forgi.threedee.visual.pymol module¶

class forgi.threedee.visual.pymol.PyMolRNA(name, color_modifier=1.0)[source]¶

Bases: future.types.newobject.newobject

add_cone(p, n, color='white', width=2.4, text='')[source]¶

add_dashed(point1, point2, width=0.1, color='purple')[source]¶

Add a dashed line from point1 to point2.

add_segment(p, n, color='green', width=0.2, text='', key='')[source]¶

Parameters:	p – start coordinates n – end-coordinates color – A color. Either a 3-element list with values from 0 to 1 for R, G and B, or a color name (as defined in this modules variable NAMED_COLORS)

add_sphere(p, color='green', width=0.2, text='')[source]¶

pymol_box_string()[source]¶

Pring out the CGO text to describe the boxes.

pymol_segments_string()[source]¶

pymol_spheres_string()[source]¶

pymol_text_string(rna_number)[source]¶

class forgi.threedee.visual.pymol.PymolPrinter[source]¶

Bases: future.types.newobject.newobject

add_cg(cg, labels, color_modifier=1.0)[source]¶

Parameters:	labels – A dictionary with element names as keys and labels as values.

add_encompassing_cylinders(rna_plotter, cg, radius=7.0)[source]¶

add_stem_like(rna_plotter, cg, text, key, color='green', width=2.4)[source]¶

add_stem_like_core(rna_plotter, coords, twists, stem_len, text, key, color='green', width=2.4)[source]¶

draw_bounding_boxes(rna_plotter, bg, s)[source]¶

Draw bounding boxes for all of the residues encompassed by a stem. But only if there is a pdb file handy.

@param bg: The BulgeGraph @param s: The name of the stem

get_element_color(elem_name)[source]¶

Get the color for this element. The color is determined by the name of the element.

@param elem_name: The name of the element. @return: A string with a color name

pymol_axis_string()[source]¶

pymol_intro_string()[source]¶

pymol_load_cgo_string(object_id)[source]¶

pymol_string()[source]¶

Output the contents of this structure into a file that can be passed in as a pymol script.

forgi.threedee.visual.pymol.pymol_color(color, modifier)[source]¶