def makeLegend(features):
"""
A function to display a legend for the features and their respective
colors.
@param features: A C{set} of feature names.
@return: A C{list} of objects to be plotted.
"""
cgo = []
colors = [[0.5, 1.0, 1.0], [1.0, 0.7, 0.2], [0.73, 0.55, 0.52],
[1.0, 0.5, 0.5], [0.6, 0.6, 0.1], [0.1, 0.6, 0.6],
[0.698, 0.13, 0.13], [0.25, 1.00, 0.75], [0.75, 0.75, 1.0],
[0.75, 1.00, 0.25], [0.0, 0.5, 1.0], [1.0, 0.5, 0.0],
[0.65, 0.9, 0.65], [1.0, 0.3, 0.3], [0.2, 1.0, 0.2],
[1.0, 0.2, 0.2], [0.55, 0.25, 0.60], [0.85, 0.20, 0.50],
[0.619607843, 0.388235294, 0.709803922],
[0.341176471, 0.090196078, 0.560784314],
[1.0, 0.819607843, 0.137254902], [0.2, 0.6, 0.2],
[0.5, 0.5, 1.0], [0.3, 0.3, 1.0], [1.0, 0.5, 1.0],
[0.819607843, 0.0, 0.309803922],
[0.090196078, 0.329411765, 0.529411765],
[1.0, 0.501960784, 0.0],
[1.0, 0.0, 1.0], [1.0, 1.0, 0.0],
[1.0, 1.0, 1.0]]
axes = [[2.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 2.0]]
textY = 0.0
sphereY = 1.0
spheres = []
for i, featureName in enumerate(features):
wire_text(cgo, plain, [0.0, textY, 0.0], featureName[1], axes=axes)
textY -= 3.0
spheres.extend([COLOR] + colors[i] +
[SPHERE, -1.5, sphereY, 0.0, 1])
sphereY -= 3.0
cgo.extend(spheres)
return cgo
def reps(self, cleanup=0):
rep_list = [
"lines", "sticks", "spheres", "surface", "mesh", "dots", "ribbon",
"cartoon"
]
try:
if not cleanup:
self.cmd.disable()
self.cmd.set("suspend_updates", 1, quiet=1)
self.cmd.mset()
self.cmd.set("movie_panel", 0)
self.cmd.load("$PYMOL_DATA/demo/pept.pdb", "rep1")
self.cmd.alter("rep1///1-5+8-13/", "ss='S'")
self.cmd.cartoon("auto")
self.cmd.hide("everything", "rep1")
for a in range(2, 9):
self.cmd.create("rep%d" % a, "rep1")
for y, x in enumerate(rep_list, 1):
self.cmd.show(x, "rep%d" % y)
self.cmd.reset()
self.cmd.zoom("rep1", 24)
util.cbay("rep2", _self=self.cmd)
util.cbac("rep3", _self=self.cmd)
util.cbas("rep4", _self=self.cmd)
util.cbab("rep5", _self=self.cmd)
util.cbaw("rep6", _self=self.cmd)
util.cbay("rep8", _self=self.cmd)
self.cmd.set("suspend_updates", 0, quiet=1)
scale = 0.5
for b in range(1, 20):
self.cmd.set("suspend_updates", 0, quiet=1)
self.cmd.refresh()
self.cmd.set("suspend_updates", 1, quiet=1)
xt = -3.2
yt = 1.6
for a in range(1, 5):
self.cmd.translate([xt * scale, yt * scale, 0],
object="rep%d" % a,
camera=0)
xt = xt + 2
yt = -yt
xt = -3.2
for a in range(5, 9):
self.cmd.translate([xt * scale, yt * scale, 0],
object="rep%d" % a,
camera=0)
xt = xt + 2
for a in range(1, 9):
self.cmd.origin("rep%d" % a, object="rep%d" % a)
self.cmd.mset("1")
st = ' '.join("rotate angle=-3,object=rep%d,axis=%s;" %
(x, 'yx'[x % 2]) for x in range(1, 9))
