def testSDF(self):
# get molecule with SDF annotations
cid = 6830
cmd.set('load_object_props_default', '')
cmd.load('CID_%d.sdf' % cid, 'm1')
self.assertEqual(None, cmd.get_property('PUBCHEM_COMPOUND_CID', 'm1'),
'property loaded, but should not')
cmd.delete('*')
cmd.load('CID_%d.sdf' % cid, 'm1', object_props='*')
self.assertEqual(cid, cmd.get_property('PUBCHEM_COMPOUND_CID', 'm1'))
v_pc = cmd.get_property('PUBCHEM_MMFF94_PARTIAL_CHARGES', 'm1')
lines = v_pc.rstrip().splitlines()
n_pc = int(lines[0])
self.assertEqual(n_pc, len(lines) - 1)
# test loading selective properties
cmd.set(
'load_object_props_default',
"PUBCHEM_COMPOUND_CID PUBCHEM_CONFORMER_RMSD PUBCHEM_CONFORMER_DIVERSEORDER"
)
cmd.load('CID_%d.sdf' % cid, 'm2')
self.assertEqual(cid, cmd.get_property('PUBCHEM_COMPOUND_CID', 'm2'))
self.assertEqual(
None, cmd.get_property('PUBCHEM_EFFECTIVE_ROTOR_COUNT', 'm2'))
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 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 testStringType(self, str1, str2):
cmd.fragment('ala')
cmd.set_property('string_property_1', str1, 'ala')
cmd.set_property('string_property_2', str2, 'ala')
self.assertEqual(cmd.get_property('string_property_1', 'ala'), str1)
self.assertEqual(cmd.get_property('string_property_2', 'ala'), str2)
# test setting boolean type by string
cmd.set_property('string_property_1', str1, 'ala', proptype=PROPERTY_STRING)
cmd.set_property('string_property_2', str1, 'ala', proptype=PROPERTY_STRING)
self.assertEqual(cmd.get_property('string_property_1', 'ala'), str1)
self.assertEqual(cmd.get_property('string_property_2', 'ala'), str1) # overwritting
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 testSimple(self):
cmd.fab('A', 'm1')
cmd.fab('A', 'm2')
v1 = 'foo'
v2 = 'bar'
v3 = 'com'
# single state
cmd.set_property('filename', v1, 'm1')
self.assertTrue('foo' == v1)
self.assertTrue(cmd.get_property('filename', 'm1') == v1)
self.assertTrue(cmd.get_property('filename', 'm2') == None)
# multiple objects
cmd.set_property('filename', v1)
self.assertTrue(cmd.get_property('filename', 'm2') == v1)
# two states
cmd.create('m1', 'm1', 1, 2)
self.assertTrue(cmd.count_states() == 2)
# set for all states
cmd.set_property('filename', v1, 'm1')
self.assertTrue(cmd.get_property('filename', 'm1', 2) == v1)
# set for particular state
cmd.set_property('filename', v2, 'm1', 2)
self.assertTrue(cmd.get_property('filename', 'm1', 1) == v1)
self.assertTrue(cmd.get_property('filename', 'm1', 2) == v2)
# set for current state
cmd.frame(2)
cmd.set_property('filename', v3, 'm1', -1)
self.assertTrue(cmd.get_property('filename', 'm1', 1) == v1)
self.assertTrue(cmd.get_property('filename', 'm1', 2) == v3)
def testSimple(self):
cmd.fab('A', 'm1')
cmd.fab('A', 'm2')
v1 = 'foo'
v2 = 'bar'
v3 = 'com'
# single state
cmd.set_property('filename', v1, 'm1')
self.assertTrue('foo' == v1)
self.assertTrue(cmd.get_property('filename', 'm1') == v1)
self.assertTrue(cmd.get_property('filename', 'm2') == None)
# multiple objects
cmd.set_property('filename', v1)
self.assertTrue(cmd.get_property('filename', 'm2') == v1)
# two states
cmd.create('m1', 'm1', 1, 2)
self.assertTrue(cmd.count_states() == 2)
# set for all states
cmd.set_property('filename', v1, 'm1')
