def mesh_geometry(mesh, seg):
# TODO: SFF format data structure mix vertices and normals, calling both vertices -- a nightmare.
# Semantics of which normal belong with which vertices unclear (consecutive in polygon?).
# Efficiency reading is horrible. Ask Paul K to make separate vertex and normal lists.
nv = mesh.num_vertices // 2
from numpy import empty, float32
va = empty((nv, 3), float32)
na = empty((nv, 3), float32)
for i, v in enumerate(mesh.vertices):
vid = v.id
if vid != i:
raise ValueError(
'Require mesh vertices be numbers consecutively from 0, got vertex id %d in position %d'
% (vid, i))
d = v.designation # 'surface' or 'normal'
if d == 'surface':
if vid % 2 == 1:
raise ValueError(
'Require odd mesh indices to be normals, got a vertex at position %d'
% vid)
va[vid // 2] = v.point
elif d == 'normal':
if vid % 2 == 0:
raise ValueError(
'Require even mesh indices to be vertices, got a normal at position %d'
% vid)
na[vid // 2] = v.point
else:
raise ValueError(
'Vertex %d designation "%s" is not "surface" or "normal"' %
(v.id, d))
'''
vids = list(set(v.id for v in mesh.vertices if v.designation == 'surface'))
vids.sort()
print ('vertex ids', vids[:3], 'num', len(vids), 'last', vids[-1])
'''
if mesh.transform_id is None:
from chimerax.geometry import Place, scale
# transform = scale((160,160,160)) * Place(seg.transforms[0].data_array)
transform = Place(seg.transforms[0].data_array) * scale(
(160, 160, 160))
else:
transform = transform_by_id(seg, mesh.transform_id)
transform.transform_points(va, in_place=True)
transform.transform_normals(na, in_place=True)
tri = []
for p in mesh.polygons:
# print ('poly', len(p.vertex_ids), p.vertex_ids[:6])
t = tuple(vid // 2 for vid in p.vertices if vid % 2 == 0)
if len(t) != 3:
raise ValueError(
'Require polygons to be single triangles, got polygon with %d vertices'
% len(t))
tri.append(t)
'''
last_vid = None
for vid in p.vertex_ids:
if vid % 2 == 0:
if last_vid is not None:
# tri.append((vid//2,last_vid//2))
tri.append((vid//2,last_vid//2,vid//2))
last_vid = vid
first_vid = p.vertex_ids[0]
tri.append((last_vid//2,first_vid//2,last_vid//2))
'''
from numpy import array, int32
ta = array(tri, int32)
return va, na, ta
def draw_slab(nd, residue, name, params):
shapes = []
standard = standard_bases[name]
ring_atom_names = standard["ring atom names"]
atoms = get_ring(residue, ring_atom_names)
if not atoms:
return shapes
plane = Plane([a.coord for a in atoms])
info = find_dimensions(params.dimensions)
tag = standard['tag']
slab_corners = info[tag]
origin = residue.find_atom(anchor(info[ANCHOR], tag)).coord
origin = plane.nearest(origin)
pts = [plane.nearest(a.coord) for a in atoms[0:2]]
y_axis = pts[0] - pts[1]
normalize_vector(y_axis)
x_axis = numpy.cross(y_axis, plane.normal)
xf = Place(matrix=((x_axis[0], y_axis[0], plane.normal[0], origin[0]),
(x_axis[1], y_axis[1], plane.normal[1], origin[1]),
(x_axis[2], y_axis[2], plane.normal[2], origin[2])))
xf = xf * standard["correction factor"]
color = residue.ring_color
half_thickness = params.thickness / 2
llx, lly = slab_corners[0]
llz = -half_thickness
urx, ury = slab_corners[1]
urz = half_thickness
center = (llx + urx) / 2, (lly + ury) / 2, 0
if params.shape == 'box':
llb = (llx, lly, llz)
urf = (urx, ury, urz)
xf2 = xf
va, na, ta = box_geometry(llb, urf)
pure_rotation = True
elif params.shape == 'muffler':
radius = (urx - llx) / 2 * _SQRT2
xf2 = xf * translation(center)
xf2 = xf2 * scale((1, 1, half_thickness * _SQRT2 / radius))
height = ury - lly
va, na, ta = get_cylinder(radius, numpy.array((0, -height / 2, 0)),
numpy.array((0, height / 2, 0)))
pure_rotation = False
elif params.shape == 'ellipsoid':
# need to reach anchor atom
xf2 = xf * translation(center)
sr = (ury - lly) / 2 * _SQRT3
xf2 = xf2 * scale(
((urx - llx) / 2 * _SQRT3 / sr, 1, half_thickness * _SQRT3 / sr))
va, na, ta = get_sphere(sr, (0, 0, 0))
pure_rotation = False
else:
raise RuntimeError('unknown base shape')
description = '%s %s' % (residue, tag)
xf2.transform_points(va, in_place=True)
xf2.transform_normals(na, in_place=True, is_rotation=pure_rotation)
shapes.append(AtomicShapeInfo(va, na, ta, color, atoms, description))
if not params.orient:
return shapes
# show slab orientation by putting "bumps" on surface
if tag == PYRIMIDINE:
center = (llx + urx) / 2.0, (lly + ury) / 2, half_thickness
va, na, ta = get_sphere(half_thickness, center)
xf.transform_points(va, in_place=True)
xf.transform_normals(na, in_place=True, is_rotation=True)
shapes.append(AtomicShapeInfo(va, na, ta, color, atoms, description))
else:
# purine
center = (llx + urx) / 2.0, lly + (ury - lly) / 3, half_thickness
va, na, ta = get_sphere(half_thickness, center)
xf.transform_points(va, in_place=True)
xf.transform_normals(na, in_place=True, is_rotation=True)
shapes.append(AtomicShapeInfo(va, na, ta, color, atoms, description))
center = (llx + urx) / 2.0, lly + (ury - lly) * 2 / 3, half_thickness
va, na, ta = get_sphere(half_thickness, center)
xf.transform_points(va, in_place=True)
xf.transform_normals(na, in_place=True, is_rotation=True)
shapes.append(AtomicShapeInfo(va, na, ta, color, atoms, description))
return shapes
