rgpycrumbs.geom.plt_rings

Draw primitive rings and the bridges between them.

Added in version 1.11.0.

The picture is chemparseplot.plot.rings: one xyzrender hull per face pydseams.yoda.ringNetwork returns, and a dashed stroke on each bridge whose ends both lie on a returned ring. Query atoms, when given, stay where the file puts them. They are a label for a Wannier centre, not the coordinate that enters a mean-square displacement.

Prefer the dispatcher:

rgpycrumbs geom plt-rings molecule.sdf rings.svg
rgpycrumbs geom plt-rings molecule.xyz rings.svg --cutoff 1.95

uv run --script on this file is the same isolated environment the dispatcher builds. An XYZ file has no bonds, so it needs --cutoff inside the gap between the longest bond and the shortest nonbonded contact. 3.5 angstrom is the ice neighbour list and is the wrong graph for a thiophene.

Attributes

warn_on_direct_script_import

Functions

main(→ None)

Render primitive rings for an SDF or an XYZ file.

Module Contents

rgpycrumbs.geom.plt_rings.warn_on_direct_script_import = None

rgpycrumbs.geom.plt_rings.main(structure: pathlib.Path, output: pathlib.Path, *, cutoff: float | None, max_depth: int, queries: pathlib.Path | None, config: str, canvas_size: int) → None

Render primitive rings for an SDF or an XYZ file.