self.assertTrue(cmd.get_property('filename', 'm1', 2) == v1)
# set for particular state
cmd.set_property('filename', v2, 'm1', 2)
self.assertTrue(cmd.get_property('filename', 'm1', 1) == v1)
self.assertTrue(cmd.get_property('filename', 'm1', 2) == v2)
# set for current state
cmd.frame(2)
cmd.set_property('filename', v3, 'm1', -1)
self.assertTrue(cmd.get_property('filename', 'm1', 1) == v1)
self.assertTrue(cmd.get_property('filename', 'm1', 2) == v3)
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 testStringType(self, str1, str2):
cmd.fragment('ala')
cmd.set_property('string_property_1', str1, 'ala')
cmd.set_property('string_property_2', str2, 'ala')
self.assertEqual(cmd.get_property('string_property_1', 'ala'), str1)
self.assertEqual(cmd.get_property('string_property_2', 'ala'), str2)
# test setting boolean type by string
cmd.set_property('string_property_1',
str1,
'ala',
proptype=PROPERTY_STRING)
cmd.set_property('string_property_2',
str1,
'ala',
proptype=PROPERTY_STRING)
self.assertEqual(cmd.get_property('string_property_1', 'ala'), str1)
self.assertEqual(cmd.get_property('string_property_2', 'ala'),
str1) # overwritting
def testFloatType(self, val1, val2):
cmd.fragment('ala')
cmd.set_property('float_property_1', val1, 'ala')
cmd.set_property('float_property_2', val2, 'ala')
self.assertAlmostEqual(cmd.get_property('float_property_1', 'ala'),
val1)
self.assertAlmostEqual(cmd.get_property('float_property_2', 'ala'),
val2)
# test setting boolean type by string
cmd.set_property('float_property_1',
str(val1),
'ala',
proptype=PROPERTY_FLOAT)
cmd.set_property('float_property_2',
str(val1),
'ala',
proptype=PROPERTY_FLOAT)
cmd.set_property('float_property_3',
str(val1),
'ala',
proptype=PROPERTY_FLOAT)
cmd.set_property('float_property_4',
str(val2),
'ala',
proptype=PROPERTY_FLOAT)
self.assertAlmostEqual(cmd.get_property('float_property_1', 'ala'),
val1)
self.assertAlmostEqual(cmd.get_property('float_property_2', 'ala'),
val1) # overwritting
self.assertAlmostEqual(cmd.get_property('float_property_3', 'ala'),
val1)
self.assertAlmostEqual(cmd.get_property('float_property_4', 'ala'),
val2)
def testIntegerType(self, val1, val2):
cmd.fragment('ala')
cmd.set_property('int_property_1', val1, 'ala')
cmd.set_property('int_property_2', val2, 'ala')
self.assertEqual(cmd.get_property('int_property_1', 'ala'), val1)
self.assertEqual(cmd.get_property('int_property_2', 'ala'), val2)
# test setting boolean type by string
cmd.set_property('int_property_1',
str(val1),
'ala',
proptype=PROPERTY_INT)
cmd.set_property('int_property_2',
str(val1),
'ala',
proptype=PROPERTY_INT)
cmd.set_property('int_property_3',
str(val1),
'ala',
proptype=PROPERTY_INT)
cmd.set_property('int_property_4',
str(val2),
'ala',
proptype=PROPERTY_INT)
self.assertEqual(cmd.get_property('int_property_1', 'ala'), val1)
self.assertEqual(cmd.get_property('int_property_2', 'ala'),
val1) # overwritting
self.assertEqual(cmd.get_property('int_property_3', 'ala'), val1)
self.assertEqual(cmd.get_property('int_property_4', 'ala'), val2)
def testBooleanType(self):
cmd.fragment('ala')
cmd.set_property('bool_property_1', True, 'ala')
cmd.set_property('bool_property_2', False, 'ala')
self.assertEqual(cmd.get_property('bool_property_1', 'ala'), True)
