render

cnotebook.render.create_img_tag(width, height, image_mime_type, image_bytes, wrap_svg=True)[source]

Create the <img> HTML tag for rendering image bytes. This could be either plain text (in the case of SVG) or base64 encoded (in binary format cases). :param width: Image width :param height: Image height :param image_mime_type: Image MIME type :param image_bytes: Image bytes :param wrap_svg: Wrap SVG in a specifically sized <div> tag for maximum control of size :return: Image tag

Parameters:
Return type:

str

cnotebook.render.oedisp_to_html(disp, *, ctx)[source]

Convert an OpenEye 2D molecule display object to HTML :param ctx: Current molecule render context :param disp: OpenEye 2D molecule display object :return: HTML image tag

Parameters:
Return type:

str

cnotebook.render.render_empty_molecule(*, ctx)[source]

Render an image that says Empty Molecule :param ctx: Render context :return: Image tag

Parameters:

ctx (CNotebookContext)

Return type:

str

cnotebook.render.render_invalid_molecule(*, ctx)[source]

Render an image that says Empty Molecule :param ctx: Render context :return: Image tag

Parameters:

ctx (CNotebookContext)

Return type:

str

cnotebook.render.render_exceeds_max_heavy_atoms(mol, *, ctx)[source]

Render a placeholder image for molecules that exceed the heavy atom limit.

Parameters:

  • mol (OEMolBase) – Molecule (used to retrieve the title).

  • ctx (CNotebookContext) – Render context.

Returns:

HTML image tag.

Return type:

str

cnotebook.render.oemol_to_disp(mol, *, ctx)[source]

Convert a valid OpenEye molecule object to a display object for depiction. Note that it is highly recommended to test that the molecule is valid first before calling this function. :param ctx: Render context :param mol: Molecule to convert :return: Display object for depiction

Parameters:
Return type:

OE2DMolDisplay

cnotebook.render.oemol_to_image(mol, *, ctx)[source]

Convert an OpenEye molecule to an OEImage.

Handles valid, empty, and invalid molecules. For valid molecules the molecule is rendered via oemol_to_disp(). Empty and invalid molecules produce placeholder images with descriptive text.

Parameters:

  • mol (OEMolBase) – Molecule to convert.

  • ctx (CNotebookContext) – Render context.

Returns:

Rendered image.

Return type:

OEImage

cnotebook.render.oedu_to_disp(du, *, ctx)[source]

Convert an OEDesignUnit to a 2D molecule display.

Extracts the ligand from the design unit and renders it as a 2D display. Returns None if the design unit has no ligand (apo structure).

Important

The returned ligand molecule must be kept alive as long as the display is in use. The OE2DMolDisplay holds an internal C++ reference to the molecule; if the molecule is garbage-collected the display will crash when rendered.

Parameters:

  • du (OEDesignUnit) – Design unit to render.

  • ctx (CNotebookContext) – Render context.

Returns:

Tuple of (display, ligand), or None if no ligand.

Return type:

tuple[OE2DMolDisplay, OEGraphMol] | None

cnotebook.render.oedu_to_image(du, *, ctx)[source]

Convert an OEDesignUnit to an OEImage.

If the design unit has a ligand, renders the ligand with a small “OEDesignUnit” label. If no ligand is present (apo structure), renders a placeholder image with “Apo DesignUnit” text.

Parameters:

  • du (OEDesignUnit) – Design unit to render.

  • ctx (CNotebookContext) – Render context.

Returns:

Rendered image.

Return type:

OEImage

cnotebook.render.oemol_to_html(mol, *, ctx)[source]

Convert an OpenEye molecule to HTML.

Parameters:

  • mol (OEMolBase) – Molecule to convert.

  • ctx (CNotebookContext) – Render context.

Returns:

HTML image tag.

Return type:

str

cnotebook.render.oedu_to_html(du, *, ctx)[source]

Convert an OEDesignUnit to HTML.

If the design unit has a ligand, renders the ligand with a small “OEDesignUnit” label. If no ligand is present (apo structure), renders a placeholder image with “Apo DesignUnit” text.

Parameters:

  • du (OEDesignUnit) – Design unit to render.

  • ctx (CNotebookContext) – Render context.

Returns:

HTML image tag.

Return type:

str

cnotebook.render.oeimage_to_html(image, *, ctx)[source]

Convert an OEImage to HTML :param ctx: Render context :param image: Image to render :return: HTML string

Parameters:
Return type:

str

Rendering Functions

The render module provides core functions for converting OpenEye molecules to HTML representations.

Key Functions

oemol_to_html

Convert an OpenEye molecule to an HTML representation (PNG or SVG image).

from cnotebook.render import oemol_to_html
from cnotebook.context import CNotebookContext

ctx = CNotebookContext(width=200, height=200, image_format="svg")
html = oemol_to_html(mol, ctx=ctx)

render_molecule

Render a molecule with optional SMARTS highlighting.

from cnotebook.render import render_molecule

# Basic rendering
render_molecule(mol)

# With SMARTS highlighting
render_molecule(mol, smarts="c1ccccc1")