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from pymol import cmd, testing, stored
class TestSetting(testing.PyMOLTestCase):
@testing.requires_version('1.7.5')
def test_indices(self):
# setting indices must not change, since they are used in session files
self.assertEqual(742, cmd.pymol.setting._get_index('collada_geometry_mode'))
def testGet(self):
name_bool = 'cartoon_fancy_helices'
name_obj = 'ala'
cmd.fragment('ala', name_obj)
cmd.set(name_bool, 1, name_obj)
self.assertEqual('off', cmd.get(name_bool))
self.assertEqual('on', cmd.get(name_bool, name_obj))
cmd.unset(name_bool, '*')
cmd.set(name_bool)
self.assertEqual('on', cmd.get(name_bool))
self.assertEqual('on', cmd.get(name_bool, name_obj))
cmd.set(name_bool, 0, name_obj)
self.assertEqual('on', cmd.get(name_bool))
self.assertEqual('off', cmd.get(name_bool, name_obj))
def testGetBond(self):
# see testSetBond
pass
def testGetSettingBoolean(self):
for v_ref in (0, 1):
cmd.set('orthoscopic', v_ref)
v = cmd.get_setting_boolean('orthoscopic')
self.assertTrue(isinstance(v, int))
self.assertEqual(v, v_ref)
def testGetSettingFloat(self):
for v_ref in (0.0, 1.0):
# bool as float
cmd.set('orthoscopic', v_ref)
v = cmd.get_setting_float('orthoscopic')
self.assertTrue(isinstance(v, float))
self.assertEqual(v, v_ref)
# float with 6 significant digits
cmd.set('sphere_scale', 1.234565)
v = cmd.get_setting_float('sphere_scale')
self.assertEqual(int(v * 1e5), 123456)
@testing.requires_version('2.4')
def testGetSettingFloatExact(self):
# PyMOL 2.4 uses pymol::pretty_f2d which rounds 7 significant digits
for v_ref in (1.234567, 1234567.e6, 9999999.0):
cmd.set('sphere_scale', v_ref)
v = cmd.get_setting_float('sphere_scale')
self.assertEqual(v, v_ref)
def testGetSettingInt(self):
cmd.set('light_count', 4)
v = cmd.get_setting_int('light_count')
self.assertTrue(isinstance(v, int))
self.assertEqual(v, 4)
# float as int gets floored
cmd.set('sphere_scale', 3.7)
v = cmd.get_setting_int('sphere_scale')
self.assertTrue(isinstance(v, int))
self.assertEqual(v, 3)
def testGetSettingText(self):
# int
cmd.set('light_count', 4)
v = cmd.get_setting_text('light_count')
self.assertTrue(isinstance(v, str))
self.assertEqual(v, '4')
# bool
cmd.set('orthoscopic', 0)
v = cmd.get_setting_text('orthoscopic')
self.assertEqual(v, 'off')
# float gets rounded to 5 digits
cmd.set('sphere_scale', 3.7)
v = cmd.get_setting_text('sphere_scale')
self.assertEqual(v, '3.70000')
# float3 gets nicely formatted
cmd.set('label_position', (0.100009, 2.3, 4.56789))
v = cmd.get_setting_text('label_position')
self.assertEqual(v, '[ 0.10001, 2.30000, 4.56789 ]')
# string
cmd.set('pdb_echo_tags', 'Hello World')
v = cmd.get_setting_text('pdb_echo_tags')
self.assertEqual(v, 'Hello World')
def testGetSettingTuple(self):
cmd.set('label_position', (1, 2, 4))
v = cmd.get_setting_tuple('label_position')
self.assertEqual(v, (4, (1.0, 2.0, 4.0)))
def testGetSettingUpdates(self):
v = cmd.get_setting_updates() # consume whatever
cmd.set('orthoscopic', 1)
v = cmd.get_setting_updates()
self.assertEqual(v, [23])
def _testGetSettingUpdates_reinitialize(self, store):
SEQ_VIEW_INDEX = 353
cmd.reinitialize("purge_defaults")
cmd.reinitialize("original_settings")
if store:
cmd.reinitialize("store")
cmd.get_setting_updates() # consume whatever
self.assertTrue(SEQ_VIEW_INDEX not in cmd.get_setting_updates())
cmd.set("seq_view")
self.assertTrue(SEQ_VIEW_INDEX in cmd.get_setting_updates())
self.assertTrue(SEQ_VIEW_INDEX not in cmd.get_setting_updates())
cmd.reinitialize()
self.assertTrue(SEQ_VIEW_INDEX in cmd.get_setting_updates())
self.assertTrue(SEQ_VIEW_INDEX not in cmd.get_setting_updates())
cmd.set("seq_view")
cmd.get_setting_updates() # consume whatever
