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 __init__(self, name="cartoon", mono=None, _self=cmd): Wizard.__init__(self,_self) self.message = [] self.last = None cmd.full_screen("off") if not mono: cmd.stereo("on") if 'last' in saved: self.last = saved['last'] self.launch(name)
def __init__(self, *arg, **kw): _self = kw.get('_self', cmd) Wizard.__init__(self, _self) self.message = [] self.last = None cmd.full_screen("off") if not ("mono" in list(kw.keys())): cmd.stereo("on") cmd.set("sphere_mode", "5") if 'last' in saved: self.last = saved['last'] if len(arg): self.launch(arg[0]) else: self.launch("cartoon")
def __init__(self,*arg,**kw): _self=kw.get('_self',cmd) Wizard.__init__(self,_self) self.message = [] self.last = None cmd.full_screen("off") if not ("mono" in list(kw.keys())): cmd.stereo("on") cmd.set("sphere_mode","5") if 'last' in saved: self.last = saved['last'] if len(arg): self.launch(arg[0]) else: self.launch("cartoon")
def testStereo(self): for (k, v) in cmd.stereo_dict.items(): if v < 1: continue cmd.stereo(k) self.assertTrue(cmd.get_setting_int('stereo')) self.assertEqual(cmd.get_setting_int('stereo_mode'), v) cmd.stereo('off') self.assertFalse(cmd.get_setting_int('stereo')) cmd.stereo('on') self.assertTrue(cmd.get_setting_int('stereo')) shift = cmd.get_setting_float('stereo_shift') cmd.stereo('swap') self.assertAlmostEqual(cmd.get_setting_float('stereo_shift'), -shift)
def testStereo(self): for (k,v) in cmd.stereo_dict.items(): if v < 1: continue cmd.stereo(k) self.assertTrue(cmd.get_setting_int('stereo')) self.assertEqual(cmd.get_setting_int('stereo_mode'), v) cmd.stereo('off') self.assertFalse(cmd.get_setting_int('stereo')) cmd.stereo('on') self.assertTrue(cmd.get_setting_int('stereo')) shift = cmd.get_setting_float('stereo_shift') cmd.stereo('swap') self.assertAlmostEqual(cmd.get_setting_float('stereo_shift'), -shift)
def initPymol(self): # set stereo mode cmd.set('stereo_mode', 3) cmd.stereo() # get rid of gui cmd.set('internal_gui', 0) # set resolution to HD for rift cmd.viewport(1920, 1080) # full screen? if self.fullscreen: cmd.full_screen('on') # load pdb if len(self.pdb) == 4 and self.pdb == re.match('[a-zA-Z0-9]*', self.pdb).group(0): cmd.fetch(self.pdb, async=0) if self.editMolecule == True: cmd.hide('everything', 'all') cmd.show('cartoon', 'all') # color each chain differently if self.editMolecule: util.cbc() # set origin at camera if self.naturalRotation: self.setOriginAtCamera() # move slab away to give a comfortable viewing area cmd.clip('move', 10) # jiggle the camera to deal with blank screen error cmd.move('z', .0001)
try: # Importing the PyMOL module will create the window. import pymol #@UnresolvedImport from pymol import cmd #@UnresolvedImport except: print "Failed to import pymol; python will stack dump next:" # Tell PyMOL we don't want any GUI features. __main__.pymol_argv = [ 'pymol', '-Gi' ] # Call the function below before using any PyMOL modules. pymol.finish_launching() cmd.stereo('walleye') cmd.set('stereo_shift', 0.23) cmd.set('stereo_angle', 1.0) cmd.spectrum() try: pdbCode = '1brv' pdbFile = urllib2.urlopen('file:///Users/jd/workspace35/cing/data/Tests/pdb/'+ pdbCode + '/pdb' + pdbCode + '.ent') cmd.read_pdbstr(pdbFile.read(), pdbCode) except: print "Unexpected error:", sys.exc_info()[0] time.sleep(5)
# cmd.show("sticks","sculpt") cmd.show("spheres", "sculpt") # cmd.set("sphere_transparency","0.75","sculpt") # cmd.set("sphere_color","grey","sculpt") cmd.frame(1) cmd.set("auto_sculpt", 1) cmd.set("sculpting", 1) cmd.sculpt_activate("sculpt") cmd.set("sculpting_cycles", "100") cmd.do("edit_mode") cmd.set("valence", "0.05") cmd.set("suspend_updates", 0, quiet=0) cmd.sculpt_iterate("sculpt") cmd.alter_state(1, "sculpt", "x=x*1.5;y=y*0.1;z=z*1.5") cmd.zoom() cmd.unpick() else: cmd.set("valence", "0") cmd.set("sculpting", 0) cmd.set("auto_sculpt", 0) cmd.delete("sculpt") cmd.mouse() if __name__ == 'pymol': pymol.wizard.stereodemo = Stereodemo() cmd.set_wizard(pymol.wizard.stereodemo) cmd.stereo("on") cmd.set("max_threads", 4)
def stereo_switch(tag): if tag == 'Off': cmd.stereo('off') elif tag == 'Quad': cmd.stereo('off') cmd.stereo('cross') cmd.stereo('quadbuffer') cmd.stereo('on') elif tag == 'Cross-Eye': cmd.stereo('off') cmd.stereo('cross') cmd.stereo('on') else: cmd.stereo('off') cmd.stereo('walleye') cmd.stereo('on')
# cmd.show("sticks","sculpt") cmd.show("spheres","sculpt") # cmd.set("sphere_transparency","0.75","sculpt") # cmd.set("sphere_color","grey","sculpt") cmd.frame(1) cmd.set("auto_sculpt",1) cmd.set("sculpting",1) cmd.sculpt_activate("sculpt") cmd.set("sculpting_cycles","100") cmd.do("edit_mode") cmd.set("valence","0.05") cmd.set("suspend_updates",0,quiet=0) cmd.sculpt_iterate("sculpt") cmd.alter_state(1,"sculpt","x=x*1.5;y=y*0.1;z=z*1.5") cmd.zoom() cmd.unpick() else: cmd.set("valence","0") cmd.set("sculpting",0) cmd.set("auto_sculpt",0) cmd.delete("sculpt") cmd.mouse() if __name__=='pymol': pymol.wizard.stereodemo = Stereodemo() cmd.set_wizard(pymol.wizard.stereodemo) cmd.stereo("on") cmd.set("max_threads",4)
def test(self): cmd.set('bg_rgb', 'red') cmd.stereo('anaglyph') self.assertImageHasColor('red')
try: # Importing the PyMOL module will create the window. import pymol #@UnresolvedImport from pymol import cmd #@UnresolvedImport except: print "Failed to import pymol; python will stack dump next:" # Tell PyMOL we don't want any GUI features. __main__.pymol_argv = ['pymol', '-Gi'] # Call the function below before using any PyMOL modules. pymol.finish_launching() cmd.stereo('walleye') cmd.set('stereo_shift', 0.23) cmd.set('stereo_angle', 1.0) cmd.spectrum() try: pdbCode = '1brv' pdbFile = urllib2.urlopen( 'file:///Users/jd/workspace35/cing/Tests/data/pdb/' + pdbCode + '/pdb' + pdbCode + '.ent') cmd.read_pdbstr(pdbFile.read(), pdbCode) except: print "Unexpected error:", sys.exc_info()[0] time.sleep(5)