def dumbbell_geometry(major_radius=1,
minor_radius=0.1,
thickness=0.1,
height=1,
nz=2,
nc1=10,
nc2=10):
from chimerax.surface.shapes import cylinder_geometry
dva, dna, dta = cylinder_geometry(major_radius, thickness, nz, nc1, True)
hva, hna, hta = cylinder_geometry(minor_radius, height, nz, nc2, False)
nv = len(dva)
vs = []
ns = []
ts = []
offset = numpy.array([0, 0, height / 2])
vs.append(dva - offset)
ns.append(dna)
ts.append(dta)
vs.append(hva)
ns.append(hna)
ts.append(hta + nv)
nv += len(hva)
vs.append(dva + offset)
ns.append(dna)
ts.append(dta + nv)
vd, nd, td = numpy.concatenate(vs), numpy.concatenate(
ns), numpy.concatenate(ts)
return vd, nd, td
def unit_cell_box_drawing(unit_cell_corners,
corner_radius=1.0,
origin_radius=2.0,
cylinder_radius=0.2):
from chimerax.graphics import Drawing
md = Drawing('Unit cell box')
cd = Drawing('Corners')
ed = Drawing('Edges')
md.add_drawing(cd)
md.add_drawing(ed)
from chimerax.surface.shapes import sphere_geometry2, cylinder_geometry
cd.set_geometry(*sphere_geometry2(80))
ed.set_geometry(*cylinder_geometry())
from chimerax.geometry import Places, cylinder_rotations
import numpy
shift_and_scale = numpy.empty((8, 4), numpy.float32)
shift_and_scale[:, :3] = unit_cell_corners
shift_and_scale[1:, 3] = corner_radius
shift_and_scale[0, 3] = origin_radius
cd.positions = Places(shift_and_scale=shift_and_scale)
edges = [[0, 1], [0, 2], [0, 4], [1, 3], [1, 5], [2, 3], [2, 6], [3, 7],
[4, 5], [4, 6], [5, 7], [6, 7]]
xyz = [[], []]
for e in edges:
for i in range(2):
xyz[i].append(unit_cell_corners[e[i]])
xyz0, xyz1 = [numpy.array(x) for x in xyz]
rot44 = numpy.empty((12, 4, 4), numpy.float32)
cylinder_rotations(xyz0, xyz1,
numpy.ones(12, numpy.float32) * cylinder_radius, rot44)
rot44[:, 3, :3] = 0.5 * (xyz0 + xyz1)
ed.positions = Places(opengl_array=rot44)
return md
def set_size(self, axis_length, axis_radius):
from chimerax.surface.shapes import cylinder_geometry, cone_geometry
vaz, naz, taz = cylinder_geometry(radius=axis_radius,
height=axis_length)
vcz, ncz, tcz = cone_geometry(radius=axis_radius * 2,
height=axis_length * 0.2,
caps=True)
from chimerax.geometry import Place
vct = Place(origin=(0, 0, axis_length / 2))
vcz = vct.transform_points(vcz)
nv = len(vaz)
tcz = tcz + nv
from numpy import concatenate
vaz = concatenate((vaz, vcz))
naz = concatenate((naz, ncz))
taz = concatenate((taz, tcz))
nv = len(vaz)
tx = Place(axes=[[0, 0, 1], [0, -1, 0], [1, 0, 0]])
vax, nax, tax = tx.transform_points(vaz), tx.transform_vectors(
naz), taz.copy() + nv
ty = Place(axes=[[1, 0, 0], [0, 0, -1], [0, 1, 0]])
vay, nay, tay = ty.transform_points(vaz), ty.transform_vectors(
naz), taz.copy() + 2 * nv
vc = self.vertex_colors
self.set_geometry(concatenate((vax, vay, vaz)),
concatenate((nax, nay, naz)),
concatenate((tax, tay, taz)))
self.vertex_colors = vc # Setting geometry clears vertex colors
def pin_geometry(handle_radius, pin_radius, total_height):
'''
Simple 3D representation of a drawing pin.
Args:
handle_radius:
The radius of the "handle" in Angstroms
pin_radius:
The radius of the "pin" in Angstroms
height:
The overall height of the drawing
'''
import numpy
from chimerax.surface.shapes import cylinder_geometry, cone_geometry
from chimerax.geometry import translation
pin_height = total_height * 5 / 12
handle_height = total_height * 7 / 12
tb_height = total_height / 4
pin = list(
cone_geometry(radius=pin_radius, height=pin_height, points_up=False))
handle_bottom = list(
cone_geometry(radius=handle_radius, height=tb_height, nc=8))
handle_middle = list(
cylinder_geometry(radius=handle_radius / 2,
height=handle_height,
nc=8,
caps=False))
handle_top = list(
cone_geometry(radius=handle_radius,
height=tb_height,
nc=8,
points_up=False))
pint = translation((0, 0, pin_height / 2))
pin[0] = pint.transform_points(pin[0])
hbt = translation((0, 0, pin_height + tb_height / 2.05))
handle_bottom[0] = hbt.transform_points(handle_bottom[0])
hmt = translation((0, 0, handle_height / 2 + pin_height))
handle_middle[0] = hmt.transform_points(handle_middle[0])
htt = translation((0, 0, total_height - tb_height / 2.05))
handle_top[0] = htt.transform_points(handle_top[0])
vertices = numpy.concatenate(
(pin[0], handle_bottom[0], handle_middle[0], handle_top[0]))
normals = numpy.concatenate(
(pin[1], handle_bottom[1], handle_middle[1], handle_top[1]))
ntri = len(pin[0])
triangles = pin[2]
for d in (handle_bottom, handle_middle, handle_top):
triangles = numpy.concatenate((triangles, d[2] + ntri))
ntri += len(d[0])
return vertices, normals, triangles
def post_geometry(radius, height, caps=False):
'''
Returns a simple cylinder, rotated and translated so its base is on
the origin and it points along (1,0,0)
'''
from chimerax.surface.shapes import cylinder_geometry
from chimerax.geometry import rotation, translation
v, n, t = cylinder_geometry(radius=radius, height=height, caps=caps, nc=6)
tr = translation([0, 0, height / 2])
tr.transform_points(v, in_place=True)
r = rotation([0, 1, 0], 90)
r.transform_points(v, in_place=True)
r.transform_vectors(n, in_place=True)
return v, n, t
def _drawing_geometry(fold_symmetry):
from chimerax.surface.shapes import cylinder_geometry
return cylinder_geometry()
def _cb_annotation(self):
from chimerax.surface.shapes import cylinder_geometry
v, n, t = cylinder_geometry(radius=0.1, height=2, nc=8, caps=True)
d = Drawing('rotamer cb indicator')
d.set_geometry(v, n, t)
return d