def test_3():
""" test for command-line tool iotbx.unique_with_biomt"""
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)
pdb_str = model.model_as_pdb()
fname = 'tst_reduce_model_with_biomt_test3.pdb'
with open(fname, 'w') as f:
f.write(pdb_str)
assert os.path.isfile(fname)
cmd = "iotbx.unique_with_biomt %s" % fname
print(cmd)
easy_run.call(cmd)
res_fname = 'tst_reduce_model_with_biomt_test3_unique_biomt_000.cif'
assert_lines_in_file(res_fname, """
ATOM 1 N . LYS 0 151 ? 72.74200 43.65400 193.22800 14.010 14.01000 N ? A ? 1 1""")
assert_lines_in_file(res_fname, """
_pdbx_struct_assembly_gen.asym_id_list
1 (1-9) A""")
cmd = "iotbx.unique_with_biomt %s chain_id_to_leave='C' output.serial=1" % fname
print(cmd)
easy_run.call(cmd)
res_fname = 'tst_reduce_model_with_biomt_test3_unique_biomt_001.cif'
assert_lines_in_file(res_fname, """
ATOM 1 N . LYS C 151 ? 186.74500 185.38200 236.77300 14.010 14.01000 N ? A ? 1 1""")
assert_lines_in_file(res_fname, """
_pdbx_struct_assembly_gen.asym_id_list
1 (1-9) A""")
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 run(args):
assert len(args) == 1
# Read file into pdb_input class
inp = iotbx.pdb.input(file_name=args[0])
# create a model manager
# Catch Sorry about MTRIX here.
model = mmtbx.model.manager(
model_input=inp,
restraint_objects=
None, # these are ligands if any [('fname', cif_object), ()]
log=null_out(),
)
print("=" * 80)
print("number of atoms with MTRIX multiplication:",
model.get_number_of_atoms())
show_ss_counts(model)
# Expand with BIOMT if needed. MTRIX are already expanded by default
# Catch case when both MTRIX and BIOMT present, or other Sorry raised by
# BIOMT handling.
# LIMITATION: this should be done before any selections made on model.manager
double_counter = 0
try:
model.expand_with_BIOMT_records()
except Sorry as e:
if str(e).startswith("Model has been already expanded"):
double_counter += 1
print("=" * 80)
print("number of atoms with BIOMT multiplication:",
model.get_number_of_atoms())
show_ss_counts(model)
# Get default params
pdb_int_params = mmtbx.model.manager.get_default_pdb_interpretation_params(
)
# Set whatever you want
pdb_int_params.pdb_interpretation.secondary_structure.protein.enabled = True
pdb_int_params.pdb_interpretation.ncs_search.enabled = True
pdb_int_params.pdb_interpretation.ncs_search.residue_match_radius = 999
pdb_int_params.pdb_interpretation.clash_guard.nonbonded_distance_threshold = None
#pdb_int_params.pdb_interpretation.nonbonded_weight = None
# set the params. Note, that GRM would be dropped, even if it was already
# constructed. In this example it is not yet constructed.
model.set_pdb_interpretation_params(params=pdb_int_params)
grm = model.get_restraints_manager()
# Not clear which one should be used at the moment
gs = model.geometry_statistics()
gs.show()
# The second way
msi = model.get_model_statistics_info()
msi.show_remark_3()
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_06():
""" Test that when building bio-molecule and then finding NCS relations
from it, we get the same rotation and translation"""
pdb_strings = [pdb_str_4, pdb_str_5]
for method, pdb_string in enumerate(pdb_strings):
pdb_inp = pdb.input(source_info=None, lines=pdb_string)
model = mmtbx.model.manager(pdb_inp, expand_with_mtrix=False)
crystal_symmetry = model.crystal_symmetry()
# The exact transforms from pdb_string
r1_expected = matrix.sqr([
0.309017, -0.951057, 0.0, 0.951057, 0.309017, -0.0, 0.0, 0.0, 1.0
])
r2_expected = matrix.sqr([
-0.809017, -0.587785, 0.0, 0.587785, -0.809017, -0.0, 0.0, 0.0, 1.0
])
t1_expected = matrix.col([0, 0, 7])
t2_expected = matrix.col([0, 0, 0])
# Look at biomt records retrieved from PDB file
if method == 0:
rec = model._model_input.process_BIOMT_records()
model.expand_with_BIOMT_records()
h = model.get_hierarchy()
else:
rec = model._model_input.process_MTRIX_records()
model.expand_with_MTRIX_records()
h = model.get_hierarchy()
r1 = rec.r[1]
r2 = rec.r[2]
t1 = rec.t[1]
t2 = rec.t[2]
assert approx_equal(r1, r1_expected, eps=0.001)
assert approx_equal(t1, t1_expected, eps=0.1)
assert approx_equal(r2, r2_expected, eps=0.001)
