def testGetColorIndices(self):
r = cmd.get_color_indices()
self.assertTrue(
set(r).issuperset([('white', 0), ('black', 1), ('blue', 2)]))
self.assertFalse(('grey50', 104) in r)
r = cmd.get_color_indices(all=1)
self.assertTrue(('grey50', 104) in r)
def testShortcutTiming(self):
names = pymol.setting.get_name_list()
colors = [c[0] for c in cmd.get_color_indices(0)]
with self.timing():
sc = cmd.Shortcut(names)
sc = cmd.Shortcut(cmd.kw_list)
sc = cmd.Shortcut(colors)
def _getColorTuple(self, color):
if isinstance(color, tuple):
return color
if isinstance(color, list):
return tuple(color)
elif isinstance(color, int):
if color in dict((k,v) for (v,k) in cmd.get_color_indices()):
return cmd.get_color_tuple(color)
else:
hexval = color & 0xffffff
return tuple(map(lambda x: x/255., [ hexval >> 16, (hexval >> 8) & 0xff, hexval & 0xff ]))
elif isinstance(color, str):
return cmd.get_color_tuple(color)
def cpk(cpknew, selection):
# Get the existing color indices from PyMOL
colorIndex = {}
for i in cmd.get_color_indices():
k, v = i
colorIndex[k] = v
# Select the right CPK dictionary
if cpknew:
cpk = CPKNewDict
suffix = 'cpknew'
else:
cpk = CPKDict
suffix = 'cpk'
# Iterate through the colors in the selected CPK dictionary
for k in cpk:
# Create a hopefully unique name for each color by concatenating
# its name in the dictionary with a suffix specifying which dictionary
# it came from
color = '%s%s' % (k, suffix)
# If PyMOL doesn't know about any of them, tell it
if color not in colorIndex:
cmd.set_color(color, cpk[k])
unk = 'not e. '
for k in cpk:
if k != 'UNK':
# Assuming ampersands mean "and" to PyMOL's selection algebra,
# this line tells PyMOL to use each color in the dictionary,
# again identified by its concatenated name (the first argument),
# to color all atoms in the selection passed to cpk() whose
# elemental symbols match the color's key in the dictionary
# (the abbreviation 'e.' in PyMOL's selection algebra can mean
# one of two things; in this case, it stands for "element symbol")
cmd.color('%s%s' % (k, suffix),
'e. %s & (%s)' % (k, selection))
# This builds a string of the format 'not e. A+B+C+D+...', where
# A, B, C, and D are element symbols. Presumably, the intent is
# to build a selection containing all atoms that don't have a
# color defined for them in the dictionary. I don't have any
# reason to believe it doesn't work, but I don't know for sure.
unk = '%s%s+' % (unk, k)
# This strips the trailing plus off of the resulting string and colors all
# atoms that both match it and are in the selection passed into cpk()
# with the unknown color 'UNK' in the dictonary.
cmd.color('UNK%s' % (suffix), '(%s) & (%s)' % (unk[:-1], selection))
def str_to_color(c):
color_map = dict(cmd.get_color_indices())
if c in color_map:
return cmd.get_color_tuple(color_map[c])
return str_to_vector(c)
def testGetColorIndices(self):
r = cmd.get_color_indices()
self.assertTrue(
set(r).issuperset([('white', 0), ('black', 1), ('blue', 2)]))
def str_to_color(c):
color_map = dict(cmd.get_color_indices())
if c in color_map:
return cmd.get_color_tuple(color_map[c])
return str_to_vector(c)
