energy-diagram

Overview

Summary: Draw a state energy diagram directly from numeric values (no structure file, no quantum/thermo calculation).

Quick reference

  • Input: Numeric energies passed via -i/--input (multiple tokens or list-like string).

  • Output: One image file (.png, .jpg, .jpeg, .svg, or .pdf).

  • Default output: energy_diagram.png.

  • State labels: Optional --label-x; defaults to S1, S2,…

  • Use when: Energies already available; only the formatted diagram is needed.

pdb2reaction energy-diagram only visualizes numbers you provide. It does not read structure files and does not run --thermo / --dft-style calculations.

Usage

pdb2reaction energy-diagram -i VALUES... [-o OUTPUT] [--label-x...] [--label-y...]

Examples

# Multiple numeric arguments
pdb2reaction energy-diagram -i 0 12.5 4.3 -o energy.png

# List string
pdb2reaction energy-diagram -i "[-205.1, -190.4, -198.7]" -o energy.png

# X/Y labels
pdb2reaction energy-diagram -i 0 12.5 4.3 --label-x R TS P --label-y "ΔE (kcal/mol)" -o energy.png

Workflow

  1. Collect values from -i/--input (supports repeated flags, multiple values after one flag, and list-like strings).

  2. Parse all input values as floats and fail early if fewer than two values are provided.

  3. Parse optional --label-x values. If omitted, labels are auto-generated as S1, S2,…

  4. Validate label count (--label-x) against value count, then render the diagram.

  5. Save the image to -o/--output and print the saved path.

CLI options

Option

Description

Default

-i, --input TEXT...

Numeric values (multiple args or list-like string).

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 a machine-readable result.json next to the output image. See JSON Output Schema for the schema.

False

Outputs

OUTPUT.(png|jpg|jpeg|svg|pdf)

  • 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.

Notes

  • Input order is used directly as plotting order.

  • At least two numeric values are required.

  • This command does not read structure files and does not compute energies.

See Also