from pymol import cmd, testing, stored, CmdException

class TestQuerying(testing.PyMOLTestCase):

    def _testMeasure(self, func, getfunc, natom, value):
        name = "m_obj"
        cmd.fragment("gly")
        
        r = func(name, *["index %d" % (i+1) for i in range(natom)])
        self.assertAlmostEqual(r, value, delta=1e-2)
        self.assertTrue(name in cmd.get_names())
        
        r = getfunc(*["index %d" % (i+1) for i in range(natom)])
        self.assertAlmostEqual(r, value, delta=1e-2)

    def testAngle(self):
        self._testMeasure(cmd.angle, cmd.get_angle, 3, 110.99)

    def testAutoMeasure(self):
        cmd.fragment("gly")

        for (N, prefix) in enumerate(["dist", "angle", "dihedral"], 2):
            cmd.set("dist_counter", 0)
            cmd.edit(*["index %d" % (i + 1) for i in range(N)])
            cmd.auto_measure()
            self.assertTrue(prefix + "01" in cmd.get_names(), prefix)

    def testCountAtoms(self):
        # used in many tests
        pass

    def testCountFrames(self):
        self.assertEqual(cmd.count_frames(), 0)
        cmd.pseudoatom("m1")
        self.assertEqual(cmd.count_frames(), 1)
        cmd.mset("1x3")
        self.assertEqual(cmd.count_frames(), 3)

    def testCountStates(self):
        self.assertEqual(cmd.count_states(), 0)
        cmd.pseudoatom("m1")
        self.assertEqual(cmd.count_states(), 1)
        cmd.create("m1", "m1", 1, 2)
        self.assertEqual(cmd.count_states(), 2)

    @testing.requires_version('2.1')
    def testDihedral(self):
        # result was 0.01318 due to numeric precision in get_angle3f
        self._testMeasure(cmd.dihedral, cmd.get_dihedral, 4, 0.0)

    def testDistance(self):
        self._testMeasure(cmd.distance, cmd.get_distance, 2, 1.46011)

    @testing.requires_version('2.2')
    def testMeasureBetweenStates(self):
        cmd.load(self.datafile('1v5a-3models.cif'), 'm1')

        # distance
        d = cmd.distance('d1', '24/CZ', 'same', state1=2, state2=3)
        self.assertAlmostEqual(d, 3.0, delta=1e-1)

        # angle
        a = cmd.angle('a1', '24/CZ', 'same', 'same', state1=2, state2=3, state3=1)
        self.assertAlmostEqual(a, 73.5, delta=1e-1)

        # visual test
        cmd.viewport(100, 100)
        cmd.set('dash_radius', 1.0)
        self.ambientOnly()
        for name in ['d1', 'a1']:
            cmd.disable('*')
            cmd.enable(name)
            cmd.zoom(name)
            self.assertImageHasColor('yellow')

    def testFindPairs(self):
        # mode 0
        cmd.fragment("gly")
        pairs = cmd.find_pairs("hydro", "elem O")
        pairs_ref = [
            (('gly', 5), ('gly', 4)),
            (('gly', 6), ('gly', 4)),
            (('gly', 7), ('gly', 4)),
        ]
        self.assertEqual(sorted(pairs), pairs_ref)

        # mode 1
        cmd.fab("GGGGG", "m2", ss=1)
        pairs = cmd.find_pairs("m2 & donor", "m2 & acceptor", mode=1)
        self.assertEqual(pairs, [(('m2', 29), ('m2', 4))])

    def testGetAngle(self):
        # see testAngle
        pass

    def testGetArea(self):
        cmd.fragment("gly")
        r = cmd.get_area(load_b=1)
        b_list = []
        cmd.iterate("elem O", "b_list.append(b)", space=locals())
        self.assertAlmostEqual(r, 82.505165, delta=1e-2)
        self.assertAlmostEqual(b_list[0], 15.47754, delta=1e-2)
        cmd.set("dot_solvent")
        self.assertAlmostEqual(cmd.get_area(), 200.145, delta=1e-2)
        cmd.set("dot_density", 4)
        self.assertAlmostEqual(cmd.get_area(), 200.888, delta=1e-2)