self.assertEqual(cmd.get_property('bool_property_2', 'ala'), False)
# test setting boolean type by string
cmd.set_property('bool_property_1',
"True",
'ala',
proptype=PROPERTY_BOOLEAN)
cmd.set_property('bool_property_2',
"True",
'ala',
proptype=PROPERTY_BOOLEAN)
cmd.set_property('bool_property_3',
"True",
'ala',
proptype=PROPERTY_BOOLEAN)
cmd.set_property('bool_property_4',
"False",
'ala',
proptype=PROPERTY_BOOLEAN)
self.assertEqual(cmd.get_property('bool_property_1', 'ala'), True)
self.assertEqual(cmd.get_property('bool_property_2', 'ala'),
True) # overwritting
self.assertEqual(cmd.get_property('bool_property_3', 'ala'), True)
self.assertEqual(cmd.get_property('bool_property_4', 'ala'), False)
def testSDF(self):
# get molecule with SDF annotations
cid = 6830
cmd.load('CID_%d.sdf' % cid, 'm1')
self.assertEqual(None, cmd.get_property('PUBCHEM_COMPOUND_CID', 'm1'),
'property loaded, but should not')
cmd.delete('*')
cmd.load('CID_%d.sdf' % cid, 'm1', object_props='*')
self.assertEqual(cid, cmd.get_property('PUBCHEM_COMPOUND_CID', 'm1'))
v_pc = cmd.get_property('PUBCHEM_MMFF94_PARTIAL_CHARGES', 'm1')
lines = v_pc.rstrip().splitlines()
n_pc = int(lines[0])
self.assertEqual(n_pc, len(lines) - 1)
# test loading selective properties
cmd.set('load_object_props_default', "PUBCHEM_COMPOUND_CID PUBCHEM_CONFORMER_RMSD PUBCHEM_CONFORMER_DIVERSEORDER")
cmd.load('CID_%d.sdf' % cid, 'm2')
self.assertEqual(cid, cmd.get_property('PUBCHEM_COMPOUND_CID', 'm2'))
self.assertEqual(None, cmd.get_property('PUBCHEM_EFFECTIVE_ROTOR_COUNT', 'm2'))
def test(self):
cmd.fragment('gly')
# atom properties
cmd.alter('index 2-4', 'p.r_custom_indexhalve = index / 2.0')
cmd.alter('index 3-5', 'p.neg_index = -index')
cmd.alter('elem C', 'p["spaced resn name"] = resn + " " + name')
# object properties
objprops = [
('first', 'Max'),
('last', 'Mustermann'),
('full name', 'Max Mustermann'),
('quoted "name"', 'Max "Mustermann"'),
]
for (key, value) in objprops:
cmd.set_property(key, value)
# save/load round-trip
with testing.mktemp('.mae') as filename:
cmd.save(filename)
cmd.delete('*')
cmd.set('load_object_props_default', '*')
cmd.set('load_atom_props_default', '*')
cmd.load(filename, 'm1')
# type conversions
cmd.alter('m1', 'p.neg_index = int(p.s_pymol_neg_index or 0)')
# atom properties
self.assertEqual(2, cmd.count_atoms('p.neg_index < -3'))
self.assertEqual(2, cmd.count_atoms('p.r_custom_indexhalve > 1.0'))
# changed in 2.3.1: undefined (<>) -> None
resnname = set()
cmd.iterate('m1', 'resnname.add(p["s_pymol_spaced resn name"] or "")', space=locals())
self.assertEqual(resnname, set(['GLY C', 'GLY CA', '']))
# object properties
for (key, value) in objprops:
self.assertEqual(cmd.get_property('s_pymol_' + key, 'm1'), value)
def testFloatType(self, val1, val2):
cmd.fragment('ala')
cmd.set_property('float_property_1', val1, 'ala')
cmd.set_property('float_property_2', val2, 'ala')
self.assertAlmostEqual(cmd.get_property('float_property_1', 'ala'), val1)
self.assertAlmostEqual(cmd.get_property('float_property_2', 'ala'), val2)
# test setting boolean type by string
cmd.set_property('float_property_1', str(val1), 'ala', proptype=PROPERTY_FLOAT)
cmd.set_property('float_property_2', str(val1), 'ala', proptype=PROPERTY_FLOAT)
