def exercise_set_sites_cart_no_ncs():
inp = iotbx.pdb.input(lines=pdb_str_5, source_info=None)
model = mmtbx.model.manager(model_input=inp, expand_with_mtrix=False)
model.search_for_ncs()
nrgl = model.get_ncs_groups()
nrgl._show()
print('n model atoms:', model.get_number_of_atoms())
print('n master atoms:', model.get_master_selection().count(True))
print('n master atoms:', model.get_master_selection().iselection().size())
print('n master atoms:', model.get_master_hierarchy().atoms_size())
assert model.get_master_selection().count(True) ==\
model.get_master_selection().iselection().size() ==\
model.get_master_hierarchy().atoms_size()
h = model.get_hierarchy()
# Warning: here here mh is not deep-copy, therefore when we change atom coords
# they are changing in model.get_hierarchy() as well
mh = model.get_master_hierarchy()
new_sites_cart = flex.vec3_double([(1.0, 1.0, 1.0)] * 42)
mh.atoms().set_xyz(new_sites_cart)
model.set_sites_cart_from_hierarchy(multiply_ncs=True)
h = model.get_hierarchy()
new_xyz = h.atoms().extract_xyz()
# print('h sites:', list(new_xyz))
# checking if setting went as supposed:
for j in range(42):
assert approx_equal(new_xyz[j], (1.0, 1.0, 1.0), eps=1e-4)
def test_2(): 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) model.search_for_ncs() model.setup_ncs_constraints_groups(filter_groups=True) assert model.ncs_constraints_present() assert not model.can_be_unique_with_biomt() assert "" == model.model_as_mmcif(try_unique_with_biomt=True)
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_set_sites_cart_ncs():
"""
No extra atoms
"""
inp = iotbx.pdb.input(lines=pdb_str_5, source_info=None)
model = mmtbx.model.manager(model_input=inp)
model.search_for_ncs()
nrgl = model.get_ncs_groups()
nrgl._show()
print('n model atoms:', model.get_number_of_atoms())
print('n master atoms:', model.get_master_selection().count(True))
print('n master atoms:', model.get_master_selection().iselection().size())
print('n master atoms:', model.get_master_hierarchy().atoms_size())
assert model.get_master_selection().count(True) ==\
model.get_master_selection().iselection().size() ==\
model.get_master_hierarchy().atoms_size()
h = model.get_hierarchy()
# print('h sites:', list(h.atoms().extract_xyz()))
# Warning: here here mh is not deep-copy, therefore when we change atom coords
# they are changing in model.get_hierarchy() as well
mh = model.get_master_hierarchy()
new_sites_cart = flex.vec3_double([(1.0, 1.0, 1.0)] * 42)
mh.atoms().set_xyz(new_sites_cart)
model.set_sites_cart_from_hierarchy(multiply_ncs=True)
h = model.get_hierarchy()
new_xyz = h.atoms().extract_xyz()
# print('h sites:', list(new_xyz))
# checking if setting went as supposed:
assert approx_equal(new_xyz[0], (1.0, 1.0, 1.0), eps=1e-4)
assert approx_equal(
new_xyz[42],
(-0.6420293330506949, 1.2600792663765976, 7.999997229451341),
eps=1e-4)
assert approx_equal(
new_xyz[84],
(-1.396802536808536, -0.22123285934616377, 1.000000038694047),
eps=1e-4)
