def exercise_bond_over_symmetry(mon_lib_srv, ener_lib):
from cctbx.geometry_restraints.linking_class import linking_class
origin_ids = linking_class()
pdb_inp = iotbx.pdb.input(source_info=None, lines=raw_records9)
params = mmtbx.model.manager.get_default_pdb_interpretation_params()
params.pdb_interpretation.restraints_library.mcl = False
model = mmtbx.model.manager(model_input=pdb_inp,
pdb_interpretation_params=params,
log=null_out(),
build_grm=True)
grm = model.get_restraints_manager().geometry
simple, asu = grm.get_all_bond_proxies()
assert (simple.size(), asu.size()) == (29, 0)
h = model.get_hierarchy()
proxy = geometry_restraints.bond_simple_proxy(
i_seqs=(32, 4),
distance_ideal=2.9,
weight=400,
origin_id=origin_ids.get_origin_id('hydrogen bonds'))
proxy2 = geometry_restraints.bond_simple_proxy(
i_seqs=(32, 24),
distance_ideal=2.9,
weight=400,
origin_id=origin_ids.get_origin_id('hydrogen bonds'))
grm.add_new_bond_restraints_in_place(proxies=[proxy, proxy2],
sites_cart=h.atoms().extract_xyz())
simple, asu = grm.get_all_bond_proxies()
assert (simple.size(), asu.size()) == (30, 2)
sites_cart = h.atoms().extract_xyz()
site_labels = model.get_xray_structure().scatterers().extract_labels()
pair_proxies = grm.pair_proxies(flags=None, sites_cart=sites_cart)
out = StringIO()
pair_proxies.bond_proxies.show_sorted(by_value="residual",
sites_cart=sites_cart,
site_labels=site_labels,
f=out,
prefix="")
outtxt = out.getvalue()
# print(outtxt)
#
# Not clear why ZN-NE2 bond adds as 2 bonds.
assert_lines_in_text(
outtxt, """\
bond pdb="ZN ZN A 8 "
pdb=" NE2 HIS B 304 "
ideal model delta sigma weight residual sym.op.
2.900 2.969 -0.069 5.00e-02 4.00e+02 1.92e+00 -x-1/2,y+1/2,-z+3/4
""")
assert_lines_in_text(
outtxt, """\
bond pdb=" NE2 HIS B 304 "
pdb="ZN ZN A 8 "
ideal model delta sigma weight residual sym.op.
2.900 2.969 -0.069 5.00e-02 4.00e+02 1.92e+00 -x-1/2,y-1/2,-z+3/4
""")
def check_cmd_line():
cmd = "mmtbx.rama_z %s" % fname
r = easy_run.fully_buffered(cmd)
stdout = r.stdout_lines
# print ("\n".join(stdout))
assert_lines_in_text("\n".join(stdout), """\
whole: -0.40 (0.66), residues: 134
helix: None (None), residues: 0
sheet: -0.06 (0.58), residues: 63
loop : -0.36 (0.69), residues: 71""")
def check_cmd_line_cryst1(prefix="tst_rama_z_01_cryst1"):
with open(fname, 'r') as f:
pdbtext = f.read()
with open(prefix + '.pdb', 'w') as f:
f.write(cryst1)
f.write(pdbtext)
cmd = "mmtbx.rama_z %s" % (prefix + '.pdb')
r = easy_run.fully_buffered(cmd)
assert r.return_code == 0
stdout = r.stdout_lines
# print ("\n".join(stdout))
assert_lines_in_text(
"\n".join(stdout), """\
whole: -0.40 (0.66), residues: 134
helix: None (None), residues: 0
sheet: -0.06 (0.58), residues: 63
loop : -0.36 (0.69), residues: 71""")
def test_1():
inp = iotbx.pdb.input(source_info=None, lines=pdb_str_0)
model = mmtbx.model.manager(model_input=inp)
model.expand_with_BIOMT_records()
model = shift_and_box_model(model)
sel = model.selection("chain '0' or chain 'C' or chain 'F' or chain 'I' or chain 'L' or chain 'O' or chain 'R' or chain 'U' or chain 'X'")
model = model.select(sel)
model.search_for_ncs()
model.setup_ncs_constraints_groups(filter_groups=True)
