def test_comprehensive(self,
filename='enk_gm.pdb',
test='test_comprehensive'):
filename = get_filename(filename)
tests = [
["", "None", "None"], # OK
[
"""sites.rotate="1 2 3" sites.translate="4 5 6" """, "None",
"None"
], # OK
[
"""sites.rotate="1 2 3" sites.translate="4 5 6" """,
"chain A or resname HOH", "not (chain A or resname HOH)"
], # OK
[
"""sites.rotate="1 2 3" sites.translate="4 5 6" """,
"chain A or chain C", "not (chain A or chain C)"
], # OK
# ["""sites.rotate="1 2 3" sites.translate="4 5 6" """, "resname HOH", "not (resname HOH)"], # FAILED
[
"""sites.rotate="1 2 3" sites.translate="4 5 6" """, "name CA",
"not (name CA)"
] # OK
]
count = 0
for shift, shift_selection, remove_selection in tests:
print(
"========= shift: %s -- shift_selection: %s -- remove_selection: %s"
% (shift, shift_selection, remove_selection))
filename_shifted = '%s.%s.shifted.pdb' % (test, count)
filename_fitted = '%s.%s.fitted.pdb' % (test, count)
cmd = """phenix.pdbtools %(filename)s output.file_name=%(filename_shifted)s selection="%(shift_selection)s" remove="%(remove_selection)s" %(shift)s""" % {
'filename': filename,
'filename_shifted': filename_shifted,
'shift': shift,
'shift_selection': shift_selection,
'remove_selection': remove_selection
}
libtbx.test_utils.run_command(command=cmd)
moving = superpose.SuperposePDB(filename_shifted,
selection=shift_selection)
target = superpose.SuperposePDB(filename,
selection=shift_selection)
rmsd, lsq = moving.superpose(target)
moving.output(lsq, filename=filename_fitted)
xs_shifted = iotbx.pdb.input(
file_name=filename_shifted).xray_structure_simple()
xs_fitted = iotbx.pdb.input(
file_name=filename_fitted).xray_structure_simple()
check = xs_fitted.mean_distance(other=xs_shifted)
if shift:
self.assertGreater(check, 5.0)
else:
self.assertAlmostEqual(check, 0)
count += 1
return
def test_rna_dna(self, test='test_rna_dna', tolerance=0.7):
filename1 = get_filename('superpose_pdbs_a.pdb')
filename2 = get_filename('superpose_pdbs_b.pdb')
filename_output = '%s.fitted.pdb' % test
moving = superpose.SuperposePDB(filename2)
target = superpose.SuperposePDB(filename1)
rmsd, lsq = moving.superpose(target)
rmsd_output = moving.output(lsq, filename=filename_output)
# ["Number of atoms for LS fitting = 8142",
# "RMSD (all matching atoms) (start): 405.009 (number of atoms: 8142)",
# "RMSD (all matching atoms) (final): 0.607 (number of atoms: 8142)"]:
self.assertLess(rmsd, tolerance)
def test_erik_vogan_case(self, test='test_erik_vogan_case'):
filename1 = get_filename('rebuild03_ckpt04.pdb')
filename2 = get_filename('2C30.pdb')
filename_output = '%s.fitted.pdb' % test
moving = superpose.SuperposePDB(filename2)
target = superpose.SuperposePDB(filename1)
rmsd, lsq = moving.superpose(target)
moving.output(lsq, filename=filename_output)
# ["Number of atoms for LS fitting = 36",
# "RMSD (all matching atoms) (start): 60.830 (number of atoms: 99)",
# "RMSD (all matching atoms) (final): 0.992 (number of atoms: 99)"]:
self.assertLess(rmsd, 1.0)
def test_example_pairwise(self):
result = {}
moving = superpose.SuperposePDB(filename="1AON.pdb")
fixed = superpose.SuperposePDB(filename="1AON.pdb")
for moving_chain in list(moving.pdb.chains())[:7]:
for fixed_chain in list(fixed.pdb.chains())[:7]:
fixed.select_update(preset='ca', chain=fixed_chain.id)
moving.select_update(preset='ca', chain=moving_chain.id)
result[(moving_chain.id,
fixed_chain.id)] = moving.superpose(fixed)
keys = set([i[0] for i in sorted(result.keys())])
print("\t" + "\t".join(keys))
for key1 in keys:
rmsds = [result[(key1, key2)][0] for key2 in keys]
print("%s:\t" % key1, "\t".join(["%0.2f" % i for i in rmsds]))
def test_altlocs_1(self, test='test_altlocs_1', tolerance=0.001):
filename1 = get_filename("fab_1.pdb")
filename2 = get_filename("fab_2.pdb")
filename_output = '%s.fitted.pdb' % test
moving = superpose.SuperposePDB(filename2)
target = superpose.SuperposePDB(filename1)
rmsd, lsq = moving.superpose(target)
moving.output(lsq, filename=filename_output)
# ["Number of atoms for LS fitting = 6",
# "RMSD between fixed and moving atoms (start): 12.830",
# "RMSD between fixed and moving atoms (final): 0.000",
# "RMSD (all matching atoms) (start): 13.164 (number of atoms: 15)",
# "RMSD (all matching atoms) (final): 0.001 (number of atoms: 15)"]:
self.assertLess(rmsd, tolerance)
def test_assert_anisou_warning_message(
self,
filename='phe_a.pdb',
test='test_assert_anisou_warning_message'):
filename = get_filename(filename)
