r_xy_2 = v[:, 0]**2 + v[:, 1]**2
## r_xy = sqrt(r_xy_2) # not needed
# to get radius, take maximum -- not sure if max(r_xy_2) would use Numeric code, but this will for sure:
i = argmax(r_xy_2)
max_xy_2 = r_xy_2[i]
radius = sqrt(max_xy_2)
# to get limits along axis (since we won't assume center is centered between them), use min/max z:
z = v[:, 2]
min_z = z[argmin(z)]
max_z = z[argmax(z)]
bcenter = chunk.abs_to_base(center)
# return, in chunk-relative coords, end1, end2, and radius of the cylinder, and color.
color = chunk.color
if color is None:
color = V(0.5, 0.5, 0.5)
# make sure it's longer than zero (in case of a single-atom chunk); in fact, add a small margin all around
# (note: this is not sufficient to enclose all atoms entirely; that's intentional)
margin = 0.2
min_z -= margin
max_z += margin
radius += margin
return (bcenter + min_z * axis, bcenter + max_z * axis, radius, color)
pass # end of class CylinderChunks
ChunkDisplayMode.register_display_mode_class(CylinderChunks)
# end
v = dot( points, matrix)
# compute xy distances-squared between axis line and atom centers
r_xy_2 = v[:,0]**2 + v[:,1]**2
## r_xy = sqrt(r_xy_2) # not needed
# to get radius, take maximum -- not sure if max(r_xy_2) would use Numeric code, but this will for sure:
i = argmax(r_xy_2)
max_xy_2 = r_xy_2[i]
radius = sqrt(max_xy_2)
# to get limits along axis (since we won't assume center is centered between them), use min/max z:
z = v[:,2]
min_z = z[argmin(z)]
max_z = z[argmax(z)]
bcenter = chunk.abs_to_base(center)
# return, in chunk-relative coords, end1, end2, and radius of the cylinder, and color.
color = chunk.color
if color is None:
color = V(0.5,0.5,0.5)
# make sure it's longer than zero (in case of a single-atom chunk); in fact, add a small margin all around
# (note: this is not sufficient to enclose all atoms entirely; that's intentional)
margin = 0.2
min_z -= margin
max_z += margin
radius += margin
return (bcenter + min_z * axis, bcenter + max_z * axis, radius, color)
pass # end of class CylinderChunks
ChunkDisplayMode.register_display_mode_class(CylinderChunks)
# end
pos1 = 2.0 * pos2 - pos3
sec[-2] = (pos1, ss1, aa1, idx1, dpos1, cbpos1)
# Make sure that the interior surface of helices
# is properly oriented.
if ss == 1:
pos2, ss2, aa2, idx2, dpos2, cbpos2 = sec[2]
pos3, ss3, aa3, idx3, dpos3, cbpos3 = sec[3]
pos4, ss4, aa4, idx4, dpos4, cbpos4 = sec[4]
xvec = cross(pos4-pos3, pos3-pos2)
sign = dot(xvec, dpos3)
if sign > 0:
# Wrong orientation, invert peptide plates
for n in range(2, len(sec)-2):
(pos1, ss1, aa1, idx1, dpos1, cbpos1) = sec[n]
dpos1 *= -1
sec[n] = (pos1, ss1, aa1, idx1, dpos1, cbpos1)
pass
# Append the secondary structure element.
structure.append((sec, ss))
n_sec += 1
sec = []
return (structure, n_ca, ca_list, n_sec)
ChunkDisplayMode.register_display_mode_class(ProteinChunks)
p = a.posn() - center
s.spheres.append(Triple(p[0], p[1], p[2]))
r = p[0]**2+p[1]**2+p[2]**2
if r > rad: rad = r
rad = sqrt(rad)
radius = rad + margin
for i in range(len(s.spheres)):
s.spheres[i] /= radius
s.radiuses[i] /= radius
color = chunk.drawing_color()
if color is None:
color = V(0.5,0.5,0.5)
# create surface
level = 3
if rad > 6 : level = 4
ts = getSphereTriangles(level)
#ts = s.TorusTriangles(0.7, 0.3, 20)
tm = s.SurfaceTriangles(ts)
nm = s.SurfaceNormals()
QApplication.restoreOverrideCursor() # Restore the cursor. Mark 060621.
env.history.message(self.cmdname + "Done.") # Mark 060621.
return (bcenter, radius, color, tm, nm)
pass # end of class SurfaceChunks
ChunkDisplayMode.register_display_mode_class(SurfaceChunks)
# end
r = p[0]**2 + p[1]**2 + p[2]**2
if r > rad: rad = r
rad = sqrt(rad)
radius = rad + margin
for i in range(len(s.spheres)):
s.spheres[i] /= radius
s.radiuses[i] /= radius
color = chunk.drawing_color()
if color is None:
color = V(0.5, 0.5, 0.5)
# create surface
level = 3
if rad > 6: level = 4
ts = getSphereTriangles(level)
#ts = s.TorusTriangles(0.7, 0.3, 20)
tm = s.SurfaceTriangles(ts)
nm = s.SurfaceNormals()
QApplication.restoreOverrideCursor(
) # Restore the cursor. Mark 060621.
env.history.message(self.cmdname + "Done.") # Mark 060621.
return (bcenter, radius, color, tm, nm)
pass # end of class SurfaceChunks
ChunkDisplayMode.register_display_mode_class(SurfaceChunks)
# end