62 lines
2.0 KiB
Python
62 lines
2.0 KiB
Python
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'''
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mmpymolx specific functionality
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See also: tests/jira/PYMOL-317.py (text_type test)
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'''
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from pymol import cmd, testing, stored
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import unittest
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@testing.requires('incentive')
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@testing.requires('no_edu')
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class TestMMPyMOLx(testing.PyMOLTestCase):
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@testing.requires('mmlibs')
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def testStereo(self):
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cmd.fragment('ala')
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cmd.remove('hydro')
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# default: S configuration
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labels = []
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cmd.iterate('name CA', 'labels.append(stereo)', space=locals())
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self.assertEqual(labels, ['S'])
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# load R configuration (moves CB)
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ala_conf_R = {
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'N' : (-0.67690, -1.23030, -0.49050),
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'CA' : (-0.00090, 0.06370, -0.49050),
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'C' : ( 1.49910, -0.11030, -0.49050),
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'O' : ( 2.03010, -1.22730, -0.50150),
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# 'CB' : (-0.50890, 0.85570, 0.72650), # S configuration
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'CB' : (-0.33784, 0.82664, -1.78310), # R configuration
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}
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cmd.alter_state(1, 'ala', '(x,y,z) = ala_conf_R.get(name)', space=locals())
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labels = []
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cmd.iterate('name CA', 'labels.append(stereo)', space=locals())
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self.assertEqual(labels, ['R'])
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@testing.requires('mmlibs')
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def testStereoPYMOL2782(self):
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# L-Cysteine has R configuration
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cmd.fragment('cys')
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labels = []
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cmd.iterate('name CA', 'labels.append(stereo)', space=locals())
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self.assertEqual(labels, ['R'])
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def testLoadMTZ(self):
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cmd.load_mtz(self.datafile('4rwb.mtz'), 'foo',
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'cryst_1/data_1/FP',
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'cryst_1/data_1/PHIC')
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self.assertEqual(cmd.get_names(), ['foo'])
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extent = cmd.get_extent('foo')
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self.assertArrayEqual(extent, [
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[ 0.000, 0.000, 0.000],
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[ 37.585, 40.586, 27.214]], delta=1e-3, msg='extend wrong')
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# min, max, mean, stdev
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mmms = cmd.get_volume_histogram('foo', 0)
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self.assertArrayEqual(mmms, [-2.6767, 4.9998, 0.0, 1.0], delta=1e-4,
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msg='histogram wrong')
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