#!/usr/bin/env python3
"""Draw primitive rings and the bridges between them.
.. versionadded:: 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.
"""
# /// script
# requires-python = ">=3.12"
# dependencies = [
# "click>=8.1",
# "numpy>=1.26",
# "matplotlib>=3.8.2",
# "pydseamslib>=2.9.1",
# "xyzrender>=0.3.8",
# "chemparseplot>=1.11",
# ]
# ///
from __future__ import annotations
from pathlib import Path
import click
from chemparseplot.plot.rings import (
format_report,
read_structure,
render_primitive_rings,
)
try:
from rgpycrumbs._aux import warn_on_direct_script_import
except ImportError: # pragma: no cover - script copy without the package root
[docs]
warn_on_direct_script_import = None
if warn_on_direct_script_import is not None:
warn_on_direct_script_import(__name__, "rgpycrumbs geom plt-rings")
@click.command()
@click.argument(
"structure",
type=click.Path(exists=True, dir_okay=False, path_type=Path),
)
@click.argument("output", type=click.Path(dir_okay=False, path_type=Path))
@click.option(
"--cutoff",
type=float,
default=None,
help="Heavy-atom cutoff in angstrom. Required for XYZ, refused for SDF.",
)
@click.option(
"--max-depth",
type=int,
default=6,
show_default=True,
help="Largest ring ringNetwork generates.",
)
@click.option(
"--queries",
type=click.Path(exists=True, dir_okay=False, path_type=Path),
default=None,
help="XYZ of query points, drawn where they sit.",
)
@click.option("--config", default="paton", show_default=True, help="xyzrender preset.")
@click.option("--canvas-size", type=int, default=900, show_default=True)
[docs]
def main(
structure: Path,
output: Path,
*,
cutoff: float | None,
max_depth: int,
queries: Path | None,
config: str,
canvas_size: int,
) -> None:
"""Render primitive rings for an SDF or an XYZ file."""
symbols, coords, bonds = read_structure(structure)
query_coords = None
if queries is not None:
_qsym, query_coords, _qbonds = read_structure(queries)
if bonds is not None and cutoff is not None:
raise SystemExit("this file already has bonds; omit --cutoff")
if bonds is None and cutoff is None:
raise SystemExit("XYZ has no bonds; pass --cutoff inside the bond/nonbonded gap")
report, assignments = render_primitive_rings(
symbols,
coords,
output,
bonds=bonds,
cutoff=cutoff,
max_depth=max_depth,
queries=query_coords,
config=config,
canvas_size=canvas_size,
)
click.echo(format_report(report, assignments))
if __name__ == "__main__":
main()
