aquaduct.visual.pymol_connector module

class BasicPymolCGO[source]

Bases: object

cgo_entity_begin = []
cgo_entity_end = []
__init__()[source]
clean()[source]
new()[source]
get()[source]
static make_color_triple(color_definition)[source]
class BasicPymolCGOLines[source]

Bases: aquaduct.visual.pymol_connector.BasicPymolCGO

cgo_entity_begin = [2.0, 1.0]
cgo_entity_end = [3.0]
add(coords=None, color=None)[source]
class BasicPymolCGOSpheres[source]

Bases: aquaduct.visual.pymol_connector.BasicPymolCGO

cgo_entity_begin = []
cgo_entity_end = []
add(coords=None, radius=None, color=None)[source]
class BasicPymolCGOPointers[source]

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)[source]
add_pointer(point=None, direction=None, length=None, color=None, reverse=False)[source]
class SimpleTarWriteHelper[source]

Bases: object

__init__()[source]
open(filename)[source]
save_object2tar(obj, name)[source]
save_file2tar(filename, name)[source]
__del__()[source]
class ConnectToPymol[source]

Bases: object

cgo_line_width = 2.0
ct_pymol = ‘pymol’
ct_file = ‘file’
__init__()[source]
decode_color(*args, **kwargs)[source]
init_pymol()[source]
init_script(filename)[source]
add_cgo_object(name, cgo_object, state=None)[source]
del_cgo_object(name, state=None)[source]
load_pdb(name, filename, state=None)[source]
orient_on(name)[source]
__del__()[source]
class SinglePathPlotter(pymol_connector, linearize=None)[source]

Bases: object

__init__(pymol_connector, linearize=None)[source]
add_single_path_continous_trace(spath, smooth=None, plot_in=True, plot_object=True, plot_out=True, **kwargs)[source]
paths_trace(spaths, smooth=None, name=’paths’, state=None, **kwargs)[source]
paths_inlets(spaths, smooth=None, color=None, plot_in=True, plot_out=True, name=’in-out-let’, state=None, **kwargs)[source]
scatter(coords, radius=0.4, color=’r’, name=’scatter’, state=None)[source]
convexhull(chull, color=’m’, name=’convexhull’, state=None)[source]