    @testing.requires_version('2.5')
    def testGetArea_flags(self):
        cmd.fragment("gly")
        area_not_O = cmd.get_area('not elem O')
        self.assertTrue(cmd.get_area() > area_not_O)
        cmd.flag('exfoliate', 'elem O')
        self.assertEqual(cmd.get_area(), area_not_O)
        cmd.flag('ignore', 'elem N')
        area_ignore_N = cmd.get_area()
        self.assertNotEqual(area_ignore_N, area_not_O)
        self.assertEqual(cmd.count_atoms(), 7)
        cmd.remove('elem N')
        self.assertEqual(cmd.count_atoms(), 6)
        self.assertEqual(cmd.get_area(), area_ignore_N)
        cmd.flag('ignore', 'all')
        self.assertEqual(cmd.get_area(), 0.0)

    def testGetAtomCoords(self):
        cmd.fragment("gly")
        coords = cmd.get_atom_coords("elem O")
        coords_ref = [0.545436, -0.974895, 1.498943]
        self.assertArrayEqual(coords, coords_ref, delta=1e-4)
        self.assertRaises(CmdException, cmd.get_atom_coords, "*")

    def testGetChains(self):
        cmd.pseudoatom("m1", chain="C")
        self.assertEqual(cmd.get_chains(), ["C"])

    def testGetColorIndex(self):
        self.assertEqual(cmd.get_color_index("blue"), 2)

    def testGetColorIndices(self):
        r = cmd.get_color_indices()
        self.assertTrue(set(r).issuperset([('white', 0), ('black', 1), ('blue', 2)]))
        self.assertFalse(('grey50', 104) in r)
        r = cmd.get_color_indices(all=1)
        self.assertTrue(('grey50', 104) in r)

    def testGetColorTuple(self):
        self.assertEqual((0.0, 0.0, 1.0), cmd.get_color_tuple("blue"))

    def testGetDihedral(self):
        # see testDihedral
        pass

    def testGetDistance(self):
        # see testDistance
        pass

    def testGetDragObjectName(self):
        cmd.fragment('gly')
        self.assertEqual(cmd.get_drag_object_name(), '')
        cmd.drag('gly')
        self.assertEqual(cmd.get_drag_object_name(), 'gly')

    def testGetExtent(self):
        cmd.load(self.datafile("1ehz-5.pdb"), "m1")
        self.assertArrayEqual(cmd.get_extent(),
                [[49.85, 40.59, 41.73], [69.99, 51.73, 56.47]], delta=1e-2)
        self.assertArrayEqual(cmd.get_extent("resi 3"),
                [[58.29, 40.87, 48.52], [64.74, 50.42, 55.29]], delta=1e-2)
        cmd.load(self.datafile("h2o-elf.cube"), "map1")
        self.assertArrayEqual(cmd.get_extent("map1"),
                [[-0.075, -0.075, -0.075], [5.925, 5.925, 5.925]], delta=1e-2)

    def testGetIdtf(self):
        cmd.fragment('gly')
        cmd.show_as('surface')
        r = cmd.get_idtf()
        self.assertTrue(isinstance(r, tuple))
        self.assertEqual(len(r), 2)
        self.assertTrue(r[0].startswith('FILE_FORMAT "IDTF"'))
        self.assertTrue('MODEL_POSITION_LIST' in r[1])
        self.assertTrue('MODEL_NORMAL_LIST' in r[1])

    def testGetLegalName(self):
        self.assertEqual(cmd.get_legal_name("foo bar baz"), "foo_bar_baz")

    def testGetModalDraw(self):
        self.assertEqual(cmd.get_modal_draw(), 0)

    def testGetModel(self):
        '''
        Test coordinates and "reference" coordinates with various
        transformations.
        '''

        # create two-state object
        # displace state 1, will do tests on state 2
        cmd.fragment('ala', 'm1')
        cmd.create('m1', 'm1', 1, 2)
        cmd.translate([1, 2, 3], 'm1', 1)

