def color_surface_cylinder(self, surf):
self.writeMessageToLog("Color cylindrically")
cc = Cylinder_Color()
try:
cmin, cmax = cc.value_range(surf.surfacePieces[0])
except:
#keep for older version of chimera, e.g. v1.2509
vertices, triangles = surf.surfacePieces[0].geometry
cmin, cmax = cc.value_range(vertices, vertex_xform=None)
if cmin is None:
cmin = 0
if cmax is None:
cmax = 1.0
crange = cmax - cmin
cc.origin = [0,0,0]
self.writeMessageToLog("%.3f,%.3f"%(cmin,cmax))
if self.colors is None:
### green, yellow, orange
data_values = (cmin, .625*crange+cmin, .75*crange+cmin, .875*crange+cmin, cmax)
#key: red,green,blue,opacity
#order: orange, yellow, green, cyan, blue
colors = [(0.8,0.4,0.1,1), (0.8,0.8,0.1,1), (0.4,0.8,0.1,1), (0.1,0.8,0.1,1), (0.1,0.8,0.8,1)]
else:
### set colors
colors = self.getColors()
data_values = (.125*crange+cmin, .5*crange+cmin, .875*crange+cmin)
cc.colormap = Color_Map(data_values, colors)
color_surface(surf, cc, caps_only = False, auto_update = False)
def color_surface_height(self, surf):
self.writeMessageToLog("Color by height")
hc = Height_Color()
hc.origin = [0, 0, 0]
try:
hmin, hmax = hc.value_range(surf.surfacePieces[0])
except:
#keep for older version of chimera, e.g. v1.2509
vertices, triangles = surf.surfacePieces[0].geometry
hmin, hmax = hc.value_range(vertices, vertex_xform=None)
hrange = hmax - hmin
self.writeMessageToLog("%.3f,%.3f" % (hmin, hmax))
#key: red,green,blue,opacity
if self.colors is None:
### red, white blue
data_values = (.125 * hrange + hmin, .25 * hrange + hmin,
.5 * hrange + hmin, .75 * hrange + hmin,
.875 * hrange + hmin)
colors = [(0.8, 0.2, 0.2, 1), (0.8, 0.5, 0.5, 1),
(0.8, 0.8, 0.8, 1), (0.5, 0.5, 0.8, 1),
(0.2, 0.2, 0.8, 1)]
else:
### set colors
colors = self.getColors()
data_values = (.125 * hrange + hmin, .5 * hrange + hmin,
.875 * hrange + hmin)
hc.colormap = Color_Map(data_values, colors)
color_surface(surf, hc, caps_only=False, auto_update=False)
def color_surface_radially(self, surf):
self.writeMessageToLog("Color radially")
rc = Radial_Color()
rc.origin = [0, 0, 0]
try:
rmin, rmax = rc.value_range(surf.surfacePieces[0])
except:
#keep for older version of chimera, e.g. v1.2509
vertices, triangles = surf.surfacePieces[0].geometry
rmin, rmax = rc.value_range(vertices, vertex_xform=None)
rrange = rmax - rmin
self.writeMessageToLog("%.3f,%.3f" % (rmin, rmax))
#key: red,green,blue,opacity
#order: red, yellow, green, cyan, blue
if self.colors is None:
data_values = (.5 * rmax, .625 * rmax, .75 * rmax, .875 * rmax,
rmax)
colors = [(0.9, 0.1, 0.1, 1), (0.9, 0.9, 0.1, 1),
(0.1, 0.9, 0.1, 1), (0.1, 0.9, 0.9, 1),
(0.1, 0.1, 0.9, 1)]
else:
### set colors
colors = self.getColors()
data_values = (.125 * rrange + rmin, .5 * rrange + rmin,
.875 * rrange + rmin)
rc.colormap = Color_Map(data_values, colors)
color_surface(surf, rc, caps_only=False, auto_update=False)
def color_surface_height(self, surf):
self.writeMessageToLog("Color by height")
hc = Height_Color()
hc.origin = [0,0,0]
try:
hmin, hmax = hc.value_range(surf.surfacePieces[0])
except:
#keep for older version of chimera, e.g. v1.2509
vertices, triangles = surf.surfacePieces[0].geometry
hmin, hmax = hc.value_range(vertices, vertex_xform=None)
hrange = hmax-hmin
self.writeMessageToLog("%.3f,%.3f"%(hmin,hmax))
#key: red,green,blue,opacity
if self.colors is None:
### red, white blue
data_values = (.125*hrange+hmin, .25*hrange+hmin, .5*hrange+hmin, .75*hrange+hmin, .875*hrange+hmin)
colors = [(0.8,0.2,0.2,1), (0.8,0.5,0.5,1), (0.8,0.8,0.8,1), (0.5,0.5,0.8,1), (0.2,0.2,0.8,1)]
else:
### set colors
colors = self.getColors()
data_values = (.125*hrange+hmin, .5*hrange+hmin, .875*hrange+hmin)
hc.colormap = Color_Map(data_values, colors)
color_surface(surf, hc, caps_only = False, auto_update = False)
def color_surface_radially(self, surf):
self.writeMessageToLog("Color radially")
rc = Radial_Color()
rc.origin = [0,0,0]
try:
rmin, rmax = rc.value_range(surf.surfacePieces[0])
except:
#keep for older version of chimera, e.g. v1.2509
vertices, triangles = surf.surfacePieces[0].geometry
rmin, rmax = rc.value_range(vertices, vertex_xform=None)
rrange = rmax-rmin
self.writeMessageToLog("%.3f,%.3f"%(rmin,rmax))
#key: red,green,blue,opacity
#order: red, yellow, green, cyan, blue
if self.colors is None:
data_values = (.5*rmax, .625*rmax, .75*rmax, .875*rmax, rmax)
colors = [(0.9,0.1,0.1,1), (0.9,0.9,0.1,1), (0.1,0.9,0.1,1), (0.1,0.9,0.9,1), (0.1,0.1,0.9,1)]
else:
### set colors
colors = self.getColors()
data_values = (.125*rrange+rmin, .5*rrange+rmin, .875*rrange+rmin)
rc.colormap = Color_Map(data_values, colors)
color_surface(surf, rc, caps_only = False, auto_update = False)
