def test_create_ncs_domain_pdb_files(self):
""" check that files are created for each NCS group as expected """
# it should create 3 files (by number of found NCS groups) and write
# there all atoms from NCS groups except chains excluded in exclude_chains
if have_phenix:
fn = 'SimpleNCSFromPDB_test.pdb'
open(fn,'w').write(pdb_str_3)
prefix = 'test_create_ncs_domain_pdb_files'
obj = simple_ncs_from_pdb.run(
args=["pdb_in=%s" % fn,
"write_ncs_domain_pdb=True",
"ncs_domain_pdb_stem=%s" % prefix])
fn_gr0 = prefix + '_group_1.pdb'
fn_gr1 = prefix + '_group_2.pdb'
fn_gr2 = prefix + '_group_3.pdb'
self.assertEqual(obj.ncs_obj.number_of_ncs_groups,3)
pdb_inp_0 = pdb.input(file_name=fn_gr0)
pdb_inp_1 = pdb.input(file_name=fn_gr1)
pdb_inp_2 = pdb.input(file_name=fn_gr2)
self.assertEqual(pdb_inp_0.atoms().size(),12)
self.assertEqual(pdb_inp_1.atoms().size(),8)
self.assertEqual(pdb_inp_2.atoms().size(),8)
else:
print "phenix not available, skipping test_create_ncs_domain_pdb_files()"
pass
def test_create_ncs_domain_pdb_files(self):
""" check that files are created for each NCS group as expected """
# it should create 3 files (by number of found NCS groups) and write
# there all atoms from NCS groups except chains excluded in exclude_chains
if have_phenix:
fn = 'SimpleNCSFromPDB_test.pdb'
open(fn, 'w').write(pdb_str_3)
prefix = 'test_create_ncs_domain_pdb_files'
obj = simple_ncs_from_pdb.run(args=[
"pdb_in=%s" % fn, "write_ncs_domain_pdb=True",
"ncs_domain_pdb_stem=%s" % prefix
])
fn_gr0 = prefix + '_group_1.pdb'
fn_gr1 = prefix + '_group_2.pdb'
fn_gr2 = prefix + '_group_3.pdb'
self.assertEqual(obj.ncs_obj.number_of_ncs_groups, 3)
pdb_inp_0 = pdb.input(file_name=fn_gr0)
pdb_inp_1 = pdb.input(file_name=fn_gr1)
pdb_inp_2 = pdb.input(file_name=fn_gr2)
self.assertEqual(pdb_inp_0.atoms().size(), 12)
self.assertEqual(pdb_inp_1.atoms().size(), 8)
self.assertEqual(pdb_inp_2.atoms().size(), 8)
else:
print "phenix not available, skipping test_create_ncs_domain_pdb_files()"
pass
def test_spec_reading(self):
""" verify creating and processing spec
This is ncs.ncs - specific functionality
"""
if have_phenix:
xrs = self.pdb_inp.xray_structure_simple()
xrs_unit_cell = xrs.orthorhombic_unit_cell_around_centered_scatterers(
buffer_size=8)
self.ph.adopt_xray_structure(xrs_unit_cell)
of = open("test_ncs_spec.pdb", "w")
print >> of, self.ph.as_pdb_string(crystal_symmetry=xrs.crystal_symmetry())
of.close()
# create a spec file
ncs_from_pdb=simple_ncs_from_pdb.run(
args=["pdb_in=test_ncs_spec.pdb", "write_spec_files=True"],
log=null_out())
else:
print "phenix not available, skipping test_spec_reading()"
pass
def test_spec_reading(self):
""" verify creating and processing spec
This is ncs.ncs - specific functionality
"""
if have_phenix:
xrs = self.pdb_inp.xray_structure_simple()
xrs_unit_cell = xrs.orthorhombic_unit_cell_around_centered_scatterers(
buffer_size=8)
self.ph.adopt_xray_structure(xrs_unit_cell)
of = open("test_ncs_spec.pdb", "w")
print >> of, self.ph.as_pdb_string(crystal_symmetry=xrs.crystal_symmetry())
of.close()
# create a spec file
ncs_from_pdb=simple_ncs_from_pdb.run(
args=["pdb_in=test_ncs_spec.pdb", "write_spec_files=True"],
log=null_out())
# reading and processing the spec file
spec_object = mmtbx.ncs.ncs.ncs()
spec_object.read_ncs(file_name="test_ncs_spec_simple_ncs_from_pdb.ncs_spec")
trans_obj = ncs.input(
spec_ncs_groups=spec_object,
# spec_file_str=test_ncs_spec, # use output string directly
hierarchy = self.pdb_inp.construct_hierarchy())
# test created object
self.assertEqual(len(trans_obj.transform_chain_assignment),3)
expected = "(chain A and (resseq 151:159)) or (chain D and (resseq 1:7))"