cmd.set_property('float_property_3', str(val1), 'ala', proptype=PROPERTY_FLOAT)
cmd.set_property('float_property_4', str(val2), 'ala', proptype=PROPERTY_FLOAT)
self.assertAlmostEqual(cmd.get_property('float_property_1', 'ala'), val1)
self.assertAlmostEqual(cmd.get_property('float_property_2', 'ala'), val1) # overwritting
self.assertAlmostEqual(cmd.get_property('float_property_3', 'ala'), val1)
self.assertAlmostEqual(cmd.get_property('float_property_4', 'ala'), val2)
def testIntegerType(self, val1, val2):
cmd.fragment('ala')
cmd.set_property('int_property_1', val1, 'ala')
cmd.set_property('int_property_2', val2, 'ala')
self.assertEqual(cmd.get_property('int_property_1', 'ala'), val1)
self.assertEqual(cmd.get_property('int_property_2', 'ala'), val2)
# test setting boolean type by string
cmd.set_property('int_property_1', str(val1), 'ala', proptype=PROPERTY_INT)
cmd.set_property('int_property_2', str(val1), 'ala', proptype=PROPERTY_INT)
cmd.set_property('int_property_3', str(val1), 'ala', proptype=PROPERTY_INT)
cmd.set_property('int_property_4', str(val2), 'ala', proptype=PROPERTY_INT)
self.assertEqual(cmd.get_property('int_property_1', 'ala'), val1)
self.assertEqual(cmd.get_property('int_property_2', 'ala'), val1) # overwritting
self.assertEqual(cmd.get_property('int_property_3', 'ala'), val1)
self.assertEqual(cmd.get_property('int_property_4', 'ala'), val2)
def testBooleanType(self):
cmd.fragment('ala')
cmd.set_property('bool_property_1', True, 'ala')
cmd.set_property('bool_property_2', False, 'ala')
self.assertEqual(cmd.get_property('bool_property_1', 'ala'), True)
self.assertEqual(cmd.get_property('bool_property_2', 'ala'), False)
# test setting boolean type by string
cmd.set_property('bool_property_1', "True", 'ala', proptype=PROPERTY_BOOLEAN)
cmd.set_property('bool_property_2', "True", 'ala', proptype=PROPERTY_BOOLEAN)
cmd.set_property('bool_property_3', "True", 'ala', proptype=PROPERTY_BOOLEAN)
cmd.set_property('bool_property_4', "False", 'ala', proptype=PROPERTY_BOOLEAN)
self.assertEqual(cmd.get_property('bool_property_1', 'ala'), True)
self.assertEqual(cmd.get_property('bool_property_2', 'ala'), True) # overwritting
self.assertEqual(cmd.get_property('bool_property_3', 'ala'), True)
self.assertEqual(cmd.get_property('bool_property_4', 'ala'), False)
def testColorTypeCmd(self):
cmd.fragment('ala')
cmd.do('set_property color_prop, red, ala, proptype=5', echo=0)
prop = cmd.get_property('color_prop', 'ala')
self.assertColorEqual(prop, 'red')
def testColorTypeCmd(self):
cmd.fragment('ala')
cmd.do('set_property color_prop, red, ala, proptype=5', echo=0)
prop = cmd.get_property('color_prop', 'ala')
self.assertColorEqual(prop, 'red')
def testColorType(self, color1, color2):
# colors are saved as integers, but can be accessed/set by either strings or hex
from pymol.querying import get_color_index_from_string_or_list
val1 = get_color_index_from_string_or_list(color1, _self=cmd)
val2 = get_color_index_from_string_or_list(color2, _self=cmd)
cmd.fragment('ala')
cmd.set_property('color_property_1',
color1,
'ala',
proptype=PROPERTY_COLOR)
cmd.set_property('color_property_2',
color2,
'ala',
proptype=PROPERTY_COLOR)
self.assertColorEqual(cmd.get_property('color_property_1', 'ala'),
val1)
