def test_ra(session):
from chimerax.core.models import Model, Drawing
m = Model('test', session)
d = Drawing('ring')
d.set_geometry(*ring_arrow_with_post(0.5, 0.05, 4, 6, 0.3, 0.1, 0.05, 1))
m.add_drawing(d)
session.models.add([m])
def _exclamation_mark(self):
v, n, t = exclamation_mark(radius=0.1, height=0.5, nc = 8)
flip = rotation((1,0,0), 180)
flip.transform_points(v, in_place=True)
flip.transform_vectors(n, in_place=True)
translation((0,1,0)).transform_points(v, in_place=True)
d = Drawing('rotamer cb indicator')
d.set_geometry(v, n, t)
return d
def _prepare_drawings(self):
if not hasattr(self, '_omega_drawing'):
od = self._omega_drawing = Drawing('cis/twisted omegas')
od.skip_bounds = True
od.pickable = False
self.add_drawing(od)
if not hasattr(self, '_rama_drawing'):
rd = self._rama_drawing = Drawing('Ramachandran score indicators')
rd.skip_bounds = True
rd.pickable = False
from chimerax.surface.shapes import sphere_geometry2
rd.set_geometry(*sphere_geometry2(80))
self.add_drawing(rd)
def simple_arrow(radius=0.1,
height=1,
nc=20,
color=[255, 0, 0, 255],
caps=True,
head_length_fraction=0.33,
head_width_ratio=1.5,
points_out=True):
from chimerax.core.models import Drawing
d = Drawing(name='Arrow')
d.color = color
d.set_geometry(
*simple_arrow_geometry(radius, height, nc, caps, head_length_fraction,
head_width_ratio, points_out))
return d
def draw_asu(xmap):
from chimerax.geometry import Place, Places
from chimerax.core.models import Drawing, Model
from chimerax.surface.shapes import sphere_geometry
d = Drawing('asu corners')
m = Model('asu box', session)
#d.vertices, d.normals, d.triangles = sphere_geometry(80)
d.set_geometry(*sphere_geometry(80))
asu = xmap.grid_asu()
grid = xmap.grid_sampling()
cell = xmap.cell()
minmax = [asu.min().coord_frac(grid).coord_orth(cell).xyz, asu.max().coord_frac(grid).coord_orth(cell).xyz]
dp = []
for i in range(2):
for j in range(2):
for k in range(2):
dp.append(Place(origin=[minmax[i][0],minmax[j][1],minmax[k][2]]))
d.positions = Places(dp)
m.add_drawing(d)
session.models.add([m])
return d
def _rota_indicator(self):
v1, n1, t1 = exclamation_mark(radius=0.1, height=0.5, nc = 8)
v2, n2, t2 = spiral(major_radius=0.3, minor_radius = 0.05, height=0.4,
turn_segments=6, circle_segments=3)
translation((0,0,-0.15)).transform_points(v2, in_place=True)
v = numpy.concatenate((v1, v2))
n = numpy.concatenate((n1, n2))
t = numpy.concatenate((t1, t2+len(v1)))
r = rotation((1,0,0),180)
r.transform_points(v, in_place=True)
r.transform_vectors(n, in_place=True)
translation((0,0.5,0.25)).transform_points(v, in_place=True)
d = Drawing('rotamer indicator')
d.skip_bounds = True
d.pickable = False
d.set_geometry(v, n, t)
return d
def draw_box(min_corner, max_corner, name='box'):
from chimerax.geometry import Place, Places
from chimerax.core.models import Drawing, Model
from chimerax.surface.shapes import sphere_geometry
d = Drawing('corners')
m = Model(name, session)
#d.vertices, d.normals, d.triangles = sphere_geometry(80)
d.set_geometry(*sphere_geometry(80))
minmax = [min_corner, max_corner]
dp = []
base_color = numpy.array([255,255,255,255])
color_increment = numpy.array([0,-32,-32,0])
colors = []
for i in range(2):
for j in range(2):
for k in range(2):
dp.append(Place(origin=[minmax[i][0],minmax[j][1],minmax[k][2]]))
colors.append(base_color-color_increment*(i+j+k));
d.positions = Places(dp)
d.colors = colors
m.add_drawing(d)
session.models.add([m])
return d
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