def add_scenes(names=None,
pause=8.0,
cut=0.0,
loop=1,
rock=-1,
period=8.0,
animate=-1,
start=0,
_self=cmd):
cmd = _self
if not start:
start = cmd.get_movie_length() + 1
animate = float(animate)
pause = float(pause)
period = float(period)
if period > pause:
period = pause
rock = int(rock)
if animate < 0:
animate = float(cmd.get("scene_animation_duration"))
if names == None:
names = cmd.get_scene_list()
elif cmd.is_str(names):
names = cmd.safe_alpha_list_eval(names)
n_scene = len(names)
duration = n_scene * (pause + animate)
fps = float(cmd.get('movie_fps'))
n_frame = int(round(fps * duration))
if not loop:
act_n_frame = int(round(fps * (duration - animate)))
else:
act_n_frame = n_frame
if rock < 0:
sweep_mode = int(cmd.get('sweep_mode'))
elif rock:
sweep_mode = rock - 1
else:
sweep_mode = 0
if n_frame > 0:
cmd.mset("1 x%d" % act_n_frame, start, freeze=1)
cnt = 0
for scene in names:
frame = start + int((cnt * n_frame) / n_scene)
cmd.mview("store", frame, scene=scene, freeze=1)
if rock:
cmd.mview("interpolate", cut=cut, wrap=0)
sweep_first = frame + 1
sweep_last = start + int(pause * fps +
(cnt * n_frame) / n_scene) - 1
if sweep_last > act_n_frame:
sweep_last = act_n_frame
n_sweep_frame = sweep_last - sweep_first + 1
if n_sweep_frame > 0:
if sweep_mode == 1: # x-axis rock
_rock(sweep_mode,
'x',
sweep_first,
sweep_last,
period,
pause,
_self=_self)
elif sweep_mode < 3: # y-axis rock
_rock(sweep_mode,
'y',
sweep_first,
sweep_last,
period,
pause,
_self=_self)
elif sweep_mode == 3:
_nutate(sweep_mode,
sweep_first,
sweep_last,
period,
pause,
_self=_self)
frame = start + int(pause * fps + (cnt * n_frame) / n_scene)
if frame <= act_n_frame:
if sweep_mode != 3:
cmd.mview("store", frame, scene=scene, freeze=1)
cnt = cnt + 1
cmd.mview("interpolate", cut=cut, wrap=loop)
if rock:
cmd.mview("smooth")
cmd.frame(start)
def add_scenes(names=None, pause=8.0, cut=0.0, loop=1,
rock=-1, period=8.0, animate=-1, start=0,
_self=cmd):
cmd = _self
if not start:
start = cmd.get_movie_length()+1
animate = float(animate)
pause = float(pause)
period = float(period)
if period>pause:
period = pause
rock = int(rock)
if animate<0:
animate = float(cmd.get("scene_animation_duration"))
if names == None:
names = cmd.get_scene_list()
elif cmd.is_str(names):
names = cmd.safe_alpha_list_eval(names)
n_scene = len(names)
duration = n_scene*(pause+animate)
fps = float(cmd.get('movie_fps'))
n_frame = int(round(fps * duration))
if not loop:
act_n_frame = int(round(fps * (duration - animate)))
else:
act_n_frame = n_frame
if rock<0:
sweep_mode = int(cmd.get('sweep_mode'))
elif rock:
sweep_mode = rock - 1
else:
sweep_mode = 0
if n_frame > 0:
cmd.mset("1 x%d"%act_n_frame,start,freeze=1)
cnt = 0
for scene in names:
frame = start+int((cnt*n_frame)/n_scene)
cmd.mview("store",frame,scene=scene,freeze=1)
if rock:
cmd.mview("interpolate",cut=cut,wrap=0)
sweep_first = frame + 1
sweep_last = start + int(pause*fps+(cnt*n_frame)/n_scene) - 1
if sweep_last > act_n_frame:
sweep_last = act_n_frame
n_sweep_frame = sweep_last - sweep_first + 1
if n_sweep_frame > 0:
if sweep_mode==1: # x-axis rock
_rock(sweep_mode, 'x', sweep_first, sweep_last,
period, pause, _self=_self)
elif sweep_mode<3: # y-axis rock
_rock(sweep_mode, 'y', sweep_first, sweep_last,
period, pause, _self=_self)
elif sweep_mode == 3:
_nutate(sweep_mode, sweep_first, sweep_last,
period, pause, _self=_self)
frame = start+int(pause*fps+(cnt*n_frame)/n_scene)
if frame <= act_n_frame:
if sweep_mode!=3:
cmd.mview("store",frame,scene=scene,freeze=1)
cnt = cnt + 1
cmd.mview("interpolate",cut=cut,wrap=loop)
if rock:
cmd.mview("smooth")
cmd.frame(start)
def ramp_new(name, map_name, range=[-1.0,0.0,1.0],
color=['red',[1.0,1.0,1.0],'blue'], state=1,
selection='', beyond=2.0, within=6.0, sigma=2.0,
zero=1, quiet=1, _self=cmd):
'''
DESCRIPTION
"ramp_new" creates a color ramp based on a map potential value or
based on proximity to a molecular object.
USAGE
ramp_new name, map_name [, range [, color [, state [, selection [,
beyond [, within [, sigma [, zero ]]]]]]]]
ARGUMENTS
name = string: name of the ramp object
map_name = string: name of the map (for potential) or molecular
object (for proximity)
range = list: values corresponding to slots in the ramp
color = list: colors corresponding to slots in the ramp
state = integer: state identifier
selection = selection: for automatic ranging
beyond = number: with automatic ranging, are we excluding
values beyond a certain distance from the selection?
within = number: with automatic ranging, are we only including
valuess within a certain distance from the selection?
sigma = number: with automatic ranging, how many standard
deviations from the mean do we go?
zero = integer: with automatic ranging, do we force the central
value to be zero?
