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 exercise_2():
"""
Same as 1 but automatic NCS search procedure does not match short chains,
in this case chains B,C, so they left out of NCS.
Not clear if we should utilize MTRIX instead of searching for NCS
because currently we don't output them and in consecutive runs NCS
search would be utilized anyway, potentially yelding different groups.
"""
inp = iotbx.pdb.input(source_info=None, lines=pdb_str_2)
pdb_int_params = mmtbx.model.manager.get_default_pdb_interpretation_params(
)
pdb_int_params.pdb_interpretation.ncs_search.enabled = True
model = mmtbx.model.manager(model_input=inp,
pdb_interpretation_params=pdb_int_params,
process_input=True,
log=null_out())
# model.get_xray_structure()
ss = model.get_ss_annotation()
assert ss.get_n_helices() == 3
assert ss.get_n_sheets() == 3
assert not model.ncs_constraints_present()
assert model.get_ncs_obj() is not None
model.setup_ncs_constraints_groups()
# print model.get_ncs_obj()
assert model.ncs_constraints_present()
assert model.get_master_hierarchy().atoms_size() == 15
# print model.get_master_hierarchy().as_pdb_string()
assert list(model.get_master_selection()).count(True) == 15
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_1():
inp = iotbx.pdb.input(source_info=None, lines=pdb_str_1)
model = mmtbx.model.manager(
model_input = inp,
log = null_out())
assert model.get_number_of_atoms() == 21
assert model.get_hierarchy().atoms_size() == 21
assert model.get_xray_structure().scatterers().size() == 21
ss = model.get_ss_annotation()
# print ss.as_pdb_str()
# STOP()
assert ss.get_n_helices() == 3
# because the second strand contains chain B which is not in ATOM records
# whole sheet got discarded.
assert ss.get_n_sheets() == 0
rm = model.get_restraints_manager()
assert rm.geometry.pair_proxies().bond_proxies.simple.size() == 6
# since No NCS was set, these functions return the whole thing and no
# master selection
assert model.get_master_hierarchy().atoms_size() == 21
assert model.get_master_selection().size() == 0
# print model.model_as_pdb()
# print "="*40
# Here we set NCS constraints
inp = iotbx.pdb.input(source_info=None, lines=pdb_str_1)
pdb_int_params = mmtbx.model.manager.get_default_pdb_interpretation_params()
pdb_int_params.pdb_interpretation.ncs_search.enabled=True
model = mmtbx.model.manager(
model_input = inp,
pdb_interpretation_params = pdb_int_params,
process_input=True,
log = null_out())
# model.get_xray_structure()
assert not model.ncs_constraints_present()
assert model.get_ncs_obj() is not None
model.setup_ncs_constraints_groups()
# print model.get_ncs_obj()
assert model.ncs_constraints_present()
assert model.get_master_hierarchy().atoms_size() == 7
# print model.get_master_hierarchy().as_pdb_string()
# print list(model.get_master_selection())
assert list(model.get_master_selection()).count(True) == 7
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)