n1 = model.get_number_of_atoms()
assert n1 == 648, n1
assert model.ncs_constraints_present()
nrgl = model.get_ncs_groups()
assert len(nrgl[0].master_iselection) == 72
assert len(nrgl[0].copies) == 8
# nrgl._show()
# print (model.can_be_unique_with_biomt())
cif_txt = model.model_as_mmcif(try_unique_with_biomt=True)
# print (cif_txt)
assert_lines_in_text(cif_txt, """
loop_
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
_pdbx_struct_assembly_gen.asym_id_list
1 (1-9) A""")
assert_lines_in_text(cif_txt, """
loop_
_pdbx_struct_assembly.id
_pdbx_struct_assembly.details
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
1 'Symmetry assembly' ? ? ? """)
assert_lines_in_text(cif_txt, """
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'point symmetry operation' ? ? 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0""")
inp = iotbx.pdb.input(source_info=None, lines=cif_txt)
m2 = mmtbx.model.manager(model_input=inp)
n2_1 = m2.get_number_of_atoms()
assert n2_1 == 72
m2.expand_with_BIOMT_records()
n2_2 = m2.get_number_of_atoms()
# print (n1, n2)
assert n1 == n2_2, "%d, %d" % (n1, n2)
def exercise_bond_over_symmetry_2(mon_lib_srv, ener_lib):
""" This test is to illustrate that bond over symmetry actually
adds 2 proxies.
"""
from cctbx.geometry_restraints.linking_class import linking_class
origin_ids = linking_class()
pdb_inp = iotbx.pdb.input(source_info=None, lines=raw_records10)
params = mmtbx.model.manager.get_default_pdb_interpretation_params()
params.pdb_interpretation.restraints_library.mcl = False
model = mmtbx.model.manager(model_input=pdb_inp,
pdb_interpretation_params=params,
log=null_out(),
build_grm=True)
grm = model.get_restraints_manager().geometry
simple, asu = grm.get_all_bond_proxies()
assert (simple.size(), asu.size()) == (0, 0)
h = model.get_hierarchy()
sites_cart = h.atoms().extract_xyz()
site_labels = model.get_xray_structure().scatterers().extract_labels()
pair_proxies = grm.pair_proxies(flags=None, sites_cart=sites_cart)
out = StringIO()
pair_proxies.bond_proxies.show_sorted(by_value="residual",
sites_cart=sites_cart,
site_labels=site_labels,
f=out,
prefix="")
outtxt = out.getvalue()
# print(outtxt)
proxy = geometry_restraints.bond_simple_proxy(
i_seqs=(0, 1),
distance_ideal=2.9,
weight=400,
origin_id=origin_ids.get_origin_id('hydrogen bonds'))
grm.add_new_bond_restraints_in_place(proxies=[proxy],
sites_cart=h.atoms().extract_xyz())
simple, asu = grm.get_all_bond_proxies()
# print(simple.size(), asu.size())
assert (simple.size(), asu.size()) == (0, 2)
sites_cart = h.atoms().extract_xyz()
site_labels = model.get_xray_structure().scatterers().extract_labels()
pair_proxies = grm.pair_proxies(flags=None, sites_cart=sites_cart)
out = StringIO()
pair_proxies.bond_proxies.show_sorted(by_value="residual",
sites_cart=sites_cart,
site_labels=site_labels,
f=out,
prefix="")
outtxt = out.getvalue()
# print(outtxt)
assert_lines_in_text(
outtxt, """\
bond pdb=" CA HIS A 2 "
pdb=" N MET A 1 "
ideal model delta sigma weight residual sym.op.
2.900 1.998 0.902 5.00e-02 4.00e+02 3.25e+02 x,y+1,z
bond pdb=" N MET A 1 "
pdb=" CA HIS A 2 "
ideal model delta sigma weight residual sym.op.
