def load_grid(fname, prefix='aa', ramp='jet'):
cmd.volume_ramp_new('ramp_jet', [
0.00,
0.00,
0.00,
1.00,
0.00,
25.00,
0.06,
0.93,
1.00,
0.05,
50.00,
0.49,
0.51,
1.00,
0.15,
75.00,
1.00,
1.00,
0.00,
0.23,
90.00,
0.80,
0.18,
1.00,
0.48,
100.00,
0.98,
0.01,
1.00,
1.00,
])
cmd.volume_ramp_new('ramp_delta', [
-1.0, 1.00, 0.00, 0.00, 0.00, -0.4, 1.00, 1.00, 0.00, 1.0, -0.2, 1.00,
0.00, 0.00, 0.00, 0.2, 0.00, 0.00, 1.00, 0.00, 0.4, 0.00, 1.00, 1.00,
1.0, 1.0, 0.00, 0.00, 1.00, 0.00
])
F = h5py.File(fname, 'r')
grid = F['step'][()]
origin = F['origin'][()]
NUCS = set(F.keys())
protected = set(['origin', 'step', 'atypes'])
NUCS -= protected
for i in NUCS:
data = F[i][()]
b = Brick.from_numpy(data, grid, origin)
bname = prefix + '_' + i
cmd.load_brick(b, bname)
volname = bname + '_volume'
cmd.volume(volname, bname)
cmd.volume_color(volname, 'ramp_jet')
def testVolume(self):
'''
cmd.volume
cmd.volume_color
cmd.volume_ramp_new
'''
self._sample_data()
cmd.volume('vol', 'map', '2fofc')
ramp = cmd.volume_color('vol')
self.assertTrue(len(ramp) > 5)
self.assertAlmostEqual(ramp[5], 1.0, delta=0.01)
cmd.volume_ramp_new('named', [
2.0, 'blue', .1,
3.0, 'yellow', .2])
cmd.volume_color('vol', 'named')
ramp = cmd.volume_color('vol')
self.assertEqual(len(ramp), 10)
self.assertArrayEqual(ramp, [2., 0., 0., 1., .1, 3., 1., 1., 0., .2], delta=0.01)
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 load_grid(fname, prefix='aa', ramp='jet'):
cmd.volume_ramp_new('ramp_DA', [
0.00,
1.00,
1.00,
1.00,
0.00,
25.00,
1.00,
0.77,
0.77,
0.02,
50.00,
1.00,
0.54,
0.54,
0.06,
75.00,
1.00,
0.38,
0.38,
0.18,
90.00,
0.93,
0.00,
0.00,
0.60,
100.00,
0.70,
0.00,
0.00,
1.00,
])
cmd.volume_ramp_new('ramp_DG', [
0.00,
1.00,
1.00,
1.00,
0.00,
25.00,
0.77,
0.77,
1.00,
0.02,
50.00,
0.54,
0.54,
1.00,
0.06,
75.00,
0.38,
0.38,
1.00,
0.18,
90.00,
0.00,
0.00,
0.93,
0.60,
100.00,
0.00,
0.00,
0.70,
1.00,
])
cmd.volume_ramp_new('ramp_DC', [
0.00,
1.00,
1.00,
1.00,
0.00,
25.00,
0.64,
1.00,
0.61,
0.02,
50.00,
0.48,
1.00,
0.47,
0.06,
75.00,
0.26,
1.00,
0.28,
0.18,
90.00,
0.04,
0.85,
0.00,
0.44,
100.00,
0.00,
0.52,
0.06,
1.00,
])
cmd.volume_ramp_new('ramp_DT', [
0.00,
1.00,
1.00,
1.00,
0.00,
25.00,
1.00,
0.99,
0.55,
0.02,
50.00,
1.00,
0.98,
0.46,
0.06,
75.00,
1.00,
0.99,
0.37,
0.19,
90.00,
0.92,
0.92,
0.00,
0.39,
100.00,
0.76,
0.73,
0.00,
1.00,
])
cmd.volume_ramp_new('ramp_P', [
0.00,
1.00,
1.00,
1.00,
0.00,
25.00,
1.00,
0.95,
0.93,
0.02,
50.00,
1.00,
0.85,
0.69,
0.06,
75.00,
1.00,
0.78,
0.55,
0.19,
90.00,
1.00,
0.66,
0.30,
0.39,
100.00,
0.97,
0.50,
0.00,
1.00,
])
cmd.volume_ramp_new('ramp_jet', [
0.00,
0.00,
0.00,
1.00,
0.00,
25.00,
0.06,
0.93,
1.00,
0.05,
50.00,
0.49,
0.51,
1.00,
0.15,
75.00,
1.00,
1.00,
0.00,
0.23,
90.00,
0.80,
0.18,
1.00,
0.48,
100.00,
0.98,
0.01,
1.00,
1.00,
])
cmd.volume_ramp_new('ramp_delta', [
-1.0, 1.00, 0.00, 0.00, 0.00, -0.4, 1.00, 1.00, 0.00, 1.0, -0.2, 1.00,
0.00, 0.00, 0.00, 0.2, 0.00, 0.00, 1.00, 0.00, 0.4, 0.00, 1.00, 1.00,
1.0, 1.0, 0.00, 0.00, 1.00, 0.00
])
F = h5py.File(fname, 'r')
# load step along every axis
# step = np.array([1.0, 1.0, 1.0])
step = F['step'][()]
# load origin of grid
# origin = np.array([0.0, 0.0, 0.0])
origin = F['origin'][()]
NUCS = set(F.keys())
protected = set(['origin', 'step', 'atypes'])