        # prepare state 2
        title = 'Alanin'
        cmd.set_title('m1', 2, title)
        cmd.reference(state=2)

        # with original coordinates
        m = cmd.get_model(state=2)
        a = m.atom[0]

        # title
        self.assertEqual(title, m.molecule.title)

        # bonds (covering count, indices and order)
        self.assertEqual(
                set(tuple(sorted(b.index)) + (b.order,) for b in m.bond),
                set([(0, 1, 1), (0, 5, 1), (1, 2, 1), (1, 4, 1), (1, 6, 1),
                    (2, 3, 2), (4, 7, 1), (4, 8, 1), (4, 9, 1)]))

        # expect equal coord and ref_coord
        coord = [-0.67689997, -1.23029995, -0.49050000]
        self.assertArrayEqual(a.ref_coord,  coord, delta=1e-4)
        self.assertArrayEqual(a.coord,      coord, delta=1e-4)

        # modify ttt
        cmd.set_object_ttt('m1', [
          0, 1, 0, 0,
         -1, 0, 0, 5,
          0, 0, 1, 0,
          0, 3, 0, 1,
        ]) # no state! API flaw, TTT object are not per state
        m = cmd.get_model('m1', state=2)
        a = m.atom[0]

        # ttt should affect both equally
        coord = [1.769700050354004, 5.6768999099731445, -0.49050000309944153]
        self.assertArrayEqual(a.ref_coord,  coord, delta=1e-4)
        self.assertArrayEqual(a.coord,      coord, delta=1e-4)

        # modify coords
        cmd.translate([10, 0, 0], state=2)
        m = cmd.get_model('m1', state=2)
        a = m.atom[0]

        # no effect of ref_coord
        ref = coord
        coord = [11.769700050354004, 5.6768999099731445, -0.49050000309944153]
        self.assertArrayEqual(a.ref_coord,  ref, delta=1e-4)
        self.assertArrayEqual(a.coord,      coord, delta=1e-4)

        # modify coords by alignment
        cmd.fragment('ala', 'm2')
        cmd.rotate('x', 90, 'm2')
        cmd.align('m1', 'm2', mobile_state=2)
        m = cmd.get_model('m1', state=2)
        a = m.atom[0]

        # no effect of ref_coord
        coord = [3.490499973297119, 5.6768999099731445, -1.230299949645996]
        self.assertArrayEqual(a.ref_coord,  ref, delta=1e-4)
        self.assertArrayEqual(a.coord,      coord, delta=1e-4)

    def testGetMovieLength(self):
        cmd.fragment('gly')
        self.assertEqual(cmd.get_movie_length(), 0)
        cmd.mset('1x10')
        self.assertEqual(cmd.get_movie_length(), 10)
        self.assertEqual(cmd.get_movie_length(images=1), 0)

    def testGetMovieLocked(self):
        self.assertEqual(cmd.get_movie_locked(), 0)
        cmd.mset('1x1')
        cmd.mdo(1, 'cmd.color("blue")')
        s = cmd.get_session()
        cmd.set_session(s)
        self.assertEqual(cmd.get_movie_locked(), 1)
        cmd.set('security', 0)
        cmd.set_session(s)
        self.assertEqual(cmd.get_movie_locked(), 0)

    def testGetMtlObj(self):
        cmd.fragment('gly')
        cmd.show_as('surface')
        r = cmd.get_mtl_obj()
        self.assertTrue(isinstance(r, tuple))
        self.assertEqual(len(r), 2)
        lines = r[1].splitlines()
        self.assertTrue(lines[0].startswith('v '))
        self.assertTrue(lines[1].startswith('v '))
        self.assertTrue(lines[2].startswith('v '))
        self.assertTrue(lines[3].startswith('vn '))
        self.assertTrue(lines[4].startswith('vn '))
        self.assertTrue(lines[5].startswith('vn '))
        self.assertTrue(lines[6].startswith('f '))
        self.assertTrue(all(len(line.split()) == 4 for line in lines))

