.gradients_iso), 0.713756592583)
assert approx_equal(flex.mean(adp_rm.gradients_aniso_cart.as_double()), -0.118959432097)
assert approx_equal(adp_rm.target, 8.97112989232)
fd(xray_structure = xray_structure, restraints_manager = geo, eps=1.e-4)
def run(args, out=sys.stdout):
if (len(args) == 0) or ("--help" in args):
raise Usage("mmtbx.rigid_bond_test model.pdb")
from mmtbx.monomer_library import pdb_interpretation
import mmtbx.restraints
import mmtbx.model
import iotbx.phil
cmdline = iotbx.phil.process_command_line_with_files(
args=args,
master_phil=master_phil,
pdb_file_def="model",
cif_file_def="restraints")
params = cmdline.work.extract()
validate_params(params)
processed_pdb_file = pdb_interpretation.run(args=[params.model] +
params.restraints)
geometry = processed_pdb_file.geometry_restraints_manager(
show_energies=True)
restraints_manager = mmtbx.restraints.manager(geometry=geometry,
normalization=True)
model = mmtbx.model.manager(
xray_structure=processed_pdb_file.xray_structure(),
pdb_hierarchy=processed_pdb_file.all_chain_proxies.pdb_hierarchy,
restraints_manager=restraints_manager,
log=out)
make_header("Rigid-bond test", out=out)
model.show_rigid_bond_test(out=out, use_id_str=True, prefix=" ")
def run (args) :
from mmtbx.monomer_library import pdb_interpretation
from cctbx import crystal
pdb = pdb_interpretation.run(args=args,
substitute_non_crystallographic_unit_cell_if_necessary=True)
geo = pdb.geometry_restraints_manager()
xrs = pdb.xray_structure()
sites_cart = xrs.sites_frac()
scatterers = xrs.scatterers()
hd_sel = xrs.hd_selection()
table_bonds = geo.shell_sym_tables[0]
table_1_4 = geo.shell_sym_tables[2]
assert len(table_1_4) == len(sites_cart)
for i_seq, sc in enumerate(scatterers) :
print sc.label
if (hd_sel[i_seq]) :
bonded = table_bonds[i_seq].keys()
for j_seq in bonded :
for k_seq in table_1_4[j_seq].keys() :
print " H/D 1_5 interaction:", scatterers[k_seq].label
else :
for j_seq in table_1_4[i_seq].keys() :
for k_seq in table_bonds[j_seq].keys() :
if (hd_sel[k_seq]) :
print " H/D 1_5 interaction:", scatterers[k_seq].label
def exercise():
if (not libtbx.env.has_module("mmtbx")):
print("Skipping exercise(): mmtbx module not available")
return
if (libtbx.env.find_in_repositories(relative_path="chem_data") is None):
print("Skipping exercise(): chem_data directory not available")
return
from mmtbx.monomer_library import pdb_interpretation
file_name = "phe_tst_adp_aniso_restraints.pdb"
open(file_name, "w").write(phe_pdb)
out = StringIO()
processed_pdb_file = pdb_interpretation.run(args=[file_name],
strict_conflict_handling=False,
log=out)
geo = processed_pdb_file.geometry_restraints_manager()
xray_structure = processed_pdb_file.xray_structure()
xray_structure.scatterers().flags_set_grads(state=False)
xray_structure.scatterers().flags_set_grad_u_iso(
iselection=xray_structure.use_u_iso().iselection())
xray_structure.scatterers().flags_set_grad_u_aniso(
iselection=xray_structure.use_u_aniso().iselection())
adp_rm = cctbx.adp_restraints.adp_aniso_restraints(
xray_structure=xray_structure, restraints_manager=geo, use_hd=False)
assert approx_equal(flex.mean(adp_rm.gradients_iso), 0.713756592583)
assert approx_equal(flex.mean(adp_rm.gradients_aniso_cart.as_double()),
-0.118959432097)
assert approx_equal(adp_rm.target, 8.97112989232)
fd(xray_structure=xray_structure, restraints_manager=geo, eps=1.e-4)
def exercise_with_pdb(verbose):
if (not libtbx.env.has_module(name="mmtbx")):
print("Skipping exercise_with_pdb():", \
"mmtbx.monomer_library.pdb_interpretation not available")
return
if (libtbx.env.find_in_repositories(relative_path="chem_data") is None):
print(
"Skipping exercise_with_pdb(): chem_data directory not available")
return
if (verbose):
out = sys.stdout
else:
out = StringIO()
with open("tmp_cctbx_geometry_restraints.pdb", "w") as f:
f.write(enk_pdb)
pdb_interpretation_params = pdb_interpretation.master_params.extract()
pdb_interpretation_params.sort_atoms = False
processed_pdb_file = pdb_interpretation.run(
args=["tmp_cctbx_geometry_restraints.pdb"],
strict_conflict_handling=False,
params=pdb_interpretation_params,
log=out,
)
geo = processed_pdb_file.geometry_restraints_manager()
site_labels = processed_pdb_file.xray_structure().scatterers() \
.extract_labels()
#
assert approx_equal(flex.min(geo.nonbonded_model_distances()), 0.4777342)
#
geo._sites_cart_used_for_pair_proxies = None
#
sel0 = geo.simple_edge_list()
assert len(sel0) == 46
assert sel0[:4] == [(0, 1), (0, 8), (0, 11), (1, 2)]
assert sel0[-4:] == [(42, 43), (42, 44), (45, 46), (45, 47)]
geo.bond_params_table[13][14].slack = 0.1
geo.bond_params_table[28][30].slack = 0.3
sel = geo.simple_edge_list()
assert sorted(set(sel0) - set(sel)) == [(13, 14), (28, 30)]
sel = geo.simple_edge_list(omit_slack_greater_than=0.2)
assert sorted(set(sel0) - set(sel)) == [(28, 30)]
#
d = geo.discard_symmetry(new_unit_cell=(10, 10, 10, 90, 90, 90))
assert d.site_symmetry_table.special_position_indices().size() == 0
#
clusters = geo.rigid_clusters_due_to_dihedrals_and_planes(
constrain_dihedrals_with_sigma_less_than=10)
assert sorted([tuple(sorted(c))
for c in clusters]) == [(0, 8, 10, 15), (0, 8, 12, 15),
(1, 2, 3, 4, 5, 6, 7, 9),
(5, 6, 7, 9), (12, 13, 14, 19),
(12, 13, 16, 19), (16, 17, 18, 29),
(16, 17, 20, 29), (20, 28, 30, 37),
(20, 28, 31, 37),
(21, 22, 23, 24, 25, 26, 27)]
def pdb_interpretation_run(args):
from mmtbx.monomer_library.pdb_interpretation import run
all_processed_pdb_files = run(args=args, return_all_processed_pdb_files=True)
for processed_pdb_file in all_processed_pdb_files:
all_proxies = processed_pdb_file.all_chain_proxies
print "update_restraints:", \
len(all_proxies.conformation_dependent_restraints_list)
for x in all_proxies.conformation_dependent_restraints_list:
x.update_restraints(sites_cart=all_proxies.sites_cart,
dihedral_proxies=all_proxies.geometry_proxy_registries.dihedral.proxies,
angle_proxies=all_proxies.geometry_proxy_registries.angle.proxies)
def test_calling_pdb_interpretation(self):
""" Make sure can create NCS object and change search parameters """
params_phil = iotbx.phil.parse(input_string=master_params,
process_includes=True)
params = params_phil.extract()
# Turn on NCS search and adjust one of the parameters
params.ncs_search.enabled = True
pdb_processed_file = pdb_interpretation.run(args=['test.pdb'],
params=params,
log=null_out())
ncs_obj = pdb_processed_file.ncs_obj
self.assertEqual(ncs_obj.number_of_ncs_groups, 2)
def run (args=(), params=None, out=None) :
if (out is None) :
out = sys.stdout
if (params is None) :
import iotbx.phil
cmdline = iotbx.phil.process_command_line_with_files(
args=args,
master_phil_string=master_phil,
pdb_file_def="adp_statistics.pdb_file",
cif_file_def="adp_statistics.cif_file",
usage_string="""\
phenix.b_factor_statistics model.pdb [restraints.cif] [selection=...]
