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aquaduct.visual.pymol_connector module
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class
BasicPymolCGO
[source]
Bases: object
-
cgo_entity_begin
= []
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cgo_entity_end
= []
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__init__
()[source]
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clean
()[source]
-
new
()[source]
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get
()[source]
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static
make_color_triple
(color_definition)[source]
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class
BasicPymolCGOLines
[source]
Bases: aquaduct.visual.pymol_connector.BasicPymolCGO
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cgo_entity_begin
= [2.0, 1.0]
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cgo_entity_end
= [3.0]
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add
(coords=None, color=None)[source]
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class
BasicPymolCGOSpheres
[source]
Bases: aquaduct.visual.pymol_connector.BasicPymolCGO
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cgo_entity_begin
= []
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cgo_entity_end
= []
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add
(coords=None, radius=None, color=None)[source]
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class
BasicPymolCGOPointers
[source]
Bases: aquaduct.visual.pymol_connector.BasicPymolCGO
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cgo_entity_begin
= []
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cgo_entity_end
= []
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add_cone
(coords1=None, coords2=None, radius1=None, radius2=None, color1=None, color2=None)[source]
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add_pointer
(point=None, direction=None, length=None, color=None, reverse=False)[source]
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class
SimpleTarWriteHelper
[source]
Bases: object
-
__init__
()[source]
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open
(filename)[source]
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save_object2tar
(obj, name)[source]
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save_file2tar
(filename, name)[source]
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__del__
()[source]
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class
ConnectToPymol
[source]
Bases: object
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cgo_line_width
= 2.0
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ct_pymol
= ‘pymol’
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ct_file
= ‘file’
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__init__
()[source]
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decode_color
(*args, **kwargs)[source]
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init_pymol
()[source]
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init_script
(filename)[source]
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add_cgo_object
(name, cgo_object, state=None)[source]
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del_cgo_object
(name, state=None)[source]
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load_pdb
(name, filename, state=None)[source]
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orient_on
(name)[source]
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__del__
()[source]
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class
SinglePathPlotter
(pymol_connector, linearize=None)[source]
Bases: object
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__init__
(pymol_connector, linearize=None)[source]
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add_single_path_continous_trace
(spath, smooth=None, plot_in=True, plot_object=True, plot_out=True, **kwargs)[source]
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paths_trace
(spaths, smooth=None, name=’paths’, state=None, **kwargs)[source]
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paths_inlets
(spaths, smooth=None, color=None, plot_in=True, plot_out=True, name=’in-out-let’, state=None, **kwargs)[source]
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scatter
(coords, radius=0.4, color=’r’, name=’scatter’, state=None)[source]
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convexhull
(chull, color=’m’, name=’convexhull’, state=None)[source]