shnitsel.vis.datasheet.figures.structure

Functions

mol_to_png(mol[, width, height])	Helper function to plot an rdkit.Mol object as a 2D structural representation
mol_to_svg(mol[, width, height])	Helper function to plot an rdkit.Mol object as a 2D structural representation using vector graphics
format_inchi(inchi[, max_line_length])	Helper function to split an inchi string across
plot_structure(mol[, name, smiles, inchi, fig, ax])	Plot function to create a 2d structure representation of a molecule mol using rdkit and create a graph with
plot_pca_structure(frames, pca_data[, fig, axs])	Function to plot the most extreme pca combinations as structure plots.

Module Contents

mol_to_png(mol, width=320, height=240)

Helper function to plot an rdkit.Mol object as a 2D structural representation

Parameters:

• mol (rdChem.Mol) – RDKit representation of the molecule to plot

• width (int, optional) – Width of the canvas to plot to. Defaults to 320.

• height (int, optional) – Height of the canvas to plot to. Defaults to 240.

Returns:

The drawn structure of the mol molecule in 2D as a sequence of bytes.

Return type:

bytes

mol_to_svg(mol, width=320, height=240)

Helper function to plot an rdkit.Mol object as a 2D structural representation using vector graphics

Parameters:

• mol (rdChem.Mol) – RDKit representation of the molecule to plot

• width (int, optional) – Width of the canvas to plot to. Defaults to 320.

• height (int, optional) – Height of the canvas to plot to. Defaults to 240.

Returns:

The drawn structure of the mol molecule in 2D as a sequence of bytes.

Return type:

bytes

format_inchi(inchi, max_line_length=30)

Helper function to split an inchi string across multiple lines to not overlap other plots in the DataSheet pages.

Parameters:

• inchi (str) – InChi string as generated by RDKit

• max_line_length (int, optional) – Maximum line length. Defaults to 30 characters

Returns:

The string broken into multiple lines with inserted n characters.

Return type:

str

plot_structure(mol, name='', smiles=None, inchi=None, fig=None, ax=None)

Plot function to create a 2d structure representation of a molecule mol using rdkit and create a graph with a 2d image representation into fig or ax with at least one of the two needing to be provided.

Parameters:

• mol (rdChem.Mol) – The RDKit molecule object to visualize.

• name (str, optional) – The name of the structure. Would be used as a plot title if not empty. Defaults to ‘’.

• smiles (str | None, optional) – Smiles strings to include in the x-axis label. Defaults to None.

• inchi (str | None, optional) – InChI strings to include in the x-axis label. Defaults to None.

• fig (Figure | SubFigure | None, optional) – Figure to plot the graphic into if ax not provided. Defaults to None.

• ax (Axes | None, optional) – Axis to plot the graphic into. Defaults to None, meaning they will be created from fig.

Returns:

The axes the graphic was plotted to.

Return type:

Axes

plot_pca_structure(frames, pca_data, fig=None, axs=None)

Function to plot the most extreme pca combinations as structure plots.

Parameters:

• frames (Frames | xr.Dataset) – The raw input data to use for extracting the positional data and structure.

• pca_data (xr.DataArray) – PCA decomposition data.

• fig (Figure | SubFigure, optional) – Figure to create axes into. If axs are provided, this can be left empty.

• axs (dict[tuple[int,str],Axes] | None, optional) – Axes to plot the extrema to. One row per pca, one column for ‘min’ or ‘max’. Defaults to None.

Returns:

The axes the extrema have been plotted to.

Return type:

dict[tuple[int,str],Axes]