Show statistics for atomic displacement parameters (ADPs) or B-factors,
including TLS contribution if present.""")
params = cmdline.work.extract()
validate_params(params)
import mmtbx.model
import mmtbx.restraints
from mmtbx.monomer_library import pdb_interpretation
processed_pdb_file = pdb_interpretation.run(
args=[params.adp_statistics.pdb_file] + params.adp_statistics.cif_file,
substitute_non_crystallographic_unit_cell_if_necessary=True,
log=out)
geometry = processed_pdb_file.geometry_restraints_manager(show_energies=True)
restraints_manager = mmtbx.restraints.manager(
geometry = geometry,
normalization = True)
model = mmtbx.model.manager(
xray_structure = processed_pdb_file.xray_structure(),
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy,
restraints_manager = restraints_manager,
log = out)
make_sub_header("Analyzing model B-factors", out=out)
if (params.adp_statistics.selection is not None) :
sel_cache = model.pdb_hierarchy().atom_selection_cache()
selection = sel_cache.selection(params.adp_statistics.selection)
n_sel = selection.count(True)
if (n_sel == 0) :
raise Sorry("No atoms in selection!")
else :
model = model.select(selection)
print >> out, "Extracted %d atoms in selection:" % n_sel
print >> out, " %s" % params.adp_statistics.selection
print >> out, ""
stats = model.adp_statistics()
stats.file_name = params.adp_statistics.pdb_file
stats.selection = params.adp_statistics.selection
stats.show_1(out=out)
return stats
def test_calling_pdb_interpretation(self):
""" Make sure can create NCS object and change search parameters """
params_phil = iotbx.phil.parse(
input_string=master_params,
process_includes=True)
params = params_phil.extract()
# Turn on NCS search and adjust one of the parameters
params.ncs_search.enabled = True
pdb_processed_file = pdb_interpretation.run(
args=['test.pdb'],
params=params,
log=null_out())
ncs_obj = pdb_processed_file.ncs_obj
self.assertEqual(ncs_obj.number_of_ncs_groups,2)
def pdb_interpretation_run(args):
from mmtbx.monomer_library.pdb_interpretation import run
all_processed_pdb_files = run(args=args,
return_all_processed_pdb_files=True)
for processed_pdb_file in all_processed_pdb_files:
all_proxies = processed_pdb_file.all_chain_proxies
print "update_restraints:", \
len(all_proxies.conformation_dependent_restraints_list)
for x in all_proxies.conformation_dependent_restraints_list:
x.update_restraints(sites_cart=all_proxies.sites_cart,
dihedral_proxies=all_proxies.
geometry_proxy_registries.dihedral.proxies,
angle_proxies=all_proxies.
geometry_proxy_registries.angle.proxies)
def run(args=(), params=None, out=None):
if (out is None):
out = sys.stdout
if (params is None):
import iotbx.phil
cmdline = iotbx.phil.process_command_line_with_files(
args=args,
master_phil_string=master_phil,
pdb_file_def="adp_statistics.pdb_file",
cif_file_def="adp_statistics.cif_file",
usage_string="""\
phenix.b_factor_statistics model.pdb [restraints.cif] [selection=...]
Show statistics for atomic displacement parameters (ADPs) or B-factors,
including TLS contribution if present.""")
params = cmdline.work.extract()
validate_params(params)
import mmtbx.model
import mmtbx.restraints
from mmtbx.monomer_library import pdb_interpretation
processed_pdb_file = pdb_interpretation.run(
args=[params.adp_statistics.pdb_file] + params.adp_statistics.cif_file,
substitute_non_crystallographic_unit_cell_if_necessary=True,
log=out)
geometry = processed_pdb_file.geometry_restraints_manager(
show_energies=True)
restraints_manager = mmtbx.restraints.manager(geometry=geometry,
normalization=True)
model = mmtbx.model.manager(
xray_structure=processed_pdb_file.xray_structure(),
pdb_hierarchy=processed_pdb_file.all_chain_proxies.pdb_hierarchy,
restraints_manager=restraints_manager,
log=out)
make_sub_header("Analyzing model B-factors", out=out)
if (params.adp_statistics.selection is not None):
sel_cache = model.pdb_hierarchy().atom_selection_cache()
selection = sel_cache.selection(params.adp_statistics.selection)
n_sel = selection.count(True)
if (n_sel == 0):
raise Sorry("No atoms in selection!")
else:
model = model.select(selection)
print >> out, "Extracted %d atoms in selection:" % n_sel
print >> out, " %s" % params.adp_statistics.selection
print >> out, ""
stats = model.adp_statistics()
stats.file_name = params.adp_statistics.pdb_file
stats.selection = params.adp_statistics.selection
stats.show_1(out=out)
return stats
def exercise_with_pdb(verbose):
if (not libtbx.env.has_module(name="mmtbx")):
print "Skipping exercise_with_pdb():", \
"mmtbx.monomer_library.pdb_interpretation not available"
return
if (libtbx.env.find_in_repositories(relative_path="chem_data") is None):
print "Skipping exercise_with_pdb(): chem_data directory not available"
return
if (verbose):
out = sys.stdout
else:
out = StringIO()
open("tmp_cctbx_geometry_restraints.pdb", "w").write(enk_pdb)
pdb_interpretation_params = pdb_interpretation.master_params.extract()
pdb_interpretation_params.sort_atoms=False
processed_pdb_file = pdb_interpretation.run(
args=["tmp_cctbx_geometry_restraints.pdb"],
strict_conflict_handling=False,
params=pdb_interpretation_params,
log=out,)
geo = processed_pdb_file.geometry_restraints_manager()
site_labels = processed_pdb_file.xray_structure().scatterers() \
.extract_labels()
#
assert approx_equal(flex.min(geo.nonbonded_model_distances()), 0.4777342)
#
geo._sites_cart_used_for_pair_proxies = None
#
sel0 = geo.simple_edge_list()
assert len(sel0) == 46
assert sel0[:4] == [(0, 1), (0, 8), (0, 11), (1, 2)]
assert sel0[-4:] == [(42, 43), (42, 44), (45, 46), (45, 47)]
geo.bond_params_table[13][14].slack = 0.1
geo.bond_params_table[28][30].slack = 0.3
sel = geo.simple_edge_list()
assert sorted(set(sel0) - set(sel)) == [(13, 14), (28, 30)]
sel = geo.simple_edge_list(omit_slack_greater_than=0.2)
assert sorted(set(sel0) - set(sel)) == [(28, 30)]
#
d = geo.discard_symmetry(new_unit_cell=(10,10,10,90,90,90))
assert d.site_symmetry_table.special_position_indices().size()==0
#
clusters = geo.rigid_clusters_due_to_dihedrals_and_planes(
constrain_dihedrals_with_sigma_less_than=10)
assert sorted([tuple(sorted(c)) for c in clusters]) == [
(0, 8, 10, 15), (0, 8, 12, 15), (1, 2, 3, 4, 5, 6, 7, 9),
(5, 6, 7, 9), (12, 13, 14, 19), (12, 13, 16, 19), (16, 17, 18, 29),
(16, 17, 20, 29), (20, 28, 30, 37), (20, 28, 31, 37),
(21, 22, 23, 24, 25, 26, 27)]
def run (args, log=sys.stdout) :
processed_pdb_file = pdb_interpretation.run(
args=args,
substitute_non_crystallographic_unit_cell_if_necessary=True,
log=log)
xray_structure = processed_pdb_file.xray_structure()
if xray_structure is None :
raise Sorry("Could not calculate X-ray structure from this PDB file. "+
"This is probably due to missing symmetry information (CRYST1 record.")
geometry = processed_pdb_file.geometry_restraints_manager(
show_energies=False)
chain_proxies = processed_pdb_file.all_chain_proxies
pdb_hierarchy = chain_proxies.pdb_hierarchy
result = restraints.combined(
pdb_hierarchy=chain_proxies.pdb_hierarchy,
xray_structure=xray_structure,
geometry_restraints_manager=geometry,
ignore_hd=True)
result.show(out=log, prefix=" ")
def run(args, log=sys.stdout):
processed_pdb_file = pdb_interpretation.run(
args=args,
substitute_non_crystallographic_unit_cell_if_necessary=True,
log=log)
xray_structure = processed_pdb_file.xray_structure()
if xray_structure is None:
raise Sorry(
"Could not calculate X-ray structure from this PDB file. " +
"This is probably due to missing symmetry information (CRYST1 record."