self.cmd.mdo(1, st)
self.cmd.set("suspend_updates", 0, quiet=1)
self.cmd.mplay()
cgo = []
axes = [[4.5, 0.0, 0.0], [0.0, 3.0, 0.0], [0.0, 0.0, 3.0]]
c = 1
for a in rep_list:
ext = self.cmd.get_extent("rep%d" % c)
pos = [(ext[0][0] + ext[1][0]) / 2,
(ext[0][1] + ext[1][1]) / 2 + 14,
(ext[0][2] + ext[1][2]) / 2]
c = c + 1
pos[0] = pos[0] - (measure_text(plain, a, axes) / 2)
wire_text(cgo, plain, pos, a, axes)
self.cmd.set("cgo_line_width", 1.5)
self.cmd.set("auto_zoom", 0)
self.cmd.load_cgo(cgo, 'reps')
self.cmd.set("auto_zoom", 1)
else:
self.cmd.delete("rep*")
self.cmd.mset()
self.cmd.mstop()
self.cmd.set("movie_panel", 1)
except:
traceback.print_exc()
def reps(self,cleanup=0):
rep_list = [ "lines","sticks","spheres","surface","mesh","dots","ribbon","cartoon" ]
try:
if not cleanup:
self.cmd.disable()
self.cmd.set("suspend_updates",1,quiet=1)
self.cmd.mset()
self.cmd.set("movie_panel", 0)
self.cmd.load("$PYMOL_DATA/demo/pept.pdb","rep1")
self.cmd.alter("rep1///1-5+8-13/","ss='S'")
self.cmd.cartoon("auto")
self.cmd.hide("everything","rep1")
for a in range(2,9):
self.cmd.create("rep%d"%a,"rep1")
for y, x in enumerate(rep_list, 1):
self.cmd.show(x, "rep%d" % y)
self.cmd.reset()
self.cmd.zoom("rep1",24)
util.cbay("rep2",_self=self.cmd)
util.cbac("rep3",_self=self.cmd)
util.cbas("rep4",_self=self.cmd)
util.cbab("rep5",_self=self.cmd)
util.cbaw("rep6",_self=self.cmd)
util.cbay("rep8",_self=self.cmd)
self.cmd.set("suspend_updates",0,quiet=1)
scale=0.5
for b in range(1,20):
self.cmd.set("suspend_updates",0,quiet=1)
self.cmd.refresh()
self.cmd.set("suspend_updates",1,quiet=1)
xt=-3.2
yt=1.6
for a in range(1,5):
self.cmd.translate([xt*scale,yt*scale,0],object="rep%d"%a,camera=0)
xt=xt+2
yt=-yt
xt=-3.2
for a in range(5,9):
self.cmd.translate([xt*scale,yt*scale,0],object="rep%d"%a,camera=0)
xt=xt+2
for a in range(1,9):
self.cmd.origin("rep%d"%a,object="rep%d"%a)
self.cmd.mset("1")
st = ' '.join("rotate angle=-3,object=rep%d,axis=%s;" % (x, 'yx'[x % 2]) for x in range(1, 9))
self.cmd.mdo(1,st)
self.cmd.set("suspend_updates",0,quiet=1)
self.cmd.mplay()
cgo = []
axes = [[4.5,0.0,0.0],[0.0,3.0,0.0],[0.0,0.0,3.0]]
c = 1
for a in rep_list:
ext = self.cmd.get_extent("rep%d"%c)
pos = [(ext[0][0]+ext[1][0])/2,
(ext[0][1]+ext[1][1])/2+14,
(ext[0][2]+ext[1][2])/2]
c = c + 1
pos[0]=pos[0]-(measure_text(plain,a,axes)/2)
wire_text(cgo,plain,pos,a,axes)
self.cmd.set("cgo_line_width",1.5)
self.cmd.set("auto_zoom",0)
self.cmd.load_cgo(cgo,'reps')
self.cmd.set("auto_zoom",1)
else:
self.cmd.delete("rep*")
self.cmd.mset()
self.cmd.mstop()
self.cmd.set("movie_panel",1)
except:
traceback.print_exc()