def testMAEsaveLoadSessions(self):
cmd.load(self.datafile('1d_smiles.mae'), '1d_smiles', object_props='*')
allpropdata = {}
objs = cmd.get_object_list()
for obj in objs:
props = cmd.get_property_list(obj)
allpropdata[obj] = {}
for prop in props:
allpropdata[obj][prop] = cmd.get_property(prop, obj)
with testing.mktemp('.pse') as psefilename:
cmd.save(psefilename)
cmd.load(psefilename)
# this is to fail the test on purpose
# cmd.set_property('i_m_ct_format', 3, '1d_smiles.mol_13')
objs = cmd.get_object_list()
for obj in objs:
props = cmd.get_property_list(obj)
# test to make sure there are no extra properties or not enough properties
self.assertEqual(set(props), set(allpropdata[obj].keys()))
# test to make sure all property values are the same
for prop in props:
try:
self.assertTrue(allpropdata[obj][prop] == cmd.get_property(prop, obj))
except:
self.fail('properties are not the same: obj=%s prop=%s' % (obj, prop))
def testDel(self):
cmd.pseudoatom('m1')
stored.keys = []
cmd.alter('all', 'p.foo = 123')
cmd.alter('all', 'p.bar = "Hello World"')
cmd.iterate('all', 'stored.keys = list(sorted(p.all))')
self.assertEqual(stored.keys, ['bar', 'foo'])
stored.keys = []
cmd.alter('all', "del p['foo']")
cmd.iterate('all', 'stored.keys = list(sorted(p.all))')
self.assertEqual(stored.keys, ['bar'])
stored.keys = []
cmd.alter('all', "p.bar = None")
cmd.iterate('all', 'stored.keys = list(sorted(p.all))')
self.assertEqual(stored.keys, [])
# object-level
cmd.set_property('bla', 456, 'm1')
stored.keys = cmd.get_property_list('m1')
self.assertEqual(stored.keys, ['bla'])
cmd.set_property('bla', None, 'm1')
stored.keys = cmd.get_property_list('m1')
self.assertEqual(stored.keys, [])
def testMAEsaveLoadSessions(self):
cmd.load(self.datafile('1d_smiles.mae'), '1d_smiles', object_props='*')
allpropdata = {}
objs = cmd.get_object_list()
for obj in objs:
props = cmd.get_property_list(obj)
allpropdata[obj] = {}
for prop in props:
allpropdata[obj][prop] = cmd.get_property(prop, obj)
with testing.mktemp('.pse') as psefilename:
cmd.save(psefilename)
cmd.load(psefilename)
# this is to fail the test on purpose
# cmd.set_property('i_m_ct_format', 3, '1d_smiles.mol_13')
objs = cmd.get_object_list()
for obj in objs:
props = cmd.get_property_list(obj)
# test to make sure there are no extra properties or not enough properties
self.assertEqual(set(props), set(allpropdata[obj].keys()))
# test to make sure all property values are the same
for prop in props:
try:
self.assertTrue(allpropdata[obj][prop] == cmd.get_property(prop, obj))
except:
self.fail('properties are not the same: obj=%s prop=%s' % (obj, prop))
def testCopyObjectProperties(self):
cmd.load(self.datafile('1molecule.mae'), 'test', object_props='*')
objs = cmd.get_object_list()
for obj in objs:
obj_copy = '%s_copy' % obj
cmd.create(obj_copy, obj, copy_properties=True)
props1 = cmd.get_property_list(obj)
props2 = cmd.get_property_list(obj_copy)
self.assertEqual(set(props1), set(props2))
for prop in props1:
prop1 = cmd.get_property(prop, obj)
prop2 = cmd.get_property(prop, obj_copy)
self.assertEqual(prop1, prop2)
def testCopyObjectProperties(self):
cmd.load(self.datafile('1molecule.mae'), 'test', object_props='*')
objs = cmd.get_object_list()
for obj in objs:
obj_copy = '%s_copy' % obj
cmd.create(obj_copy, obj, copy_properties=True)
props1 = cmd.get_property_list(obj)
props2 = cmd.get_property_list(obj_copy)
self.assertEqual(set(props1), set(props2))
for prop in props1:
prop1 = cmd.get_property(prop, obj)
prop2 = cmd.get_property(prop, obj_copy)
self.assertEqual(prop1, prop2)
def testMAEloadSomePropertiesEmptyList(self):
props = []
cmd.load(self.datafile('1d_smiles.mae'), '1d_smiles', object_props=' '.join(props))
objs = cmd.get_object_list()
for obj in objs:
allprops = cmd.get_property_list(obj)
self.assertIsNone(allprops)
def testMAEloadSomePropertiesDontExist(self):
props = ['s_knime_origin_file_name', 's_knime_origin_hostname', 'dontexist']
cmd.load(self.datafile('1d_smiles.mae'), '1d_smiles', object_props=' '.join(props))
objs = cmd.get_object_list()
for obj in objs:
allprops = cmd.get_property_list(obj)
self.assertIsNotNone(allprops)
def testMAEloadSomeProperties(self):
