def test_rotate(self):
from chempy import cpv
from math import pi
get_coord_list = lambda s: cmd.get_model(s).get_coord_list()
cmd.fragment('ala')
cmd.select('s1', 'hydro')
c1_hydro = get_coord_list('s1')
c1_other = get_coord_list('not s1')
c1_hydro_rot = cpv.transform_array(
cpv.rotation_matrix(pi * 0.25, [0,0,1]), c1_hydro)
cmd.rotate('z', 45, 's1', camera=0, origin=(0,0,0))
c2_hydro = get_coord_list('s1')
c2_other = get_coord_list('not s1')
self.assertArrayEqual(c2_other, c1_other)
self.assertArrayEqual(c2_hydro, c1_hydro_rot, 0.001)
def test_rotate(self):
from chempy import cpv
from math import pi
get_coord_list = lambda s: cmd.get_model(s).get_coord_list()
cmd.fragment('ala')
cmd.select('s1', 'hydro')
c1_hydro = get_coord_list('s1')
c1_other = get_coord_list('not s1')
c1_hydro_rot = cpv.transform_array(
cpv.rotation_matrix(pi * 0.25, [0, 0, 1]), c1_hydro)
cmd.rotate('z', 45, 's1', camera=0, origin=(0, 0, 0))
c2_hydro = get_coord_list('s1')
c2_other = get_coord_list('not s1')
self.assertArrayEqual(c2_other, c1_other)
self.assertArrayEqual(c2_hydro, c1_hydro_rot, 0.001)
def torus(center=(0., 0., 0.), normal=(0., 0., 1.), radius=1., color='',
cradius=.25, samples=20, csamples=20):
'''
Generate and return a torus CGO with given center, normal
and ring radius.
'''
from math import cos, sin, pi
if color and isinstance(color, str):
color = list(cmd.get_color_tuple(color))
obj = []
axis = cpv.cross_product(normal, (0., 0., 1.))
angle = -cpv.get_angle(normal, (0., 0., 1.))
matrix = cpv.rotation_matrix(angle, cpv.normalize(axis))
obj_vertex = lambda x, y, z: obj.extend([VERTEX] + cpv.add(center,
cpv.transform(matrix, [x, y, z])))
obj_normal = lambda x, y, z: obj.extend([NORMAL] +
cpv.transform(matrix, [x, y, z]))
r = radius
cr = cradius
rr = 1.5 * cr
dv = 2 * pi / csamples
dw = 2 * pi / samples
v = 0.0
w = 0.0
while w < 2 * pi:
v = 0.0
c_w = cos(w)
s_w = sin(w)
c_wdw = cos(w + dw)
s_wdw = sin(w + dw)
obj.append(BEGIN)
obj.append(TRIANGLE_STRIP)
if color:
obj.append(COLOR)
obj.extend(color)
while v < 2 * pi + dv:
c_v = cos(v)
s_v = sin(v)
c_vdv = cos(v + dv)
s_vdv = sin(v + dv)
obj_normal(
(r + rr * c_v) * c_w - (r + cr * c_v) * c_w,
(r + rr * c_v) * s_w - (r + cr * c_v) * s_w,
(rr * s_v - cr * s_v))
obj_vertex(
(r + cr * c_v) * c_w,
(r + cr * c_v) * s_w,
cr * s_v)
obj_normal(
(r + rr * c_vdv) * c_wdw - (r + cr * c_vdv) * c_wdw,
(r + rr * c_vdv) * s_wdw - (r + cr * c_vdv) * s_wdw,
rr * s_vdv - cr * s_vdv)
obj_vertex(
(r + cr * c_vdv) * c_wdw,
(r + cr * c_vdv) * s_wdw,
cr * s_vdv)
v += dv
obj.append(END)
w += dw
return obj
def torus(center=(0., 0., 0.), normal=(0., 0., 1.), radius=1., color='',
cradius=.25, samples=20, csamples=20, _self=cmd):
'''
Generate and return a torus CGO with given center, normal
and ring radius.