self.assertColorEqual(cmd.get_property('color_property_2', 'ala'),
val2)
self.assertColorEqual(cmd.get_property('color_property_1', 'ala'),
color1)
self.assertColorEqual(cmd.get_property('color_property_2', 'ala'),
color2)
cmd.set_property('color_property_1',
str(val1),
'ala',
proptype=PROPERTY_COLOR)
cmd.set_property('color_property_2',
str(val1),
'ala',
proptype=PROPERTY_COLOR)
cmd.set_property('color_property_3',
str(val1),
'ala',
proptype=PROPERTY_COLOR)
cmd.set_property('color_property_4',
str(val2),
'ala',
proptype=PROPERTY_COLOR)
self.assertColorEqual(cmd.get_property('color_property_1', 'ala'),
color1)
self.assertColorEqual(cmd.get_property('color_property_1', 'ala'),
val1)
self.assertColorEqual(cmd.get_property('color_property_2', 'ala'),
color1) # overwritting
self.assertColorEqual(cmd.get_property('color_property_2', 'ala'),
val1)
self.assertColorEqual(cmd.get_property('color_property_3', 'ala'),
color1)
self.assertColorEqual(cmd.get_property('color_property_3', 'ala'),
val1)
self.assertColorEqual(cmd.get_property('color_property_4', 'ala'),
color2)
self.assertColorEqual(cmd.get_property('color_property_4', 'ala'),
val2)
def testMAEloadNoProperties(self):
cmd.load(self.datafile('1d_smiles.mae'), '1d_smiles')
objs = cmd.get_object_list()
for obj in objs:
props = cmd.get_property('', obj)
self.assertIsNone(props)
def testColorType(self, color1, color2):
# colors are saved as integers, but can be accessed/set by either strings or hex
from pymol.querying import get_color_index_from_string_or_list
val1 = get_color_index_from_string_or_list(color1, _self=cmd)
val2 = get_color_index_from_string_or_list(color2, _self=cmd)
cmd.fragment('ala')
cmd.set_property('color_property_1', color1, 'ala', proptype=PROPERTY_COLOR)
cmd.set_property('color_property_2', color2, 'ala', proptype=PROPERTY_COLOR)
self.assertColorEqual(cmd.get_property('color_property_1', 'ala'), val1)
self.assertColorEqual(cmd.get_property('color_property_2', 'ala'), val2)
self.assertColorEqual(cmd.get_property('color_property_1', 'ala'), color1)
self.assertColorEqual(cmd.get_property('color_property_2', 'ala'), color2)
cmd.set_property('color_property_1', str(val1), 'ala', proptype=PROPERTY_COLOR)
cmd.set_property('color_property_2', str(val1), 'ala', proptype=PROPERTY_COLOR)
cmd.set_property('color_property_3', str(val1), 'ala', proptype=PROPERTY_COLOR)
cmd.set_property('color_property_4', str(val2), 'ala', proptype=PROPERTY_COLOR)
self.assertColorEqual(cmd.get_property('color_property_1', 'ala'), color1)
self.assertColorEqual(cmd.get_property('color_property_1', 'ala'), val1)
self.assertColorEqual(cmd.get_property('color_property_2', 'ala'), color1) # overwritting
self.assertColorEqual(cmd.get_property('color_property_2', 'ala'), val1)
self.assertColorEqual(cmd.get_property('color_property_3', 'ala'), color1)
self.assertColorEqual(cmd.get_property('color_property_3', 'ala'), val1)
self.assertColorEqual(cmd.get_property('color_property_4', 'ala'), color2)
self.assertColorEqual(cmd.get_property('color_property_4', 'ala'), val2)
def testMAEloadNoProperties(self):
cmd.load(self.datafile('1d_smiles.mae'), '1d_smiles')
objs = cmd.get_object_list()
for obj in objs:
props = cmd.get_property('', obj)
self.assertIsNone(props)