props = ['s_knime_origin_file_name', 's_knime_origin_hostname']
cmd.load(self.datafile('1d_smiles.mae'), '1d_smiles', object_props=' '.join(props))
objs = cmd.get_object_list()
for obj in objs:
allprops = cmd.get_property_list(obj)
self.assertEqual(len(props), len(allprops))
def testMAEloadSomePropertiesEmptyList(self):
props = []
cmd.load(self.datafile('1d_smiles.mae'), '1d_smiles', object_props=' '.join(props))
objs = cmd.get_object_list()
for obj in objs:
allprops = cmd.get_property_list(obj)
self.assertIsNone(allprops)
def testMAEloadSomeProperties(self):
props = ['s_knime_origin_file_name', 's_knime_origin_hostname']
cmd.load(self.datafile('1d_smiles.mae'), '1d_smiles', object_props=' '.join(props))
objs = cmd.get_object_list()
for obj in objs:
allprops = cmd.get_property_list(obj)
self.assertEqual(len(props), len(allprops))
def testMAEloadSomePropertiesDontExist(self):
props = ['s_knime_origin_file_name', 's_knime_origin_hostname', 'dontexist']
cmd.load(self.datafile('1d_smiles.mae'), '1d_smiles', object_props=' '.join(props))
objs = cmd.get_object_list()
for obj in objs:
allprops = cmd.get_property_list(obj)
self.assertIsNotNone(allprops)
def testMAEchempy(self, molfilename):
cmd.load(self.datafile(molfilename), 'test', object_props='*', atom_props='*')
objs = cmd.get_object_list()
for obj in objs:
idxToVal = {}
natoms = cmd.count_atoms(obj)
for i in range(natoms):
idxToVal[i+1] = i*10
cmd.set_atom_property('test_prop', i*10, "index %d and %s" % (i+1, obj))
model = cmd.get_model(obj)
# test to make sure the properties that exist are the same
prop_list= cmd.get_property_list(obj)
mol_prop_list = [x[0] for x in model.molecule_properties]
self.assertEqual(set(prop_list), set(mol_prop_list))
# need to test whether the values are the same
for prop, val in model.molecule_properties:
propval = cmd.get_property(prop, obj)
self.assertEqual(propval, val)
self.assertEqual(natoms, len(model.atom))
# need to test values of all atom properties, including the ones that were set above
stored.prop_lookup = {}
cmd.iterate(obj, "stored.prop_lookup[index-1] = properties.all")
idx = 0
for at in model.atom:
for prop in at.atom_properties.keys():
val = at.atom_properties[prop]
self.assertEqual(val, stored.prop_lookup[idx][prop])
idx += 1
def testLoadNoProperties(self, molfilename):
cmd.set('load_object_props_default', '')
cmd.load(self.datafile(molfilename), 'test')
objs = cmd.get_object_list()
for obj in objs:
prop_list= cmd.get_property_list(obj)
self.assertEquals(prop_list, None)
def testMAEchempy(self):
cmd.load(self.datafile('1d_smiles.mae'), '1d_smiles', object_props='*')
objs = cmd.get_object_list()
for obj in objs:
model = cmd.get_model(obj)
prop_list= cmd.get_property_list(obj)
mol_prop_list = [x[0] for x in model.molecule_properties]
self.assertEqual(set(prop_list), set(mol_prop_list))
def testMAEchempy(self):
cmd.load(self.datafile('1d_smiles.mae'), '1d_smiles', object_props='*')
objs = cmd.get_object_list()
for obj in objs:
model = cmd.get_model(obj)
prop_list= cmd.get_property_list(obj)
mol_prop_list = map(lambda x: x[0], model.molecule_properties)
self.assertEqual(set(prop_list), set(mol_prop_list))
def testMAEloadAllProperties(self):
cmd.load(self.datafile('1d_smiles.mae'), '1d_smiles', object_props='*')
objs = cmd.get_object_list()
for obj in objs:
props = cmd.get_property_list(obj)
self.assertIsNotNone(props)
def testMAEloadAllProperties(self):
cmd.load(self.datafile('1d_smiles.mae'), '1d_smiles', object_props='*')
objs = cmd.get_object_list()
for obj in objs:
props = cmd.get_property_list(obj)
self.assertIsNotNone(props)
def testPdbHeader(self, load_object_props_default, object_props, truth):
cmd.set('load_object_props_default', load_object_props_default)
cmd.load(self.datafile('1rx1.pdb'), 'm1', object_props=object_props)
self.assertEqual(truth, 'pdb_header' in (cmd.get_property_list('m1')
or ()))
def testPdbHeader(self, load_object_props_default, object_props, truth):
cmd.set('load_object_props_default', load_object_props_default)
cmd.load(self.datafile('1rx1.pdb'), 'm1', object_props=object_props)
self.assertEqual(truth, 'pdb_header' in (cmd.get_property_list('m1') or ()))
