def test_options_shelxe_resolution_ok(self):
"""Check we don't accidently turn it off if above limit
"""
options = AMPLEConfigOptions()
argso = argparse_util.process_command_line(
args=['-mtz', 'foo', '-fasta', 'bar'])
options.populate(argso)
self.assertTrue(options.d['use_shelxe']) # default so should be true
options.d['shelxe_rebuild'] = True
options.d['mtz_min_resolution'] = SHELXE_MAX_PERMITTED_RESOLUTION - 1
options_processor.process_mr_options(options.d)
self.assertTrue(options.d['use_shelxe'])
self.assertTrue(options.d['shelxe_rebuild'])
def test_options_shelxe_resolution_cc(self):
"""Check limit with coiled-coil mode turned on
"""
options = AMPLEConfigOptions()
argso = argparse_util.process_command_line(
args=['-mtz', 'foo', '-fasta', 'bar', '-coiled_coil', 'True'])
options.populate(argso)
options.d['shelxe_rebuild'] = True
limit = random.uniform(SHELXE_MAX_PERMITTED_RESOLUTION,
SHELXE_MAX_PERMITTED_RESOLUTION_CC)
options.d['mtz_min_resolution'] = limit
options_processor.process_mr_options(options.d)
self.assertTrue(options.d['use_shelxe'])
self.assertTrue(options.d['shelxe_rebuild'])
def test_options_shelxe_resolution_max(self):
"""Make sure we turn off shelxe if resolution is outside limit
"""
options = AMPLEConfigOptions()
argso = argparse_util.process_command_line(
args=['-mtz', 'foo', '-fasta', 'bar'])
options.populate(argso)
self.assertTrue(options.d['use_shelxe']) # default so should be true
options.d['shelxe_rebuild'] = True
# Set resolution below limit
options.d['mtz_min_resolution'] = SHELXE_MAX_PERMITTED_RESOLUTION + 1
options_processor.process_mr_options(options.d)
self.assertFalse(options.d['use_shelxe'])
self.assertFalse(options.d['shelxe_rebuild'])
def test_options_shelxe_resolution_cmd(self):
"""Check limit with coiled-coil mode turned on
Need to see if we can override and extend the original limit
"""
limit = random.uniform(SHELXE_MAX_PERMITTED_RESOLUTION_CC,
REBUILD_MAX_PERMITTED_RESOLUTION)
options = AMPLEConfigOptions()
argso = argparse_util.process_command_line(args=[
'-mtz', 'foo', '-fasta', 'bar', '-coiled_coil', 'True',
'-shelxe_max_resolution',
str(limit)
])
options.populate(argso)
options.d['use_shelxe'] = True
options.d['shelxe_rebuild'] = True
options.d['mtz_min_resolution'] = random.uniform(
limit, REBUILD_MAX_PERMITTED_RESOLUTION)
options_processor.process_mr_options(options.d)
self.assertTrue(options.d['use_shelxe'])
self.assertTrue(options.d['shelxe_rebuild'])
def test_process_mr_options(self):
"""Make sure we handle resolution limits around SHELXE use properly
"""
options = AMPLEConfigOptions()
argso = argparse_util.process_command_line(args=['-mtz', 'foo',
'-fasta', 'bar'])
options.populate(argso)
# Make sure we turn off shelxe if resolution is outside limit
self.assertTrue(options.d['use_shelxe']) # default so should be true
options.d['shelxe_rebuild'] = True
# Set resolution below limit
options.d['mtz_min_resolution'] = SHELXE_MAX_PERMITTED_RESOLUTION + 1
options_processor.process_mr_options(options.d)
self.assertFalse(options.d['use_shelxe'])
self.assertFalse(options.d['shelxe_rebuild'])
# Check we don't accidently turn it off if above limit
options.d['use_shelxe'] = True
options.d['shelxe_rebuild'] = True
options.d['mtz_min_resolution'] = SHELXE_MAX_PERMITTED_RESOLUTION - 1
options_processor.process_mr_options(options.d)
self.assertTrue(options.d['use_shelxe'])
self.assertTrue(options.d['shelxe_rebuild'])
def test_process_mr_options(self):
"""Make sure we handle resolution limits around SHELXE use properly
"""
options = AMPLEConfigOptions()
argso = argparse_util.process_command_line(
args=['-mtz', 'foo', '-fasta', 'bar'])
options.populate(argso)
# Make sure we turn off shelxe if resolution is outside limit
self.assertTrue(options.d['use_shelxe']) # default so should be true
options.d['shelxe_rebuild'] = True
# Set resolution below limit
options.d['mtz_min_resolution'] = SHELXE_MAX_PERMITTED_RESOLUTION + 1
options_processor.process_mr_options(options.d)
self.assertFalse(options.d['use_shelxe'])
self.assertFalse(options.d['shelxe_rebuild'])
# Check we don't accidently turn it off if above limit
options.d['use_shelxe'] = True
options.d['shelxe_rebuild'] = True
options.d['mtz_min_resolution'] = SHELXE_MAX_PERMITTED_RESOLUTION - 1
options_processor.process_mr_options(options.d)
self.assertTrue(options.d['use_shelxe'])
self.assertTrue(options.d['shelxe_rebuild'])