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(
pdb_file=fn,
quiet=True,
exclude_chains=['D','E'],
suppress_print=True,
write_ncs_domain_pdb=True,
ncs_domain_pdb_stem=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(),6)
self.assertEqual(pdb_inp_1.atoms().size(),8)
self.assertEqual(pdb_inp_2.atoms().size(),4)
else:
print "phenix not available, skipping test_create_ncs_domain_pdb_files()"
pass
def test_spec_reading(self):
""" verify creating and processing spec """
if have_phenix:
# print sys._getframe().f_code.co_name
# creating a spec file
params = master_params.extract()
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(
pdb_file="test_ncs_spec.pdb",
quiet=True,
log=null_out(),
params=params)
# reading and processing the spec file
trans_obj = ncs.input(
file_name="simple_ncs_from_pdb.ncs_spec",
# spec_file_str=test_ncs_spec, # use output string directly
pdb_hierarchy_inp = self.pdb_obj)
# 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['004'].r
r2 = trans_obj.ncs_transform['002'].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,{'001', '002', '003', '004', '005'})
#
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
