def testGetVolumeHistogram(self):
cmd.load(self.datafile('h2o-elf.cube'), 'map1')
hist1 = cmd.get_volume_histogram('map1', 10)
self.assertEqual(len(hist1), 14)
hist2 = cmd.get_volume_histogram('map1', 2)
self.assertArrayEqual(
hist2, [-0.0151, 0.9292, 0.0692, 0.1720, 63812.0, 188.0],
delta=1e-4)
self.assertArrayEqual(hist1[:4], hist2[:4])
self.assertEqual(sum(hist1[4:]), sum(hist2[4:]))
hist2 = cmd.get_volume_histogram('map1', 2, (0.3, 0.7))
self.assertArrayEqual(hist2,
[0.3, 0.7, 0.0692, 0.172, 62263.0, 1737.0],
delta=1e-4)
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')
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')
def volume_esp(name, map, stops=[0.1, 1.0], neg='red', pos='blue',
opacity=0.2, quiet=1):
'''
DESCRIPTION
Create a volume object from a map object with default coloring
for electrostatic potential (similar to positive and negative
isosurface).
ARGUMENTS
name = string: name for the new volume object
map = string: name of the map object to use
stops = list of floats: 2 or 3 values in standard deviations for creating
the volume ramp {default: [0.1, 1.0]}
neg = string: color for negative volume {default: red}
pos = string: color for positive volume {default: blue}
opacity = float: maximum opacity in volume ramp {default: 0.2}
SEE ALSO
volume
'''
from .setting import set_temporary
opacity, quiet = float(opacity), int(quiet)
if isinstance(stops, str):
stops = cmd.safe_list_eval(stops)
try:
from pymol.colorramping import ColorRamp
except ImportError:
print(' Warning: volume_esp is deprecated')
stdevD = cmd.get_volume_histogram(map, 0)[3]
stops = [s * stdevD for s in stops]
ramp = [
-stops[1], neg, opacity,
-stops[0], neg, 0.0,
stops[0], pos, 0.0,
stops[1], pos, opacity,
]
if len(stops) == 3:
ramp = [-stops[2], neg, opacity] + ramp + [stops[2], pos, opacity]
cmd.volume(name, map, ramp, quiet=quiet)
return
c_neg = cmd.get_color_tuple(neg)
c_pos = cmd.get_color_tuple(pos)
c_pos_0 = c_pos + (0.0,)
c_pos_1 = c_pos + (opacity,)
c_neg_0 = c_neg + (0.0,)
c_neg_1 = c_neg + (opacity,)
if len(stops) == 2:
cstops = [(c_neg_1, -999), (c_neg_1, -stops[1]), (c_neg_0, -stops[0]),
(c_pos_0, stops[0]), (c_pos_1, stops[1]), (c_pos_1, 999)]
elif len(stops) == 3:
cstops = [(c_neg_0, -999), (c_neg_0, -stops[2]), (c_neg_1, -stops[1]),
(c_neg_0, -stops[0]), (c_pos_0, stops[0]), (c_pos_1, stops[1]),
(c_pos_0, stops[2]), (c_pos_0, 999)]
else:
print(' Error: need 2 or 3 stops')
raise CmdException
cmd.volume(name, map, quiet=quiet)
# get_volume_histogram returns zeros without refresh
with set_temporary(suspend_updates='off'):
cmd.refresh()
minD, maxD, meanD, stdevD = cmd.get_volume_histogram(name)[:4]
v_ramp = []
c_ramp = ColorRamp(360)
for c, s in cstops:
i = int(360 * ((s * stdevD) - minD) / (maxD - minD))
i = min(max(i, 0), 359)
v_ramp.append(i)
v_ramp.extend(c)
c_ramp.addColor(i, c)
cmd.set_volume_ramp(name, v_ramp)
cmd.volume_color(name, c_ramp.getRamp())
cmd.recolor(name)
def volume_esp(name,
map,
stops=[0.1, 1.0],
neg='red',
pos='blue',
opacity=0.2,
quiet=1):
'''
DESCRIPTION
Create a volume object from a map object with default coloring
for electrostatic potential (similar to positive and negative
isosurface).
ARGUMENTS
name = string: name for the new volume object
map = string: name of the map object to use
stops = list of floats: 2 or 3 values in standard deviations for creating
the volume ramp {default: [0.1, 1.0]}
neg = string: color for negative volume {default: red}
pos = string: color for positive volume {default: blue}
opacity = float: maximum opacity in volume ramp {default: 0.2}
SEE ALSO
volume
'''
from .setting import set_temporary
opacity, quiet = float(opacity), int(quiet)
if isinstance(stops, str):
stops = cmd.safe_list_eval(stops)
try:
from pymol.colorramping import ColorRamp
except ImportError:
print(' Warning: volume_esp is deprecated')
stdevD = cmd.get_volume_histogram(map, 0)[3]
stops = [s * stdevD for s in stops]
ramp = [
-stops[1],
neg,
opacity,
-stops[0],
neg,
0.0,
stops[0],
pos,
0.0,
stops[1],
pos,
opacity,
]
if len(stops) == 3:
ramp = [-stops[2], neg, opacity] + ramp + [stops[2], pos, opacity]
cmd.volume(name, map, ramp, quiet=quiet)
return
c_neg = cmd.get_color_tuple(neg)
c_pos = cmd.get_color_tuple(pos)
c_pos_0 = c_pos + (0.0, )
c_pos_1 = c_pos + (opacity, )
c_neg_0 = c_neg + (0.0, )
c_neg_1 = c_neg + (opacity, )
if len(stops) == 2:
cstops = [(c_neg_1, -999), (c_neg_1, -stops[1]), (c_neg_0, -stops[0]),
(c_pos_0, stops[0]), (c_pos_1, stops[1]), (c_pos_1, 999)]
elif len(stops) == 3:
cstops = [(c_neg_0, -999), (c_neg_0, -stops[2]), (c_neg_1, -stops[1]),
(c_neg_0, -stops[0]), (c_pos_0, stops[0]),
(c_pos_1, stops[1]), (c_pos_0, stops[2]), (c_pos_0, 999)]
else:
print(' Error: need 2 or 3 stops')
raise CmdException
cmd.volume(name, map, quiet=quiet)
# get_volume_histogram returns zeros without refresh
with set_temporary(suspend_updates='off'):
cmd.refresh()
minD, maxD, meanD, stdevD = cmd.get_volume_histogram(name)[:4]
v_ramp = []
c_ramp = ColorRamp(360)
for c, s in cstops:
i = int(360 * ((s * stdevD) - minD) / (maxD - minD))
i = min(max(i, 0), 359)
v_ramp.append(i)
v_ramp.extend(c)
c_ramp.addColor(i, c)
cmd.set_volume_ramp(name, v_ramp)
cmd.volume_color(name, c_ramp.getRamp())
cmd.recolor(name)
def test(self, normalize, ref):
cmd.set('volume_data_range', 0)
cmd.set('normalize_ccp4_maps', normalize)
cmd.load(self.datafile('emd_1155.ccp4'), 'map')
mmms = cmd.get_volume_histogram('map', 0)
self.assertArrayEqual(mmms, ref, delta=0.05)