def png(self, filename, *args, **kwargs):
'''
Save image to filename, with antialias=0.
'''
cmd.unset('antialias')
cmd.png(filename, *args, **kwargs)
cmd.draw()
def test(self):
cmd.set('suspend_updates')
cmd.set('depth_cue', 0)
cmd.set('ambient', 1)
cmd.set('specular', 0)
cmd.set('stereo_angle', 10)
cmd.pseudoatom()
cmd.show_as('sphere')
cmd.zoom()
cmd.stereo('anaglyph')
cmd.set('suspend_updates', 0)
wh = (40, 40)
cmd.draw(*wh, antialias=0)
cmd.sync()
img = self.get_imagearray(prior=1)
self.assertEqual(wh, img.shape[:2])
# ray tracing and shaders in PyMOL 1.7.6+:
# 0xe50000
# 0x00e5e5
# -> delta=26 (0x1a)
self.assertImageHasColor('0xff0000', img, delta=0x1a)
self.assertImageHasColor('0x00ffff', img, delta=0x1a)
def testDirtyDelete(self):
cmd.pseudoatom('m1')
cmd.pseudoatom('m2')
cmd.group('g1', 'm1 m2')
cmd.set_wizard(MockWizard())
cmd.draw()
v = cmd.get_object_list('(g1)')
self.assertEqual(v, ['m1', 'm2'])
def testPngExists(self):
'''
Save a PNG image with width/height specified and
check if the file exists.
'''
cmd.pseudoatom('m1')
cmd.show('spheres')
with testing.mktemp('.png') as filename:
cmd.png(filename, width=100, height=100, ray=0)
cmd.draw()
self.assertTrue(os.path.exists(filename), 'png file not written')
def test(self, ribbon_as_cylinders):
cmd.set('ribbon_as_cylinders', ribbon_as_cylinders)
cmd.set('ribbon_width', 8)
cmd.fab('AG')
cmd.color('red', 'resn ALA')
cmd.color('blue', 'resn GLY')
cmd.show_as('ribbon')
cmd.orient()
self.ambientOnly()
cmd.viewport(100, 100)
cmd.draw(100, 100)
img = self.get_imagearray()
self.assertImageHasColor('red', img)
self.assertImageHasColor('blue', img)
def render_false_color_image(width, height, filename=''):
global tmpdir
tmpFile = get_temporary_file(filename)
# draw with antialiasing disabled
cmd.draw(width, height, 0)
cmd.png(tmpFile)
while not os.path.exists(tmpFile):
time.sleep(1)
if DEBUG:
print "created temporary file %s" % tmpFile
return tmpFile
def test(self, ribbon_as_cylinders):
cmd.set('ribbon_as_cylinders', ribbon_as_cylinders)
cmd.set('ribbon_width', 8)
cmd.fab('AG')
cmd.color('red', 'resn ALA')
cmd.color('blue', 'resn GLY')
cmd.show_as('ribbon')
cmd.orient()
self.ambientOnly()
cmd.viewport(100, 100)
cmd.draw(100, 100)
img = self.get_imagearray()
self.assertImageHasColor('red', img)
self.assertImageHasColor('blue', img)
def testAsyncBuilds(self, rep, async_builds):
target = "1aon"
if async_builds:
msg = '%s cpus' % max_threads
else:
msg = '1 cpu'
cmd.set("async_builds", async_builds)
cmd.load(self.datafile('1aon.pdb.gz'), target)
for x in cmd.get_chains():
cmd.create("Chain_%s" % x, target + " & c. " + x)
cmd.delete(target)
with self.timing('%s' % msg):
cmd.show_as(rep)
cmd.draw()
# NLS
for r in range(680, 742):
cmd.color('firebrick', 'resi {0} and S009'.format(r))
###### SETVIEW
cmd.set_view ('\
0.636402488, 0.699312985, -0.325504273,\
-0.565354168, 0.135798618, -0.813591778,\
-0.524754405, 0.701796234, 0.481783271,\
0.000000000, 0.000000000, -429.757751465,\
-69.421409607, 7.238445282, 72.295677185,\
338.824279785, 520.691223145, -20.000000000 ')
###### POSTAMBLE
cmd.select(None)
cmd.set('specular', "off")
cmd.draw(width=1000, height=1000)
cmd.png('{0}_{1}.png'.format(structure, metric), ray=1)
cmd.rotate('y', angle=180)
cmd.draw(width=1000, height=1000)
cmd.png('{0}_{1}_y.png'.format(structure, metric), ray=1)
cmd.rotate('y', angle=180)
cmd.rotate('x', angle=90)
cmd.draw(width=1000, height=1000)
cmd.png('{0}_{1}_x.png'.format(structure, metric), ray=1)
def _pngExistsAsync(self, filename, sync_in_thread):
cmd.png(filename, width=100, height=100, ray=0)
cmd.draw()
if sync_in_thread:
cmd.sync()
def test2668(self):
cmd.pseudoatom('m1', pos=(-.4, 0, 0))
cmd.pseudoatom('m2', pos=(.4, 0, 0))
cmd.distance('d0', 'm1', 'm2')
cmd.draw()
def _pngExistsAsync(self, filename, sync_in_thread):
cmd.png(filename, width=100, height=100, ray=0)
cmd.draw()
if sync_in_thread:
cmd.sync()
assert (len(min_rmsd_key) == 1)
max_id1 = max_rmsd_key[0][0]
max_id2 = max_rmsd_key[0][1]
print('The maximum rmsd arose from a comparison of ' + max_id1 + ' and ' +
max_id2 + ' with a rmsd value of: ' + str(round(max_rmsd, 2)))
min_id1 = min_rmsd_key[0][0]
min_id2 = min_rmsd_key[0][1]
print('The maximum rmsd arose from a comparison of ' + min_id1 + ' and ' +
min_id2 + ' with a rmsd value of: ' + str(round(min_rmsd, 2)))
## set your best and worst protein structures up to take an image, and capture this to your working directory
print 'Build best.pdb from {} and {}'.format(max_id1, max_id2)
sys.stdout.flush()
pdb_merge(max_id1, max_id2, 'best.pdb')
print 'Build worst.pdb from {} and {}'.format(min_id1, min_id2)
sys.stdout.flush()
pdb_merge(min_id1, min_id2, 'worst.pdb')
cmd.load('best.pdb')
cmd.cartoon('putty', 'best')
cmd.draw()
cmd.save('best.png')
cmd.load('worst.pdb')
cmd.cartoon('putty', 'worst')
cmd.draw()
cmd.save('worst.png')