'''
from math import cos, sin, pi
if color and isinstance(color, str):
color = list(_self.get_color_tuple(color))
obj = []
axis = cpv.cross_product(normal, (0., 0., 1.))
angle = -cpv.get_angle(normal, (0., 0., 1.))
matrix = cpv.rotation_matrix(angle, cpv.normalize(axis))
obj_vertex = lambda x, y, z: obj.extend([VERTEX] + cpv.add(center,
cpv.transform(matrix, [x, y, z])))
obj_normal = lambda x, y, z: obj.extend([NORMAL] +
cpv.transform(matrix, [x, y, z]))
r = radius
cr = cradius
rr = 1.5 * cr
dv = 2 * pi / csamples
dw = 2 * pi / samples
v = 0.0
w = 0.0
while w < 2 * pi:
v = 0.0
c_w = cos(w)
s_w = sin(w)
c_wdw = cos(w + dw)
s_wdw = sin(w + dw)
obj.append(BEGIN)
obj.append(TRIANGLE_STRIP)
if color:
obj.append(COLOR)
obj.extend(color)
while v < 2 * pi + dv:
c_v = cos(v)
s_v = sin(v)
c_vdv = cos(v + dv)
s_vdv = sin(v + dv)
obj_normal(
(r + rr * c_v) * c_w - (r + cr * c_v) * c_w,
(r + rr * c_v) * s_w - (r + cr * c_v) * s_w,
(rr * s_v - cr * s_v))
obj_vertex(
(r + cr * c_v) * c_w,
(r + cr * c_v) * s_w,
cr * s_v)
obj_normal(
(r + rr * c_vdv) * c_wdw - (r + cr * c_vdv) * c_wdw,
(r + rr * c_vdv) * s_wdw - (r + cr * c_vdv) * s_wdw,
rr * s_vdv - cr * s_vdv)
obj_vertex(
(r + cr * c_vdv) * c_wdw,
(r + cr * c_vdv) * s_wdw,
cr * s_vdv)
v += dv
obj.append(END)
w += dw
return obj
def rebuild(self) -> None:
"""
Rebuilds torus
"""
obj = []
axis = cpv.cross_product(self.normal.array(), (0., 0., 1.))
angle = -cpv.get_angle(self.normal.array(), (0., 0., 1.))
matrix = cpv.rotation_matrix(angle, cpv.normalize(axis))
def obj_vertex(x, y, z):
return [cgo.VERTEX] + cpv.add(self.center.array(),
cpv.transform(matrix, [x, y, z]))
def obj_normal(x, y, z):
return [cgo.NORMAL] + cpv.transform(matrix, [x, y, z])
r = self.radius
cr = self.cradius
rr = 1.5 * cr
dv = 2 * math.pi / self.csamples
dw = 2 * math.pi / self.samples
v = 0.0
w = 0.0
while w < 2 * math.pi:
v = 0.0
c_w = math.cos(w)
s_w = math.sin(w)
c_wdw = math.cos(w + dw)
s_wdw = math.sin(w + dw)
obj.append(cgo.BEGIN)
obj.append(cgo.TRIANGLE_STRIP)
obj.append(cgo.COLOR)
obj.extend(self.color.array())
while v < 2 * math.pi + dv:
c_v = math.cos(v)
s_v = math.sin(v)
c_vdv = math.cos(v + dv)
s_vdv = math.sin(v + dv)
obj.extend(
obj_normal((r + rr * c_v) * c_w - (r + cr * c_v) * c_w,
(r + rr * c_v) * s_w - (r + cr * c_v) * s_w,
(rr * s_v - cr * s_v)))
obj.extend(
obj_vertex((r + cr * c_v) * c_w, (r + cr * c_v) * s_w,
cr * s_v))
obj.extend(
obj_normal(
(r + rr * c_vdv) * c_wdw - (r + cr * c_vdv) * c_wdw,
(r + rr * c_vdv) * s_wdw - (r + cr * c_vdv) * s_wdw,
rr * s_vdv - cr * s_vdv))
obj.extend(
obj_vertex((r + cr * c_vdv) * c_wdw,
(r + cr * c_vdv) * s_wdw, cr * s_vdv))
v += dv
obj.append(cgo.END)
w += dw
self._data = obj