    def testGetNames(self):
        cmd.fragment('gly')
        cmd.fragment('cys')
        cmd.ramp_new('ramp1', 'none')  # non-molecular object
        cmd.select('foo', 'none')
        self.assertEqual(cmd.get_names(), ['gly', 'cys', 'ramp1'])
        self.assertEqual(cmd.get_names(selection="elem S"), ['cys'])
        cmd.disable('gly')
        cmd.disable('ramp1')
        self.assertEqual(cmd.get_names(enabled_only=1), ['cys'])
        self.assertEqual(cmd.get_names('selections'), ['foo'])
        self.assertEqual(cmd.get_names('all'), ['gly', 'cys', 'ramp1', 'foo'])

    @testing.requires_version('1.6')
    def testGetNamesOfType(self):
        cmd.fragment('gly', 'm1')
        cmd.fragment('ala', 'm2')
        cmd.ramp_new('ramp1', 'none')
        self.assertEqual(cmd.get_names_of_type('object:molecule'), ['m1', 'm2'])
        self.assertEqual(cmd.get_names_of_type('object:ramp'), ['ramp1'])
        self.assertEqual(cmd.get_names_of_type('object:map'), [])

    def testGetObjectColorIndex(self):
        cmd.fragment('gly', 'm1')
        cmd.color(3, 'm1')
        self.assertEqual(cmd.get_object_color_index('m1'), 3)
        cmd.color(5, '(m1)')
        self.assertEqual(cmd.get_object_color_index('m1'), 3)
        cmd.color(5, 'm1')
        self.assertEqual(cmd.get_object_color_index('m1'), 5)
        cmd.set_object_color('m1', 7)
        self.assertEqual(cmd.get_object_color_index('m1'), 7)

    def testGetObjectList(self):
        cmd.fragment('gly')
        cmd.fragment('cys')
        cmd.ramp_new('ramp1', 'none')  # non-molecular object
        self.assertEqual(cmd.get_object_list(), ['gly', 'cys'])
        self.assertEqual(cmd.get_object_list('elem S'), ['cys'])

    @testing.requires_version('1.6')
    def testGetObjectMatrix(self):
        identity = (
            1.0, 0.0, 0.0, 0.0,
            0.0, 1.0, 0.0, 0.0,
            0.0, 0.0, 1.0, 0.0,
            0.0, 0.0, 0.0, 1.0)
        mat_x90 = (
            1.0, 0.0,  0.0, 0.0,
            0.0, 0.0, -1.0, 0.0,
            0.0, 1.0,  0.0, 0.0,
            0.0, 0.0,  0.0, 1.0)

        cmd.fragment('ala', 'm1')
        cmd.fragment('gly', 'm2')

        # default/identity
        mat = cmd.get_object_matrix('m1', incl_ttt=1)
        self.assertTrue(isinstance(mat, tuple))
        self.assertArrayEqual(mat, identity, delta=1e-6)
        mat = cmd.get_object_matrix('m1', incl_ttt=0)
        self.assertArrayEqual(mat, identity, delta=1e-6)

        # TTT
        cmd.rotate('x', 90, object='m1', camera=0, object_mode=0)
        mat = cmd.get_object_matrix('m1', incl_ttt=1)
        self.assertArrayEqual(mat, mat_x90, delta=1e-6)
        mat = cmd.get_object_matrix('m1', incl_ttt=0)
        self.assertArrayEqual(mat, identity, delta=1e-6)