)
geometry = processed_pdb_file.geometry_restraints_manager(
show_energies=False)
chain_proxies = processed_pdb_file.all_chain_proxies
pdb_hierarchy = chain_proxies.pdb_hierarchy
result = restraints.combined(pdb_hierarchy=chain_proxies.pdb_hierarchy,
xray_structure=xray_structure,
geometry_restraints_manager=geometry,
ignore_hd=True)
result.show(out=log, prefix=" ")
def process_clash_score(file_name):
pdb_processed_file = pdb_inter.run(
args=[file_name],
assume_hydrogens_all_missing=False,
hard_minimum_nonbonded_distance=0.0,
nonbonded_distance_threshold=None,
substitute_non_crystallographic_unit_cell_if_necessary=True,
log=null_out())
grm = pdb_processed_file.geometry_restraints_manager()
xrs = pdb_processed_file.xray_structure()
sites_cart = xrs.sites_cart()
site_labels = xrs.scatterers().extract_labels()
hd_sel = xrs.hd_selection()
macro_mol_sel = cs.get_macro_mol_sel(pdb_processed_file)
clash_score_info = cs.info(
geometry_restraints_manager=grm,
macro_molecule_selection=macro_mol_sel,
sites_cart=sites_cart,
site_labels=site_labels,
hd_sel=hd_sel)
return clash_score_info
def run(args, out=sys.stdout):
if (len(args) == 0) or ("--help" in args):
raise Usage("mmtbx.rigid_bond_test model.pdb")
from mmtbx.monomer_library import pdb_interpretation
import mmtbx.restraints
import mmtbx.model
import iotbx.phil
cmdline = iotbx.phil.process_command_line_with_files(
args=args, master_phil=master_phil, pdb_file_def="model", cif_file_def="restraints"
)
params = cmdline.work.extract()
validate_params(params)
processed_pdb_file = pdb_interpretation.run(args=[params.model] + params.restraints)
geometry = processed_pdb_file.geometry_restraints_manager(show_energies=True)
restraints_manager = mmtbx.restraints.manager(geometry=geometry, normalization=True)
model = mmtbx.model.manager(
xray_structure=processed_pdb_file.xray_structure(),
pdb_hierarchy=processed_pdb_file.all_chain_proxies.pdb_hierarchy,
restraints_manager=restraints_manager,
log=out,
)
make_header("Rigid-bond test", out=out)
model.show_rigid_bond_test(out=out, use_id_str=True, prefix=" ")
def exercise_na_restraints_output_to_geo(verbose=False):
for dependency in ("chem_data", "ksdssp"):
if not libtbx.env.has_module(dependency):
print "Skipping exercise_na_restraints_output_to_geo(): %s not available" %(
dependency)
return
pdb_str_1dpl_cutted="""\
CRYST1 24.627 42.717 46.906 90.00 90.00 90.00 P 21 21 21 8
ATOM 184 P DG A 9 9.587 13.026 19.037 1.00 6.28 P
ATOM 185 OP1 DG A 9 9.944 14.347 19.602 1.00 8.07 O
ATOM 186 OP2 DG A 9 10.654 12.085 18.639 1.00 8.27 O
ATOM 187 O5' DG A 9 8.717 12.191 20.048 1.00 5.88 O
ATOM 188 C5' DG A 9 7.723 12.833 20.854 1.00 5.45 C
ATOM 189 C4' DG A 9 7.145 11.818 21.807 1.00 5.40 C
ATOM 190 O4' DG A 9 6.435 10.777 21.087 1.00 5.77 O
ATOM 191 C3' DG A 9 8.142 11.036 22.648 1.00 5.10 C
ATOM 192 O3' DG A 9 8.612 11.838 23.723 1.00 5.90 O
ATOM 193 C2' DG A 9 7.300 9.857 23.068 1.00 5.97 C
ATOM 194 C1' DG A 9 6.619 9.536 21.805 1.00 5.97 C
ATOM 195 N9 DG A 9 7.390 8.643 20.931 1.00 5.97 N
ATOM 196 C8 DG A 9 8.074 8.881 19.775 1.00 6.62 C
ATOM 197 N7 DG A 9 8.647 7.820 19.249 1.00 6.57 N
ATOM 198 C5 DG A 9 8.308 6.806 20.141 1.00 6.22 C
ATOM 199 C6 DG A 9 8.620 5.431 20.136 1.00 6.03 C
ATOM 200 O6 DG A 9 9.297 4.803 19.296 1.00 7.21 O
ATOM 201 N1 DG A 9 8.101 4.773 21.247 1.00 6.10 N
ATOM 202 C2 DG A 9 7.365 5.351 22.260 1.00 6.24 C
ATOM 203 N2 DG A 9 6.948 4.569 23.241 1.00 7.88 N
ATOM 204 N3 DG A 9 7.051 6.652 22.257 1.00 6.53 N
ATOM 205 C4 DG A 9 7.539 7.295 21.184 1.00 5.69 C
ATOM 206 P DC A 10 10.081 11.538 24.300 1.00 5.91 P
ATOM 207 OP1 DC A 10 10.273 12.645 25.291 1.00 7.27 O
ATOM 208 OP2 DC A 10 11.063 11.363 23.228 1.00 6.84 O
ATOM 209 O5' DC A 10 9.953 10.128 25.026 1.00 5.75 O
ATOM 210 C5' DC A 10 9.077 9.959 26.149 1.00 5.87 C
ATOM 211 C4' DC A 10 9.188 8.549 26.672 1.00 5.56 C
ATOM 212 O4' DC A 10 8.708 7.612 25.667 1.00 5.70 O
ATOM 213 C3' DC A 10 10.580 8.059 27.007 1.00 5.27 C
ATOM 214 O3' DC A 10 11.010 8.447 28.315 1.00 5.83 O
ATOM 215 C2' DC A 10 10.422 6.549 26.893 1.00 5.34 C
ATOM 216 C1' DC A 10 9.436 6.405 25.754 1.00 5.23 C
ATOM 217 N1 DC A 10 10.113 6.168 24.448 1.00 5.30 N
ATOM 218 C2 DC A 10 10.514 4.871 24.152 1.00 5.28 C
ATOM 219 O2 DC A 10 10.283 3.972 25.000 1.00 5.75 O
ATOM 220 N3 DC A 10 11.131 4.627 22.965 1.00 5.65 N
ATOM 221 C4 DC A 10 11.395 5.628 22.138 1.00 5.80 C
ATOM 222 N4 DC A 10 12.034 5.327 21.005 1.00 6.75 N
ATOM 223 C5 DC A 10 11.029 6.970 22.449 1.00 5.99 C
ATOM 224 C6 DC A 10 10.394 7.203 23.612 1.00 5.56 C
ATOM 226 O5' DG B 11 12.424 -4.393 18.427 1.00 22.70 O
ATOM 227 C5' DG B 11 12.380 -5.516 19.282 1.00 14.75 C
ATOM 228 C4' DG B 11 11.969 -5.112 20.676 1.00 10.42 C
ATOM 229 O4' DG B 11 12.972 -4.192 21.210 1.00 10.51 O
ATOM 230 C3' DG B 11 10.649 -4.394 20.782 1.00 8.57 C
ATOM 231 O3' DG B 11 9.618 -5.363 20.846 1.00 8.69 O
ATOM 232 C2' DG B 11 10.822 -3.597 22.051 1.00 8.63 C
ATOM 233 C1' DG B 11 12.236 -3.233 21.980 1.00 9.81 C
ATOM 234 N9 DG B 11 12.509 -1.902 21.305 1.00 8.66 N
ATOM 235 C8 DG B 11 13.175 -1.667 20.135 1.00 9.57 C
ATOM 236 N7 DG B 11 13.255 -0.407 19.824 1.00 9.04 N
ATOM 237 C5 DG B 11 12.613 0.235 20.869 1.00 7.63 C
ATOM 238 C6 DG B 11 12.388 1.612 21.119 1.00 7.05 C
ATOM 239 O6 DG B 11 12.723 2.590 20.419 1.00 7.81 O
ATOM 240 N1 DG B 11 11.715 1.819 22.317 1.00 6.27 N
ATOM 241 C2 DG B 11 11.264 0.828 23.159 1.00 6.05 C
ATOM 242 N2 DG B 11 10.611 1.219 24.248 1.00 5.85 N
ATOM 243 N3 DG B 11 11.483 -0.457 22.942 1.00 6.55 N
ATOM 244 C4 DG B 11 12.150 -0.687 21.797 1.00 6.84 C
ATOM 245 P DC B 12 8.134 -5.009 20.350 1.00 8.13 P
ATOM 246 OP1 DC B 12 7.367 -6.252 20.459 1.00 10.02 O
ATOM 247 OP2 DC B 12 8.172 -4.307 19.052 1.00 9.79 O
ATOM 248 O5' DC B 12 7.564 -3.912 21.389 1.00 8.18 O
ATOM 249 C5' DC B 12 7.275 -4.296 22.719 1.00 8.00 C
ATOM 250 C4' DC B 12 6.856 -3.057 23.487 1.00 8.01 C
ATOM 251 O4' DC B 12 8.006 -2.146 23.615 1.00 7.35 O
ATOM 252 C3' DC B 12 5.763 -2.208 22.890 1.00 7.04 C
ATOM 253 O3' DC B 12 4.456 -2.800 23.100 1.00 9.82 O
ATOM 254 C2' DC B 12 6.019 -0.916 23.630 1.00 6.50 C
ATOM 255 C1' DC B 12 7.467 -0.808 23.608 1.00 7.35 C
ATOM 256 N1 DC B 12 8.040 -0.143 22.396 1.00 6.64 N
ATOM 257 C2 DC B 12 8.017 1.257 22.382 1.00 5.68 C
ATOM 258 O2 DC B 12 7.524 1.832 23.357 1.00 6.32 O
ATOM 259 N3 DC B 12 8.543 1.930 21.312 1.00 6.18 N
ATOM 260 C4 DC B 12 9.009 1.236 20.266 1.00 6.48 C
ATOM 261 N4 DC B 12 9.518 1.926 19.243 1.00 7.43 N
ATOM 262 C5 DC B 12 9.012 -0.198 20.248 1.00 6.83 C
ATOM 263 C6 DC B 12 8.502 -0.825 21.311 1.00 6.80 C
"""
identical_portions = [
"""\
Histogram of bond lengths:
1.23 - 1.31: 5
1.31 - 1.39: 25
1.39 - 1.46: 27
1.46 - 1.54: 25
1.54 - 1.61: 5
Bond restraints: 87""",
"""\
Histogram of bond angle deviations from ideal:
99.49 - 105.87: 23
105.87 - 112.26: 36
112.26 - 118.65: 28
118.65 - 125.04: 30
125.04 - 131.42: 13
Bond angle restraints: 130"""
]
open("tst_cctbx_geometry_restraints_2_na.pdb", "w").write(pdb_str_1dpl_cutted)
out1 = StringIO()
out2 = StringIO()
from mmtbx.monomer_library.server import MonomerLibraryServerError
try:
processed_pdb_file = pdb_interpretation.run(
args=["tst_cctbx_geometry_restraints_2_na.pdb"],
strict_conflict_handling=False,
log=out1)
except MonomerLibraryServerError:
print "Skipping exercise_na_restraints_output_to_geo(): Encountered MonomerLibraryServerError.\n"
print "Is the CCP4 monomer library installed and made available through environment variables MMTBX_CCP4_MONOMER_LIB or CLIBD_MON?"
