polymerist.rdutils.rdkdraw
==========================

.. py:module:: polymerist.rdutils.rdkdraw

.. autoapi-nested-parse::

   Tools for drawing and visulaizing RDKit molecules



Functions
---------

.. autoapisummary::

   polymerist.rdutils.rdkdraw.set_rdkdraw_size
   polymerist.rdutils.rdkdraw.enable_substruct_highlights
   polymerist.rdutils.rdkdraw.disable_substruct_highlights
   polymerist.rdutils.rdkdraw.enable_kekulized_drawing
   polymerist.rdutils.rdkdraw.disable_kekulized_drawing
   polymerist.rdutils.rdkdraw.clear_highlights
   polymerist.rdutils.rdkdraw.tight_norm_for_rdmol_prop
   polymerist.rdutils.rdkdraw.rdmol_prop_heatmap
   polymerist.rdutils.rdkdraw.rdmol_prop_heatmap_colorscaled


Module Contents
---------------

.. py:function:: set_rdkdraw_size(dim: int = 300, aspect: float = 3 / 2)

   Change image size and shape of RDKit Mol images


.. py:function:: enable_substruct_highlights() -> None

   Turns on highlighting of found substructures when performing substructure matches


.. py:function:: disable_substruct_highlights() -> None

   Turns off highlighting of found substructures when performing substructure matches


.. py:function:: enable_kekulized_drawing() -> None

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


.. py:function:: disable_kekulized_drawing() -> None

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


.. py:function:: clear_highlights(rdmol: rdkit.Chem.rdchem.Mol) -> None

   Removes the highlighted atoms flags from an RDKit Mol if present


.. py:function:: tight_norm_for_rdmol_prop(rdmol: rdkit.Chem.rdchem.Mol, prop: str, prop_type: Union[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


.. py:function:: rdmol_prop_heatmap(rdmol: rdkit.Chem.rdchem.Mol, prop: str, cmap: matplotlib.colors.Colormap, norm: Optional[matplotlib.colors.Normalize] = 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


.. py:function:: rdmol_prop_heatmap_colorscaled(rdmol: rdkit.Chem.rdchem.Mol, prop: str, cmap: matplotlib.colors.Colormap = plt.get_cmap('turbo'), norm: Optional[matplotlib.colors.Normalize] = None, ticks: Optional[tuple[float]] = None, cbar_label: str = '', orient: Optional[str] = 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