        # state matrix
        cmd.rotate('x', 90, object='m2', camera=0, object_mode=1)
        mat = cmd.get_object_matrix('m2', incl_ttt=1)
        self.assertArrayEqual(mat, mat_x90, delta=1e-6)
        mat = cmd.get_object_matrix('m2', incl_ttt=0)
        self.assertArrayEqual(mat, mat_x90, delta=1e-6)

    def assertPhiPsiEqual(self, pp, pp_ref):
        self.assertEqual(len(pp), len(pp_ref))
        for key in pp:
            self.assertArrayEqual(pp[key], pp_ref[key], delta=1e-2)

    def _testGetPhipsi(self, func):
        cmd.load(self.datafile("1oky-frag.pdb"), "m1")
        pp = func("resi 1-81")
        self.assertPhiPsiEqual(pp, {
            ('m1', 13): (-43.4902, -42.8589),
            ('m1', 20): (-61.0592, -19.4712),
            ('m1', 29): (-72.9009, -8.8334)
        })
        pp = func("resi 117- & name CA")
        self.assertPhiPsiEqual(pp, {
            ('m1', 316): (-59.7243, -43.9939),
            ('m1', 326): (-61.4714, -47.4775)
        })

    def testGetPhipsi(self):
        return self._testGetPhipsi(cmd.get_phipsi)

    def testGetPosition(self):
        cmd.pseudoatom(pos=(1, 2, 3))
        self.assertArrayEqual(cmd.get_position(), [0., 0., 0.], delta=1e-4)
        cmd.zoom(animate=0)
        self.assertArrayEqual(cmd.get_position(), [1., 2., 3.], delta=1e-4)

    def testGetPovray(self):
        cmd.fragment('gly')
        cmd.show_as('sticks')
        pov = cmd.get_povray()
        self.assertTrue(isinstance(pov, tuple))
        self.assertEqual(len(pov), 2)
        self.assertTrue(pov[0].startswith('camera {direction<0.0,0.0'))
        self.assertTrue(pov[1].startswith('cylinder{<'))

    def testGetRawAlignment(self):
        from collections import defaultdict
        cmd.fab('ACDEGGKLMN', 'm1')
        cmd.fab('CDEFFGGK', 'm2')
        cmd.fab('ASDEKLMNFY', 'm3')
        cmd.align('m2 & guide', 'm1 & guide', cycles=0, object='aln')
        cmd.align('m3 & guide', 'm1 & guide', cycles=0, object='aln')
        cmd.disable('m2')
        # expecting alignment:
        # m1 ACDE--GGKLMN--
        # m2 -CDEFFGGK-----
        # m3 ASDE----KLMQFY
        guideids = defaultdict(list)
        cmd.iterate('guide', 'guideids[model].append(index)', space=locals())
        idx = lambda m, i: (m, guideids[m][i])
        aln_expect = [
            [idx('m1', 0),               idx('m3', 0)],
            [idx('m1', 1), idx('m2', 0), idx('m3', 1)],
            [idx('m1', 2), idx('m2', 1), idx('m3', 2)],
            [idx('m1', 3), idx('m2', 2), idx('m3', 3)],
            [idx('m1', 4), idx('m2', 5),             ],
            [idx('m1', 5), idx('m2', 6),             ],
            [idx('m1', 6), idx('m2', 7), idx('m3', 4)],
            [idx('m1', 7),               idx('m3', 5)],
            [idx('m1', 8),               idx('m3', 6)],
            [idx('m1', 9),               idx('m3', 7)],
        ]
        dictify = lambda aln: [dict(col) for col in aln]
        aln_expect = dictify(aln_expect)

        aln = cmd.get_raw_alignment('aln', 0)
        self.assertEqual(dictify(aln), aln_expect)

        # remove m2 from alignment
        for d in aln_expect:
            d.pop('m2', None)

        aln = cmd.get_raw_alignment('aln', 1)
        self.assertEqual(dictify(aln), aln_expect)

    def testGetRenderer(self):
        r = cmd.get_renderer()
        self.assertEqual(len(r), 3)

    @testing.requires_version('1.5')
    def testGetSymmetry(self):
        cmd.load(self.datafile('1rx1.pdb'))
        sym = cmd.get_symmetry('1rx1')
        self.assertArrayEqual(sym[:6],
                [34.455, 45.370, 98.701, 90.0, 90.0, 90.0], delta=1e-3)
        self.assertEqual(sym[6], 'P 21 21 21')

        cmd.fragment('gly', 'm1')
        self.assertTrue(cmd.get_symmetry('m1') is None)

    def testGetTitle(self):
        cmd.fragment('gly', 'm1')
        cmd.create('m1', 'm1', 1, 2)
        title = cmd.get_title('m1', 1)
        self.assertEqual(title, '')
        cmd.set_title('m1', 1, 'foo bar')
        title = cmd.get_title('m1', 1)
        self.assertEqual(title, 'foo bar')
        title = cmd.get_title('m1', 2)
        self.assertEqual(title, '')
        cmd.set_title('m1', 2, 'second state')
        title = cmd.get_title('m1', 2)
        self.assertEqual(title, 'second state')