assert approx_equal(t2, t2_expected, eps=0.1)
# Look at the rotation and translation found by the NCS search
s = h.as_pdb_string(crystal_symmetry=crystal_symmetry)
ncs_obj = ncs.input(hierarchy=pdb.input(source_info=None,
lines=s).construct_hierarchy())
nrgl = ncs_obj.get_ncs_restraints_group_list()
assert approx_equal(r1_expected, nrgl[0].copies[0].r, eps=0.001)
assert approx_equal(t1_expected, nrgl[0].copies[0].t, eps=0.1)
assert approx_equal(r2_expected, nrgl[0].copies[1].r, eps=0.001)
assert approx_equal(t2_expected, nrgl[0].copies[1].t, eps=0.1)
if method == 0:
assert nrgl.get_n_groups() == 1
elif method == 1:
assert nrgl.get_n_groups() == 2
def exercise_biomt():
inp = iotbx.pdb.input(lines=biomt_txt+ss_txt+atoms_txt, source_info=None)
model = mmtbx.model.manager(
model_input = inp)
assert model.get_number_of_atoms() == 300, model.get_number_of_atoms()
assert model.get_hierarchy().atoms_size() == 300
assert model.get_xray_structure().scatterers().size() == 300
ss_ann = model.get_ss_annotation()
assert ss_ann.get_n_helices() == 2
assert ss_ann.get_n_sheets() == 1
model.expand_with_BIOMT_records()
assert model.get_number_of_atoms() == 900, model.get_number_of_atoms()
assert model.get_hierarchy().atoms_size() == 900
assert model.get_xray_structure().scatterers().size() == 900, model.get_xray_structure().scatterers().size()
ss_ann = model.get_ss_annotation()
assert ss_ann.get_n_helices() == 6
assert ss_ann.get_n_sheets() == 3
def exercise_04():
"""Test MTRIX record processing"""
expected = """\
CRYST1 10.000 10.000 10.000 90.00 90.00 90.00 P 1
SCALE1 0.100000 0.000000 0.000000 0.00000
SCALE2 0.000000 0.100000 0.000000 0.00000
SCALE3 0.000000 0.000000 0.100000 0.00000
ATOM 1 N ILE A 40 1.000 1.000 1.000 1.00162.33 C
ATOM 2 CA LEU A 40 94.618 -5.253 91.582 1.00 87.10 C
TER
ATOM 3 C ARG B 40 62.395 51.344 80.786 1.00107.25 C
TER
HETATM 4 C1 EDO A 40 39.954 51.526 72.372 0.33 60.93 C
ATOM 1 N ILE C 40 1.000 -1.000 1.000 1.00162.33 C
ATOM 2 CA LEU C 40 94.618 -91.582 -5.253 1.00 87.10 C
TER
ATOM 3 C ARG D 40 62.395 -80.786 51.344 1.00107.25 C
TER
HETATM 4 C1 EDO C 40 39.954 -72.372 51.526 0.33 60.93 C
ATOM 1 N ILE E 40 1.000 1.000 -1.000 1.00162.33 C
ATOM 2 CA LEU E 40 91.582 -5.253 -94.618 1.00 87.10 C
TER
ATOM 3 C ARG F 40 80.786 51.344 -62.395 1.00107.25 C
TER
HETATM 4 C1 EDO E 40 72.372 51.526 -39.954 0.33 60.93 C
ATOM 1 N ILE G 40 -1.000 1.000 1.000 1.00162.33 C
ATOM 2 CA LEU G 40 5.253 94.618 91.582 1.00 87.10 C
TER
ATOM 3 C ARG H 40 -51.344 62.395 80.786 1.00107.25 C
TER
HETATM 4 C1 EDO G 40 -51.526 39.954 72.372 0.33 60.93 C
ATOM 1 N ILE I 40 1.000 1.000 -1.000 1.00162.33 C
ATOM 2 CA LEU I 40 91.582 -5.253 -94.618 1.00 87.10 C
TER
ATOM 3 C ARG J 40 80.786 51.344 -62.395 1.00107.25 C
TER
HETATM 4 C1 EDO I 40 72.372 51.526 -39.954 0.33 60.93 C
ATOM 1 N ILE K 40 -1.000 1.000 -1.000 1.00162.33 C
ATOM 2 CA LEU K 40 5.253 91.582 -94.618 1.00 87.10 C
TER
ATOM 3 C ARG L 40 -51.344 80.786 -62.395 1.00107.25 C
TER
HETATM 4 C1 EDO K 40 -51.526 72.372 -39.954 0.33 60.93 C
ATOM 1 N ILE M 40 -0.366 1.366 1.000 1.00162.33 C
ATOM 2 CA LEU M 40 51.858 79.315 91.582 1.00 87.10 C
TER
ATOM 3 C ARG N 40 -13.268 79.708 80.786 1.00107.25 C
TER
HETATM 4 C1 EDO M 40 -24.646 60.364 72.372 0.33 60.93 C
ATOM 1 N ILE O 40 -1.366 0.366 1.000 1.00162.33 C
ATOM 2 CA LEU O 40 -42.760 84.568 91.582 1.00 87.10 C
TER
ATOM 3 C ARG P 40 -75.663 28.364 80.786 1.00107.25 C
TER
HETATM 4 C1 EDO O 40 -64.600 8.838 72.372 0.33 60.93 C
ATOM 1 N ILE Q 40 1.000 1.500 1.000 1.00162.33 C
ATOM 2 CA LEU Q 40 94.618 -4.753 91.582 1.00 87.10 C
TER
ATOM 3 C ARG R 40 62.395 51.844 80.786 1.00107.25 C
TER
HETATM 4 C1 EDO Q 40 39.954 52.026 72.372 0.33 60.93 C
ATOM 1 N ILE S 40 -1.366 0.366 0.000 1.00162.33 C
ATOM 2 CA LEU S 40 -42.760 84.568 90.582 1.00 87.10 C
TER
ATOM 3 C ARG T 40 -75.663 28.364 79.786 1.00107.25 C
TER
HETATM 4 C1 EDO S 40 -64.600 8.838 71.372 0.33 60.93 C
END
"""
pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str_3)
model = mmtbx.model.manager(pdb_inp, expand_with_mtrix=False)
model.expand_with_BIOMT_records()
assert not show_diff(expected, model.model_as_pdb())
