cgsmiles.drawing module

Utilities for drawing molecules and cgsmiles graphs.

cgsmiles.drawing.draw_molecule(graph, ax=None, layout_method='vespr_refined', pos=None, cg_mapping=True, colors=None, labels=None, scale=2, outline=False, use_weights=False, align_with='diag', fontsize=10, text_color='black', edge_widths=3, mapped_edge_width=20, default_bond=1, layout_kwargs={})[source]

Draw the graph of a molecule optionally with a coarse-grained projection if cg_mapping is set to True. The membership of atoms to the CG projection is taken from the ‘fragid’ node attribute.

Positions or one of three layout methods must be specified. The layout options are vespr_refined, vespr, and circular. Note that the vespr_refined is slow but yields the best quality results. For a quick look vespr is recommended. The drawing function also accepts a layout_kwarg dictionary specifiying options to be given to the chosen layout method. See also cgsmiles.graph_layout.

For example to draw Benzene using the Martini 3 mapping:

>>> import matplotlib.pyplot as plt
>>> from cgsmiles import MoleculeResolver
>>> from cgsmiles import draw_molecule

>>> cgsmiles_str = "{[#TC5]1[#TC5][#TC5]1}.{#TC5=[$]cc[$]}"
>>> resolver = MoleculeResolver.from_string(cgsmiles_str)
>>> cg_mol, aa_mol = resolver.resolve()
>>> draw_molecule(aa_mol, layout_method="vespr_refined")
>>> plt.show()

The drawing is always of fixed size based on the canvas size. This means that molecules drawn on a canvas with the same size will have the same dimensions (i.e. bond length, atom size). Using the scale argument a drawing can be scaled to make it larger or smaller on a given canvas. That means if your molecule is too small or large redraw it setting a different scale parameter.

Parameters:

  • ax (matplotlib.axes.Axes) – mpl axis object

  • layout_method (str) – choice of vespr, vespr_refined, circular (default: ‘vespr_refined’)

  • pos (dict) – a dict mapping nodes to 2D positions

  • cg_mapping (bool) – draw outline for the CG mapping (default: True)

  • colors (dict) – a dict mapping nodes to colors or fragids to colors depending on if cg_mapping is True

  • labels (list) – list of node_labels; must follow the order of nodes in graph

  • scale (float) – scale the drawing relative to the total canvas size

  • outline (bool) – draw an outline around each node

  • use_weights (bool) – color nodes according to weight attribute (default: False)

  • align_with (str or numpy.ndarray) – align the longest distance in molecule with one of x, y, diag or a custom axis as numpy 2D array

  • fontsize (float) – fontsize of labels

  • text_color (str) – color of the node labels (default: black)

  • edge_widths (float) – the width of the bonds

  • mapped_edge_widths (float) – the width of the mapped projection

  • default_bond (float) – default bond length (default: 1)

  • layout_kwargs (dict) – dict with arguments passed to the layout methods

Returns:

  • matplotlib.axes.Axes – the updated axis object

  • dict – a dict of positions