filename_output = '%s.noaniso.pdb' % test
moving = superpose.SuperposePDB(filename)
target = superpose.SuperposePDB(filename)
rmsd, lsq = moving.superpose(target)
moving.output(lsq, filename=filename_output)
pi = iotbx.pdb.input(file_name=filename_output)
ph = pi.construct_hierarchy()
pa = ph.atoms()
uij = pa.extract_uij().as_double()
print(uij.all_eq(-1.0))
assert uij.all_eq(-1.0)
def test_same_models_many_differently_ordered_chains_2(
self,
test='test_same_models_many_differently_ordered_chains_2',
tolerance=0.13):
filename1 = get_filename("a2.pdb")
filename2 = get_filename("b2.pdb")
filename_output = '%s.fitted.pdb' % test
moving = superpose.SuperposePDB(filename2)
target = superpose.SuperposePDB(filename1)
rmsd, lsq = moving.superpose(target)
rmsd_output = moving.output(lsq, filename=filename_output)
# ["Number of atoms for LS fitting = 1284",
# "RMSD (all matching atoms) (start): 159.830 (number of atoms: 26184)",
# "RMSD (all matching atoms) (final): 67.995 (number of atoms: 26184)"]
self.assertLess(rmsd, tolerance)
def test_same_models_many_differently_ordered_chains_1(
self,
test='test_same_models_many_differently_ordered_chains_1',
tolerance=0.03):
filename1 = get_filename("a1.pdb")
filename2 = get_filename("b1.pdb")
filename_output = '%s.fitted.pdb' % test
moving = superpose.SuperposePDB(filename2)
target = superpose.SuperposePDB(filename1)
rmsd, lsq = moving.superpose(target)
rmsd_output = moving.output(lsq, filename=filename_output)
# ["Number of atoms for LS fitting = 33",
# "RMSD between fixed and moving atoms (start): 153.279",
# "RMSD between fixed and moving atoms (final): 0.025"]:
self.assertLess(rmsd, tolerance)
def test_alignment_used_1(self,
filename='fab_a_cut_1.pdb',
test='test_alignment_used_1',
tolerance=0.003):
filename = get_filename(filename)
filename_shifted = "%s.shifted.pdb" % test
cmd = """phenix.pdbtools %(filename)s output.file_name=%(filename_shifted)s remove="%(gap_selection)s" %(shift)s""" % {
'filename': filename,
'filename_shifted': filename_shifted,
'gap_selection': "chain A and (resid 5:30 or resid 32:50)",
'shift': 'sites.rotate="10 20 30" sites.translate="10 20 30"'
}
libtbx.test_utils.run_command(command=cmd,
result_file_names=[filename_shifted])
moving = superpose.SuperposePDB(filename_shifted)
target = superpose.SuperposePDB(filename)
rmsd, lsq = moving.superpose(target)
self.assertLess(rmsd, tolerance)
def test_example_multiple(self):
# Open multiple models for fitting and align chain A Ca's.
fixed = superpose.SuperposePDB(filename="1OAN.pdb",
desc='fixed',
preset='ca')
models = superpose.SuperposePDB.open_models(filename="1S6N.pdb",
desc='moving',
preset='ca')
for model in models:
rmsd, lsq = model.superpose(fixed)
def test_example_presets(self):
# Do a basic Ca fitting (default)
fixed = superpose.SuperposePDB(filename="1CBS.pdb",
desc='fixed',
preset='ca')
moving = superpose.SuperposePDB(filename="1HMT.pdb",
desc='moving',
preset='ca')
rmsd, lsq = moving.superpose(fixed)
# ... or will all atoms
moving.select_update(preset="all")
rmsd, lsq = moving.superpose(fixed)
# ... or with a specific selection string.
moving.select_update(selection="""pepnames and (name ca) chain A""")
rmsd, lsq = moving.superpose(fixed)
# ... or use the Select-o-matic.
moving.selectomatic(fixed)
rmsd, lsq = moving.superpose(fixed)
def test_alignment_used_2(self,
filename='fab_a_cut.pdb',
test='test_alignment_used_2',
tolerance=0.003):
filename = get_filename(filename)
for attempt in range(1):
filename_shifted = '%s.%s.shifted.pdb' % (test, attempt)
gap_selection = "chain A and (resid %s:%s or resid %s:%s or resid %s:%s)" % (
tuple(
random_pair(0, 15) + random_pair(16, 35) +
random_pair(36, 50)))
cmd = """phenix.pdbtools %(filename)s output.file_name=%(filename_shifted)s remove="%(gap_selection)s" %(shift)s""" % {
'filename': filename,
'filename_shifted': filename_shifted,
'gap_selection': gap_selection,
'shift': 'sites.rotate="10 20 30" sites.translate="10 20 30"'
}
libtbx.test_utils.run_command(command=cmd,
result_file_names=[filename_shifted])
moving = superpose.SuperposePDB(filename_shifted)
target = superpose.SuperposePDB(filename)
rmsd, lsq = moving.superpose(target)
self.assertLess(rmsd, tolerance)
return
def test_example_na(self):
# Fit nucleic acid -- note the default settings will realize it's NA.
fixed = superpose.SuperposePDB(filename="na1.pdb", desc='fixed')
moving = superpose.SuperposePDB(filename="na2.pdb", desc='moving')
rmsd, lsq = moving.superpose(fixed)