return
geo1 = processed_pdb_file.geometry_restraints_manager()
hbp = geo1.get_n_hbond_proxies()
from mmtbx import monomer_library
params = monomer_library.pdb_interpretation.master_params.extract()
params.secondary_structure.enabled=True
processed_pdb_file = pdb_interpretation.run(
args=["tst_cctbx_geometry_restraints_2_na.pdb"],
params=params,
strict_conflict_handling=False,
log=out2)
geo2 = processed_pdb_file.geometry_restraints_manager()
hbp = geo2.get_n_hbond_proxies()
v_out1 = out1.getvalue()
v_out2 = out2.getvalue()
assert v_out2.find("""\
Restraints generated for nucleic acids:
6 hydrogen bonds
12 hydrogen bond angles
0 basepair planarities
2 basepair parallelities
2 stacking parallelities""") > 0
for v in [v_out1, v_out2]:
for portion in identical_portions:
if not v.find(portion) > 0:
print "This portion was not found:\n%s\n=====End of portion." % portion
assert 0, "the portion above does not match expected portion."
# check .geo output
geo_identical_portions = ["Bond restraints: 87",
"Bond angle restraints: 130", "Dihedral angle restraints: 33",
"Chirality restraints: 15",
"Planarity restraints: 4"]
ss_geo_portions = ["Bond-like restraints: 6",
"Noncovalent bond angle restraints: 12", "Parallelity restraints: 4",
"Nonbonded interactions: 504"]
non_ss_geo_portions = ["Bond-like restraints: 0",
"Noncovalent bond angle restraints: 0", "Parallelity restraints: 0",
"Nonbonded interactions: 526"]
acp = processed_pdb_file.all_chain_proxies
sites_cart = acp.sites_cart_exact()
site_labels = [atom.id_str() for atom in acp.pdb_atoms]
geo_out1 = StringIO()
geo_out2 = StringIO()
geo1.show_sorted(sites_cart=sites_cart, site_labels=site_labels, f=geo_out1)
geo2.show_sorted(sites_cart=sites_cart, site_labels=site_labels, f=geo_out2)
v_geo_out_noss = geo_out1.getvalue()
v_geo_out_ss = geo_out2.getvalue()
for portion in geo_identical_portions+ss_geo_portions:
assert v_geo_out_ss.find(portion) >= 0
for portion in geo_identical_portions+non_ss_geo_portions:
assert v_geo_out_noss.find(portion) >= 0
def run(args, out=None):
"""
Calculates number of non-bonded atoms overlaps in a model
prints to log:
When verbose=True the function print detailed results to log
When verbose=False it will print:
nb_overlaps_macro_molecule,
nb_overlaps_due_to_sym_op,
nb_overlaps_all
Args:
args (list): list of options.
model=input_file input PDB file
cif=input_file input CIF file for additional model information
keep_hydrogens=True keep input hydrogen files (otherwise regenerate)
nuclear=False use nuclear x-H distances and vdW radii
verbose=True verbose text output
time_limit=120 Time limit (sec) for Reduce optimization
show_overlap_type=all what type of overlaps to show
show_normalized_nbo=False Show non-bonded overlaps per 1000 atoms
substitute_non_crystallographic_unit_cell_if_necessary=false
fix CRYST1 records if needed
out : where to wrote the output to.
Returns:
nb_overlaps (obj): Object containing overlap and overlap per thousand
atoms information
"""
if not out: out = sys.stdout
if not args:
print >> out, usage_string
return None
cmdline = iotbx.phil.process_command_line_with_files(
args=args,
master_phil_string=master_phil_str,
pdb_file_def="model",
cif_file_def="cif",
usage_string=usage_string)
params = cmdline.work.extract()
if (params.model is None):
raise Usage(usage_string)
pdb_file_name = [x for x in args if x.endswith('.pdb')]
cif_file_name = [x for x in args if x.endswith('.cif')]
assert pdb_file_name
pdb_file_name = pdb_file_name[0]
if not params.skip_hydrogen_test:
pdb_with_h, h_were_added = mvc.check_and_add_hydrogen(
file_name=pdb_file_name,
model_number=0,
nuclear=params.nuclear,
verbose=params.verbose,
time_limit=params.time_limit,
keep_hydrogens=params.keep_hydrogens,
allow_multiple_models=False,
log=out)
if h_were_added:
pdb_file_name = pdb_file_name.replace('.pdb', '_with_h.pdb')
open(pdb_file_name, 'w').write(pdb_with_h)
files = [pdb_file_name]
if cif_file_name:
files += cif_file_name
pdb_processed_file = pdb_inter.run(
args=files,
assume_hydrogens_all_missing=False,
hard_minimum_nonbonded_distance=0.0,
nonbonded_distance_threshold=None,
substitute_non_crystallographic_unit_cell_if_necessary=params.
substitute_non_crystallographic_unit_cell_if_necessary,
log=null_out())
# test that CRYST1 records are ok
sps = pdb_processed_file.all_chain_proxies.special_position_settings
if not sps:
msg = 'None valid CRSYT1 records.\n'
msg += 'Consider running mmtbx.nonbonded_overlaps with the option:\n'
msg += 'substitute_non_crystallographic_unit_cell_if_necessary=true'
raise Sorry(msg)
grm = pdb_processed_file.geometry_restraints_manager()
xrs = pdb_processed_file.xray_structure()
sites_cart = xrs.sites_cart()
site_labels = xrs.scatterers().extract_labels()
hd_sel = xrs.hd_selection()
macro_mol_sel = nbo.get_macro_mol_sel(pdb_processed_file)
nb_overlaps = nbo.info(geometry_restraints_manager=grm,
macro_molecule_selection=macro_mol_sel,
sites_cart=sites_cart,
site_labels=site_labels,
hd_sel=hd_sel)
if params.verbose:
nb_overlaps.show(log=out,
nbo_type=params.show_overlap_type,
normalized_nbo=params.show_normalized_nbo)
else:
all = nb_overlaps.result.nb_overlaps_all
macro_molecule = nb_overlaps.result.nb_overlaps_macro_molecule
sym = nb_overlaps.result.nb_overlaps_due_to_sym_op
out_list = map(lambda x: str(round(x, 2)), [macro_molecule, sym, all])
print >> out, ', '.join(out_list)
return nb_overlaps
def run_test(params, pdb_files, other_files, callback=None, log=None):
if (log is None): log = sys.stdout
if (params.random_seed is not None):
random.seed(params.random_seed)
flex.set_random_seed(value=params.random_seed)
#
if (len(pdb_files) != 0):
print >> log, "PDB files:"
for file_name in pdb_files:
print >> log, " ", file_name
print >> log
if (len(other_files) != 0):
print >> log, "Other files:"
for file_name in other_files:
print >> log, " ", file_name
print >> log
#
assert len(pdb_files) in [1, 2]
#
pdb_interpretation_params = pdb_interpretation.master_params.extract()
pdb_interpretation_params.dihedral_function_type \
= params.dihedral_function_type
processed_pdb_files = pdb_interpretation.run(
args=pdb_files[-1:]+other_files,
params=pdb_interpretation_params,
strict_conflict_handling=False,
substitute_non_crystallographic_unit_cell_if_necessary=True,
return_all_processed_pdb_files=True,
log=log)
assert len(processed_pdb_files) == 1
print >> log
#
xs = processed_pdb_files[0].xray_structure()
geo_manager = processed_pdb_files[0].geometry_restraints_manager()
labels = [sc.label for sc in xs.scatterers()]
ideal_sites_cart = xs.sites_cart()
sites = ideal_sites_cart
masses = xs.atomic_weights()
tardy_tree_simple_connectivity = geo_manager.construct_tardy_tree(sites=sites)
rmsd_calculator = tardy_tree_simple_connectivity.rmsd_calculator()
#
if (params.tardy_displacements is not None):
def get_tardy_model_no_potential():
return scitbx.rigid_body.tardy_model(
labels=labels,
sites=sites,
masses=masses,
tardy_tree=tardy_tree_simple_connectivity,
potential_obj=None)
def get_tardy_model_no_density():
tardy_tree = scitbx.graph.tardy_tree.construct(
n_vertices=len(sites), edge_list=[])
tardy_tree.build_tree()
potential_obj = potential_object(
density_map=None,
geo_manager=geo_manager,
reduced_geo_manager=None,
prolsq_repulsion_function_changes=
params.prolsq_repulsion_function_changes,
real_space_gradients_delta=None,
real_space_target_weight=None,
ideal_sites_cart=None)
return scitbx.rigid_body.tardy_model(
labels=labels,
sites=sites,
masses=masses,
tardy_tree=tardy_tree,
potential_obj=potential_obj)
if (params.tardy_displacements is Auto):
auto_params = params.tardy_displacements_auto
target_rmsd = \
params.structure_factors_high_resolution \
* auto_params.rmsd_vs_high_resolution_factor
target_rmsd_tol = \
params.structure_factors_high_resolution \
* auto_params.rmsd_tolerance