EXAMPLES
ramp_new e_pot_color, e_pot_map, [-10,0,10], [red,white,blue]
NOTES
Color ramps are extremely powerful but complicated to use.
In the simplest case, they can be used to color representations
based on the potential values found in a map object at the
corresponding positions in space.
In another simple case, representations can be colored based on
proximity to a target. Note that since ramp targets must
themselves be real objects (not merely selections), the "create"
command may be needed in order to generate an appropriate target.
In more complicated cases, they can be used to color
representations on one object based atoms found in another.
Ramps can operate recursively. In other words, the output color
from one ramp can be used as the input color for another. For
example, you could color by map potential within a certain
distance of the target object, beyond which, a uniform color is applied.
PYMOL API
def ramp_new(string name, string map_name, list range, list color,
int state, string selection, float beyond, float
within, float sigma, int zero, int quiet)
SEE ALSO
load, color, create, slice, gradient
'''
r = DEFAULT_ERROR
safe_color = string.strip(str(color))
if(safe_color[0:1]=="["): # looks like a list
color = safe_alpha_list_eval(str(safe_color))
else: # looks like a literal
color = str(color)
new_color = []
# preprocess selection
if selection!='':
selection = selector.process(selection)
# coerce range
try:
if isinstance(range, str):
range = safe_list_eval(range)
range = map(float, range)
except:
raise pymol.CmdException('invalid range')
if is_list(color):
for a in color:
if not is_list(a):
new_color.append(list(_self.get_color_tuple(a,4))) # incl negative RGB special colors
else:
new_color.append(a)
elif is_string(color):
new_color = ramp_spectrum_dict[ramp_spectrum_sc.auto_err(str(color),'ramp color spectrum')]
else:
new_color=int(color)
try:
_self.lock(_self)
r = _cmd.ramp_new(_self._COb,str(name),str(map_name),range,new_color,
int(state)-1,str(selection),float(beyond),float(within),
float(sigma),int(zero),int(quiet))
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise pymol.CmdException
return r
def ramp_new(name,
map_name,
range=[-1.0, 0.0, 1.0],
color=['red', [1.0, 1.0, 1.0], 'blue'],
state=1,
selection='',
beyond=2.0,
within=6.0,
sigma=2.0,
zero=1,
quiet=1,
_self=cmd):
'''
DESCRIPTION
"ramp_new" creates a color ramp based on a map potential value or
based on proximity to a molecular object.
USAGE
ramp_new name, map_name [, range [, color [, state [, selection [,
beyond [, within [, sigma [, zero ]]]]]]]]
ARGUMENTS
name = string: name of the ramp object
map_name = string: name of the map (for potential) or molecular
object (for proximity)
range = list: values corresponding to slots in the ramp
color = list: colors corresponding to slots in the ramp
state = integer: state identifier
selection = selection: for automatic ranging
beyond = number: with automatic ranging, are we excluding
values beyond a certain distance from the selection?
within = number: with automatic ranging, are we only including
valuess within a certain distance from the selection?
sigma = number: with automatic ranging, how many standard
deviations from the mean do we go?
zero = integer: with automatic ranging, do we force the central
value to be zero?
EXAMPLES
ramp_new e_pot_color, e_pot_map, [-10,0,10], [red,white,blue]
NOTES
Color ramps are extremely powerful but complicated to use.
In the simplest case, they can be used to color representations
based on the potential values found in a map object at the
corresponding positions in space.
In another simple case, representations can be colored based on
proximity to a target. Note that since ramp targets must
themselves be real objects (not merely selections), the "create"
command may be needed in order to generate an appropriate target.
In more complicated cases, they can be used to color
representations on one object based atoms found in another.
Ramps can operate recursively. In other words, the output color
from one ramp can be used as the input color for another. For
example, you could color by map potential within a certain
distance of the target object, beyond which, a uniform color is applied.
PYMOL API
def ramp_new(string name, string map_name, list range, list color,
int state, string selection, float beyond, float
within, float sigma, int zero, int quiet)
SEE ALSO
load, color, create, slice, gradient
'''
r = DEFAULT_ERROR
safe_color = string.strip(str(color))
if (safe_color[0:1] == "["): # looks like a list
color = safe_alpha_list_eval(str(safe_color))
else: # looks like a literal
color = str(color)
new_color = []
# preprocess selection
if selection != '':
selection = selector.process(selection)
# coerce range
try:
if isinstance(range, str):
range = safe_list_eval(range)
range = map(float, range)
except:
raise pymol.CmdException('invalid range')
if is_list(color):
for a in color:
if not is_list(a):
new_color.append(list(_self.get_color_tuple(
a, 4))) # incl negative RGB special colors
else:
new_color.append(a)
elif is_string(color):
new_color = ramp_spectrum_dict[ramp_spectrum_sc.auto_err(
str(color), 'ramp color spectrum')]
else:
new_color = int(color)
try:
_self.lock(_self)
r = _cmd.ramp_new(_self._COb, str(name), str(map_name), range,
new_color,
int(state) - 1, str(selection), float(beyond),
float(within), float(sigma), int(zero),
int(quiet))
finally:
_self.unlock(r, _self)
if _self._raising(r, _self): raise pymol.CmdException
return r