self.assertEqual(trans_obj.ncs_selection_str,expected)
# check that static parts are included in NCS and ASU
self.assertEqual(len(trans_obj.ncs_atom_selection),3*9+2*7+3+3)
self.assertEqual(trans_obj.ncs_atom_selection.count(True),9+7+3+3)
#
expected = {
"chain A and (resseq 151:159)":
["chain B and (resseq 151:159)","chain C and (resseq 151:159)"],
"chain D and (resseq 1:7)":
["chain E and (resseq 1:7)"]}
self.assertEqual(trans_obj.ncs_to_asu_selection,expected)
# check ncs_transform
group_ids = [x.ncs_group_id for x in trans_obj.ncs_transform.itervalues()]
tran_sn = {x.serial_num for x in trans_obj.ncs_transform.itervalues()}
group_keys = {x for x in trans_obj.ncs_transform.iterkeys()}
r1 = trans_obj.ncs_transform['0000000004'].r
r2 = trans_obj.ncs_transform['0000000002'].r
#
self.assertEqual(len(group_ids),5)
self.assertEqual(set(group_ids),{1,2})
self.assertEqual(tran_sn,{1,2,3,4,5})
self.assertEqual(group_keys,{'0000000001', '0000000002', '0000000003', '0000000004', '0000000005'})
#
self.assertTrue(r1.is_r3_identity_matrix())
expected_r = matrix.sqr(
[0.4966,0.8679,-0.0102,-0.6436,0.3761,0.6666,0.5824,-0.3245,0.7453])
d = r2 - expected_r.transpose()
d = map(abs,d)
self.assertTrue(max(d)<0.01)
else:
print "phenix not available, skipping test_spec_reading()"
pass
def test_spec_reading(self):
""" verify creating and processing spec
This is ncs.ncs - specific functionality
"""
if have_phenix:
xrs = self.pdb_inp.xray_structure_simple()
xrs_unit_cell = xrs.orthorhombic_unit_cell_around_centered_scatterers(
buffer_size=8)
self.ph.adopt_xray_structure(xrs_unit_cell)
of = open("test_ncs_spec.pdb", "w")
print >> of, self.ph.as_pdb_string(
crystal_symmetry=xrs.crystal_symmetry())
of.close()
# create a spec file
ncs_from_pdb = simple_ncs_from_pdb.run(
args=["pdb_in=test_ncs_spec.pdb", "write_spec_files=True"],
log=null_out())
# reading and processing the spec file
spec_object = mmtbx.ncs.ncs.ncs()
spec_object.read_ncs(
file_name="test_ncs_spec_simple_ncs_from_pdb.ncs_spec")
trans_obj = ncs.input(
spec_ncs_groups=spec_object,
# spec_file_str=test_ncs_spec, # use output string directly
hierarchy=self.pdb_inp.construct_hierarchy())
# test created object
self.assertEqual(len(trans_obj.transform_chain_assignment), 3)
expected = "(chain A and (resseq 151:159)) or (chain D and (resseq 1:7))"
self.assertEqual(trans_obj.ncs_selection_str, expected)
# check that static parts are included in NCS and ASU
self.assertEqual(len(trans_obj.ncs_atom_selection),
3 * 9 + 2 * 7 + 3 + 3)
self.assertEqual(trans_obj.ncs_atom_selection.count(True),
9 + 7 + 3 + 3)
#
expected = {
"chain A and (resseq 151:159)": [
"chain B and (resseq 151:159)",
"chain C and (resseq 151:159)"
],
"chain D and (resseq 1:7)": ["chain E and (resseq 1:7)"]
}
self.assertEqual(trans_obj.ncs_to_asu_selection, expected)
# check ncs_transform
group_ids = [
x.ncs_group_id for x in trans_obj.ncs_transform.itervalues()
]
tran_sn = {
x.serial_num
for x in trans_obj.ncs_transform.itervalues()
}
group_keys = {x for x in trans_obj.ncs_transform.iterkeys()}
r1 = trans_obj.ncs_transform['0000000004'].r
r2 = trans_obj.ncs_transform['0000000002'].r
#
self.assertEqual(len(group_ids), 5)
self.assertEqual(set(group_ids), {1, 2})
self.assertEqual(tran_sn, {1, 2, 3, 4, 5})
self.assertEqual(
group_keys, {
'0000000001', '0000000002', '0000000003', '0000000004',
'0000000005'
})
#
self.assertTrue(r1.is_r3_identity_matrix())
expected_r = matrix.sqr([
0.4966, 0.8679, -0.0102, -0.6436, 0.3761, 0.6666, 0.5824,
-0.3245, 0.7453
])
d = r2 - expected_r.transpose()
d = map(abs, d)
self.assertTrue(max(d) < 0.01)
else:
print "phenix not available, skipping test_spec_reading()"
pass