assert target_rmsd > 0
assert target_rmsd_tol > 0
print >> log, "Random displacements (%s):" \
% params.tardy_displacements_auto.parameterization
print >> log, " high resolution: %.6g" \
% params.structure_factors_high_resolution
print >> log, " target rmsd: %.6g" % target_rmsd
print >> log, " target rmsd tolerance: %.6g" % target_rmsd_tol
log.flush()
def raise_max_steps_exceeded(var_name, rmsd_history):
msg = [
"tardy_displacements_auto.max_steps exceeded:",
" % -13s rmsd" % var_name]
for var_rmsd in rmsd_history:
msg.append(" %13.6e %13.6e" % var_rmsd)
raise Sorry("\n".join(msg))
if (params.tardy_displacements_auto.parameterization == "cartesian"):
multiplier = 1.5
rmsd_history = []
for i_step in xrange(auto_params.max_steps):
sites = cartesian_random_displacements(
sites_cart=ideal_sites_cart,
target_rmsd=target_rmsd*multiplier)
tardy_model = get_tardy_model_no_density()
tardy_model.minimization(max_iterations=20)
sites = tardy_model.sites_moved()
sites_moved = sites
rmsd = rmsd_calculator(sites_moved, ideal_sites_cart)
rmsd_history.append((multiplier, rmsd))
print >> log, " multiplier, rmsd: %13.6e, %13.6e" \
% rmsd_history[-1]
log.flush()
if (rmsd < target_rmsd - target_rmsd_tol):
if (rmsd != 0):
multiplier = min(
multiplier*2, max(
multiplier*1.2,
target_rmsd / rmsd))
else:
multiplier *= 2
else:
if (rmsd <= target_rmsd + target_rmsd_tol):
tardy_model.minimization(max_iterations=500)
sites = tardy_model.sites_moved()
sites_moved = sites
rmsd = rmsd_calculator(sites_moved, ideal_sites_cart)
rmsd_history.append((0, rmsd))
print >> log, " multiplier, rmsd: %13.6e, %13.6e" \
% rmsd_history[-1]
log.flush()
break
multiplier *= max(0.5, target_rmsd/rmsd)
else:
raise_max_steps_exceeded(
var_name="multiplier", rmsd_history=rmsd_history)
del rmsd_history
print >> log, " actual rmsd: %.6g" % rmsd
print >> log
elif (params.tardy_displacements_auto.parameterization == "constrained"):
tardy_model = get_tardy_model_no_potential()
tardy_model.assign_random_velocities()
delta_t = auto_params.first_delta_t
rmsd_history = []
assert auto_params.max_steps > 0
for i_step in xrange(auto_params.max_steps):
prev_q = tardy_model.pack_q()
prev_qd = tardy_model.pack_qd()
tardy_model.dynamics_step(delta_t=delta_t)
sites_moved = tardy_model.sites_moved()
rmsd = rmsd_calculator(sites_moved, ideal_sites_cart)
rmsd_history.append((delta_t, rmsd))
if (rmsd < target_rmsd - target_rmsd_tol):
delta_t *= 2 - rmsd / target_rmsd
else:
if (rmsd <= target_rmsd + target_rmsd_tol):
break
tardy_model.unpack_q(q_packed=prev_q)
tardy_model.unpack_qd(qd_packed=prev_qd)
delta_t *= 0.5
prev_q = None
prev_qd = None
else:
raise_max_steps_exceeded(
var_name="delta_t", rmsd_history=rmsd_history)
del rmsd_history
print >> log, " actual rmsd: %.6g" % rmsd
print >> log, " tardy_displacements=%s" % ",".join(
["%.6g" % v for v in tardy_model.pack_q()])
print >> log
sites = tardy_model.sites_moved()
else:
raise AssertionError
else:
tardy_model = get_tardy_model_no_potential()
q = tardy_model.pack_q()
if (len(params.tardy_displacements) != len(q)):
print >> log, "tardy_displacements:", params.tardy_displacements
hinge_edges = tardy_model.tardy_tree.cluster_manager.hinge_edges
assert len(hinge_edges) == tardy_model.bodies_size()
dofej = tardy_model.degrees_of_freedom_each_joint()
qsej = tardy_model.q_size_each_joint()
for ib,(i,j) in enumerate(hinge_edges):
if (i == -1): si = "root"
else: si = tardy_model.labels[i]
sj = tardy_model.labels[j]
print >> log, "%21s - %-21s: %d dof, %d q_size" % (
si, sj, dofej[ib], qsej[ib])
print >> log, "Zero displacements:"
print >> log, " tardy_displacements=%s" % ",".join(
[str(v) for v in q])
raise Sorry("Incompatible tardy_displacements.")
tardy_model.unpack_q(q_packed=flex.double(params.tardy_displacements))
sites = tardy_model.sites_moved()
#
if (params.emulate_cartesian):
tardy_tree = scitbx.graph.tardy_tree.construct(
n_vertices=len(sites), edge_list=[])
tardy_tree.build_tree()
else:
tardy_tree = tardy_tree_simple_connectivity
print >> log, "tardy_tree summary:"
tardy_tree.show_summary(vertex_labels=labels, out=log, prefix=" ")
print >> log
#
if (len(pdb_files) == 2):
ideal_pdb_inp = iotbx.pdb.input(file_name=pdb_files[0])
ideal_pdb_hierarchy = ideal_pdb_inp.construct_hierarchy()
assert ideal_pdb_hierarchy.is_similar_hierarchy(
processed_pdb_files[0].all_chain_proxies.pdb_hierarchy)
ideal_sites_cart = ideal_pdb_hierarchy.atoms().extract_xyz()
xs.set_sites_cart(sites_cart=ideal_sites_cart)
fft_map = xs.structure_factors(
d_min=params.structure_factors_high_resolution).f_calc().fft_map()
fft_map.apply_sigma_scaling()
#
assert not params.orca_experiments or not params.emulate_cartesian
if (params.orca_experiments):
from mmtbx.refinement import orca
x = orca.expand(
labels=labels,
sites_cart=sites,
masses=masses,
geo_manager=geo_manager)
labels = x.labels
sites = x.sites_cart
masses = x.masses
geo_manager = x.geo_manager
tardy_tree = x.tardy_tree
x_ideal_sites_cart = flex.vec3_double()
for i_orc,i_seq in x.indices:
x_ideal_sites_cart.append(ideal_sites_cart[i_seq])
ideal_sites_cart = x_ideal_sites_cart
rmsd_calculator = x.rmsd_calculator(
tardy_tree_rmsd_calculator=rmsd_calculator)
#
if (params.emulate_cartesian or params.keep_all_restraints):
reduced_geo_manager = None
else:
reduced_geo_manager = geo_manager.reduce_for_tardy(tardy_tree=tardy_tree)
real_space_gradients_delta = \
params.structure_factors_high_resolution \
* params.real_space_gradients_delta_resolution_factor
potential_obj = potential_object(
density_map=fft_map.real_map(),
geo_manager=geo_manager,
reduced_geo_manager=reduced_geo_manager,
prolsq_repulsion_function_changes=params.prolsq_repulsion_function_changes,
real_space_gradients_delta=real_space_gradients_delta,
real_space_target_weight=params.real_space_target_weight,
ideal_sites_cart=ideal_sites_cart,
site_labels=labels,
orca_experiments=params.orca_experiments)
tardy_model = scitbx.rigid_body.tardy_model(
labels=labels,
sites=sites,
masses=masses,
tardy_tree=tardy_tree,
potential_obj=potential_obj)
mmtbx.refinement.tardy.action(
tardy_model=tardy_model,
params=params,
rmsd_calculator=rmsd_calculator,
callback=callback,
log=log)
print >> log
def run (args, viewer_class=selection_editor_mixin) :
import cStringIO
pdb_files = []
cif_files = []
show_ss_restraints = False
fast_connectivity = True
for arg in args :
if os.path.isfile(arg) :
import iotbx.pdb
if iotbx.pdb.is_pdb_file(arg) :
pdb_files.append(os.path.abspath(arg))
elif arg.endswith(".cif") :
cif_files.append(os.path.abspath(arg))
elif arg == "--ss" :
show_ss_restraints = True
elif arg in ["--thorough", "--slow", "--use_monomer_library"] :
fast_connectivity = False
if len(pdb_files) == 0 :
print "Please specify a PDB file (and optional CIFs) on the command line."
return
a = App(viewer_class=viewer_class)
a.frame.Show()
out = sys.stdout
if not "--debug" in args :
out = cStringIO.StringIO()
for file_name in pdb_files :
print "Reading PDB file %s" % file_name
from iotbx import file_reader
from mmtbx.monomer_library import pdb_interpretation
from mmtbx import secondary_structure
t1 = time.time()
if fast_connectivity :
pdb_in = file_reader.any_file(file_name, force_type="pdb")
pdb_hierarchy = pdb_in.file_object.hierarchy
atomic_bonds = pdb_hierarchy.distance_based_simple_two_way_bond_sets()
acp_selection = None
else :
processed_pdb_file = pdb_interpretation.run(args=[file_name]+cif_files,
log=out)
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
pdb_hierarchy.atoms().reset_i_seq()
grm = processed_pdb_file.geometry_restraints_manager()
acp_selection = processed_pdb_file.all_chain_proxies.selection
if grm is None or grm.shell_sym_tables is None :
raise Sorry("Atomic bonds could not be calculated for this model. "+
"This is probably due to a missing CRYST1 record in the PDB file.")
