`energy-diagram`¶

Draw a state energy diagram directly from numeric values you provide — it does not read structure files and runs no quantum / thermo / MLIP calculations (--thermo / --dft). Use it when numeric state energies are already known (e.g. from summary.json) and only the formatted diagram is needed. It produces one image file and an optional machine-readable sidecar.

Examples¶

# Command form
pdb2reaction energy-diagram {-i VALUE ... | -i "[VALUE, ...]"} [-o OUTPUT] [--label-x...] [--label-y...]

# List string (recommended for ad-hoc plots)
pdb2reaction energy-diagram -i "[0, 12.5, 4.3]" -o energy.png

# Repeated flag form (use one `-i` per value)
pdb2reaction energy-diagram -i 0 -i 12.5 -i 4.3 -o energy.png

# X/Y labels — same applies to --label-x / --label-y
pdb2reaction energy-diagram -i "[0, 12.5, 4.3]" \
    --label-x "['R','TS','P']" --label-y "ΔE (kcal/mol)" -o energy.png

Workflow¶

Collect values from -i/--input (supports repeated flags and a single list-like string).
Parse all input values as floats and fail early if fewer than two values are provided.
Parse optional --label-x values. If omitted, labels are auto-generated as S1, S2,…
Validate label count (--label-x) against value count, then render the diagram.
Save the image to -o/--output and print the saved path.

Outputs¶

OUTPUT.(png|jpg|jpeg|svg|pdf)
result.json   # Authoritative optional sidecar: status, n_points, files, and the standard envelope
summary.json  # Byte-identical compatibility mirror on a successful --out-json run

If -o/--output is omitted, energy_diagram.png is written to the current directory.
When output has no extension, .png is appended automatically.
Parent directories are created automatically when needed.

CLI options¶

Option	Description	Default
`-i, --input TEXT`	Repeat once per numeric value, or pass one quoted list-like string. Multiple bare values after a single `-i` are rejected.	Required
`-o, --output PATH`	Output image path (`.png/.jpg/.jpeg/.svg/.pdf`).	`energy_diagram.png`
`--label-x TEXT...`	X-axis state labels. Count must match input value count.	`S1, S2,...`
`--label-y TEXT`	Y-axis label.	`ΔE (kcal/mol)`
`--out-json/--no-out-json`	Write authoritative `result.json` and its identical `summary.json` mirror next to the image. See JSON Output Schema.	`False`

The full flag list is in the generated command reference.

Notes¶

Input order is used directly as plotting order.
Values are plotted unchanged; set --label-y to their unit.
At least two numeric values are required.

energy-diagram¶