rgpycrumbs.geom.plt_rings_track

Track a query point across primitive rings.

Added in version 1.12.0.

Each frame is labelled by chemparseplot.plot.rings. The label is the nearest ring centroid or junction midpoint. A block hop is a change of the terminal ring, and that ring is its atom set. A frame spent on a bridge keeps the terminal ring. The query coordinate is the caller’s Wannier centre. It is not replaced by the centroid.

Prefer the dispatcher:

rgpycrumbs geom plt-rings-track molecule.sdf centres.xyz
rgpycrumbs geom plt-rings-track molecule.xyz centres.xyz --cutoff 1.95

One molecule frame is reused for every centre frame. Several molecule frames pair with the centre frames one to one. An XYZ molecule has no bonds, so it needs --cutoff inside the bond/nonbonded gap. 3.5 angstrom is the ice neighbour list.

Attributes

warn_on_direct_script_import

Functions

main(→ None)

Count terminal-ring hops for centres stored in an XYZ trajectory.

Module Contents

rgpycrumbs.geom.plt_rings_track.warn_on_direct_script_import = None

rgpycrumbs.geom.plt_rings_track.main(molecule: pathlib.Path, queries: pathlib.Path, *, cutoff: float | None, max_depth: int, csv_path: pathlib.Path | None) → None

Count terminal-ring hops for centres stored in an XYZ trajectory.