posebutcher.o3d

Module Contents

Functions

sphere([radius, position, resolution, legacy])
arrow(origin, direction, length[, radius, color])
cylinder(origin, direction[, length, radius, legacy, ...])
cone(origin, direction, half_angle, length[, ...])
rotation_matrix_from_vectors(vec1, vec2)	Find the rotation matrix that aligns vec1 to vec2
render(mesh[, raw_mode, show_ui, wireframe])
paint(mesh, colour)
material(color[, alpha, shiny])
glass()
compute_vertex_normals(mesh)
union(mesh1, mesh2)
is_point_in_mesh(mesh, point[, within, tolerance])
signed_distance(mesh, point)
combine_many(meshes)
convex_hull(mesh)
tensor_from_legacy(mesh)
subtract_atoms(mesh, group[, r_scale, use_covalent])
mesh_fix(mesh[, sample_points, nbr_sz, ...])
dump_mesh(path, mesh[, verbosity])
load_mesh(path[, verbosity])
material_to_dict(material)
material_from_dict(d)
union_mesh_from_atoms(atoms[, skip_hydrogen])
mesh_from_AtomGroup(group[, r_scale, use_covalent, ...])
mesh_from_pdb(path[, gauss])
test_sphere()
test_2spheres()
test_3spheres()

Attributes

logger

posebutcher.o3d.logger

posebutcher.o3d.sphere(radius=1.0, position=None, resolution=20, legacy=False)

posebutcher.o3d.arrow(origin, direction, length, radius=0.5, color=[0, 1, 0])

posebutcher.o3d.cylinder(origin, direction, length=None, radius=0.25, legacy=False, resolution=20)

posebutcher.o3d.cone(origin, direction, half_angle, length, resolution=30, legacy=False)

posebutcher.o3d.rotation_matrix_from_vectors(vec1, vec2)

Find the rotation matrix that aligns vec1 to vec2 :param vec1: A 3d “source” vector :param vec2: A 3d “destination” vector :return mat: A transform matrix (3x3) which when applied to vec1, aligns it with vec2.

posebutcher.o3d.render(mesh, raw_mode=False, show_ui=True, wireframe=False)

posebutcher.o3d.paint(mesh, colour)

posebutcher.o3d.material(color, alpha=1.0, shiny=False)

posebutcher.o3d.glass()

posebutcher.o3d.compute_vertex_normals(mesh)

posebutcher.o3d.union(mesh1, mesh2)

posebutcher.o3d.is_point_in_mesh(mesh, point, within=0.0, tolerance=0.1)

posebutcher.o3d.signed_distance(mesh, point)

posebutcher.o3d.combine_many(meshes)

posebutcher.o3d.convex_hull(mesh)

posebutcher.o3d.tensor_from_legacy(mesh)

posebutcher.o3d.subtract_atoms(mesh, group, r_scale=1.0, use_covalent=False)

posebutcher.o3d.mesh_fix(mesh, sample_points=2000, nbr_sz=20, sample_spacing=None, temp_path='_meshfix.ply', clip_to_hull=False)

posebutcher.o3d.dump_mesh(path, mesh, verbosity=True, **kwargs)

posebutcher.o3d.load_mesh(path, verbosity=True)

posebutcher.o3d.material_to_dict(material)

posebutcher.o3d.material_from_dict(d)

posebutcher.o3d.union_mesh_from_atoms(atoms, skip_hydrogen=True)

posebutcher.o3d.mesh_from_AtomGroup(group, r_scale=1.0, use_covalent=False, licorice=True, licorice_radius=0.3)

posebutcher.o3d.mesh_from_pdb(path, gauss=False)

posebutcher.o3d.test_sphere()

posebutcher.o3d.test_2spheres()

posebutcher.o3d.test_3spheres()