atomic_bonds = grm.shell_sym_tables[0].full_simple_connectivity()
t2 = time.time()
print "%.2fs" % (t2-t1)
a.view_objects.add_model(file_name, pdb_hierarchy, atomic_bonds,
mmtbx_selection_function=acp_selection)
sec_str = secondary_structure.manager(
pdb_hierarchy=pdb_hierarchy,
xray_structure=None)
a.view_objects.set_sec_str(file_name, sec_str.selections_as_ints())
if show_ss_restraints and acp_selection is not None :
bonds_table = secondary_structure.process_structure(params=None,
processed_pdb_file=processed_pdb_file,
tmp_dir=os.getcwd(),
log=sys.stderr)
a.view_objects.set_noncovalent_bonds(file_name, bonds_table.bonds)
a.view_objects.flag_show_noncovalent_bonds = True
a.view_objects.set_model_base_color([1.0,1.0,1.0], file_name)
a.view_objects.set_color_mode("element")
a.view_objects.force_update(recenter=True)
a.MainLoop()
def exercise () :
from mmtbx.monomer_library import pdb_interpretation
import cStringIO
open("tmp.pdb", "w").write("""\
CRYST1 50.800 50.800 155.300 90.00 90.00 90.00 P 43 21 2 8
ATOM 4 N SER A 1 8.753 29.755 61.685 1.00 49.13
ATOM 5 CA SER A 1 9.242 30.200 62.974 1.00 46.62
ANISOU 5 CA SER A 1 343 490 2719 -45 -169 617
ATOM 6 C SER A 1 10.453 29.500 63.579 1.00 41.99
ATOM 7 O SER A 1 10.593 29.607 64.814 1.00 43.24
ANISOU 7 O SER A 1 343 490 2719 -45 -169 617
ATOM 8 CB SER A 1 8.052 30.189 63.974 1.00 53.00
ATOM 9 OG SER A 1 7.294 31.409 63.930 1.00 57.79
ATOM 10 N ARG A 2 11.360 28.819 62.827 1.00 36.48
ATOM 11 CA ARG A 2 12.548 28.316 63.532 1.00 30.20
ATOM 12 C ARG A 2 13.502 29.501 63.500 1.00 25.54
ATOM 13 O ARG A 2 13.730 30.037 62.407 1.00 23.86
ATOM 14 CB ARG A 2 13.241 27.119 62.861 1.00 27.44
ATOM 15 CG ARG A 2 12.412 25.849 62.964 1.00 23.66
ATOM 16 CD ARG A 2 13.267 24.651 63.266 1.00 23.98
ATOM 17 NE ARG A 2 13.948 24.115 62.135 1.00 22.71
ATOM 18 CZ ARG A 2 15.114 23.487 62.201 1.00 21.38
ATOM 19 NH1 ARG A 2 15.845 23.331 63.301 1.00 19.34
ATOM 20 NH2 ARG A 2 15.575 23.030 61.051 1.00 26.66
ATOM 21 N PRO A 3J 13.947 29.997 64.680 1.00 22.94
ATOM 22 CA PRO A 3J 14.902 31.100 64.827 1.00 20.19
ATOM 23 C PRO A 3J 16.195 30.718 64.086 1.00 18.44
ATOM 24 O PRO A 3J 16.545 29.521 64.086 1.00 19.76
ATOM 25 CB PRO A 3J 15.133 31.218 66.313 1.00 19.17
ATOM 26 CG PRO A 3J 14.065 30.364 66.951 1.00 15.12
ATOM 27 CD PRO A 3J 13.816 29.289 65.966 1.00 19.56
ATOM 28 N AILE A 4 16.953 31.648 63.512 1.00 15.29
ATOM 29 CA AILE A 4 18.243 31.372 62.859 1.00 14.32
ATOM 30 C AILE A 4 19.233 32.112 63.743 1.00 13.54
ATOM 31 O AILE A 4 19.105 33.315 64.009 1.00 11.84
ATOM 32 CB AILE A 4 18.298 31.951 61.406 1.00 13.62
ATOM 33 CG1AILE A 4 17.157 31.300 60.620 1.00 18.39
ATOM 34 CG2AILE A 4 19.661 31.747 60.743 1.00 13.64
ATOM 35 CD1AILE A 4 16.879 32.102 59.355 1.00 16.69
ATOM 28 N BILE A 4 16.953 31.648 63.512 1.00 15.29
ATOM 29 CA BILE A 4 18.243 31.372 62.859 1.00 14.32
ATOM 30 C BILE A 4 19.233 32.112 63.743 1.00 13.54
ATOM 31 O BILE A 4 19.105 33.315 64.009 1.00 11.84
ATOM 32 CB BILE A 4 18.298 31.951 61.406 1.00 13.62
ATOM 33 CG1BILE A 4 17.157 31.300 60.620 1.00 18.39
ATOM 34 CG2BILE A 4 19.661 31.747 60.743 1.00 13.64
ATOM1200035 CD1BILE A 4 16.879 32.102 59.355 1.00 16.69
HETATM 1475 S SO4 S 188 31.424 42.923 60.396 1.00 55.69 S4+
HETATM 1476 O1 SO4 S 188 31.631 41.513 60.336 1.00 59.84 O1-
HETATM 1477 O2 SO4 S 188 32.533 43.699 59.932 1.00 49.98 O1-
HETATM 1478 O3 SO4 S 188 31.128 43.217 61.738 1.00 59.44 O1-
HETATM 1479 O4 SO4 S 188 30.353 43.201 59.539 1.00 60.54 O1-
HETATM 1480 O HOH W 200 29.478 23.354 61.364 1.00 8.67 WATE
END""")
out = cStringIO.StringIO()
processed_pdb_file = pdb_interpretation.run(args=["tmp.pdb"], log=out)
m = mouse_selection_manager()
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
pdb_hierarchy.atoms().reset_i_seq()
m.update_selection_handlers(
pdb_hierarchy=pdb_hierarchy,
mmtbx_selection_function=processed_pdb_file.all_chain_proxies.selection)
assert m.selection_size() == 0
m.apply_selection("chain A")
assert m.selection_size() == 40
m.clear_selection()
m.toggle_chain_selection(5)
assert m.selection_size() == 40
m.toggle_residue_selection(10)
assert m.selection_size() == 29
m.toggle_atom_selection(10) # XXX: doesn't work!
assert m.selection_size() == 29
m.toggle_atom_selection(20)
assert m.selection_size() == 28
from iotbx import pdb
from scitbx.array_family import flex
pdb_hierarchy = pdb.input(source_info=None, lines=flex.split_lines("""\
HETATM 4049 O HOH W 1 2.954 13.042 11.632 1.00 37.53 O
HETATM 4050 O HOH W 2 5.539 14.595 10.951 1.00 31.25 O
HETATM 4051 O HOH W 3 -2.971 14.661 14.669 1.00 38.68 O
HETATM 4052 O HOH W 4 6.281 34.000 7.684 1.00 39.58 O
HETATM 4053 O HOH W 5 16.004 9.039 10.335 1.00 37.31 O
HETATM 4054 O HOH W 6 2.144 5.718 20.447 1.00 49.77 O
HETATM 4055 O HOH W 7 -1.180 10.517 14.630 1.00 32.95 O
HETATM 4056 O AHOH W 8 9.227 8.636 12.535 1.00 32.52 O
HETATM 4056 O BHOH W 8 9.227 8.636 12.535 1.00 32.52 O
HETATM 4057 O AHOH W 9 11.070 -0.570 15.047 1.00 30.24 O
HETATM 4057 O BHOH W 9 11.070 -0.570 15.047 1.00 30.24 O
HETATM 4058 O AHOH W 10 15.630 -6.169 12.853 1.00 31.08 O
HETATM 4058 O BHOH W 10 15.630 -6.169 12.853 1.00 31.08 O
HETATM 4059 O HOH W 11 14.854 -8.299 16.887 1.00 32.65 O
HETATM 4060 O HOH W 12 27.586 0.391 24.184 1.00 31.29 O
HETATM 4061 O HOH W 13 3.240 7.801 38.401 1.00 32.09 O
END""")).construct_hierarchy()
m = mouse_selection_manager()
pdb_hierarchy.atoms().reset_i_seq()
m.update_selection_handlers(pdb_hierarchy=pdb_hierarchy,
mmtbx_selection_function=None)
assert m.selection_size() == 0
m.apply_selection("chain W")
assert m.selection_size() == 16
m.start_range_selection(5)
m.end_range_selection(15, deselect=False, ignore_altloc=True)
assert m.selection_size() == 11
m.start_range_selection(6)
m.end_range_selection(10, deselect=False, ignore_altloc=True)
assert m.selection_size() == 11 # no change because of deselect=False
m.start_range_selection(6)
m.end_range_selection(9, deselect=True, ignore_altloc=True)
assert m.selection_size() == 6
m.start_range_selection(10)
m.end_range_selection(12, deselect=True, ignore_altloc=False)
assert m.selection_size() == 5
print "OK"
def run(args, viewer_class=selection_editor_mixin):
import cStringIO
pdb_files = []
cif_files = []
show_ss_restraints = False
fast_connectivity = True
for arg in args:
if os.path.isfile(arg):
import iotbx.pdb
if iotbx.pdb.is_pdb_file(arg):
pdb_files.append(os.path.abspath(arg))
elif arg.endswith(".cif"):
cif_files.append(os.path.abspath(arg))
elif arg == "--ss":
show_ss_restraints = True
elif arg in ["--thorough", "--slow", "--use_monomer_library"]:
fast_connectivity = False
if len(pdb_files) == 0:
print(
"Please specify a PDB file (and optional CIFs) on the command line."