cmd.reinitialize("settings")
self.assertTrue(SEQ_VIEW_INDEX in cmd.get_setting_updates())
self.assertTrue(SEQ_VIEW_INDEX not in cmd.get_setting_updates())
cmd.set("seq_view")
cmd.get_setting_updates() # consume whatever
cmd.reinitialize("original_settings")
self.assertTrue(SEQ_VIEW_INDEX in cmd.get_setting_updates())
self.assertTrue(SEQ_VIEW_INDEX not in cmd.get_setting_updates())
def testGetSettingUpdates_reinitialize(self):
self._testGetSettingUpdates_reinitialize(False)
self._testGetSettingUpdates_reinitialize(True)
@testing.foreach.product(
('', 'ala', '(elem O)'),
('sphere_scale',),
(2.3,),
(1.0,),
)
@testing.requires_version('1.7')
def testSet(self, sele, name, value, defaultvalue):
cmd.fragment('ala')
cmd.set(name, value, sele)
n = cmd.iterate('first (%s)' % (sele or 'all'), 'stored.v = s.' + name)
self.assertEqual(n, 1)
self.assertAlmostEqual(stored.v, value)
if sele:
cmd.unset(name, sele)
n = cmd.iterate('first (%s)' % (sele or 'all'), 'stored.v = s.' + name)
self.assertEqual(n, 1)
self.assertEqual(stored.v, defaultvalue)
@testing.requires_version('1.8.4')
def testSetBond(self):
value = 2.3
cmd.fragment('ala')
cmd.set_bond('stick_radius', value, '*', '*')
v_list = cmd.get_bond('stick_radius', 'first *', '*')
self.assertAlmostEqual(v_list[0][1][0][2], value)
# unset
# before 1.8.4, get_bond reported [0,0,0] after unset_bond
cmd.unset_bond('stick_radius', '*', '*')
v_list = cmd.get_bond('stick_radius', 'first *', '*')
self.assertEqual(v_list[0][1][0][2], None)
@testing.requires_version('2.5')
def testUnset(self):
# unset with selection: see testSet
# unset global settings since PyMOL 2.5:
for name, value in [
('light_count', 5), # int, non-zero-default
('sphere_scale', 2.0), # float, non-zero default
('ray_shadow', 'off'), # bool, non-zero-default
('orthoscopic', 'on'), # bool, zero-default
('cartoon_highlight_color', 'blue'), # color
('fetch_path', '/some/path'), # string
]:
old_value = cmd.get(name)
cmd.set(name, value)
assert old_value != cmd.get(name)
cmd.unset(name)
self.assertEqual(old_value, cmd.get(name))
def testUnsetBond(self):
# see testSetBond
pass
@testing.requires_version('1.8.3')
def testUnsetDeep(self):
cmd.fragment('ala')
cmd.fragment('gly')
cmd.fragment('his')
# global
sphere_scale_global = 0.8
cmd.set('sphere_scale', sphere_scale_global)
cmd.set('stick_color', 'blue')
# object-level
cmd.set('sphere_scale', .5, 'ala')
cmd.set('stick_radius', .4, 'gly')
# atom-level
cmd.set('sphere_scale', .3, 'index 1-3')
cmd.set('sphere_color', 'yellow', 'index 2-4')
# bond-level
cmd.set('stick_radius', .6, 'elem C')
cmd.set('stick_color', 'red', 'index 1-5')
cmd.unset_deep()
names = cmd.get_object_list()
for oname in names:
# object-level check
for sname in ['sphere_scale', 'sphere_color']:
self.assertEqual(cmd.get(sname), cmd.get(sname, oname))
# atom-level check (1)
# type float
sname = 'sphere_scale'
a_level_values = set()
cmd.iterate(oname, 'a_level_values.add(s.' + sname + ')', space=locals())
self.assertEqual(len(a_level_values), 1)
self.assertAlmostEqual(sphere_scale_global, list(a_level_values)[0], delta=1e-4)
# atom-level check (2)
# type color ('default' -> None)
sname = 'sphere_color'
a_level_values = set()
cmd.iterate(oname, 'a_level_values.add(s.' + sname + ')', space=locals())
self.assertEqual(len(a_level_values), 1)
self.assertEqual(None, list(a_level_values)[0])
# bond-level check (None for unset settings)
for sname in ['stick_radius', 'stick_color']:
b_level_values = cmd.get_bond(sname, '*')
for o_set in b_level_values:
for b_set in o_set[1]:
self.assertEqual(None, b_set[2], msg=sname + ' ' + o_set[0] + ' ' + str(b_set))
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