for i in range(3):
for j in range(42):
assert approx_equal(new_xyz[42 * i + j], new_xyz[42 * i], eps=1e-4)
def exercise_set_sites_cart_ncs_with_extra_atoms():
inp = iotbx.pdb.input(lines=test_pdb_6, source_info=None)
model = mmtbx.model.manager(model_input=inp)
model.search_for_ncs()
nrgl = model.get_ncs_groups()
nrgl._show(brief=False)
print('n model atoms:', model.get_number_of_atoms())
print('n master atoms:', model.get_master_selection().count(True))
print('n master atoms:', model.get_master_selection().iselection().size())
print('n master isel:', list(model.get_master_selection().iselection()))
print('n master atoms:', model.get_master_hierarchy().atoms_size())
print('n master hierarchy:\n',
model.get_master_hierarchy().as_pdb_string())
# Note that "HETATM 32 C2 NDG H" and "HETATM 35 C2 NDG L"
# don't belong to any master/copy
assert not show_diff(
model.get_master_hierarchy().as_pdb_string(), """\
ATOM 1 N ASP H 5 91.286 -31.834 73.572 1.00 77.83 N
ATOM 2 CA ASP H 5 90.511 -32.072 72.317 1.00 78.04 C
ATOM 3 C ASP H 5 90.136 -30.762 71.617 1.00 77.70 C
ATOM 4 O ASP H 5 89.553 -29.857 72.225 1.00 77.56 O
ATOM 5 N THR H 6 91.286 -31.834 73.572 1.00 77.83 N
ATOM 6 CA THR H 6 90.511 -32.072 72.317 1.00 78.04 C
TER
ATOM 7 N GLY I 501 91.286 -31.834 73.572 1.00 77.83 N
ATOM 8 CA GLY I 501 90.511 -32.072 72.317 1.00 78.04 C
ATOM 9 C GLY I 501 90.136 -30.762 71.617 1.00 77.70 C
ATOM 10 O GLY I 501 89.553 -29.857 72.225 1.00 77.56 O
TER
HETATM 31 C1 NDG H 640 91.286 -31.834 73.572 1.00 77.83 C
HETATM 32 C2 NDG H 640 91.286 -31.834 73.572 1.00 77.83 C
HETATM 35 C2 NDG L 646 61.028 -14.273 81.262 1.00 69.80 C
""")
mh = model.get_master_hierarchy()
# Note that atoms outside NCS are getting 2.0 as xyz
new_sites_cart = flex.vec3_double(
[(1.0, 1.0, 1.0), (1.0, 1.0, 1.0), (1.0, 1.0, 1.0), (1.0, 1.0, 1.0),
(1.0, 1.0, 1.0), (1.0, 1.0, 1.0)] + [(3.0, 3.0, 3.0)] * 4 +
[
(1.0, 1.0, 1.0), # <--- Note this atom belongs the first NCS group
(2.0, 2.0, 2.0),
(2.0, 2.0, 2.0)
])
mh.atoms().set_xyz(new_sites_cart)
# print('='*80)
# print (mh.as_pdb_string())
model.set_sites_cart_from_hierarchy(multiply_ncs=True)
h = model.get_hierarchy()
new_xyz = h.atoms().extract_xyz()
# print(model.model_as_pdb())
# print (list(new_xyz))
assert approx_equal(new_xyz[31], (2.0, 2.0, 2.0), eps=1e-4)
assert approx_equal(new_xyz[34], (2.0, 2.0, 2.0), eps=1e-4)
assert approx_equal(new_xyz[0], (1.0, 1.0, 1.0), eps=1e-4)
assert approx_equal(new_xyz[5], (1.0, 1.0, 1.0), eps=1e-4)
assert approx_equal(new_xyz[6], (3.0, 3.0, 3.0), eps=1e-4)
assert approx_equal(new_xyz[9], (3.0, 3.0, 3.0), eps=1e-4)
assert nrgl.check_for_max_rmsd(sites_cart=new_xyz, chain_max_rmsd=0.0)
for i in [[0, 1, 2, 3, 4, 5, 30], [10, 11, 12, 13, 14, 15, 32],
[20, 21, 22, 23, 24, 25, 33]]:
for j in i:
assert approx_equal(new_xyz[j], new_xyz[i[0]], eps=1e-4)
for i in [[6, 7, 8, 9], [16, 17, 18, 19], [26, 27, 28, 29]]:
for j in i:
assert approx_equal(new_xyz[j], new_xyz[i[0]], eps=1e-4)