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