NUCS -= protected
for i in NUCS:
# load data: 3D array
data = F[i][()]
# Create brick
b = Brick.from_numpy(data, step, origin)
bname = prefix + '_' + i
# load brick into pymol
cmd.load_brick(b, bname)
volname = bname + '_volume'
# assign ramp to the brick
cmd.volume(volname, bname)
if ramp == 'nuc':
cmd.volume_color(volname, 'ramp_' + i)
elif ramp == 'delta':
cmd.volume_color(volname, 'ramp_delta')
else:
cmd.volume_color(volname, 'ramp_jet')
def load_meta_grid(fname, prefix='meta'):
F = h5py.File(fname, 'r')
step = F['step'][()]
origin = F['origin'][()]
NUCS = set(F.keys())
protected = set(['origin', 'step', 'atypes'])
NUCS -= protected
for i in NUCS:
data = F[i][()]
b = Brick.from_numpy(data, step, origin)
bname = prefix + '_' + i
cmd.load_brick(b, bname)
volname = bname + '_volume'
d_min = np.min(data)
d_max = np.max(data)
v = np.linspace(d_min, d_max, 6)
cmd.volume(volname, bname)
print('ramp_%s' % i)
cmd.volume_ramp_new('ramp_grid', [
v[0],
0.00,
0.00,
1.00,
0.70,
v[1],
0.06,
0.93,
1.00,
0.50,
v[2],
0.49,
0.51,
1.00,
0.30,
v[3],
1.00,
1.00,
0.00,
0.10,
v[4],
0.80,
0.18,
1.00,
0.05,
v[5],
0.98,
0.01,
1.00,
0.00,
])
cmd.volume_color(volname, 'ramp_grid')
def load_sites(fname, prefix='sites', ramp='jet', top=42):
cmd.volume_ramp_new('ramp_DA', [
0.00,
1.00,
1.00,
1.00,
0.00,
25.00,
1.00,
0.77,
0.77,
0.02,
50.00,
1.00,
0.54,
0.54,
0.06,
75.00,
1.00,
0.38,
0.38,
0.18,
90.00,
0.93,
0.00,
0.00,
0.60,
100.00,
0.70,
0.00,
0.00,
1.00,
])
cmd.volume_ramp_new('ramp_DG', [
0.00,
1.00,
1.00,
1.00,
0.00,
25.00,
0.77,
0.77,
1.00,
0.02,
50.00,
0.54,
0.54,
1.00,
0.06,
75.00,
0.38,
0.38,
1.00,
0.18,
90.00,
0.00,
0.00,
0.93,
0.60,
100.00,
0.00,
0.00,
0.70,
1.00,
])
cmd.volume_ramp_new('ramp_DC', [
0.00,
1.00,
1.00,
1.00,
0.00,
25.00,
0.64,
1.00,
0.61,
0.02,
50.00,
0.48,
1.00,
0.47,
0.06,
75.00,
0.26,
1.00,
0.28,
0.18,
90.00,
0.04,
0.85,
0.00,
0.44,
100.00,
0.00,
0.52,
0.06,
1.00,
])
cmd.volume_ramp_new('ramp_DT', [
0.00,
1.00,
1.00,
1.00,
0.00,
25.00,
1.00,
0.99,
0.55,
0.02,
50.00,
1.00,
0.98,
0.46,
0.06,
75.00,
1.00,
0.99,
0.37,
0.19,
90.00,
0.92,
0.92,
0.00,
0.39,
100.00,
0.76,
0.73,
0.00,
1.00,
])
cmd.volume_ramp_new('ramp_P', [
0.00,
1.00,
1.00,
1.00,
0.00,
25.00,
1.00,
0.95,
0.93,
0.02,
50.00,
1.00,
0.85,
0.69,
0.06,
75.00,
1.00,
0.78,
0.55,
0.19,
90.00,
1.00,
0.66,
0.30,
0.39,
100.00,
0.97,
0.50,
0.00,
1.00,
])
cmd.volume_ramp_new('ramp_jet', [
0.00,
0.00,
0.00,
1.00,
0.00,
25.00,
0.06,
0.93,
1.00,
0.05,
50.00,
0.49,
0.51,
1.00,
0.15,
75.00,
1.00,
1.00,
0.00,
0.23,
90.00,
0.80,
0.18,
1.00,
0.48,
100.00,
0.98,
0.01,
1.00,
1.00,
])
cmd.volume_ramp_new('ramp_delta', [
-1.0, 1.00, 0.00, 0.00, 0.00, -0.4, 1.00, 1.00, 0.00, 1.0, -0.2, 1.00,
0.00, 0.00, 0.00, 0.2, 0.00, 0.00, 1.00, 0.00, 0.4, 0.00, 1.00, 1.00,
1.0, 1.0, 0.00, 0.00, 1.00, 0.00
])
F = h5py.File(fname, 'r')
NUCS = natsort.natsorted(F.keys())
if int(top) < 1:
print('top should be greater than 1')
return
top_ = min(int(top), len(NUCS))
NUCS_ = NUCS[:top_]
for i in NUCS_:
data = F[i]['data'][()]
origin = F[i]['origin'][()]
step = F[i]['step'][()]
b = Brick.from_numpy(data, step, origin)
bname = prefix + '_' + i
cmd.load_brick(b, bname)
volname = bname + '_volume'
cmd.volume(volname, bname)
cmd.volume_color(volname, 'ramp_' + ramp)