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 update_object_list(self):
"""
update the internal state list
"""
# purge list of removed objects
pubObj = self.cmd.get_names("public_objects")
object_list_copy = self.object_list.copy()
for x in object_list_copy:
if x not in pubObj:
del self.object_list[x]
# for all VOLUME type objects not known to the list
for x in self.cmd.get_names("public_objects"):
if "object:volume"==cmd.get_type(x):
if x not in self.object_list.keys():
if self.cmd.get_volume_is_updated(x) == 0:
continue
# make a default pair for this volume object
tmpMap = VolumeHist(self.cmd.get_volume_histogram(x,self.cmd),nBins=64)
tmpRamp = ColorRamp(360,name=x)
self.object_list[x] = (tmpRamp,tmpMap)
if self.ramp_update.has_key(x) and self.ramp_update[x]:
tmpRamp.addColor(0, (0,0,1,0))
tmpRamp.addColor(359, (0,0,1,0))
for data, alpha, col, kind in self.ramp_update[x]:
self.addWithoutGUINow(x, data, alpha, col, kind=kind)
self.ramp_update[x] = []
tmpRamp.updateRamp()
self.cmd.volume_color(x, tmpRamp.getRamp())
self.cmd.set_volume_ramp(x, tmpRamp.getRampList())
else:
ramp_list = self.cmd.get_volume_ramp(x, self.cmd)
if ramp_list:
while ramp_list:
tmpRamp.addColor(ramp_list[0],
(ramp_list[1], ramp_list[2], ramp_list[3], ramp_list[4]))
ramp_list = ramp_list[5:]
else:
tmpRamp.addColor(0, (0,0,1,0))
tmpRamp.addColor(359, (0,0,1,0))
tmpRamp.addColor(200, (0.0, 0.0, 1.0, 0.0))
tmpRamp.addColor(210, (0.0, 0.8, 1.0, 0.2))
tmpRamp.addColor(220, (0.0, 0.0, 1.0, 0.0))
else:
# need to regenerate the histogram
(tmpRamp,tmpMap) = self.object_list[x]
tmpMap = VolumeHist(self.cmd.get_volume_histogram(x,self.cmd),nBins=64)
self.object_list[x] = (tmpRamp,tmpMap)
if len(self.object_list.keys())!=0:
# guaranteed to exist
k = self.object_list.keys()[0]
self.active_ramp, self.active_map = self.object_list[k]
self.active = k
self.update_transferframe()
def update_object_list(self):
"""
update the internal state list
"""
# purge list of removed objects
pubObj = self.cmd.get_names("public_objects")
object_list_copy = self.object_list.copy()
for x in object_list_copy:
if x not in pubObj:
del self.object_list[x]
# for all VOLUME type objects not known to the list
for x in self.cmd.get_names("public_objects"):
if "object:volume" == cmd.get_type(x):
if x not in self.object_list.keys():
if self.cmd.get_volume_is_updated(x) == 0:
continue
# make a default pair for this volume object
tmpMap = VolumeHist(self.cmd.get_volume_histogram(
x, self.cmd),
nBins=64)
tmpRamp = ColorRamp(360, name=x)
self.object_list[x] = (tmpRamp, tmpMap)
if self.ramp_update.has_key(x) and self.ramp_update[x]:
tmpRamp.addColor(0, (0, 0, 1, 0))
tmpRamp.addColor(359, (0, 0, 1, 0))
for data, alpha, col, kind in self.ramp_update[x]:
self.addWithoutGUINow(x,
data,
alpha,
col,
kind=kind)
self.ramp_update[x] = []
tmpRamp.updateRamp()
self.cmd.volume_color(x, tmpRamp.getRamp())
self.cmd.set_volume_ramp(x, tmpRamp.getRampList())
else:
ramp_list = self.cmd.get_volume_ramp(x, self.cmd)
if ramp_list:
while ramp_list:
tmpRamp.addColor(ramp_list[0],
(ramp_list[1], ramp_list[2],
ramp_list[3], ramp_list[4]))
ramp_list = ramp_list[5:]
else:
tmpRamp.addColor(0, (0, 0, 1, 0))
tmpRamp.addColor(359, (0, 0, 1, 0))
tmpRamp.addColor(200, (0.0, 0.0, 1.0, 0.0))
tmpRamp.addColor(210, (0.0, 0.8, 1.0, 0.2))
tmpRamp.addColor(220, (0.0, 0.0, 1.0, 0.0))
else:
# need to regenerate the histogram
(tmpRamp, tmpMap) = self.object_list[x]
tmpMap = VolumeHist(self.cmd.get_volume_histogram(
x, self.cmd),
nBins=64)
self.object_list[x] = (tmpRamp, tmpMap)
if len(self.object_list.keys()) != 0:
# guaranteed to exist
k = self.object_list.keys()[0]
self.active_ramp, self.active_map = self.object_list[k]
self.active = k
self.update_transferframe()
