Compiled graphics object API

ammolite.draw_cgo(cgo_list, name=None, pymol_instance=None)

Draw geometric shapes using Compiled Graphics Objects (CGOs).

Each CGO is represented by a list of floats, which can be obtained via the get_xxx_cgo() functions.

Parameters
cgo_listlist of list of float

The CGOs to draw. It is recommended to use a get_xxx_cgo() function to obtain the elements for this list, if possible. Otherwise, shapes may be drawn incorrectly or omitted entirely, if a CGO is incorrectly formatted.

namestr, optional

The name of the newly created CGO object. If omitted, a unique name is generated.

pymol_instancemodule or SingletonPyMOL or PyMOL, optional

If PyMOL is used in library mode, the PyMOL or SingletonPyMOL object is given here. If otherwise PyMOL is used in GUI mode, the pymol module is given. By default the currently used PyMOL instance (ammolite.pymol) is used. If no PyMOL instance is currently running, PyMOL is started in library mode.

ammolite.get_cylinder_cgo(start, end, radius, start_color, end_color)

Get the CGO for a cylinder.

Parameters
start, endarray-like, shape=(3,)

The start and end position of the cylinder.

radiusfloat

The radius of the cylinder

start_color, end_colorarray-like, shape=(3,)

The color at the start and end of the cylinder given as RGB values in the range (0, 1).

ammolite.get_cone_cgo(start, end, start_radius, end_radius, start_color, end_color, start_cap, end_cap)

Get the CGO for a cone.

Parameters
start, endarray-like, shape=(3,)

The start and end position of the cone.

start_radius, end_radiusfloat

The radius of the cone at the start and end.

start_color, end_colorarray-like, shape=(3,)

The color at the start and end of the cone given as RGB values in the range (0, 1).

start_cap, end_capbool

If true, a cap is drawn at the start or end of the cone. Otherwise the cone is displayed as open.

ammolite.get_sphere_cgo(pos, radius, color)

Get the CGO for a sphere.

Parameters
posarray-like, shape=(3,)

The position of the sphere.

radiusfloat

The radius of the sphere.

colorarray-like, shape=(3,)

The color of the sphere given as RGB values in the range (0, 1).


ammolite.draw_arrows(start, end, radius=0.1, head_radius=0.2, head_length=0.5, color=(0.5, 0.5, 0.5), head_color=None, name=None, pymol_instance=None)

Draw three-dimensional arrows using Compiled Graphics Objects (CGOs).

Parameters
start, endarray-like, shape=(n,3)

The start and end position of each arrow.

radius, head_radius: float or array-like, shape=(n,), optional

The radius of the tail and head for each arrow. Uniform for all arrows, if a single value is given.

head_length: float or array-like, shape=(n,), optional

The length of each arrow head. Uniform for all arrows, if a single value is given.

color, head_colorarray-like, shape=(3,) or shape=(n,3), optional

The color of the tail and head for each arrow, given as RGB values in the range (0, 1). Uniform for all arrows, if a single value is given. If no head_color is given, the arrows are single-colored.

namestr, optional

The name of the newly created CGO object. If omitted, a unique name is generated.

pymol_instancemodule or SingletonPyMOL or PyMOL, optional

If PyMOL is used in library mode, the PyMOL or SingletonPyMOL object is given here. If otherwise PyMOL is used in GUI mode, the pymol module is given. By default the currently used PyMOL instance (ammolite.pymol) is used. If no PyMOL instance is currently running, PyMOL is started in library mode.