polymerist.rdutils.rdkdraw

Tools for drawing and visulaizing RDKit molecules

Functions

set_rdkdraw_size([dim, aspect])	Change image size and shape of RDKit Mol images
enable_substruct_highlights(→ None)	Turns on highlighting of found substructures when performing substructure matches
disable_substruct_highlights(→ None)	Turns off highlighting of found substructures when performing substructure matches
enable_kekulized_drawing(→ None)	Turns on automatic kekulization of aromatic bonds before drawing molecules in Jupyter Notebooks
disable_kekulized_drawing(→ None)	Turns off automatic kekulization of aromatic bonds before drawing molecules in Jupyter Notebooks
clear_highlights(→ None)	Removes the highlighted atoms flags from an RDKit Mol if present
tight_norm_for_rdmol_prop(...)	Generate a matplotlib Normalize object with bounds matching the maxima, minima, and midpoint of a numeric Prop
rdmol_prop_heatmap() → PIL.Image.Image)	Take a charged RDKit Mol and color atoms based on the magnitude of a particular atomwise property
rdmol_prop_heatmap_colorscaled(, norm, ticks, ...)	Plot a labelled heatmap of the charge differences between 2 structurally identical RDKit Molecules with different partial charges

Module Contents

polymerist.rdutils.rdkdraw.set_rdkdraw_size(dim: int = 300, aspect: float = 3 / 2)

Change image size and shape of RDKit Mol images

polymerist.rdutils.rdkdraw.enable_substruct_highlights() → None

Turns on highlighting of found substructures when performing substructure matches

polymerist.rdutils.rdkdraw.disable_substruct_highlights() → None

Turns off highlighting of found substructures when performing substructure matches

polymerist.rdutils.rdkdraw.enable_kekulized_drawing() → None

Turns on automatic kekulization of aromatic bonds before drawing molecules in Jupyter Notebooks

polymerist.rdutils.rdkdraw.disable_kekulized_drawing() → None

Turns off automatic kekulization of aromatic bonds before drawing molecules in Jupyter Notebooks

polymerist.rdutils.rdkdraw.clear_highlights(rdmol: rdkit.Chem.rdchem.Mol) → None

Removes the highlighted atoms flags from an RDKit Mol if present

polymerist.rdutils.rdkdraw.tight_norm_for_rdmol_prop(rdmol: rdkit.Chem.rdchem.Mol, prop: str, prop_type: Type[int] | Type[float]) → tuple[matplotlib.colors.Normalize, tuple[int, Ellipsis]]

Generate a matplotlib Normalize object with bounds matching the maxima, minima, and midpoint of a numeric Prop

polymerist.rdutils.rdkdraw.rdmol_prop_heatmap(rdmol: rdkit.Chem.rdchem.Mol, prop: str, cmap: matplotlib.colors.Colormap, norm: matplotlib.colors.Normalize | None = None, annotate: bool = False, annotate_precision: int = 5, img_size: tuple[int, int] = (1000, 1000)) → PIL.Image.Image

Take a charged RDKit Mol and color atoms based on the magnitude of a particular atomwise property

polymerist.rdutils.rdkdraw.rdmol_prop_heatmap_colorscaled(rdmol: rdkit.Chem.rdchem.Mol, prop: str, cmap: matplotlib.colors.Colormap = plt.get_cmap('turbo'), norm: matplotlib.colors.Normalize | None = None, ticks: tuple[float] | None = None, cbar_label: str = '', orient: str | None = None, **heatmap_args) → tuple[matplotlib.pyplot.Figure, matplotlib.pyplot.Axes]

Plot a labelled heatmap of the charge differences between 2 structurally identical RDKit Molecules with different partial charges