)
return
a = App(viewer_class=viewer_class)
a.frame.Show()
out = sys.stdout
if not "--debug" in args:
out = cStringIO.StringIO()
for file_name in pdb_files:
print("Reading PDB file %s" % file_name)
from iotbx import file_reader
from mmtbx.monomer_library import pdb_interpretation
from mmtbx import secondary_structure
t1 = time.time()
if fast_connectivity:
pdb_in = file_reader.any_file(file_name, force_type="pdb")
pdb_hierarchy = pdb_in.file_object.hierarchy
atomic_bonds = pdb_hierarchy.distance_based_simple_two_way_bond_sets(
)
acp_selection = None
else:
processed_pdb_file = pdb_interpretation.run(args=[file_name] +
cif_files,
log=out)
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
pdb_hierarchy.atoms().reset_i_seq()
grm = processed_pdb_file.geometry_restraints_manager()
acp_selection = processed_pdb_file.all_chain_proxies.selection
if grm is None or grm.shell_sym_tables is None:
raise Sorry(
"Atomic bonds could not be calculated for this model. " +
"This is probably due to a missing CRYST1 record in the PDB file."
)
atomic_bonds = grm.shell_sym_tables[0].full_simple_connectivity()
t2 = time.time()
print("%.2fs" % (t2 - t1))
a.view_objects.add_model(file_name,
pdb_hierarchy,
atomic_bonds,
mmtbx_selection_function=acp_selection)
sec_str = secondary_structure.manager(pdb_hierarchy=pdb_hierarchy,
xray_structure=None)
a.view_objects.set_sec_str(file_name, sec_str.selections_as_ints())
if show_ss_restraints and acp_selection is not None:
bonds_table = secondary_structure.process_structure(
params=None,
processed_pdb_file=processed_pdb_file,
tmp_dir=os.getcwd(),
log=sys.stderr)
a.view_objects.set_noncovalent_bonds(file_name, bonds_table.bonds)
a.view_objects.flag_show_noncovalent_bonds = True
a.view_objects.set_model_base_color([1.0, 1.0, 1.0], file_name)
a.view_objects.set_color_mode("element")
a.view_objects.force_update(recenter=True)
a.MainLoop()
def exercise_na_restraints_output_to_geo(verbose=False):
for dependency in ("chem_data", "ksdssp"):
if not libtbx.env.has_module(dependency):
print(
"Skipping exercise_na_restraints_output_to_geo(): %s not available"
% (dependency))
return
pdb_str_1dpl_cutted = """\
CRYST1 24.627 42.717 46.906 90.00 90.00 90.00 P 21 21 21 8
ATOM 184 P DG A 9 9.587 13.026 19.037 1.00 6.28 P
ATOM 185 OP1 DG A 9 9.944 14.347 19.602 1.00 8.07 O
ATOM 186 OP2 DG A 9 10.654 12.085 18.639 1.00 8.27 O
ATOM 187 O5' DG A 9 8.717 12.191 20.048 1.00 5.88 O
ATOM 188 C5' DG A 9 7.723 12.833 20.854 1.00 5.45 C
ATOM 189 C4' DG A 9 7.145 11.818 21.807 1.00 5.40 C
ATOM 190 O4' DG A 9 6.435 10.777 21.087 1.00 5.77 O
ATOM 191 C3' DG A 9 8.142 11.036 22.648 1.00 5.10 C
ATOM 192 O3' DG A 9 8.612 11.838 23.723 1.00 5.90 O
ATOM 193 C2' DG A 9 7.300 9.857 23.068 1.00 5.97 C
ATOM 194 C1' DG A 9 6.619 9.536 21.805 1.00 5.97 C
ATOM 195 N9 DG A 9 7.390 8.643 20.931 1.00 5.97 N
ATOM 196 C8 DG A 9 8.074 8.881 19.775 1.00 6.62 C
ATOM 197 N7 DG A 9 8.647 7.820 19.249 1.00 6.57 N
ATOM 198 C5 DG A 9 8.308 6.806 20.141 1.00 6.22 C
ATOM 199 C6 DG A 9 8.620 5.431 20.136 1.00 6.03 C
ATOM 200 O6 DG A 9 9.297 4.803 19.296 1.00 7.21 O
ATOM 201 N1 DG A 9 8.101 4.773 21.247 1.00 6.10 N
ATOM 202 C2 DG A 9 7.365 5.351 22.260 1.00 6.24 C
ATOM 203 N2 DG A 9 6.948 4.569 23.241 1.00 7.88 N
ATOM 204 N3 DG A 9 7.051 6.652 22.257 1.00 6.53 N
ATOM 205 C4 DG A 9 7.539 7.295 21.184 1.00 5.69 C
ATOM 206 P DC A 10 10.081 11.538 24.300 1.00 5.91 P
ATOM 207 OP1 DC A 10 10.273 12.645 25.291 1.00 7.27 O
ATOM 208 OP2 DC A 10 11.063 11.363 23.228 1.00 6.84 O
ATOM 209 O5' DC A 10 9.953 10.128 25.026 1.00 5.75 O
ATOM 210 C5' DC A 10 9.077 9.959 26.149 1.00 5.87 C
ATOM 211 C4' DC A 10 9.188 8.549 26.672 1.00 5.56 C
ATOM 212 O4' DC A 10 8.708 7.612 25.667 1.00 5.70 O
ATOM 213 C3' DC A 10 10.580 8.059 27.007 1.00 5.27 C
ATOM 214 O3' DC A 10 11.010 8.447 28.315 1.00 5.83 O
ATOM 215 C2' DC A 10 10.422 6.549 26.893 1.00 5.34 C
ATOM 216 C1' DC A 10 9.436 6.405 25.754 1.00 5.23 C
ATOM 217 N1 DC A 10 10.113 6.168 24.448 1.00 5.30 N
ATOM 218 C2 DC A 10 10.514 4.871 24.152 1.00 5.28 C
ATOM 219 O2 DC A 10 10.283 3.972 25.000 1.00 5.75 O
ATOM 220 N3 DC A 10 11.131 4.627 22.965 1.00 5.65 N
ATOM 221 C4 DC A 10 11.395 5.628 22.138 1.00 5.80 C
ATOM 222 N4 DC A 10 12.034 5.327 21.005 1.00 6.75 N
ATOM 223 C5 DC A 10 11.029 6.970 22.449 1.00 5.99 C
ATOM 224 C6 DC A 10 10.394 7.203 23.612 1.00 5.56 C
ATOM 226 O5' DG B 11 12.424 -4.393 18.427 1.00 22.70 O
ATOM 227 C5' DG B 11 12.380 -5.516 19.282 1.00 14.75 C
ATOM 228 C4' DG B 11 11.969 -5.112 20.676 1.00 10.42 C
ATOM 229 O4' DG B 11 12.972 -4.192 21.210 1.00 10.51 O
ATOM 230 C3' DG B 11 10.649 -4.394 20.782 1.00 8.57 C
ATOM 231 O3' DG B 11 9.618 -5.363 20.846 1.00 8.69 O
ATOM 232 C2' DG B 11 10.822 -3.597 22.051 1.00 8.63 C
ATOM 233 C1' DG B 11 12.236 -3.233 21.980 1.00 9.81 C
ATOM 234 N9 DG B 11 12.509 -1.902 21.305 1.00 8.66 N
ATOM 235 C8 DG B 11 13.175 -1.667 20.135 1.00 9.57 C
ATOM 236 N7 DG B 11 13.255 -0.407 19.824 1.00 9.04 N
ATOM 237 C5 DG B 11 12.613 0.235 20.869 1.00 7.63 C
ATOM 238 C6 DG B 11 12.388 1.612 21.119 1.00 7.05 C
ATOM 239 O6 DG B 11 12.723 2.590 20.419 1.00 7.81 O
ATOM 240 N1 DG B 11 11.715 1.819 22.317 1.00 6.27 N
ATOM 241 C2 DG B 11 11.264 0.828 23.159 1.00 6.05 C
ATOM 242 N2 DG B 11 10.611 1.219 24.248 1.00 5.85 N
ATOM 243 N3 DG B 11 11.483 -0.457 22.942 1.00 6.55 N
ATOM 244 C4 DG B 11 12.150 -0.687 21.797 1.00 6.84 C
ATOM 245 P DC B 12 8.134 -5.009 20.350 1.00 8.13 P
ATOM 246 OP1 DC B 12 7.367 -6.252 20.459 1.00 10.02 O
ATOM 247 OP2 DC B 12 8.172 -4.307 19.052 1.00 9.79 O
ATOM 248 O5' DC B 12 7.564 -3.912 21.389 1.00 8.18 O
ATOM 249 C5' DC B 12 7.275 -4.296 22.719 1.00 8.00 C
ATOM 250 C4' DC B 12 6.856 -3.057 23.487 1.00 8.01 C
ATOM 251 O4' DC B 12 8.006 -2.146 23.615 1.00 7.35 O
ATOM 252 C3' DC B 12 5.763 -2.208 22.890 1.00 7.04 C
ATOM 253 O3' DC B 12 4.456 -2.800 23.100 1.00 9.82 O
ATOM 254 C2' DC B 12 6.019 -0.916 23.630 1.00 6.50 C
ATOM 255 C1' DC B 12 7.467 -0.808 23.608 1.00 7.35 C
ATOM 256 N1 DC B 12 8.040 -0.143 22.396 1.00 6.64 N
ATOM 257 C2 DC B 12 8.017 1.257 22.382 1.00 5.68 C
ATOM 258 O2 DC B 12 7.524 1.832 23.357 1.00 6.32 O
ATOM 259 N3 DC B 12 8.543 1.930 21.312 1.00 6.18 N
ATOM 260 C4 DC B 12 9.009 1.236 20.266 1.00 6.48 C
ATOM 261 N4 DC B 12 9.518 1.926 19.243 1.00 7.43 N
ATOM 262 C5 DC B 12 9.012 -0.198 20.248 1.00 6.83 C
ATOM 263 C6 DC B 12 8.502 -0.825 21.311 1.00 6.80 C
"""
identical_portions = [