    @testing.requires_version('1.6')
    def testGetType(self):
        cmd.fragment('gly', 'm1')
        self.assertEqual(cmd.get_type('m1'), 'object:molecule')
        cmd.ramp_new('ramp1', 'none')
        self.assertEqual(cmd.get_type('ramp1'), 'object:ramp')
        cmd.select('s1', 'elem C')
        self.assertEqual(cmd.get_type('s1'), 'selection')

    def testGetUnusedName(self):
        n1 = cmd.get_unused_name()
        self.assertEqual(n1, "tmp01")
        n2 = cmd.get_unused_name("foo", 0)
        self.assertEqual(n2, "foo")
        cmd.pseudoatom("foo")
        n3 = cmd.get_unused_name("foo", 0)
        self.assertEqual(n3, "foo01")
        cmd.pseudoatom("foo01")
        cmd.pseudoatom("foo02")
        n4 = cmd.get_unused_name("foo")
        self.assertEqual(n4, "foo03")
        cmd.delete('*')
        n5 = cmd.get_unused_name("foo")
        self.assertEqual(n5, "foo01")

    def testGetVersion(self):
        # see tests/api/get_version.py
        pass

    @testing.requires_version('1.7.3.0')
    def testGetVolumeField(self):
        import numpy
        cmd.load(self.datafile('emd_1155.ccp4'), 'map1')
        fieldcopy = cmd.get_volume_field('map1')
        field = cmd.get_volume_field('map1', copy=0)
        self.assertEqual(field.shape, (141, 91, 281))
        self.assertTrue(numpy.allclose(field, fieldcopy))

        # data manipulation with copy=0
        mean1 = field.mean()
        field += 5.0
        mean2 = cmd.get_volume_field('map1', copy=0)[:].mean()
        self.assertAlmostEqual(mean1 + 5.0, mean2, delta=1e-2)

    @testing.requires_version('1.7.3.0')
    def testGetVolumeHistogram(self):
        cmd.load(self.datafile('h2o-elf.cube'), 'map1')
        hist1 = cmd.get_volume_histogram('map1', 10)
        self.assertEqual(len(hist1), 14)
        hist2 = cmd.get_volume_histogram('map1', 2)
        self.assertArrayEqual(hist2, [-0.0151, 0.9292, 0.0692, 0.1720, 63812.0, 188.0], delta=1e-4)
        self.assertArrayEqual(hist1[:4], hist2[:4])
        self.assertEqual(sum(hist1[4:]), sum(hist2[4:]))
        hist2 = cmd.get_volume_histogram('map1', 2, (0.3, 0.7))
        self.assertArrayEqual(hist2, [0.3, 0.7, 0.0692, 0.172, 62263.0, 1737.0], delta=1e-4)

    def testGetVrml(self):
        cmd.fragment('gly')
        cmd.show_as('sticks')
        s = cmd.get_vrml()
        self.assertTrue(s.startswith('#VRML V'))
        self.assertTrue('geometry Cylinder' in s)
        cmd.show_as('spheres')
        s = cmd.get_vrml()
        self.assertFalse('geometry Cylinder' in s)
        self.assertTrue('geometry Sphere' in s)

    def testIdAtom(self):
        cmd.fragment('gly', 'm1')
        self.assertEqual(cmd.id_atom('ID 3'), 3)
        self.assertEqual(cmd.id_atom('ID 3', 1), ('m1', 3))
        cmd.feedback("disable", "cmd", "errors")
        self.assertRaises(CmdException, cmd.id_atom, 'ID 3+4')
        self.assertRaises(CmdException, cmd.id_atom, 'ID 100')

