def test_join_states():
cmd.reinitialize()
cmd.load(DATA_PATH / "1nmr-frag-nohydro.pdb", "m1", multiplex=1)
assert len(cmd.get_names()) == 4
assert cmd.count_states() == 1
psico.creating.join_states("m2", "m1_*", discrete=0)
assert cmd.count_states("m2") == 4
assert cmd.count_discrete("m2") == 0
assert cmd.count_atoms("m2") == 241
psico.creating.join_states("m3", "m1_*", discrete=1)
assert cmd.count_states("m3") == 4
assert cmd.count_discrete("m3") == 1
assert cmd.count_atoms("m3") == 241 * 4
def testCreateDiscrete(self, discrete_source):
self.create_many_states("methanol", "m1", 2)
self.create_many_states("benzene", "m2", 2)
pymol.editing.set_discrete("m1", discrete=discrete_source)
pymol.editing.set_discrete("m2", discrete=discrete_source)
# create new
cmd.create('dm', 'm1', 0, -1, discrete=1)
self.assertTrue(cmd.count_discrete('dm'))
self.assertEqual(cmd.count_states('dm'), 2)
self.assertEqual(cmd.count_atoms('dm'), 2 * 6)
self.assertEqual(len(cmd.get_bonds('dm')), 5)
# append to existing
cmd.create('dm', 'm2', 0, -1, discrete=1)
self.assertTrue(cmd.count_discrete('dm'))
self.assertEqual(cmd.count_states('dm'), 4)
self.assertEqual(cmd.count_atoms('dm'), 2 * 6 + 2 * 12)
self.assertEqual(len(cmd.get_bonds('dm', 1)), 5)
self.assertEqual(len(cmd.get_bonds('dm', 4)), 12)
self.assertEqual(len(cmd.get_bonds('dm', 0)), 2 * 5 + 2 * 12)
def test_set_discrete(self):
import pymol
cmd.fragment('ala', 'm1')
cmd.create('m1', 'm1', 1, 2)
self.assertEqual(0, cmd.count_discrete('*'))
self.assertEqual(2, cmd.count_states())
self.assertEqual(10, cmd.count_atoms())
pymol.editing.set_discrete('m1', 1)
self.assertEqual(1, cmd.count_discrete('*'))
self.assertEqual(2, cmd.count_states())
self.assertEqual(20, cmd.count_atoms())
pymol.editing.set_discrete('m1', 0)
self.assertEqual(0, cmd.count_discrete('*'))
self.assertEqual(2, cmd.count_states())
self.assertEqual(10, cmd.count_atoms())
def test_set_discrete(self):
import pymol
cmd.fragment('ala', 'm1')
cmd.create('m1', 'm1', 1, 2)
self.assertEqual(0, cmd.count_discrete('*'))
self.assertEqual(2, cmd.count_states())
self.assertEqual(10, cmd.count_atoms())
pymol.editing.set_discrete('m1', 1)
self.assertEqual(1, cmd.count_discrete('*'))
self.assertEqual(2, cmd.count_states())
self.assertEqual(20, cmd.count_atoms())
pymol.editing.set_discrete('m1', 0)
self.assertEqual(0, cmd.count_discrete('*'))
self.assertEqual(2, cmd.count_states())
self.assertEqual(10, cmd.count_atoms())
def testLoad_multi(self, ext, discrete):
'''
Load multi-state files with discrete=0/1 and multiplex=0/1
'''
N = 10
filename = self.datafile('ligs3d.' + ext)
# mutiplex=0
cmd.load(filename, discrete=discrete, multiplex=0)
self.assertEqual(cmd.count_discrete('*'), discrete)
self.assertEqual(cmd.count_states(), N)
self.assertEqual(len(cmd.get_object_list()), 1)
if ext in ['mmd']:
return
# mutiplex=1
cmd.delete('*')
cmd.load(filename, discrete=discrete, multiplex=1)
self.assertEqual(cmd.count_discrete('*'), discrete * N)
self.assertEqual(cmd.count_states(), 1)
self.assertEqual(len(cmd.get_object_list()), N)
def testLoad_multi(self, ext, discrete):
'''
Load multi-state files with discrete=0/1 and multiplex=0/1
'''
N = 10
filename = self.datafile('ligs3d.' + ext)
# mutiplex=0
cmd.load(filename, discrete=discrete, multiplex=0)
self.assertEqual(cmd.count_discrete('*'), discrete)
self.assertEqual(cmd.count_states(), N)
self.assertEqual(len(cmd.get_object_list()), 1)
if ext in ['mmd']:
return
# mutiplex=1
cmd.delete('*')
cmd.load(filename, discrete=discrete, multiplex=1)
self.assertEqual(cmd.count_discrete('*'), discrete * N)
self.assertEqual(cmd.count_states(), 1)
self.assertEqual(len(cmd.get_object_list()), N)
def testSelectByAtomType(self):
cmd.load(self.datafile('1oky.pdb.gz'))
cmd.remove("alt 'B'")
cmd.select('foo', "resn STU and text_type 'C.3'")
self.assertEquals(cmd.count_atoms('foo'), 8)
# discrete object
cmd.delete('*')
cmd.load(self.datafile('ligs3d.sdf'))
self.assertTrue(cmd.count_discrete('*') > 0)
n = cmd.select('foo', "text_type 'C.3'")
self.assertEquals(n, 115)
# only run label test if selection tests passed. Don't wnat
# more than one failing tests for builds with NO_MMLIBS
cmd.delete('*')
self._testLabelByAtomType()
def testLoadMae(self, multiplex, discrete):
cmd.load(self.datafile('multimae.maegz'), 'm',
multiplex=multiplex, discrete=discrete)
nstate = 4
natoms = 79
nmodel = 1
ndiscrete = discrete
if multiplex:
natoms *= nstate
ndiscrete *= nstate
nmodel = nstate
nstate = 1
elif discrete:
self.assertEqual(cmd.count_atoms(state=1), natoms)
natoms *= nstate
self.assertEqual(cmd.count_states(), nstate)
self.assertEqual(cmd.count_discrete('*'), ndiscrete)
self.assertEqual(cmd.count_atoms(), natoms)
self.assertEqual(len(cmd.get_object_list()), nmodel)
def testLoadMae(self, multiplex, discrete):
cmd.load(self.datafile('multimae.maegz'),
'm',
multiplex=multiplex,
discrete=discrete)
nstate = 4
natoms = 79
nmodel = 1
ndiscrete = discrete
if multiplex:
natoms *= nstate
ndiscrete *= nstate
nmodel = nstate
nstate = 1
elif discrete:
self.assertEqual(cmd.count_atoms(state=1), natoms)
natoms *= nstate
self.assertEqual(cmd.count_states(), nstate)
self.assertEqual(cmd.count_discrete('*'), ndiscrete)
self.assertEqual(cmd.count_atoms(), natoms)
self.assertEqual(len(cmd.get_object_list()), nmodel)