export-knot-xyz

name	export-knot-xyz
description	Run ~/.local/bin/export_xyz to generate one or many knot conformations as XYZ files from the local SQLite database ~/.local/share/rust_knot/knots_data.db. Use when Codex needs command construction, batch export loops, or quick troubleshooting for knot id and atom count exports.

Export Knot XYZ

Entrypoint

• BIN=~/.local/bin/export_xyz
• DB=~/.local/share/rust_knot/knots_data.db

Quick Use

Single knot:

$BIN --knot 3_1 --atoms 200 --db "$DB" -o 3_1_200.xyz

Batch knots:

for knot in 3_1 4_1 5_1 5_2; do
  $BIN --knot "$knot" --atoms 240 --db "$DB" -o "${knot}_240.xyz"
done

Different atom counts:

for atoms in 120 180 240 360; do
  $BIN --knot 6_1 --atoms "$atoms" --db "$DB" -o "6_1_${atoms}.xyz"
done

Rules

• Always pass --knot, --atoms, --db.
• Keep --atoms >= 2.
• If -o is omitted, output defaults to <knot>_<atoms>.xyz.
• If user gives a custom DB path, use user path instead of $DB.