"""\
Histogram of bond lengths:
1.23 - 1.31: 5
1.31 - 1.39: 25
1.39 - 1.46: 27
1.46 - 1.54: 25
1.54 - 1.61: 5
Bond restraints: 87""",
'''\
Histogram of bond angle deviations from ideal:
99.49 - 105.87: 23
105.87 - 112.26: 36
112.26 - 118.65: 28
118.65 - 125.04: 30
125.04 - 131.42: 13
Bond angle restraints: 130''',
]
open("tst_cctbx_geometry_restraints_2_na.pdb",
"w").write(pdb_str_1dpl_cutted)
out1 = StringIO()
out2 = StringIO()
from mmtbx.monomer_library.server import MonomerLibraryServerError
try:
processed_pdb_file = pdb_interpretation.run(
args=["tst_cctbx_geometry_restraints_2_na.pdb"],
strict_conflict_handling=False,
log=out1)
except MonomerLibraryServerError:
print(
"Skipping exercise_na_restraints_output_to_geo(): Encountered MonomerLibraryServerError.\n"
)
print(
"Is the CCP4 monomer library installed and made available through environment variables MMTBX_CCP4_MONOMER_LIB or CLIBD_MON?"
)
return
geo1 = processed_pdb_file.geometry_restraints_manager()
hbp = geo1.get_n_hbond_proxies()
from mmtbx import monomer_library
params = monomer_library.pdb_interpretation.master_params.extract()
params.secondary_structure.enabled = True
processed_pdb_file = pdb_interpretation.run(
args=["tst_cctbx_geometry_restraints_2_na.pdb"],
params=params,
strict_conflict_handling=False,
log=out2)
geo2 = processed_pdb_file.geometry_restraints_manager()
hbp = geo2.get_n_hbond_proxies()
v_out1 = out1.getvalue()
v_out2 = out2.getvalue()
assert v_out2.find("""\
Restraints generated for nucleic acids:
6 hydrogen bonds
12 hydrogen bond angles
0 basepair planarities
2 basepair parallelities
2 stacking parallelities""") > 0
for v in [v_out1, v_out2]:
for portion in identical_portions:
if not v.find(portion) > 0:
print("This portion was not found:\n%s\n=====End of portion." %
portion)
assert 0, "the portion above does not match expected portion."
# check .geo output
geo_identical_portions = [
"Bond restraints: 87", "Bond angle restraints: 130",
"Dihedral angle restraints: 33", "Chirality restraints: 15",
"Planarity restraints: 4"
]
ss_geo_portions = [
"Bond-like restraints: 6",
'Secondary Structure restraints around h-bond angle restraints: 12',
"Parallelity restraints: 4", "Nonbonded interactions: 504"
]
non_ss_geo_portions = [
#"Bond-like restraints: 0",
#'Secondary Structure restraints around h-bond angle restraints: 0',
"Parallelity restraints: 0",
"Nonbonded interactions: 526"
]
acp = processed_pdb_file.all_chain_proxies
sites_cart = acp.sites_cart_exact()
site_labels = [atom.id_str() for atom in acp.pdb_atoms]
geo_out1 = StringIO()
geo_out2 = StringIO()
geo1.show_sorted(sites_cart=sites_cart,
site_labels=site_labels,
f=geo_out1)
geo2.show_sorted(sites_cart=sites_cart,
site_labels=site_labels,
f=geo_out2)
v_geo_out_noss = geo_out1.getvalue()
v_geo_out_ss = geo_out2.getvalue()
for portion in geo_identical_portions + ss_geo_portions:
assert v_geo_out_ss.find(portion) >= 0
for portion in geo_identical_portions + non_ss_geo_portions:
assert v_geo_out_noss.find(portion) >= 0
def run (args, out=None) :
"""
Calculates number of non-bonded atoms overlaps in a model
prints to log:
When verbose=True the function print detailed results to log
When verbose=False it will print:
nb_overlaps_macro_molecule,
nb_overlaps_due_to_sym_op,
nb_overlaps_all
Args:
args (list): list of options.
model=input_file input PDB file
cif=input_file input CIF file for additional model information
keep_hydrogens=True keep input hydrogen files (otherwise regenerate)
nuclear=False use nuclear x-H distances and vdW radii
verbose=True verbose text output
time_limit=120 Time limit (sec) for Reduce optimization
show_overlap_type=all what type of overlaps to show
show_normalized_nbo=False Show non-bonded overlaps per 1000 atoms
substitute_non_crystallographic_unit_cell_if_necessary=false
fix CRYST1 records if needed
out : where to wrote the output to.
Returns:
nb_overlaps (obj): Object containing overlap and overlap per thousand
atoms information
"""
if not out: out = sys.stdout
if not args:
print >> out,usage_string
return None
cmdline = iotbx.phil.process_command_line_with_files(
args=args,
master_phil_string=master_phil_str,
pdb_file_def="model",
cif_file_def="cif",
usage_string=usage_string)
params = cmdline.work.extract()
if (params.model is None) :
raise Usage(usage_string)
pdb_file_name = [x for x in args if x.endswith('.pdb')]
cif_file_name = [x for x in args if x.endswith('.cif')]
assert pdb_file_name
pdb_file_name = pdb_file_name[0]
if not params.skip_hydrogen_test:
pdb_with_h, h_were_added = mvc.check_and_add_hydrogen(
file_name=pdb_file_name,
model_number=0,
nuclear=params.nuclear,
verbose=params.verbose,
time_limit=params.time_limit,
keep_hydrogens=params.keep_hydrogens,
allow_multiple_models=False,
log=out)
if h_were_added:
pdb_file_name = pdb_file_name.replace('.pdb','_with_h.pdb')
open(pdb_file_name,'w').write(pdb_with_h)
files = [pdb_file_name]
if cif_file_name:
files += cif_file_name
pdb_processed_file = pdb_inter.run(
args=files,
assume_hydrogens_all_missing=False,
hard_minimum_nonbonded_distance=0.0,
nonbonded_distance_threshold=None,
substitute_non_crystallographic_unit_cell_if_necessary=
params.substitute_non_crystallographic_unit_cell_if_necessary,
log=null_out() )
# test that CRYST1 records are ok
sps = pdb_processed_file.all_chain_proxies.special_position_settings
if not sps:
msg = 'None valid CRSYT1 records.\n'
msg += 'Consider running phenix.clashscore with the option:\n'
msg += 'substitute_non_crystallographic_unit_cell_if_necessary=true'
raise Sorry(msg)
grm = pdb_processed_file.geometry_restraints_manager()
xrs = pdb_processed_file.xray_structure()
sites_cart = xrs.sites_cart()
site_labels = xrs.scatterers().extract_labels()
hd_sel = xrs.hd_selection()
macro_mol_sel = nbo.get_macro_mol_sel(pdb_processed_file)
nb_overlaps = nbo.info(
geometry_restraints_manager=grm,
macro_molecule_selection=macro_mol_sel,
sites_cart=sites_cart,
site_labels=site_labels,
hd_sel=hd_sel)
if params.verbose:
nb_overlaps.show(
log=out,
nbo_type=params.show_overlap_type,
normalized_nbo=params.show_normalized_nbo)
else:
all = nb_overlaps.result.nb_overlaps_all
macro_molecule = nb_overlaps.result.nb_overlaps_macro_molecule
sym = nb_overlaps.result.nb_overlaps_due_to_sym_op
out_list = map(lambda x: str(round(x,2)),[macro_molecule,sym,all])
print >> out,', '.join(out_list)
return nb_overlaps