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'''
test various settings
'''
import numpy
from pymol import cmd, testing
class TestSettings(testing.PyMOLTestCase):
def assertNumColorsEqual(self, img, count, delta=0):
self.assertTrue(len(numpy.unique(img[...,:3] // (delta + 1))) == count)
@testing.foreach(True, False)
def testStickBall(self, use_shader):
'''
Test some stick_ball* settings
'''
cmd.viewport(100, 100)
cmd.set('use_shaders', use_shader)
self.ambientOnly()
cmd.set('stick_ball')
cmd.set('stick_ball_ratio', 2.0)
cmd.set('stick_ball_color', 'blue')
cmd.set('stick_color', 'red')
cmd.fragment('gly')
cmd.orient()
cmd.color('green')
cmd.show_as('sticks')
img = self.get_imagearray()
self.assertImageHasColor('blue', img)
self.assertImageHasColor('red', img)
self.assertImageHasNotColor('green', img)
@testing.requires_version('1.7.5')
@testing.requires('no_edu')
@testing.requires('gui')
def testTransparencyMode3(self):
'''
Test if something gets rendered in transparency_mode=3
'''
cmd.viewport(100, 100)
cmd.fragment('gly')
cmd.zoom()
cmd.set('transparency_mode', 3)
cmd.set('transparency', 0.5)
cmd.set('stick_transparency', 0.5)
cmd.set('sphere_transparency', 0.5)
cmd.set('cartoon_transparency', 0.5)
for rep in ['sphere', 'stick', 'surface']:
cmd.show_as(rep)
# check on black screen to see if any shader failed
img = self.get_imagearray()
self.assertTrue(img[...,:3].any())
@testing.requires_version('1.7.4')
@testing.requires('incentive')
@testing.requires('no_edu')
@testing.requires('gui')
def testAA(self):
'''
Make a black/white image and check if gray pixels are found with
antialias_shader=1/2
'''
cmd.viewport(100, 100)
cmd.set('use_shaders', True)
self.ambientOnly()
cmd.fragment('gly')
cmd.show_as('spheres')
cmd.color('white')
cmd.zoom()
# b/w image, we expect only two color values
img = self.get_imagearray()
self.assertNumColorsEqual(img, 2)
for aa in (1, 2):
cmd.set('antialias_shader', aa)
# smoothed edges, we expect more than two color values
img = self.get_imagearray()
self.assertTrue(len(numpy.unique(img[...,:3])) > 2)
@testing.foreach(0, 1)
@testing.requires_version('1.7.5')
@testing.requires('gui')
def testTrilines(self, trilines):
cmd.viewport(100, 100)
cmd.set('use_shaders', True)
self.ambientOnly()
cmd.set('dynamic_width', 0)
cmd.set('line_width', 5)
cmd.set('line_smooth', 0)
cmd.fragment('ethylene')
cmd.show_as('lines')
cmd.color('white')
cmd.orient()
cmd.set('trilines', trilines)
# check percentage of covered pixels
img = self.get_imagearray()
npixels = img.shape[0] * img.shape[1]
covered = numpy.count_nonzero(img[...,:3])
ratio = covered / float(npixels)
msg = "covered=%d npixels=%d ratio=%f" % (covered, npixels, ratio)
self.assertTrue(0.14 < ratio < 0.165, msg)
@testing.requires_version('1.7.5')
@testing.requires('gui')
def testChromadepth(self):
cmd.viewport(100, 100)
self.ambientOnly()
cmd.set('use_shaders')
cmd.set('chromadepth')
cmd.set('orthoscopic')
cmd.pseudoatom(pos=(0, 0, -5))
cmd.pseudoatom(pos=(0, 0, 5))
cmd.color('gray')
cmd.show_as('spheres')
cmd.zoom()
cmd.turn('y', 20)
img = self.get_imagearray()
self.assertImageHasColor('blue', img)
self.assertImageHasColor('red', img)
@testing.requires_version('2.3')
def testAtomCartoonTransparency(self):
'''
Test atom-level cartoon_transparency
'''
cmd.load(self.datafile('1oky-frag.pdb'))
cmd.select('sele', 'resi 106-111', 0)
# hide blended parts between residues
cmd.cartoon('skip', 'resi 105+112')
return self._testAtomCartoonTransparency()
@testing.requires_version('2.3')
def testAtomCartoonTransparencyCylHelices(self):
'''
Test atom-level cartoon_transparency with cylindrical helices
'''
cmd.load(self.datafile('1oky-frag.pdb'))
cmd.select('sele', 'resi 113-', 0)
# hide blended parts between residues
cmd.cartoon('skip', 'resi 112')
cmd.set('cartoon_cylindrical_helices')
return self._testAtomCartoonTransparency()
@testing.requires_version('2.3')
def testAtomCartoonTransparencyNuc(self):
'''