    def testIdentify(self):
        cmd.fragment('gly', 'm1')
        cmd.select('s1', 'ID 3+4')
        r = cmd.identify('s1')
        self.assertItemsEqual(r, [3, 4])
        r = cmd.identify('s1', 1)
        self.assertItemsEqual(r, [('m1', 3), ('m1', 4)])

    def testIndex(self):
        cmd.fragment('gly', 'm1')
        r = cmd.index('index 3+4')
        self.assertItemsEqual(r, [('m1', 3), ('m1', 4)])

    def testOverlap(self):
        # unsupported command
        cmd.pseudoatom('m1', vdw=2.0)
        cmd.pseudoatom('m2', vdw=2.0, pos=(2., 0., 0.))
        r = cmd.overlap('m1', 'm2')
        # this is actually half the vdw overlap
        self.assertEqual(r, 1.0)

    def testPhiPsi(self):
        return self._testGetPhipsi(cmd.phi_psi)

    @testing.requires_version('2.1')
    def testGetBonds(self):
        self.assertEqual([], cmd.get_bonds())
        cmd.fragment('gly')
        self.assertEqual([], cmd.get_bonds('none'))
        self.assertEqual([
            (0, 1, 1), # C-C
            (1, 2, 2), # C=O
        ], cmd.get_bonds('elem C+O'))
        self.assertEqual([
            (0, 1, 1),
            (0, 4, 1),
            (1, 2, 1),
            (1, 5, 1),
            (1, 6, 1),
            (2, 3, 2),
        ], cmd.get_bonds())

    @testing.requires('incentive')
    @testing.requires_version('2.4')
    def testPiInteractions(self):
        # 1rx1 has 4 pi-pi and 1 pi-cation
        coords_ref_pi_pi = [
                30.962, 56.116,  4.616, 27.154, 59.807,  4.965,
                23.588, 39.248, 24.729, 18.578, 38.629, 23.297,
                28.754, 34.308, 11.073, 31.535, 31.381, 12.396,
                36.444, 30.384, 13.916, 31.535, 31.381, 12.396]
        coords_ref_pi_cat = [
                24.198, 57.834, 15.137, 25.219, 59.507, 17.986]
        coords_ref_pi = coords_ref_pi_pi + coords_ref_pi_cat

        cmd.load(self.datafile('1rx1.pdb'))

        cmd.pi_interactions('p1')
        coords = cmd.get_session('p1', 1)['names'][0][5][2][0][1]
        self.assertArrayEqual(coords, coords_ref_pi, delta=1e-2)

        cmd.distance('p2', '1rx1', 'same', mode=6)
        coords = cmd.get_session('p2', 1)['names'][0][5][2][0][1]
        self.assertArrayEqual(coords, coords_ref_pi_pi, delta=1e-2)

        cmd.distance('p3', '1rx1', 'same', mode=7)
        coords = cmd.get_session('p3', 1)['names'][0][5][2][0][1]
        self.assertArrayEqual(coords, coords_ref_pi_cat, delta=1e-2)

    # incentive: 1.8.4, open-source: 2.1
    @testing.requires_version('2.1')
    def test_get_object_settings(self):
        cmd.pseudoatom("m1")
        # global (should have no influence)
        cmd.set("half_bonds")
        # object-level
        cmd.set("cartoon_gap_cutoff", 5, "m1")
        cmd.set("grid_slot", 3, "m1")
        cmd.set("wildcard", "#", "m1")
        # ostate-level
        cmd.set("cartoon_gap_cutoff", 7, "m1", 1)
        cmd.set("ribbon_sampling", 9, "m1", 1)
        # object-level
        s = cmd.get_object_settings("m1")
        self.assertEqual(s, [[412, 6, '#'], [579, 2, 3], [750, 2, 5]])
        # ostate-level
        s = cmd.get_object_settings("m1", state=1)
        self.assertEqual(s, [[19, 2, 9], [750, 2, 7]])