aquaduct.visual.pymol_connector module

class BasicPymolCGO

Bases: object

cgo_entity_begin = []

cgo_entity_end = []

__init__()

clean(empty=False)

new()

get()

static make_color_triple(color_definition)

class BasicPymolCGOLines

Bases: aquaduct.visual.pymol_connector.BasicPymolCGO

cgo_entity_begin = [2.0, 1.0]

cgo_entity_end = [3.0]

add(coords=None, color=None)

class BasicPymolCGOSpheres

Bases: aquaduct.visual.pymol_connector.BasicPymolCGO

cgo_entity_begin = []

cgo_entity_end = []

add(coords=None, radius=None, color=None)

class BasicPymolCGOPointers

Bases: aquaduct.visual.pymol_connector.BasicPymolCGO

cgo_entity_begin = []

cgo_entity_end = []

add_cone(coords1=None, coords2=None, radius1=None, radius2=None, color1=None, color2=None)

add_pointer(point=None, direction=None, length=None, color=None, reverse=False)

class SimpleTarWriteHelper

Bases: object

__init__()

open(filename)

save_object2tar(obj, name)

save_file2tar(filename, name)

__del__()

class ConnectToPymol

Bases: object

cgo_line_width = 2.0

ct_pymol = 'pymol'

ct_file = 'file'

__init__()

decode_color(*args, **kwargs)

init_pymol()

init_script(filename)

add_cgo_object(name, cgo_object, state=None)

del_cgo_object(name, state=None)

load_pdb(name, filename, state=None)

orient_on(name)

__del__()

class SinglePathPlotter(pymol_connector, linearize=None)

Bases: object

__init__(pymol_connector, linearize=None)

add_single_path_continous_trace(spath, smooth=None, plot_in=True, plot_object=True, plot_out=True, plot_walk=True, **kwargs)

paths_trace(spaths, smooth=None, name='paths', state=None, **kwargs)

paths_inlets(spaths, smooth=None, color=None, plot_in=True, plot_out=True, name='in-out-let', state=None, **kwargs)

scatter(coords, radius=0.4, color='r', name='scatter', state=None)

convexhull(chull, color='m', name='convexhull', state=None)