Test atom-level cartoon_transparency with nucleic acid
'''
cmd.load(self.datafile('1ehz-5.pdb'))
cmd.select('sele', 'resi 4-', 0)
# hide blended parts between residues
cmd.cartoon('skip', 'resi 3')
return self._testAtomCartoonTransparency()
def _testAtomCartoonTransparency(self):
self.ambientOnly()
cmd.viewport(100, 100)
cmd.set('opaque_background')
cmd.set('ray_shadow', 0)
cmd.orient()
cmd.color('0xFF0000')
cmd.color('0x0000FF', 'sele')
# all opaque
img = self.get_imagearray()
self.assertImageHasColor('0xFF0000', img)
self.assertImageHasColor('0x0000FF', img)
# object-level transparency
cmd.set('cartoon_transparency', 0.4)
img = self.get_imagearray()
self.assertImageHasColor('0x990000', img) # 40%
self.assertImageHasColor('0x000099', img) # 40%
self.assertImageHasNotColor('0xFF0000', img)
self.assertImageHasNotColor('0x0000FF', img)
# atom-level full-opaque
cmd.set('cartoon_transparency', 0.0, 'sele')
img = self.get_imagearray()
self.assertImageHasColor('0x990000', img) # 40%
self.assertImageHasColor('0x0000FF', img) # 0%
self.assertImageHasNotColor('0xFF0000', img)
self.assertImageHasNotColor('0x000099', img)
# atom-level semi-transparent
cmd.set('cartoon_transparency', 0.6, 'sele')
img = self.get_imagearray()
self.assertImageHasColor('0x990000', img) # 40%
self.assertImageHasColor('0x000066', img, delta=1) # 60%
self.assertImageHasNotColor('0xFF0000', img)
self.assertImageHasNotColor('0x0000FF', img)
self.assertImageHasNotColor('0x000099', img)
# atom-level full-transparent (expect only two color values)
cmd.set('cartoon_transparency', 0.0)
cmd.set('cartoon_transparency', 1.0, 'sele')
img = self.get_imagearray()
self.assertImageHasColor('0xFF0000', img)
# need delta=1 with clang, but not with gcc
self.assertNumColorsEqual(img, 2, delta=1)
def _testTransparency(self, rep, setting_name):
cmd.fab('GGGG')
cmd.remove('resi 2+3')
cmd.select('sele', 'resi 4', 0)
self.ambientOnly()
cmd.viewport(100, 100)
cmd.set('opaque_background')
cmd.set('ray_shadow', 0)
cmd.orient()
cmd.color('0xFF0000')
cmd.show_as(rep)
# all opaque
img = self.get_imagearray()
self.assertImageHasColor('0xFF0000', img)
# object-level transparency
cmd.set(setting_name, 0.4)
img = self.get_imagearray()
self.assertImageHasColor('0x990000', img) # 40%
self.assertImageHasNotColor('0xFF0000', img)
# atom-level full-opaque
cmd.set(setting_name, 0.0, 'sele')
img = self.get_imagearray()
self.assertImageHasColor('0x990000', img) # 40%
self.assertImageHasColor('0xFF0000', img) # 0%
# atom-level semi-transparent
cmd.set(setting_name, 0.6, 'sele')
img = self.get_imagearray()
self.assertImageHasColor('0x990000', img) # 40%
self.assertImageHasColor('0x660000', img, delta=1) # 60%
self.assertImageHasNotColor('0xFF0000', img)
# atom-level full-transparent (expect only two color values)
cmd.set(setting_name, 0.0)
cmd.set(setting_name, 1.0, 'sele')
img = self.get_imagearray()
self.assertImageHasColor('0xFF0000', img)
# need delta=1 with clang, but not with gcc
self.assertNumColorsEqual(img, 2, delta=1)
def testStickTransparency(self):
self._testTransparency('sticks', 'stick_transparency')
def testSphereTransparency(self):
self._testTransparency('spheres', 'sphere_transparency')
def testSurfaceTransparency(self):
self._testTransparency('surface', 'transparency')
@testing.requires_version('2.5')
def testIsomeshTransparency(self):
self.ambientOnly()
cmd.set('opaque_background')
cmd.set('gaussian_b_floor', 30)
cmd.set('mesh_width', 5)
cmd.fragment('gly', 'm1')
cmd.hide('everything')
cmd.map_new('map1', 'gaussian', 0.5, 'm1')
cmd.isomesh('mesh1', 'map1')
# global
cmd.set('transparency', 0.75)
img = self.get_imagearray(width=100, height=100)
self.assertImageHasColor('0x3F3F3F', img)
self.assertImageHasNotColor('0xFFFFFF', img)
# object-level
cmd.set('transparency', 0.25, 'mesh1')
img = self.get_imagearray(width=100, height=100)
self.assertImageHasColor('0xBFBFBF', img)
self.assertImageHasNotColor('0xFFFFFF', img)
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