2.900 1.998 0.902 5.00e-02 4.00e+02 3.25e+02 x,y-1,z
""")
es = grm.energies_sites(sites_cart=sites_cart, compute_gradients=True)
out = StringIO()
es.show(f=out)
outtxt = out.getvalue()
# print(outtxt)
# do for x coordinate
# ATOM 1 N MET A 1 9.821 1.568 5.000 1.00 66.07 N
# ATOM 2 CA HIS A 2 9.946 12.171 5.357 1.00 66.55 C
# calculation is from geometry_restraints/bond.h: gradient_0()
# weight * 2 * delta_slack * d_distance_d_site_0(epsilon);
# print("X gradient:", 400*2*0.902*(9.946-9.821)) # 90
# Note that n=2 but residual sum is 325.349. 349 is chopped off in rounding in
# cctbx/geometry_restraints/__init__py, def _bond_show_sorted_impl(...)
# where %6.2e is used. in cctbx/geometry_restraints/energies.py: def show()
# %.6g is used which is showing more numbers.
assert_lines_in_text(outtxt, """\
bond_residual_sum (n=2): 325.349""")
# print("Gradients:", list(es.gradients))
# Seems that gradients were splitted in half (note the X gradient is 90 8 lines above)
assert approx_equal(
list(es.gradients),
[(45.135801792665134, -708.451544937652, 128.90784991984805),
(-45.13580179266516, 708.4515449376522, -128.90784991984813)])
def exercise_add_when_restraint_is_present():
"""
Trying to 'add' values for existing covalent
"""
edits = """
geometry_restraints.edits {
excessive_bond_distance_limit = 10
bond {
action = *add delete change
atom_selection_1 = name N
atom_selection_2 = name CA
symmetry_operation = None
distance_ideal = 4
sigma = 0.5
slack = None
}
angle {
action = *add delete change
atom_selection_1 = name N
atom_selection_2 = name CA
atom_selection_3 = name C
angle_ideal = 130
sigma = 3
}
dihedral {
action = *add delete change
atom_selection_1 = name N
atom_selection_2 = name CA
atom_selection_3 = name CB
atom_selection_4 = name CG
angle_ideal = 90
sigma = 10
periodicity = 1
}
}
"""
def_params = mmtbx.model.manager.get_default_pdb_interpretation_scope()
edits_phil = iotbx.phil.parse(edits)
working_phil = def_params.fetch(edits_phil)
params = working_phil.extract()
inp = iotbx.pdb.input(lines=raw_records1, source_info=None)
model = mmtbx.model.manager(model_input=inp)
geo = model.restraints_as_geo(force=True)
print(geo)
assert_lines_in_text(geo, """Bond restraints: 8""")
assert_lines_in_text(
geo, """bond pdb=" N LYS A 135 "
pdb=" CA LYS A 135 "
ideal model delta sigma weight residual
1.458 1.477 -0.019 1.90e-02 2.77e+03 1.01e+00""")
assert_lines_in_text(
geo, """angle pdb=" N LYS A 135 "
pdb=" CA LYS A 135 "
pdb=" C LYS A 135 "
ideal model delta sigma weight residual
111.00 107.25 3.75 2.80e+00 1.28e-01 1.79e+00""")
assert_lines_in_text(
geo, """dihedral pdb=" N LYS A 135 "
pdb=" CA LYS A 135 "
pdb=" CB LYS A 135 "
pdb=" CG LYS A 135 "
ideal model delta sinusoidal sigma weight residual
-60.00 -54.19 -5.81 3 1.50e+01 4.44e-03 2.18e-01""")
# Now with modifications
print("*" * 80)
model2 = mmtbx.model.manager(model_input=inp,
pdb_interpretation_params=params)
geo2 = model2.restraints_as_geo(force=True)
print(geo2)
# !!! Note that bond-restraint was applied: one less standard, one more
# nonstandard.
assert_lines_in_text(geo2, """Bond restraints: 7""")
assert_lines_in_text(
geo2, """User supplied restraints: 1
Sorted by residual:
bond pdb=" N LYS A 135 "
pdb=" CA LYS A 135 "
ideal model delta sigma weight residual
4.000 1.477 2.523 5.00e-01 4.00e+00 2.55e+01""")
#
# Angles and dihedrals were not changed...
assert_lines_in_text(
geo2, """angle pdb=" N LYS A 135 "
pdb=" CA LYS A 135 "
pdb=" C LYS A 135 "
ideal model delta sigma weight residual
111.00 107.25 3.75 2.80e+00 1.28e-01 1.79e+00""")
assert_lines_in_text(
geo2, """dihedral pdb=" N LYS A 135 "
pdb=" CA LYS A 135 "
pdb=" CB LYS A 135 "
pdb=" CG LYS A 135 "
ideal model delta sinusoidal sigma weight residual
-60.00 -54.19 -5.81 3 1.50e+01 4.44e-03 2.18e-01""")
